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source: trunk/GSASIIIO.py @ 3217

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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2018-01-08 22:37:12 +0000 (Mon, 08 Jan 2018) $
4	# $Author: toby $
5	# $Revision: 3217 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 3217 2018-01-08 22:37:12Z toby $
8	########### SVN repository information ###################
9	'''
10	GSASIIIO: Misc I/O routines
11	=============================
12
13	Module with miscellaneous routines for input and output. Many
14	are GUI routines to interact with user.
15
16	Includes support for image reading.
17
18	Also includes base classes for data import routines.
19
20	This module needs some work to separate wx from non-wx routines
21	'''
22	# If this is being used for GSASIIscriptable, don't depend on wx
23	from __future__ import division, print_function
24	try:
25	import wx
26	except ImportError:
27	class Placeholder(object):
28	def __init__(self):
29	self.Dialog = object
30	wx = Placeholder()
31	import math
32	import numpy as np
33	import copy
34	import platform
35	if '2' in platform.python_version_tuple()[0]:
36	import cPickle
37	else:
38	import _pickle as cPickle
39	import sys
40	import re
41	import glob
42	import random as ran
43	import GSASIIpath
44	GSASIIpath.SetVersionNumber("$Revision: 3217 $")
45	try:
46	import GSASIIdataGUI as G2gd
47	except ImportError:
48	pass
49	import GSASIIobj as G2obj
50	import GSASIIlattice as G2lat
51	import GSASIImath as G2mth
52	try:
53	import GSASIIpwdGUI as G2pdG
54	import GSASIIimgGUI as G2imG
55	except ImportError:
56	pass
57	import GSASIIimage as G2img
58	import GSASIIElem as G2el
59	import GSASIIstrIO as G2stIO
60	import GSASIImapvars as G2mv
61	try:
62	import GSASIIctrlGUI as G2G
63	except ImportError:
64	pass
65	import os
66	import os.path as ospath
67
68	DEBUG = False #=True for various prints
69	TRANSP = False #=true to transpose images for testing
70	if GSASIIpath.GetConfigValue('Transpose'): TRANSP = True
71	npsind = lambda x: np.sin(x*np.pi/180.)
72
73	def sfloat(S):
74	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
75	if S.strip():
76	try:
77	return float(S)
78	except ValueError:
79	pass
80	return 0.0
81
82	def sint(S):
83	'Convert a string to int. An empty field is treated as zero'
84	if S.strip():
85	return int(S)
86	else:
87	return 0
88
89	def trim(val):
90	'''Simplify a string containing leading and trailing spaces
91	as well as newlines, tabs, repeated spaces etc. into a shorter and
92	more simple string, by replacing all ranges of whitespace
93	characters with a single space.
94
95	:param str val: the string to be simplified
96
97	:returns: the (usually) shortened version of the string
98	'''
99	return re.sub('\s+', ' ', val).strip()
100
101	def FileDlgFixExt(dlg,file):
102	'this is needed to fix a problem in linux wx.FileDialog'
103	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
104	if ext not in file:
105	file += ext
106	return file
107
108	def GetPowderPeaks(fileName):
109	'Read powder peaks from a file'
110	sind = lambda x: math.sin(x*math.pi/180.)
111	asind = lambda x: 180.*math.asin(x)/math.pi
112	wave = 1.54052
113	File = open(fileName,'Ur')
114	Comments = []
115	peaks = []
116	S = File.readline()
117	while S:
118	if S[:1] == '#':
119	Comments.append(S[:-1])
120	else:
121	item = S.split()
122	if len(item) == 1:
123	peaks.append([float(item[0]),1.0])
124	elif len(item) > 1:
125	peaks.append([float(item[0]),float(item[0])])
126	S = File.readline()
127	File.close()
128	if Comments:
129	print ('Comments on file:')
130	for Comment in Comments:
131	print (Comment)
132	if 'wavelength' in Comment:
133	wave = float(Comment.split('=')[1])
134	Peaks = []
135	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
136	for peak in peaks:
137	dsp = peak[0]
138	sth = wave/(2.0*dsp)
139	if sth < 1.0:
140	tth = 2.0*asind(sth)
141	else:
142	break
143	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
144	else: #2-thetas - assume Cuka (for now)
145	for peak in peaks:
146	tth = peak[0]
147	dsp = wave/(2.0*sind(tth/2.0))
148	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
149	limits = [1000.,0.]
150	for peak in Peaks:
151	limits[0] = min(limits[0],peak[0])
152	limits[1] = max(limits[1],peak[0])
153	limits[0] = max(1.,(int(limits[0]-1.)/5)*5.)
154	limits[1] = min(170.,(int(limits[1]+1.)/5)*5.)
155	return Comments,Peaks,limits,wave
156
157	def GetCheckImageFile(G2frame,treeId):
158	'''Try to locate an image file if the project and image have been moved
159	together. If the image file cannot be found, request the location from
160	the user.
161
162	:param wx.Frame G2frame: main GSAS-II Frame and data object
163	:param wx.Id treeId: Id for the main tree item for the image
164	:returns: Npix,imagefile,imagetag with (Npix) number of pixels,
165	imagefile, if it exists, or the name of a file that does exist or False if the user presses Cancel
166	and (imagetag) an optional image number
167
168	'''
169	Npix,Imagefile,imagetag = G2frame.GPXtree.GetImageLoc(treeId)
170	if isinstance(Imagefile,list):
171	imagefile,imagetag = Imagefile
172	else:
173	imagefile = Imagefile
174	if not os.path.exists(imagefile):
175	print ('Image file '+imagefile+' not found')
176	fil = imagefile.replace('\\','/') # windows?!
177	# see if we can find a file with same name or in a similarly named sub-dir
178	pth,fil = os.path.split(fil)
179	prevpth = None
180	while pth and pth != prevpth:
181	prevpth = pth
182	if os.path.exists(os.path.join(G2frame.dirname,fil)):
183	print ('found image file '+os.path.join(G2frame.dirname,fil))
184	imagefile = os.path.join(G2frame.dirname,fil)
185	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
186	return Npix,imagefile,imagetag
187	pth,enddir = os.path.split(pth)
188	fil = os.path.join(enddir,fil)
189	# not found as a subdirectory, drop common parts of path for last saved & image file names
190	# if image was .../A/B/C/imgs/ima.ge
191	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
192	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
193	Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
194	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
195	imgPath = imagefile.replace('\\','/').split('/')
196	for p1,p2 in zip(gpxPath,imgPath):
197	if p1 == p2:
198	gpxPath.pop(0),imgPath.pop(0)
199	else:
200	break
201	fil = os.path.join(*imgPath) # file with non-common prefix elements
202	prevpth = None
203	pth = os.path.abspath(G2frame.dirname)
204	while pth and pth != prevpth:
205	prevpth = pth
206	if os.path.exists(os.path.join(pth,fil)):
207	print ('found image file '+os.path.join(pth,fil))
208	imagefile = os.path.join(pth,fil)
209	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
210	return Npix,imagefile,imagetag
211	pth,enddir = os.path.split(pth)
212	#GSASIIpath.IPyBreak()
213
214	if not os.path.exists(imagefile):
215	prevnam = os.path.split(imagefile)[1]
216	prevext = os.path.splitext(imagefile)[1]
217	wildcard = 'Image format ('+prevext+')\|'+prevext
218	dlg = wx.FileDialog(G2frame, 'Previous image file ('+prevnam+') not found; open here', '.', prevnam,
219	wildcard,wx.FD_OPEN)
220	try:
221	dlg.SetFilename(''+ospath.split(imagefile)[1])
222	if dlg.ShowModal() == wx.ID_OK:
223	imagefile = dlg.GetPath()
224	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
225	else:
226	imagefile = False
227	finally:
228	dlg.Destroy()
229	return Npix,imagefile,imagetag
230
231	def EditImageParms(parent,Data,Comments,Image,filename):
232	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
233	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
234	def onClose(event):
235	dlg.EndModal(wx.ID_OK)
236	mainsizer = wx.BoxSizer(wx.VERTICAL)
237	h,w = Image.shape[:2]
238	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
239	0,wx.ALIGN_LEFT\|wx.ALL, 2)
240
241	vsizer = wx.BoxSizer(wx.HORIZONTAL)
242	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
243	0,wx.ALIGN_LEFT\|wx.ALL, 2)
244	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
245	vsizer.Add(wdgt)
246	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
247
248	vsizer = wx.BoxSizer(wx.HORIZONTAL)
249	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
250	0,wx.ALIGN_LEFT\|wx.ALL, 2)
251	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
252	size=(50,-1))
253	vsizer.Add(wdgt)
254	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),wx.ALIGN_LEFT\|wx.ALL, 2)
255	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,size=(50,-1))
256	vsizer.Add(wdgt)
257	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
258
259	vsizer = wx.BoxSizer(wx.HORIZONTAL)
260	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
261	0,wx.ALIGN_LEFT\|wx.ALL, 2)
262	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
263	vsizer.Add(wdgt)
264	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
265
266	vsizer = wx.BoxSizer(wx.HORIZONTAL)
267	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
268	0,wx.ALIGN_LEFT\|wx.ALL, 2)
269	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,size=(75,-1))
270	vsizer.Add(wdgt)
271	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),wx.ALIGN_LEFT\|wx.ALL, 2)
272	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,size=(75,-1))
273	vsizer.Add(wdgt)
274	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
275
276	vsizer = wx.BoxSizer(wx.HORIZONTAL)
277	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
278	0,wx.ALIGN_LEFT\|wx.ALL, 2)
279	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
280	vsizer.Add(wdgt)
281	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
282
283	btnsizer = wx.StdDialogButtonSizer()
284	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
285	OKbtn.SetDefault()
286	OKbtn.Bind(wx.EVT_BUTTON,onClose)
287	btnsizer.AddButton(OKbtn) # not sure why this is needed
288	btnsizer.Realize()
289	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
290	dlg.SetSizer(mainsizer)
291	dlg.CenterOnParent()
292	dlg.ShowModal()
293
294	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
295	'''Load an image into the tree. Saves the location of the image, as well as the
296	ImageTag (where there is more than one image in the file), if defined.
297	'''
298	ImgNames = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
299	TreeLbl = 'IMG '+os.path.basename(imagefile)
300	ImageTag = Data.get('ImageTag')
301	if ImageTag:
302	TreeLbl += ' #'+'%04d'%(ImageTag)
303	imageInfo = (imagefile,ImageTag)
304	else:
305	imageInfo = imagefile
306	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
307	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=TreeName)
308	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
309	Imax = np.amax(Image)
310	if G2frame.imageDefault:
311	Data = copy.copy(G2frame.imageDefault)
312	Data['showLines'] = True
313	Data['ring'] = []
314	Data['rings'] = []
315	Data['cutoff'] = 10
316	Data['pixLimit'] = 20
317	Data['edgemin'] = 100000000
318	Data['calibdmin'] = 0.5
319	Data['calibskip'] = 0
320	Data['ellipses'] = []
321	Data['calibrant'] = ''
322	Data['GonioAngles'] = [0.,0.,0.]
323	Data['DetDepthRef'] = False
324	else:
325	Data['type'] = 'PWDR'
326	Data['color'] = GSASIIpath.GetConfigValue('Contour_color','Paired')
327	Data['tilt'] = 0.0
328	Data['rotation'] = 0.0
329	Data['showLines'] = False
330	Data['ring'] = []
331	Data['rings'] = []
332	Data['cutoff'] = 10
333	Data['pixLimit'] = 20
334	Data['calibdmin'] = 0.5
335	Data['calibskip'] = 0
336	Data['edgemin'] = 100000000
337	Data['ellipses'] = []
338	Data['GonioAngles'] = [0.,0.,0.]
339	Data['DetDepth'] = 0.
340	Data['DetDepthRef'] = False
341	Data['calibrant'] = ''
342	Data['IOtth'] = [2.0,5.0]
343	Data['LRazimuth'] = [0.,180.]
344	Data['azmthOff'] = 0.0
345	Data['outChannels'] = 2500
346	Data['outAzimuths'] = 1
347	Data['centerAzm'] = False
348	Data['fullIntegrate'] = False
349	Data['setRings'] = False
350	Data['background image'] = ['',-1.0]
351	Data['dark image'] = ['',-1.0]
352	Data['Flat Bkg'] = 0.0
353	Data['setDefault'] = False
354	Data['range'] = [(0,Imax),[0,Imax]]
355	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Image Controls'),Data)
356	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(0,Imax),[0,Imax]]}
357	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Masks'),Masks)
358	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Stress/Strain'),
359	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
360	G2frame.GPXtree.SetItemPyData(Id,[Npix,imageInfo])
361	G2frame.PickId = Id
362	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
363	G2frame.Image = Id
364
365	def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None,FormatName=''):
366	'''Read a single image with an image importer. This is called to reread an image
367	after it has already been imported with :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
368	(or :func:`ReadImages` in Auto Integration) so it is not necessary to reload metadata.
369
370	:param wx.Frame G2frame: main GSAS-II Frame and data object.
371	:param str imagefile: name of image file
372	:param bool imageOnly: If True return only the image,
373	otherwise (default) return more (see below)
374	:param int/str ImageTag: specifies a particular image to be read from a file.
375	First image is read if None (default).
376	:param str formatName: the image reader formatName
377
378	:returns: an image as a numpy array or a list of four items:
379	Comments, Data, Npix and the Image, as selected by imageOnly
380
381	'''
382	# determine which formats are compatible with this file
383	primaryReaders = []
384	secondaryReaders = []
385	for rd in G2frame.ImportImageReaderlist:
386	flag = rd.ExtensionValidator(imagefile)
387	if flag is None:
388	secondaryReaders.append(rd)
389	elif flag:
390	if not FormatName:
391	primaryReaders.append(rd)
392	elif FormatName == rd.formatName:
393	primaryReaders.append(rd)
394	if len(secondaryReaders) + len(primaryReaders) == 0:
395	print('Error: No matching format for file '+imagefile)
396	raise Exception('No image read')
397	errorReport = ''
398	if not imagefile:
399	return
400	for rd in primaryReaders+secondaryReaders:
401	rd.ReInitialize() # purge anything from a previous read
402	rd.errors = "" # clear out any old errors
403	if not rd.ContentsValidator(imagefile): # rejected on cursory check
404	errorReport += "\n "+rd.formatName + ' validator error'
405	if rd.errors:
406	errorReport += ': '+rd.errors
407	continue
408	if imageOnly:
409	ParentFrame = None # prevent GUI access on reread
410	else:
411	ParentFrame = G2frame
412	if GSASIIpath.GetConfigValue('debug'):
413	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
414	else:
415	flag = False
416	try:
417	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
418	except rd.ImportException as detail:
419	rd.errors += "\n Read exception: "+str(detail)
420	except Exception as detail:
421	import traceback
422	rd.errors += "\n Unhandled read exception: "+str(detail)
423	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
424	if flag: # this read succeeded
425	if rd.Image is None:
426	raise Exception('No image read. Strange!')
427	if GSASIIpath.GetConfigValue('Transpose'):
428	print ('Transposing Image!')
429	rd.Image = rd.Image.T
430	#rd.readfilename = imagefile
431	if imageOnly:
432	return rd.Image
433	else:
434	return rd.Comments,rd.Data,rd.Npix,rd.Image
435	else:
436	print('Error reading file '+imagefile)
437	print('Error messages(s)\n'+errorReport)
438	raise Exception('No image read')
439
440	def ReadImages(G2frame,imagefile):
441	'''Read one or more images from a file and put them into the Tree
442	using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
443
444	ToDo: Images are most commonly read in :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
445	which is called from :meth:`GSASIIdataGUI.GSASII.OnImportImage`
446	it would be good if these routines used a common code core so that changes need to
447	be made in only one place.
448
449	:param wx.Frame G2frame: main GSAS-II Frame and data object.
450	:param str imagefile: name of image file
451
452	:returns: a list of the id's of the IMG tree items created
453	'''
454	# determine which formats are compatible with this file
455	primaryReaders = []
456	secondaryReaders = []
457	for rd in G2frame.ImportImageReaderlist:
458	flag = rd.ExtensionValidator(imagefile)
459	if flag is None:
460	secondaryReaders.append(rd)
461	elif flag:
462	primaryReaders.append(rd)
463	if len(secondaryReaders) + len(primaryReaders) == 0:
464	print('Error: No matching format for file '+imagefile)
465	raise Exception('No image read')
466	errorReport = ''
467	rdbuffer = {} # create temporary storage for file reader
468	for rd in primaryReaders+secondaryReaders:
469	rd.ReInitialize() # purge anything from a previous read
470	rd.errors = "" # clear out any old errors
471	if not rd.ContentsValidator(imagefile): # rejected on cursory check
472	errorReport += "\n "+rd.formatName + ' validator error'
473	if rd.errors:
474	errorReport += ': '+rd.errors
475	continue
476	ParentFrame = G2frame
477	block = 0
478	repeat = True
479	CreatedIMGitems = []
480	while repeat: # loop if the reader asks for another pass on the file
481	block += 1
482	repeat = False
483	if GSASIIpath.GetConfigValue('debug'):
484	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
485	else:
486	flag = False
487	try:
488	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
489	except rd.ImportException as detail:
490	rd.errors += "\n Read exception: "+str(detail)
491	except Exception as detail:
492	import traceback
493	rd.errors += "\n Unhandled read exception: "+str(detail)
494	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
495	if flag: # this read succeeded
496	if rd.Image is None:
497	raise Exception('No image read. Strange!')
498	if GSASIIpath.GetConfigValue('Transpose'):
499	print ('Transposing Image!')
500	rd.Image = rd.Image.T
501	rd.Data['ImageTag'] = rd.repeatcount
502	rd.readfilename = imagefile
503	# Load generic metadata, as configured
504	GetColumnMetadata(rd)
505	LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
506	repeat = rd.repeat
507	CreatedIMGitems.append(G2frame.Image)
508	if CreatedIMGitems: return CreatedIMGitems
509	else:
510	print('Error reading file '+imagefile)
511	print('Error messages(s)\n'+errorReport)
512	return []
513	#raise Exception('No image read')
514
515	def SaveMultipleImg(G2frame):
516	if not G2frame.GPXtree.GetCount():
517	print ('no images!')
518	return
519	choices = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
520	if len(choices) == 1:
521	names = choices
522	else:
523	dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices)
524	dlg.SetSelections([])
525	names = []
526	if dlg.ShowModal() == wx.ID_OK:
527	names = [choices[sel] for sel in dlg.GetSelections()]
528	dlg.Destroy()
529	if not names: return
530	for name in names:
531	Id = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, name)
532	Npix,imagefile,imagetag = G2frame.GPXtree.GetImageLoc(Id)
533	imroot = os.path.splitext(imagefile)[0]
534	if imagetag:
535	imroot += '_' + str(imagetag)
536	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Image Controls'))
537	print('Writing '+imroot+'.imctrl')
538	File = open(imroot+'.imctrl','w')
539	keys = ['type','wavelength','calibrant','distance','center',
540	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth',
541	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
542	'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg',
543	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image']
544	for key in keys:
545	if key not in Data: continue #uncalibrated!
546	File.write(key+':'+str(Data[key])+'\n')
547	File.close()
548	mask = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Masks'))
549	G2imG.CleanupMasks(mask)
550	print('Writing '+imroot+'.immask')
551	File = open(imroot+'.immask','w')
552	for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
553	File.write(key+':'+str(mask[key])+'\n')
554	File.close()
555
556	def PutG2Image(filename,Comments,Data,Npix,image):
557	'Write an image as a python pickle - might be better as an .edf file?'
558	File = open(filename,'wb')
559	cPickle.dump([Comments,Data,Npix,image],File,2)
560	File.close()
561	return
562
563	def ProjFileOpen(G2frame,showProvenance=True):
564	'Read a GSAS-II project file and load into the G2 data tree'
565	if not os.path.exists(G2frame.GSASprojectfile):
566	print ('\n*** Error attempt to open project file that does not exist:\n '+
567	str(G2frame.GSASprojectfile))
568	return
569	LastSavedUsing = None
570	file = open(G2frame.GSASprojectfile,'rb')
571	if showProvenance: print ('loading from file: '+G2frame.GSASprojectfile)
572	#G2frame.SetTitle("GSAS-II data tree: "+
573	# os.path.split(G2frame.GSASprojectfile)[1])
574	G2frame.SetTitle("GSAS-II data tree: "+
575	os.path.split(G2frame.GSASprojectfile)[1],1)
576	wx.BeginBusyCursor()
577	try:
578	while True:
579	try:
580	if '2' in platform.python_version_tuple()[0]:
581	data = cPickle.load(file)
582	else:
583	data = cPickle.load(file,encoding='latin-1')
584	except EOFError:
585	break
586	datum = data[0]
587
588	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=datum[0])
589	if datum[0].startswith('PWDR'):
590	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
591	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
592	G2frame.GPXtree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
593	elif datum[0].startswith('HKLF'):
594	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
595	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
596	G2frame.GPXtree.SetItemPyData(Id,datum[1])
597	else:
598	G2frame.GPXtree.SetItemPyData(Id,datum[1])
599	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
600	LastSavedUsing = datum[1]['LastSavedUsing']
601	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance:
602	print('Packages used to create .GPX file:')
603	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
604	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
605	print(" {:<14s}: {:s}".format(p[0],p[1]))
606	else:
607	for p in datum[1]['PythonVersions']:
608	print(" {:<12s} {:s}".format(p[0]+':',p[1]))
609	oldPDF = False
610	for datus in data[1:]:
611	#patch - 1/23/17 PDF cleanup
612	if datus[0][:4] in ['I(Q)','S(Q)','F(Q)','G(R)']:
613	oldPDF = True
614	data[1][1][datus[0][:4]] = copy.deepcopy(datus[1][:2])
615	continue
616	#end PDF cleanup
617	sub = G2frame.GPXtree.AppendItem(Id,datus[0])
618	#patch
619	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
620	if datum[0].startswith('PWDR'):
621	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
622	else:
623	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
624	for item in datus[1][0]: #zip makes tuples - now make lists!
625	datus[1][0][item] = list(datus[1][0][item])
626	#end patch
627	G2frame.GPXtree.SetItemPyData(sub,datus[1])
628	if 'PDF ' in datum[0][:4] and oldPDF:
629	sub = G2frame.GPXtree.AppendItem(Id,'PDF Peaks')
630	G2frame.GPXtree.SetItemPyData(sub,{'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
631	if datum[0].startswith('IMG'): #retrieve image default flag & data if set
632	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls'))
633	if Data['setDefault']:
634	G2frame.imageDefault = Data
635	file.close()
636	if LastSavedUsing:
637	print('GPX load successful. Last saved with GSAS-II revision '+LastSavedUsing)
638	else:
639	print('project load successful')
640	G2frame.NewPlot = True
641	except:
642	msg = wx.MessageDialog(G2frame,message="Error reading file "+
643	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
644	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
645	msg.ShowModal()
646	finally:
647	wx.EndBusyCursor()
648	G2frame.Status.SetStatusText('Mouse RB drag/drop to reorder',0)
649
650	def ProjFileSave(G2frame):
651	'Save a GSAS-II project file'
652	if not G2frame.GPXtree.IsEmpty():
653	file = open(G2frame.GSASprojectfile,'wb')
654	print ('save to file: '+G2frame.GSASprojectfile)
655	# stick the file name into the tree and version info into tree so they are saved.
656	# (Controls should always be created at this point)
657	try:
658	Controls = G2frame.GPXtree.GetItemPyData(
659	G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
660	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
661	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
662	Controls['PythonVersions'] = G2frame.PackageVersions
663	except:
664	pass
665	wx.BeginBusyCursor()
666	try:
667	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
668	while item:
669	data = []
670	name = G2frame.GPXtree.GetItemText(item)
671	data.append([name,G2frame.GPXtree.GetItemPyData(item)])
672	item2, cookie2 = G2frame.GPXtree.GetFirstChild(item)
673	while item2:
674	name = G2frame.GPXtree.GetItemText(item2)
675	data.append([name,G2frame.GPXtree.GetItemPyData(item2)])
676	item2, cookie2 = G2frame.GPXtree.GetNextChild(item, cookie2)
677	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
678	cPickle.dump(data,file,2)
679	file.close()
680	pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
681	if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
682	G2frame.LastGPXdir = pth
683	finally:
684	wx.EndBusyCursor()
685	print('project save successful')
686
687	def SaveIntegration(G2frame,PickId,data,Overwrite=False):
688	'Save image integration results as powder pattern(s)'
689	azms = G2frame.Integrate[1]
690	X = G2frame.Integrate[2][:-1]
691	N = len(X)
692	Id = G2frame.GPXtree.GetItemParent(PickId)
693	name = G2frame.GPXtree.GetItemText(Id)
694	name = name.replace('IMG ',data['type']+' ')
695	Comments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Comments'))
696	Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
697	if 'PWDR' in name:
698	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
699	codes = [0 for i in range(12)]
700	elif 'SASD' in name:
701	names = ['Type','Lam','Zero','Azimuth']
702	codes = [0 for i in range(4)]
703	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
704	Xminmax = [X[0],X[-1]]
705	Azms = []
706	dazm = 0.
707	if data['fullIntegrate'] and data['outAzimuths'] == 1:
708	Azms = [45.0,] #a poor man's average?
709	else:
710	for i,azm in enumerate(azms[:-1]):
711	if azm > 360. and azms[i+1] > 360.:
712	Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
713	else:
714	Azms.append(G2img.meanAzm(azm,azms[i+1]))
715	dazm = np.min(np.abs(np.diff(azms)))/2.
716	G2frame.IntgOutList = []
717	for i,azm in enumerate(azms[:-1]):
718	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
719	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
720	# if Overwrite delete any duplicate
721	if Overwrite and G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname):
722	print('Replacing '+Aname)
723	item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname)
724	G2frame.GPXtree.Delete(item)
725	else:
726	nOcc = 0
727	while item:
728	Name = G2frame.GPXtree.GetItemText(item)
729	if Aname in Name:
730	nOcc += 1
731	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
732	if nOcc:
733	Aname += '(%d)'%(nOcc)
734	Sample = G2obj.SetDefaultSample() #set as Debye-Scherrer
735	Sample['Gonio. radius'] = data['distance']
736	Sample['Omega'] = data['GonioAngles'][0]
737	Sample['Chi'] = data['GonioAngles'][1]
738	Sample['Phi'] = data['GonioAngles'][2]
739	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
740	polariz = 0.99 #set default polarization for synchrotron radiation!
741	for item in Comments:
742	if 'polariz' in item:
743	try:
744	polariz = float(item.split('=')[1])
745	except:
746	polariz = 0.99
747	for key in ('Temperature','Pressure','Time','FreePrm1','FreePrm2','FreePrm3','Omega',
748	'Chi','Phi'):
749	if key.lower() in item.lower():
750	try:
751	Sample[key] = float(item.split('=')[1])
752	except:
753	pass
754	if 'label_prm' in item.lower():
755	for num in ('1','2','3'):
756	if 'label_prm'+num in item.lower():
757	Controls['FreePrm'+num] = item.split('=')[1].strip()
758	if 'PWDR' in Aname:
759	parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0,0.0001,Azms[i]]
760	elif 'SASD' in Aname:
761	Sample['Trans'] = data['SampleAbs'][0]
762	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
763	Y = G2frame.Integrate[0][i]
764	Ymin = np.min(Y)
765	Ymax = np.max(Y)
766	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
767	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=Aname)
768	G2frame.IntgOutList.append(Id)
769	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
770	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Limits'),copy.deepcopy([tuple(Xminmax),Xminmax]))
771	if 'PWDR' in Aname:
772	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
773	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
774	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
775	for item in inst[0]:
776	inst[0][item] = list(inst[0][item])
777	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),inst)
778	if 'PWDR' in Aname:
779	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
780	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
781	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Index Peak List'),[[],[]])
782	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Unit Cells List'),[])
783	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection Lists'),{})
784	elif 'SASD' in Aname:
785	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
786	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
787	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
788	valuesdict = {
789	'wtFactor':1.0,
790	'Dummy':False,
791	'ranId':ran.randint(0,sys.maxsize),
792	'Offset':[0.0,0.0],'delOffset':0.02Ymax,'refOffset':-0.1Ymax,'refDelt':0.1*Ymax,
793	'qPlot':False,'dPlot':False,'sqrtPlot':False,'Yminmax':[Ymin,Ymax]
794	}
795	G2frame.GPXtree.SetItemPyData(
796	Id,[valuesdict,
797	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
798	return Id #last powder pattern generated
799
800	def XYsave(G2frame,XY,labelX='X',labelY='Y',names=None):
801	'Save XY table data'
802	pth = G2G.GetExportPath(G2frame)
803	dlg = wx.FileDialog(
804	G2frame, 'Enter csv filename for XY table', pth, '',
805	'XY table file (.csv)\|.csv',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
806	try:
807	if dlg.ShowModal() == wx.ID_OK:
808	filename = dlg.GetPath()
809	filename = os.path.splitext(filename)[0]+'.csv'
810	File = open(filename,'w')
811	else:
812	filename = None
813	finally:
814	dlg.Destroy()
815	if not filename:
816	return
817	for i in range(len(XY)):
818	if names != None:
819	header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
820	else:
821	header = '%s,%s(%d)\n'%(labelX,labelY,i)
822	File.write(header)
823	for x,y in XY[i].T:
824	File.write('%.3f,%.3f\n'%(x,y))
825	File.close()
826	print (' XY data saved to: '+filename)
827
828	def askSaveDirectory(G2frame):
829	'''Ask the user to supply a directory name. Path name is used as the
830	starting point for the next export path search.
831
832	:returns: a directory name (str) or None if Cancel is pressed
833	'''
834	pth = G2G.GetExportPath(G2frame)
835	dlg = wx.DirDialog(
836	G2frame, 'Input directory where file(s) will be written', pth,
837	wx.DD_DEFAULT_STYLE)
838	dlg.CenterOnParent()
839	try:
840	if dlg.ShowModal() == wx.ID_OK:
841	filename = dlg.GetPath()
842	G2frame.LastExportDir = filename
843	else:
844	filename = None
845	finally:
846	dlg.Destroy()
847	return filename
848
849	def askSaveFile(G2frame,defnam,extension,longFormatName):
850	'''Ask the user to supply a file name
851
852	:returns: a file name (str) or None if Cancel is pressed
853	'''
854
855	pth = G2G.GetExportPath(G2frame)
856	dlg = wx.FileDialog(
857	G2frame, 'Input name for file to write', pth, defnam,
858	longFormatName+' ('+extension+')\|'+extension,
859	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
860	dlg.CenterOnParent()
861	try:
862	if dlg.ShowModal() == wx.ID_OK:
863	filename = dlg.GetPath()
864	G2frame.LastExportDir = os.path.split(filename)[0]
865	filename = os.path.splitext(filename)[0]+extension # make sure extension is correct
866	else:
867	filename = None
868	finally:
869	dlg.Destroy()
870	return filename
871
872	def PDFSave(G2frame,exports,PDFsaves):
873	'Save a PDF I(Q), S(Q), F(Q) and G(r) in column formats'
874	import scipy.interpolate as scintp
875	if len(exports) > 1:
876	dirname = askSaveDirectory(G2frame)
877	if not dirname: return
878	else:
879	defnam = exports[0].replace(' ','_')[5:]
880	filename = askSaveFile(G2frame,defnam,'.gr','G(r) file, etc.')
881	if not filename: return
882	dirname,filename = os.path.split(filename)
883	filename = os.path.splitext(filename)[0]
884	for export in exports:
885	if len(exports) > 1:
886	filename = export.replace(' ','_')[5:]
887	PickId = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, export)
888	PDFControls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame, PickId,'PDF Controls'))
889	if PDFsaves[0]: #I(Q)
890	iqfilename = ospath.join(dirname,filename+'.iq')
891	iqdata = PDFControls['I(Q)'][0]
892	iqfxn = scintp.interp1d(iqdata[0],iqdata[1],kind='linear')
893	iqfile = open(iqfilename,'w')
894	iqfile.write('#T I(Q) %s\n'%(export))
895	iqfile.write('#L Q I(Q)\n')
896	qnew = np.arange(iqdata[0][0],iqdata[0][-1],0.005)
897	iqnew = zip(qnew,iqfxn(qnew))
898	for q,iq in iqnew:
899	iqfile.write("%15.6g %15.6g\n" % (q,iq))
900	iqfile.close()
901	print (' I(Q) saved to: '+iqfilename)
902
903	if PDFsaves[1]: #S(Q)
904	sqfilename = ospath.join(dirname,filename+'.sq')
905	sqdata = PDFControls['S(Q)'][1]
906	sqfxn = scintp.interp1d(sqdata[0],sqdata[1],kind='linear')
907	sqfile = open(sqfilename,'w')
908	sqfile.write('#T S(Q) %s\n'%(export))
909	sqfile.write('#L Q S(Q)\n')
910	qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
911	sqnew = zip(qnew,sqfxn(qnew))
912	for q,sq in sqnew:
913	sqfile.write("%15.6g %15.6g\n" % (q,sq))
914	sqfile.close()
915	print (' S(Q) saved to: '+sqfilename)
916
917	if PDFsaves[2]: #F(Q)
918	fqfilename = ospath.join(dirname,filename+'.fq')
919	fqdata = PDFControls['F(Q)'][1]
920	fqfxn = scintp.interp1d(fqdata[0],fqdata[1],kind='linear')
921	fqfile = open(fqfilename,'w')
922	fqfile.write('#T F(Q) %s\n'%(export))
923	fqfile.write('#L Q F(Q)\n')
924	qnew = np.arange(fqdata[0][0],fqdata[0][-1],0.005)
925	fqnew = zip(qnew,fqfxn(qnew))
926	for q,fq in fqnew:
927	fqfile.write("%15.6g %15.6g\n" % (q,fq))
928	fqfile.close()
929	print (' F(Q) saved to: '+fqfilename)
930
931	if PDFsaves[3]: #G(R)
932	grfilename = ospath.join(dirname,filename+'.gr')
933	grdata = PDFControls['G(R)'][1]
934	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
935	grfile = open(grfilename,'w')
936	grfile.write('#T G(R) %s\n'%(export))
937	grfile.write('#L R G(R)\n')
938	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
939	grnew = zip(rnew,grfxn(rnew))
940	for r,gr in grnew:
941	grfile.write("%15.6g %15.6g\n" % (r,gr))
942	grfile.close()
943	print (' G(R) saved to: '+grfilename)
944
945	if PDFsaves[4]: #pdfGUI file for G(R)
946	pId = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, 'PWDR'+export[4:])
947	Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame, pId,'Instrument Parameters'))[0]
948	Limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame, pId,'Limits'))
949	grfilename = ospath.join(dirname,filename+'.gr')
950	grdata = PDFControls['G(R)'][1]
951	qdata = PDFControls['I(Q)'][1][0]
952	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
953	grfile = open(grfilename,'w')
954	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
955	grnew = zip(rnew,grfxn(rnew))
956
957	grfile.write('[DEFAULT]\n')
958	grfile.write('\n')
959	grfile.write('version = GSAS-II-v'+str(GSASIIpath.GetVersionNumber())+'\n')
960	grfile.write('\n')
961	grfile.write('# input and output specifications\n')
962	grfile.write('dataformat = Qnm\n')
963	grfile.write('inputfile = %s\n'%(PDFControls['Sample']['Name']))
964	grfile.write('backgroundfile = %s\n'%(PDFControls['Sample Bkg.']['Name']))
965	grfile.write('outputtype = gr\n')
966	grfile.write('\n')
967	grfile.write('# PDF calculation setup\n')
968	if 'x' in Inst['Type']:
969	grfile.write('mode = %s\n'%('xray'))
970	elif 'N' in Inst['Type']:
971	grfile.write('mode = %s\n'%('neutron'))
972	wave = G2mth.getMeanWave(Inst)
973	grfile.write('wavelength = %.5f\n'%(wave))
974	formula = ''
975	for el in PDFControls['ElList']:
976	formula += el
977	num = PDFControls['ElList'][el]['FormulaNo']
978	if num == round(num):
979	formula += '%d'%(int(num))
980	else:
981	formula += '%.2f'%(num)
982	grfile.write('composition = %s\n'%(formula))
983	grfile.write('bgscale = %.3f\n'%(-PDFControls['Sample Bkg.']['Mult']))
984	highQ = 2.*np.pi/G2lat.Pos2dsp(Inst,Limits[1][1])
985	grfile.write('qmaxinst = %.2f\n'%(highQ))
986	grfile.write('qmin = %.5f\n'%(qdata[0]))
987	grfile.write('qmax = %.4f\n'%(qdata[-1]))
988	grfile.write('rmin = %.2f\n'%(PDFControls['Rmin']))
989	grfile.write('rmax = %.2f\n'%(PDFControls['Rmax']))
990	grfile.write('rstep = 0.01\n')
991
992
993	grfile.write('\n')
994	grfile.write('# End of config '+63*'-')
995	grfile.write('\n')
996	grfile.write('#### start data\n')
997	grfile.write('#S 1\n')
998	grfile.write('#L r($\AA$) G($\AA^{-2}$)\n')
999	for r,gr in grnew:
1000	grfile.write("%15.2F %15.6F\n" % (r,gr))
1001	grfile.close()
1002	print (' G(R) saved to: '+grfilename)
1003
1004	def PeakListSave(G2frame,file,peaks):
1005	'Save powder peaks to a data file'
1006	print ('save peak list to file: '+G2frame.peaklistfile)
1007	if not peaks:
1008	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1009	try:
1010	dlg.ShowModal()
1011	finally:
1012	dlg.Destroy()
1013	return
1014	for peak in peaks:
1015	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1016	(peak[0],peak[2],peak[4],peak[6]))
1017	print ('peak list saved')
1018
1019	def IndexPeakListSave(G2frame,peaks):
1020	'Save powder peaks from the indexing list'
1021	file = open(G2frame.peaklistfile,'wa')
1022	print ('save index peak list to file: '+G2frame.peaklistfile)
1023	wx.BeginBusyCursor()
1024	try:
1025	if not peaks:
1026	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1027	try:
1028	dlg.ShowModal()
1029	finally:
1030	dlg.Destroy()
1031	return
1032	for peak in peaks:
1033	file.write("%12.6f\n" % (peak[7]))
1034	file.close()
1035	finally:
1036	wx.EndBusyCursor()
1037	print ('index peak list saved')
1038
1039	class MultipleChoicesDialog(wx.Dialog):
1040	'''A dialog that offers a series of choices, each with a
1041	title and a wx.Choice widget. Intended to be used Modally.
1042	typical input:
1043
1044	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1045	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1046
1047	selections are placed in self.chosen when OK is pressed
1048
1049	Also see GSASIIctrlGUI
1050	'''
1051	def __init__(self,choicelist,headinglist,
1052	head='Select options',
1053	title='Please select from options below',
1054	parent=None):
1055	self.chosen = []
1056	wx.Dialog.__init__(
1057	self,parent,wx.ID_ANY,head,
1058	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1059	panel = wx.Panel(self)
1060	mainSizer = wx.BoxSizer(wx.VERTICAL)
1061	mainSizer.Add((10,10),1)
1062	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1063	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1064	self.ChItems = []
1065	for choice,lbl in zip(choicelist,headinglist):
1066	mainSizer.Add((10,10),1)
1067	self.chosen.append(0)
1068	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1069	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1070	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1071	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1072
1073	OkBtn = wx.Button(panel,-1,"Ok")
1074	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1075	cancelBtn = wx.Button(panel,-1,"Cancel")
1076	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1077	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1078	btnSizer.Add((20,20),1)
1079	btnSizer.Add(OkBtn)
1080	btnSizer.Add((20,20),1)
1081	btnSizer.Add(cancelBtn)
1082	btnSizer.Add((20,20),1)
1083	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1084	panel.SetSizer(mainSizer)
1085	panel.Fit()
1086	self.Fit()
1087
1088	def OnOk(self,event):
1089	parent = self.GetParent()
1090	if parent is not None: parent.Raise()
1091	# save the results from the choice widgets
1092	self.chosen = []
1093	for w in self.ChItems:
1094	self.chosen.append(w.GetSelection())
1095	self.EndModal(wx.ID_OK)
1096
1097	def OnCancel(self,event):
1098	parent = self.GetParent()
1099	if parent is not None: parent.Raise()
1100	self.chosen = []
1101	self.EndModal(wx.ID_CANCEL)
1102
1103	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1104	confirmoverwrite=True, parent=None,
1105	multipleselect=False):
1106	'''If the filename is a zip file, extract a file from that
1107	archive.
1108
1109	:param list Selection: used to predefine the name of the file
1110	to be extracted. Filename case and zip directory name are
1111	ignored in selection; the first matching file is used.
1112
1113	:param bool confirmread: if True asks the user to confirm before expanding
1114	the only file in a zip
1115
1116	:param bool confirmoverwrite: if True asks the user to confirm
1117	before overwriting if the extracted file already exists
1118
1119	:param bool multipleselect: if True allows more than one zip
1120	file to be extracted, a list of file(s) is returned.
1121	If only one file is present, do not ask which one, otherwise
1122	offer a list of choices (unless selection is used).
1123
1124	:returns: the name of the file that has been created or a
1125	list of files (see multipleselect)
1126
1127	If the file is not a zipfile, return the name of the input file.
1128	If the zipfile is empty or no file has been selected, return None
1129	'''
1130	import zipfile # do this now, since we can save startup time by doing this only on need
1131	import shutil
1132	zloc = os.path.split(filename)[0]
1133	if not zipfile.is_zipfile(filename):
1134	#print("not zip")
1135	return filename
1136
1137	z = zipfile.ZipFile(filename,'r')
1138	zinfo = z.infolist()
1139
1140	if len(zinfo) == 0:
1141	#print('Zip has no files!')
1142	zlist = [-1]
1143	if selection:
1144	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1145	if selection.lower() in choices:
1146	zlist = [choices.index(selection.lower())]
1147	else:
1148	print('debug: file '+str(selection)+' was not found in '+str(filename))
1149	zlist = [-1]
1150	elif len(zinfo) == 1 and confirmread:
1151	result = wx.ID_NO
1152	dlg = wx.MessageDialog(
1153	parent,
1154	'Is file '+str(zinfo[0].filename)+
1155	' what you want to extract from '+
1156	str(os.path.split(filename)[1])+'?',
1157	'Confirm file',
1158	wx.YES_NO \| wx.ICON_QUESTION)
1159	try:
1160	result = dlg.ShowModal()
1161	finally:
1162	dlg.Destroy()
1163	if result == wx.ID_NO:
1164	zlist = [-1]
1165	else:
1166	zlist = [0]
1167	elif len(zinfo) == 1:
1168	zlist = [0]
1169	elif multipleselect:
1170	# select one or more from a from list
1171	choices = [i.filename for i in zinfo]
1172	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1173	'Choose file(s)',choices)
1174	if dlg.ShowModal() == wx.ID_OK:
1175	zlist = dlg.GetSelections()
1176	else:
1177	zlist = []
1178	dlg.Destroy()
1179	else:
1180	# select one from a from list
1181	choices = [i.filename for i in zinfo]
1182	dlg = wx.SingleChoiceDialog(parent,
1183	'Select file to extract from zip file'+str(filename),'Choose file',
1184	choices,)
1185	if dlg.ShowModal() == wx.ID_OK:
1186	zlist = [dlg.GetSelection()]
1187	else:
1188	zlist = [-1]
1189	dlg.Destroy()
1190
1191	outlist = []
1192	for zindex in zlist:
1193	if zindex >= 0:
1194	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1195	if os.path.exists(efil) and confirmoverwrite:
1196	result = wx.ID_NO
1197	dlg = wx.MessageDialog(parent,
1198	'File '+str(efil)+' already exists. OK to overwrite it?',
1199	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1200	try:
1201	result = dlg.ShowModal()
1202	finally:
1203	dlg.Destroy()
1204	if result == wx.ID_NO:
1205	zindex = -1
1206	if zindex >= 0:
1207	# extract the file to the current directory, regardless of it's original path
1208	#z.extract(zinfo[zindex],zloc)
1209	eloc,efil = os.path.split(zinfo[zindex].filename)
1210	outfile = os.path.join(zloc, efil)
1211	fpin = z.open(zinfo[zindex])
1212	fpout = file(outfile, "wb")
1213	shutil.copyfileobj(fpin, fpout)
1214	fpin.close()
1215	fpout.close()
1216	outlist.append(outfile)
1217	z.close()
1218	if multipleselect and len(outlist) >= 1:
1219	return outlist
1220	elif len(outlist) == 1:
1221	return outlist[0]
1222	else:
1223	return None
1224
1225	######################################################################
1226	# base classes for reading various types of data files
1227	# not used directly, only by subclassing
1228	######################################################################
1229	def BlockSelector(ChoiceList, ParentFrame=None,title='Select a block',
1230	size=None, header='Block Selector',useCancel=True):
1231	''' Provide a wx dialog to select a block if the file contains more
1232	than one set of data and one must be selected
1233	'''
1234	if useCancel:
1235	dlg = wx.SingleChoiceDialog(
1236	ParentFrame,title, header,ChoiceList)
1237	else:
1238	dlg = wx.SingleChoiceDialog(
1239	ParentFrame,title, header,ChoiceList,
1240	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1241	if size: dlg.SetSize(size)
1242	dlg.CenterOnParent()
1243	if dlg.ShowModal() == wx.ID_OK:
1244	sel = dlg.GetSelection()
1245	return sel
1246	else:
1247	return None
1248	dlg.Destroy()
1249
1250	def MultipleBlockSelector(ChoiceList, ParentFrame=None,
1251	title='Select a block',size=None, header='Block Selector'):
1252	'''Provide a wx dialog to select a block of data if the
1253	file contains more than one set of data and one must be
1254	selected.
1255
1256	:returns: a list of the selected blocks
1257	'''
1258	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1259	wx.CHOICEDLG_STYLE)
1260	dlg.CenterOnScreen()
1261	if size: dlg.SetSize(size)
1262	if dlg.ShowModal() == wx.ID_OK:
1263	sel = dlg.GetSelections()
1264	else:
1265	return []
1266	dlg.Destroy()
1267	selected = []
1268	if len(ChoiceList) in sel:
1269	return range(len(ChoiceList))
1270	else:
1271	return sel
1272	return selected
1273
1274	def MultipleChoicesSelector(choicelist, headinglist, ParentFrame=None, **kwargs):
1275	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1276	widget. Typical input:
1277
1278	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1279
1280	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1281
1282	optional keyword parameters are: head (window title) and title
1283	returns a list of selected indicies for each choice (or None)
1284	'''
1285	result = None
1286	dlg = MultipleChoicesDialog(choicelist,headinglist,
1287	parent=ParentFrame, **kwargs)
1288	dlg.CenterOnParent()
1289	if dlg.ShowModal() == wx.ID_OK:
1290	result = dlg.chosen
1291	dlg.Destroy()
1292	return result
1293
1294	def PhaseSelector(ChoiceList, ParentFrame=None,
1295	title='Select a phase', size=None,header='Phase Selector'):
1296	''' Provide a wx dialog to select a phase if the file contains more
1297	than one phase
1298	'''
1299	return BlockSelector(ChoiceList,ParentFrame,title,
1300	size,header)
1301
1302	######################################################################
1303	def striphist(var,insChar=''):
1304	'strip a histogram number from a var name'
1305	sv = var.split(':')
1306	if len(sv) <= 1: return var
1307	if sv[1]:
1308	sv[1] = insChar
1309	return ':'.join(sv)
1310	class ExportBaseclass(object):
1311	'''Defines a base class for the exporting of GSAS-II results.
1312
1313	This class is subclassed in the various exports/G2export_*.py files. Those files
1314	are imported in :meth:`GSASIIdataGUI.GSASII._init_Exports` which defines the
1315	appropriate menu items for each one and the .Exporter method is called
1316	directly from the menu item.
1317
1318	Routines may also define a .Writer method, which is used to write a single
1319	file without invoking any GUI objects.
1320	'''
1321	# TODO: review exporters producing exceptions where .Writer can't be used where G2frame is None (see CIF)
1322	# TODO: review conflicting uses of .Writer with mode (SeqRef) & elsewhere
1323	# TODO: move this class to G2fil
1324	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1325	self.G2frame = G2frame
1326	self.formatName = formatName # short string naming file type
1327	self.extension = extension
1328	if longFormatName: # longer string naming file type
1329	self.longFormatName = longFormatName
1330	else:
1331	self.longFormatName = formatName
1332	self.OverallParms = {}
1333	self.Phases = {}
1334	self.Histograms = {}
1335	self.powderDict = {}
1336	self.xtalDict = {}
1337	self.parmDict = {}
1338	self.sigDict = {}
1339	# updated in InitExport:
1340	self.currentExportType = None # type of export that has been requested
1341	# updated in ExportSelect (when used):
1342	self.phasenam = None # a list of selected phases
1343	self.histnam = None # a list of selected histograms
1344	self.filename = None # name of file to be written (single export) or template (multiple files)
1345	self.dirname = '' # name of directory where file(s) will be written
1346	self.fullpath = '' # name of file being written -- full path
1347
1348	# items that should be defined in a subclass of this class
1349	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1350	# The following types are defined: 'project', "phase", "powder", "single"
1351	self.multiple = False # set as True if the class can export multiple phases or histograms
1352	# self.multiple is ignored for "project" exports
1353
1354	def InitExport(self,event):
1355	'''Determines the type of menu that called the Exporter and
1356	misc initialization.
1357	'''
1358	self.filename = None # name of file to be written (single export)
1359	self.dirname = '' # name of file to be written (multiple export)
1360	if event:
1361	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1362
1363	def MakePWDRfilename(self,hist):
1364	'''Make a filename root (no extension) from a PWDR histogram name
1365
1366	:param str hist: the histogram name in data tree (starts with "PWDR ")
1367	'''
1368	file0 = ''
1369	file1 = hist[5:]
1370	# replace repeated blanks
1371	while file1 != file0:
1372	file0 = file1
1373	file1 = file0.replace(' ',' ').strip()
1374	file0 = file1.replace('Azm= ','A')
1375	# if angle has unneeded decimal places on aziumuth, remove them
1376	if file0[-3:] == '.00': file0 = file0[:-3]
1377	file0 = file0.replace('.','_')
1378	file0 = file0.replace(' ','_')
1379	return file0
1380
1381	def ExportSelect(self,AskFile='ask'):
1382	'''Selects histograms or phases when needed. Sets a default file name when
1383	requested into self.filename; always sets a default directory in self.dirname.
1384
1385	:param bool AskFile: Determines how this routine processes getting a
1386	location to store the current export(s).
1387
1388	* if AskFile is 'ask' (default option), get the name of the file to be written;
1389	self.filename and self.dirname are always set. In the case where
1390	multiple files must be generated, the export routine should do this
1391	based on self.filename as a template.
1392	* if AskFile is 'dir', get the name of the directory to be used;
1393	self.filename is not used, but self.dirname is always set. The export routine
1394	will always generate the file name.
1395	* if AskFile is 'single', get only the name of the directory to be used when
1396	multiple items will be written (as multiple files) are used
1397	or a complete file name is requested when a single file
1398	name is selected. self.dirname is always set and self.filename used
1399	only when a single file is selected.
1400	* if AskFile is 'default', creates a name of the file to be used from
1401	the name of the project (.gpx) file. If the project has not been saved,
1402	then the name of file is requested.
1403	self.filename and self.dirname are always set. In the case where
1404	multiple file names must be generated, the export routine should do this
1405	based on self.filename.
1406	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1407	file. If the project has not been saved, then a directory is requested.
1408	self.filename is not used.
1409
1410	:returns: True in case of an error
1411	'''
1412
1413	numselected = 1
1414	if self.currentExportType == 'phase':
1415	if len(self.Phases) == 0:
1416	self.G2frame.ErrorDialog(
1417	'Empty project',
1418	'Project does not contain any phases.')
1419	return True
1420	elif len(self.Phases) == 1:
1421	self.phasenam = self.Phases.keys()
1422	elif self.multiple:
1423	choices = sorted(self.Phases.keys())
1424	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1425	if phasenum is None: return True
1426	self.phasenam = [choices[i] for i in phasenum]
1427	if not self.phasenam: return True
1428	numselected = len(self.phasenam)
1429	else:
1430	choices = sorted(self.Phases.keys())
1431	phasenum = G2G.ItemSelector(choices,self.G2frame)
1432	if phasenum is None: return True
1433	self.phasenam = [choices[phasenum]]
1434	numselected = len(self.phasenam)
1435	elif self.currentExportType == 'single':
1436	if len(self.xtalDict) == 0:
1437	self.G2frame.ErrorDialog(
1438	'Empty project',
1439	'Project does not contain any single crystal data.')
1440	return True
1441	elif len(self.xtalDict) == 1:
1442	self.histnam = self.xtalDict.values()
1443	elif self.multiple:
1444	choices = sorted(self.xtalDict.values())
1445	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1446	if not hnum: return True
1447	self.histnam = [choices[i] for i in hnum]
1448	numselected = len(self.histnam)
1449	else:
1450	choices = sorted(self.xtalDict.values())
1451	hnum = G2G.ItemSelector(choices,self.G2frame)
1452	if hnum is None: return True
1453	self.histnam = [choices[hnum]]
1454	numselected = len(self.histnam)
1455	elif self.currentExportType == 'powder':
1456	if len(self.powderDict) == 0:
1457	self.G2frame.ErrorDialog(
1458	'Empty project',
1459	'Project does not contain any powder data.')
1460	return True
1461	elif len(self.powderDict) == 1:
1462	self.histnam = self.powderDict.values()
1463	elif self.multiple:
1464	choices = sorted(self.powderDict.values())
1465	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1466	if not hnum: return True
1467	self.histnam = [choices[i] for i in hnum]
1468	numselected = len(self.histnam)
1469	else:
1470	choices = sorted(self.powderDict.values())
1471	hnum = G2G.ItemSelector(choices,self.G2frame)
1472	if hnum is None: return True
1473	self.histnam = [choices[hnum]]
1474	numselected = len(self.histnam)
1475	elif self.currentExportType == 'image':
1476	if len(self.Histograms) == 0:
1477	self.G2frame.ErrorDialog(
1478	'Empty project',
1479	'Project does not contain any images.')
1480	return True
1481	elif len(self.Histograms) == 1:
1482	self.histnam = self.Histograms.keys()
1483	else:
1484	choices = sorted(self.Histograms.keys())
1485	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1486	if self.multiple:
1487	if not hnum: return True
1488	self.histnam = [choices[i] for i in hnum]
1489	else:
1490	if hnum is None: return True
1491	self.histnam = [choices[hnum]]
1492	numselected = len(self.histnam)
1493	if self.currentExportType == 'map':
1494	# search for phases with maps
1495	mapPhases = []
1496	choices = []
1497	for phasenam in sorted(self.Phases):
1498	phasedict = self.Phases[phasenam] # pointer to current phase info
1499	if len(phasedict['General']['Map'].get('rho',[])):
1500	mapPhases.append(phasenam)
1501	if phasedict['General']['Map'].get('Flip'):
1502	choices.append('Charge flip map: '+str(phasenam))
1503	elif phasedict['General']['Map'].get('MapType'):
1504	choices.append(
1505	str(phasedict['General']['Map'].get('MapType'))
1506	+ ' map: ' + str(phasenam))
1507	else:
1508	choices.append('unknown map: '+str(phasenam))
1509	# select a map if needed
1510	if len(mapPhases) == 0:
1511	self.G2frame.ErrorDialog(
1512	'Empty project',
1513	'Project does not contain any maps.')
1514	return True
1515	elif len(mapPhases) == 1:
1516	self.phasenam = mapPhases
1517	else:
1518	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1519	if self.multiple:
1520	if not phasenum: return True
1521	self.phasenam = [mapPhases[i] for i in phasenum]
1522	else:
1523	if phasenum is None: return True
1524	self.phasenam = [mapPhases[phasenum]]
1525	numselected = len(self.phasenam)
1526
1527	# items selected, now set self.dirname and usually self.filename
1528	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1529	AskFile == 'default' and not self.G2frame.GSASprojectfile
1530	):
1531	filename = self.askSaveFile()
1532	if not filename: return True
1533	self.dirname,self.filename = os.path.split(filename)
1534	elif AskFile == 'dir' or AskFile == 'single' or (
1535	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1536	):
1537	self.dirname = self.askSaveDirectory()
1538	if not self.dirname: return True
1539	elif AskFile == 'default-dir' or AskFile == 'default':
1540	self.dirname,self.filename = os.path.split(
1541	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1542	)
1543	else:
1544	raise Exception('This should not happen!')
1545
1546	def loadParmDict(self):
1547	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1548	refined values to those from the last cycle and set the uncertainties for the
1549	refined parameters in another dict (self.sigDict).
1550
1551	Expands the parm & sig dicts to include values derived from constraints.
1552	'''
1553	self.parmDict = {}
1554	self.sigDict = {}
1555	rigidbodyDict = {}
1556	covDict = {}
1557	consDict = {}
1558	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1559	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1560	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1561	while item:
1562	name = self.G2frame.GPXtree.GetItemText(item)
1563	if name == 'Rigid bodies':
1564	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(item)
1565	elif name == 'Covariance':
1566	covDict = self.G2frame.GPXtree.GetItemPyData(item)
1567	elif name == 'Constraints':
1568	consDict = self.G2frame.GPXtree.GetItemPyData(item)
1569	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1570	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1571	self.parmDict.update(rbDict)
1572	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1573	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1574	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1575	self.parmDict.update(phaseDict)
1576	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
1577	Phases,Histograms,Print=False,resetRefList=False)
1578	self.parmDict.update(hapDict)
1579	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1580	self.parmDict.update(histDict)
1581	self.parmDict.update(zip(
1582	covDict.get('varyList',[]),
1583	covDict.get('variables',[])))
1584	self.sigDict = dict(zip(
1585	covDict.get('varyList',[]),
1586	covDict.get('sig',[])))
1587	# expand to include constraints: first compile a list of constraints
1588	constList = []
1589	for item in consDict:
1590	if item.startswith('_'): continue
1591	constList += consDict[item]
1592	# now process the constraints
1593	G2mv.InitVars()
1594	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
1595	varyList = covDict.get('varyListStart')
1596	if varyList is None and len(constDict) == 0:
1597	# no constraints can use varyList
1598	varyList = covDict.get('varyList')
1599	elif varyList is None:
1600	# old GPX file from before pre-constraint varyList is saved
1601	print (' * Old refinement: Please use Calculate/Refine to redo *')
1602	raise Exception(' * Export aborted *')
1603	else:
1604	varyList = list(varyList)
1605	try:
1606	groups,parmlist = G2mv.GroupConstraints(constDict)
1607	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
1608	except:
1609	# this really should not happen
1610	print (' * ERROR - constraints are internally inconsistent *')
1611	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
1612	print ('Errors'+errmsg)
1613	if warnmsg: print ('Warnings'+warnmsg)
1614	raise Exception(' * CIF creation aborted *')
1615	# add the constrained values to the parameter dictionary
1616	G2mv.Dict2Map(self.parmDict,varyList)
1617	# and add their uncertainties into the esd dictionary (sigDict)
1618	if covDict.get('covMatrix') is not None:
1619	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
1620
1621	def loadTree(self):
1622	'''Load the contents of the data tree into a set of dicts
1623	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
1624	& self.xtalDict)
1625
1626	* The childrenless data tree items are overall parameters/controls for the
1627	entire project and are placed in self.OverallParms
1628	* Phase items are placed in self.Phases
1629	* Data items are placed in self.Histogram. The key for these data items
1630	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
1631	'''
1632	self.OverallParms = {}
1633	self.powderDict = {}
1634	self.xtalDict = {}
1635	self.Phases = {}
1636	self.Histograms = {}
1637	self.SeqRefdata = None
1638	self.SeqRefhist = None
1639	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1640	histType = None
1641	if self.currentExportType == 'phase':
1642	# if exporting phases load them here
1643	sub = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Phases')
1644	if not sub:
1645	print ('no phases found')
1646	return True
1647	item, cookie = self.G2frame.GPXtree.GetFirstChild(sub)
1648	while item:
1649	phaseName = self.G2frame.GPXtree.GetItemText(item)
1650	self.Phases[phaseName] = self.G2frame.GPXtree.GetItemPyData(item)
1651	item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie)
1652	return
1653	elif self.currentExportType == 'single':
1654	histType = 'HKLF'
1655	elif self.currentExportType == 'powder':
1656	histType = 'PWDR'
1657	elif self.currentExportType == 'image':
1658	histType = 'IMG'
1659
1660	if histType: # Loading just one kind of tree entry
1661	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1662	while item:
1663	name = self.G2frame.GPXtree.GetItemText(item)
1664	if name.startswith(histType):
1665	if self.Histograms.get(name): # there is already an item with this name
1666	print('Histogram name '+str(name)+' is repeated. Renaming')
1667	if name[-1] == '9':
1668	name = name[:-1] + '10'
1669	elif name[-1] in '012345678':
1670	name = name[:-1] + str(int(name[-1])+1)
1671	else:
1672	name += '-1'
1673	self.Histograms[name] = {}
1674	# the main info goes into Data, but the 0th
1675	# element contains refinement results, carry
1676	# that over too now.
1677	self.Histograms[name]['Data'] = self.G2frame.GPXtree.GetItemPyData(item)[1]
1678	self.Histograms[name][0] = self.G2frame.GPXtree.GetItemPyData(item)[0]
1679	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1680	while item2:
1681	child = self.G2frame.GPXtree.GetItemText(item2)
1682	self.Histograms[name][child] = self.G2frame.GPXtree.GetItemPyData(item2)
1683	item2, cookie2 = self.G2frame.GPXtree.GetNextChild(item, cookie2)
1684	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1685	# index powder and single crystal histograms by number
1686	for hist in self.Histograms:
1687	if hist.startswith("PWDR"):
1688	d = self.powderDict
1689	elif hist.startswith("HKLF"):
1690	d = self.xtalDict
1691	else:
1692	return
1693	i = self.Histograms[hist].get('hId')
1694	if i is None and not d.keys():
1695	i = 0
1696	elif i is None or i in d.keys():
1697	i = max(d.keys())+1
1698	d[i] = hist
1699	return
1700	# else standard load: using all interlinked phases and histograms
1701	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1702	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1703	while item:
1704	name = self.G2frame.GPXtree.GetItemText(item)
1705	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1706	if not item2:
1707	self.OverallParms[name] = self.G2frame.GPXtree.GetItemPyData(item)
1708	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1709	# index powder and single crystal histograms
1710	for hist in self.Histograms:
1711	i = self.Histograms[hist]['hId']
1712	if hist.startswith("PWDR"):
1713	self.powderDict[i] = hist
1714	elif hist.startswith("HKLF"):
1715	self.xtalDict[i] = hist
1716
1717	def dumpTree(self,mode='type'):
1718	'''Print out information on the data tree dicts loaded in loadTree.
1719	Used for testing only.
1720	'''
1721	if self.SeqRefdata and self.SeqRefhist:
1722	print('Note that dumpTree does not show sequential results')
1723	print ('\nOverall')
1724	if mode == 'type':
1725	def Show(arg): return type(arg)
1726	else:
1727	def Show(arg): return arg
1728	for key in self.OverallParms:
1729	print (' '+key+Show(self.OverallParms[key]))
1730	print ('Phases')
1731	for key1 in self.Phases:
1732	print (' '+key1+Show(self.Phases[key1]))
1733	print ('Histogram')
1734	for key1 in self.Histograms:
1735	print (' '+key1+Show(self.Histograms[key1]))
1736	for key2 in self.Histograms[key1]:
1737	print (' '+key2+Show(self.Histograms[key1][key2]))
1738
1739	def defaultSaveFile(self):
1740	return os.path.abspath(
1741	os.path.splitext(self.G2frame.GSASprojectfile
1742	)[0]+self.extension)
1743
1744	def askSaveFile(self):
1745	'''Ask the user to supply a file name
1746
1747	:returns: a file name (str) or None if Cancel is pressed
1748	'''
1749
1750	pth = G2G.GetExportPath(self.G2frame)
1751	defnam = os.path.splitext(
1752	os.path.split(self.G2frame.GSASprojectfile)[1]
1753	)[0]+self.extension
1754	dlg = wx.FileDialog(
1755	self.G2frame, 'Input name for file to write', pth, defnam,
1756	self.longFormatName+' ('+self.extension+')\|'+self.extension,
1757	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
1758	dlg.CenterOnParent()
1759	try:
1760	if dlg.ShowModal() == wx.ID_OK:
1761	filename = dlg.GetPath()
1762	self.G2frame.LastExportDir = os.path.split(filename)[0]
1763	filename = os.path.splitext(filename)[0]+self.extension # make sure extension is correct
1764	else:
1765	filename = None
1766	finally:
1767	dlg.Destroy()
1768	return filename
1769
1770	def askSaveDirectory(self):
1771	'''Ask the user to supply a directory name. Path name is used as the
1772	starting point for the next export path search.
1773
1774	:returns: a directory name (str) or None if Cancel is pressed
1775	'''
1776	pth = G2G.GetExportPath(self.G2frame)
1777	dlg = wx.DirDialog(
1778	self.G2frame, 'Input directory where file(s) will be written', pth,
1779	wx.DD_DEFAULT_STYLE)
1780	dlg.CenterOnParent()
1781	try:
1782	if dlg.ShowModal() == wx.ID_OK:
1783	filename = dlg.GetPath()
1784	self.G2frame.LastExportDir = filename
1785	else:
1786	filename = None
1787	finally:
1788	dlg.Destroy()
1789	return filename
1790
1791	# Tools for file writing.
1792	def OpenFile(self,fil=None,mode='w'):
1793	'''Open the output file
1794
1795	:param str fil: The name of the file to open. If None (default)
1796	the name defaults to self.dirname + self.filename.
1797	If an extension is supplied, it is not overridded,
1798	but if not, the default extension is used.
1799	:returns: the file object opened by the routine which is also
1800	saved as self.fp
1801	'''
1802	if mode == 'd': # debug mode
1803	self.fullpath = '(stdout)'
1804	self.fp = sys.stdout
1805	return
1806	if not fil:
1807	if not os.path.splitext(self.filename)[1]:
1808	self.filename += self.extension
1809	fil = os.path.join(self.dirname,self.filename)
1810	self.fullpath = os.path.abspath(fil)
1811	self.fp = open(self.fullpath,mode)
1812	return self.fp
1813
1814	def Write(self,line):
1815	'''write a line of output, attaching a line-end character
1816
1817	:param str line: the text to be written.
1818	'''
1819	self.fp.write(line+'\n')
1820
1821	def CloseFile(self,fp=None):
1822	'''Close a file opened in OpenFile
1823
1824	:param file fp: the file object to be closed. If None (default)
1825	file object self.fp is closed.
1826	'''
1827	if self.fp == sys.stdout: return # debug mode
1828	if fp is None:
1829	fp = self.fp
1830	self.fp = None
1831	if fp is not None: fp.close()
1832
1833	def SetSeqRef(self,data,hist):
1834	'''Set the exporter to retrieve results from a sequential refinement
1835	rather than the main tree
1836	'''
1837	self.SeqRefdata = data
1838	self.SeqRefhist = hist
1839	data_name = data[hist]
1840	for i,val in zip(data_name['varyList'],data_name['sig']):
1841	self.sigDict[i] = val
1842	self.sigDict[striphist(i)] = val
1843	for i in data_name['parmDict']:
1844	self.parmDict[striphist(i)] = data_name['parmDict'][i]
1845	self.parmDict[i] = data_name['parmDict'][i]
1846	# zero out the dA[xyz] terms, they would only bring confusion
1847	key = i.split(':')
1848	if len(key) < 3: continue
1849	if key[2].startswith('dA'):
1850	self.parmDict[i] = 0.0
1851	for i,(val,sig) in data_name.get('depParmDict',{}).iteritems():
1852	self.parmDict[i] = val
1853	self.sigDict[i] = sig
1854	#GSASIIpath.IPyBreak()
1855
1856	def SetFromArray(self,hist,histname):
1857	'''Load a histogram into the exporter in preparation for use of the .Writer
1858	rather than the main tree. This is used in GSASIIscriptable when wx
1859	is not present.
1860	'''
1861	self.Histograms[histname] = {}
1862	self.Histograms[histname]['Data'] = hist['data'][1]
1863	self.Histograms[histname]['Instrument Parameters'] = hist['Instrument Parameters']
1864	self.Histograms[histname]['Sample Parameters'] = hist['Sample Parameters']
1865
1866	# Tools to pull information out of the data arrays
1867	def GetCell(self,phasenam):
1868	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1869
1870	:param str phasenam: the name for the selected phase
1871	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1872	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1873	cell values and `cellSig` has their uncertainties.
1874	"""
1875	if self.SeqRefdata and self.SeqRefhist:
1876	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
1877	phasedict = self.Phases[phasenam] # pointer to current phase info
1878	try:
1879	pfx = str(phasedict['pId'])+'::'
1880	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
1881	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
1882	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
1883	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
1884	return cellList,cellSig
1885	except KeyError:
1886	cell = phasedict['General']['Cell'][1:]
1887	return cell,7*[0]
1888
1889	def GetSeqCell(self,phasenam,data_name):
1890	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1891	and histogram in a sequential fit
1892
1893	:param str phasenam: the name for the selected phase
1894	:param dict data_name: the sequential refinement parameters for the selected histogram
1895	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1896	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1897	cell values and `cellSig` has their uncertainties.
1898	"""
1899	phasedict = self.Phases[phasenam]
1900	SGdata = phasedict['General']['SGData']
1901	pId = phasedict['pId']
1902	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
1903	ESDlookup = {}
1904	Dlookup = {}
1905	varied = [striphist(i) for i in data_name['varyList']]
1906	for item,val in data_name['newCellDict'].iteritems():
1907	if item in varied:
1908	ESDlookup[val[0]] = item
1909	Dlookup[item] = val[0]
1910	A = RecpCellTerms[:]
1911	for i in range(6):
1912	var = str(pId)+'::A'+str(i)
1913	if var in ESDlookup:
1914	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
1915	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
1916	zeroDict = {i:0.0 for i in cellDict}
1917	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
1918	covData = {
1919	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
1920	'covMatrix': data_name['covMatrix']
1921	}
1922	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
1923
1924	def GetAtoms(self,phasenam):
1925	"""Gets the atoms associated with a phase. Can be used with standard
1926	or macromolecular phases
1927
1928	:param str phasenam: the name for the selected phase
1929	:returns: a list of items for eac atom where each item is a list containing:
1930	label, typ, mult, xyz, and td, where
1931
1932	* label and typ are the atom label and the scattering factor type (str)
1933	* mult is the site multiplicity (int)
1934	* xyz is contains a list with four pairs of numbers:
1935	x, y, z and fractional occupancy and
1936	their standard uncertainty (or a negative value)
1937	* td is contains a list with either one or six pairs of numbers:
1938	if one number it is U\ :sub:`iso` and with six numbers it is
1939	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
1940	paired with their standard uncertainty (or a negative value)
1941	"""
1942	phasedict = self.Phases[phasenam] # pointer to current phase info
1943	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1944	cfrac = cx+3
1945	fpfx = str(phasedict['pId'])+'::Afrac:'
1946	atomslist = []
1947	for i,at in enumerate(phasedict['Atoms']):
1948	if phasedict['General']['Type'] == 'macromolecular':
1949	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1950	else:
1951	label = at[ct-1]
1952	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
1953	fsig = self.sigDict.get(fpfx+str(i),-0.009)
1954	mult = at[cs+1]
1955	typ = at[ct]
1956	xyz = []
1957	for j,v in enumerate(('x','y','z')):
1958	val = at[cx+j]
1959	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
1960	val = self.parmDict.get(pfx, val)
1961	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
1962	sig = self.sigDict.get(dpfx,-0.000009)
1963	xyz.append((val,sig))
1964	xyz.append((fval,fsig))
1965	td = []
1966	if at[cia] == 'I':
1967	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
1968	val = self.parmDict.get(pfx,at[cia+1])
1969	sig = self.sigDict.get(pfx,-0.0009)
1970	td.append((val,sig))
1971	else:
1972	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
1973	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
1974	val = self.parmDict.get(pfx,at[cia+2+i])
1975	sig = self.sigDict.get(pfx,-0.0009)
1976	td.append((val,sig))
1977	atomslist.append((label,typ,mult,xyz,td))
1978	return atomslist
1979	######################################################################
1980	def ExportPowderList(G2frame):
1981	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
1982	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1983
1984	:param wx.Frame G2frame: the GSAS-II main data tree window
1985	'''
1986	extList = []
1987	for obj in G2frame.exporterlist:
1988	if 'powder' in obj.exporttype:
1989	try:
1990	obj.Writer
1991	extList.append(obj.extension)
1992	except AttributeError:
1993	pass
1994	return extList
1995
1996	def ExportPowder(G2frame,TreeName,fileroot,extension):
1997	'''Writes a single powder histogram using the Export routines.
1998	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1999
2000	:param wx.Frame G2frame: the GSAS-II main data tree window
2001	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
2002	:param str fileroot: name for file to be written, extension ignored
2003	:param str extension: extension for file to be written (start with '.'). Must
2004	match a powder export routine that has a Writer object.
2005	'''
2006	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
2007	for obj in G2frame.exporterlist:
2008	if obj.extension == extension and 'powder' in obj.exporttype:
2009	obj.currentExportType = 'powder'
2010	obj.InitExport(None)
2011	obj.loadTree() # load all histograms in tree into dicts
2012	if TreeName not in obj.Histograms:
2013	raise Exception('Histogram not found: '+str(TreeName))
2014	try:
2015	obj.Writer
2016	except AttributeError:
2017	continue
2018	try:
2019	obj.Writer(TreeName,filename)
2020	print('wrote file '+filename)
2021	return
2022	except Exception:
2023	print('Export Routine for '+extension+' failed.')
2024	else:
2025	print('No Export routine supports extension '+extension)
2026
2027	def ExportSequential(G2frame,data,obj,exporttype):
2028	'''
2029	Used to export from every phase/dataset in a sequential refinement using
2030	a .Writer method for either projects or phases. Prompts to select histograms
2031	and for phase exports, which phase(s).
2032
2033	:param wx.Frame G2frame: the GSAS-II main data tree window
2034	:param dict data: the sequential refinement data object
2035	:param str exporttype: indicates the type of export ('project' or 'phase')
2036	'''
2037	if len(data['histNames']) == 0:
2038	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
2039	obj.InitExport(None)
2040	obj.loadTree()
2041	obj.loadParmDict()
2042	if len(data['histNames']) == 1:
2043	histlist = data['histNames']
2044	else:
2045	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
2046	'Select histograms',data['histNames'])
2047	if dlg.ShowModal() == wx.ID_OK:
2048	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
2049	dlg.Destroy()
2050	else:
2051	dlg.Destroy()
2052	return
2053	if exporttype == 'Phase':
2054	phaselist = list(obj.Phases.keys())
2055	if len(obj.Phases) == 0:
2056	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
2057	return
2058	elif len(obj.Phases) > 1:
2059	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
2060	'Select phases', phaselist)
2061	if dlg.ShowModal() == wx.ID_OK:
2062	phaselist = [phaselist[l] for l in dlg.GetSelections()]
2063	dlg.Destroy()
2064	else:
2065	dlg.Destroy()
2066	return
2067	filename = obj.askSaveFile()
2068	if not filename: return True
2069	obj.dirname,obj.filename = os.path.split(filename)
2070	print('Writing output to file '+str(obj.filename)+"...")
2071	mode = 'w'
2072	for p in phaselist:
2073	for h in histlist:
2074	obj.SetSeqRef(data,h)
2075	#GSASIIpath.IPyBreak()
2076	obj.Writer(h,phasenam=p,mode=mode)
2077	mode = 'a'
2078	print('...done')
2079	elif exporttype == 'Project': # note that the CIF exporter is not yet ready for this
2080	filename = obj.askSaveFile()
2081	if not filename: return True
2082	obj.dirname,obj.filename = os.path.split(filename)
2083	print('Writing output to file '+str(obj.filename)+"...")
2084	mode = 'w'
2085	for h in histlist:
2086	obj.SetSeqRef(data,h)
2087	obj.Writer(h,mode=mode)
2088	print('\t'+str(h)+' written')
2089	mode = 'a'
2090	print('...done')
2091	elif exporttype == 'Powder':
2092	filename = obj.askSaveFile()
2093	if not filename: return True
2094	obj.dirname,obj.filename = os.path.split(filename)
2095	print('Writing output to file '+str(obj.filename)+"...")
2096	mode = 'w'
2097	for h in histlist:
2098	obj.SetSeqRef(data,h)
2099	obj.Writer(h,mode=mode)
2100	print('\t'+str(h)+' written')
2101	mode = 'a'
2102	print('...done')
2103
2104	def ReadDIFFaX(DIFFaXfile):
2105	print ('read '+DIFFaXfile)
2106	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
2107	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
2108	df = open(DIFFaXfile,'r')
2109	lines = df.readlines()
2110	df.close()
2111	struct = False
2112	Struct = []
2113	stack = False
2114	Stack = []
2115	trans = False
2116	Trans = []
2117	for diff in lines:
2118	diff = diff[:-1].lower()
2119	if '!' in diff:
2120	continue
2121	while '}' in diff: #strip comments
2122	iB = diff.index('{')
2123	iF = diff.index('}')+1
2124	if iB:
2125	diff = diff[:iB]
2126	else:
2127	diff = diff[iF:]
2128	if not diff:
2129	continue
2130	if diff.strip() == 'instrumental':
2131	continue
2132	if diff.strip() == 'structural':
2133	struct = True
2134	continue
2135	elif diff.strip() == 'stacking':
2136	struct = False
2137	stack = True
2138	continue
2139	elif diff.strip() == 'transitions':
2140	stack = False
2141	trans = True
2142	continue
2143	diff = diff.strip()
2144	if struct:
2145	if diff:
2146	Struct.append(diff)
2147	elif stack:
2148	if diff:
2149	Stack.append(diff)
2150	elif trans:
2151	if diff:
2152	Trans.append(diff)
2153
2154	#STRUCTURE records
2155	laueRec = Struct[1].split()
2156	Layer['Laue'] = laueRec[0]
2157	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2158	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2159	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2160	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2161	cell = Struct[0].split()
2162	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2163	nLayers = int(Struct[2])
2164	N = 3
2165	if 'layer' not in Struct[3]:
2166	N = 4
2167	if Struct[3] != 'infinite':
2168	width = Struct[3].split()
2169	Layer['Width'][0] = [float(width[0]),float(width[1])]
2170	for nL in range(nLayers):
2171	if '=' in Struct[N]:
2172	name = Struct[N].split('=')
2173	sameas = int(name[1])-1
2174	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2175	N += 1
2176	continue
2177	Symm = 'None'
2178	if 'centro' in Struct[N+1]: Symm = '-1'
2179	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2180	N += 2
2181	while 'layer' not in Struct[N]:
2182	atom = Struct[N][4:].split()
2183	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2184	if atomType not in Layer['AtInfo']:
2185	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2186	atomName = '%s(%s)'%(atomType,atom[0])
2187	newVals = []
2188	for val in atom[1:6]:
2189	if '/' in val:
2190	newVals.append(eval(val+'.'))
2191	else:
2192	newVals.append(float(val))
2193	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2194	Layer['Layers'][-1]['Atoms'].append(atomRec)
2195	N += 1
2196	if N > len(Struct)-1:
2197	break
2198	#TRANSITIONS records
2199	transArray = []
2200	N = 0
2201	for i in range(nLayers):
2202	transArray.append([])
2203	for j in range(nLayers):
2204	vals = Trans[N].split()
2205	newVals = []
2206	for val in vals[:4]:
2207	if '/' in val:
2208	newVals.append(eval(val+'.'))
2209	else:
2210	newVals.append(float(val))
2211	transArray[-1].append(newVals+['',False])
2212	N += 1
2213	Layer['Transitions'] = transArray
2214	#STACKING records
2215	Layer['Stacking'] = [Stack[0],'']
2216	if Stack[0] == 'recursive':
2217	Layer['Stacking'][1] = Stack[1]
2218	elif Stack[0] == 'explicit':
2219	if Stack[1] == 'random':
2220	Layer['Stacking'][1] = Stack[1]
2221	else:
2222	Layer['Stacking'][1] = 'list'
2223	Layer['Stacking'].append('')
2224	for stack in Stack[2:]:
2225	Layer['Stacking'][2] += ' '+stack
2226	return Layer
2227
2228	def readColMetadata(imagefile):
2229	'''Reads image metadata from a column-oriented metadata table
2230	(1-ID style .par file). Called by :func:`GetColumnMetadata`
2231
2232	The .par file has any number of columns separated by spaces.
2233	The directory for the file must be specified in
2234	Config variable ``Column_Metadata_directory``.
2235	As an index to the .par file a second "label file" must be specified with the
2236	same file root name as the .par file but the extension must be .XXX_lbls (where
2237	.XXX is the extension of the image) or if that is not present extension
2238	.lbls.
2239
2240	:param str imagefile: the full name of the image file (with extension, directory optional)
2241
2242	:returns: a dict with parameter values. Named parameters will have the type based on
2243	the specified Python function, named columns will be character strings
2244
2245	The contents of the label file will look like this::
2246
2247	# define keywords
2248	filename:lambda x,y: "{}_{:0>6}".format(x,y)\|33,34
2249	distance: float \| 75
2250	wavelength:lambda keV: 12.398425/float(keV)\|9
2251	pixelSize:lambda x: [74.8, 74.8]\|0
2252	ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)\|0,1,2,3,4
2253	Temperature: float\|53
2254	FreePrm2: int \| 34 \| Free Parm2 Label
2255	# define other variables
2256	0:day
2257	1:month
2258	2:date
2259	3:time
2260	4:year
2261	7:I_ring
2262
2263	This file contains three types of lines in any order.
2264	* Named parameters are evaluated with user-supplied Python code (see
2265	subsequent information). Specific named parameters are used
2266	to determine values that are used for image interpretation (see table,
2267	below). Any others are copied to the Comments subsection of the Image
2268	tree item.
2269	* Column labels are defined with a column number (integer) followed by
2270	a colon (:) and a label to be assigned to that column. All labeled
2271	columns are copied to the Image's Comments subsection.
2272	* Comments are any line that does not contain a colon.
2273
2274	Note that columns are numbered starting at zero.
2275
2276	Any named parameter may be defined provided it is not a valid integer,
2277	but the named parameters in the table have special meanings, as descibed.
2278	The parameter name is followed by a colon. After the colon, specify
2279	Python code that defines or specifies a function that will be called to
2280	generate a value for that parameter.
2281
2282	Note that several keywords, if defined in the Comments, will be found and
2283	placed in the appropriate section of the powder histogram(s)'s Sample
2284	Parameters after an integration: ``Temperature``,``Pressure``,``Time``,
2285	``FreePrm1``,``FreePrm2``,``FreePrm3``,``Omega``,``Chi``, and ``Phi``.
2286
2287	After the Python code, supply a vertical bar (\|) and then a list of one
2288	more more columns that will be supplied as arguments to that function.
2289
2290	Note that the labels for the three FreePrm items can be changed by
2291	including that label as a third item with an additional vertical bar. Labels
2292	will be ignored for any other named parameters.
2293
2294	The examples above are discussed here:
2295
2296	``filename:lambda x,y: "{}_{:0>6}".format(x,y)\|33,34``
2297	Here the function to be used is defined with a lambda statement::
2298
2299	lambda x,y: "{}_{:0>6}".format(x,y)
2300
2301	This function will use the format function to create a file name from the
2302	contents of columns 33 and 34. The first parameter (x, col. 33) is inserted directly into
2303	the file name, followed by a underscore (_), followed by the second parameter (y, col. 34),
2304	which will be left-padded with zeros to six characters (format directive ``:0>6``).
2305
2306	When there will be more than one image generated per line in the .par file, an alternate way to
2307	generate list of file names takes into account the number of images generated::
2308
2309	lambda x,y,z: ["{}_{:0>6}".format(x,int(y)+i) for i in range(int(z))]
2310
2311	Here a third parameter is used to specify the number of images generated, where
2312	the image number is incremented for each image.
2313
2314	``distance: float \| 75``
2315	Here the contents of column 75 will be converted to a floating point number
2316	by calling float on it. Note that the spaces here are ignored.
2317
2318	``wavelength:lambda keV: 12.398425/float(keV)\|9``
2319	Here we define an algebraic expression to convert an energy in keV to a
2320	wavelength and pass the contents of column 9 as that input energy
2321
2322	``pixelSize:lambda x: [74.8, 74.8]\|0``
2323	In this case the pixel size is a constant (a list of two numbers). The first
2324	column is passed as an argument as at least one argument is required, but that
2325	value is not used in the expression.
2326
2327	``ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)\|0,1,2,3,4``
2328	This example defines a parameter that takes items in the first five columns
2329	and formats them in a different way. This parameter is not one of the pre-defined
2330	parameter names below. Some external code could be used to change the month string
2331	(argument ``m``) to a integer from 1 to 12.
2332
2333	``FreePrm2: int \| 34 \| Free Parm2 Label``
2334	In this example, the contents of column 34 will be converted to an integer and
2335	placed as the second free-named parameter in the Sample Parameters after an
2336	integration. The label for this parameter will be changed to "Free Parm2 Label".
2337
2338	Pre-defined parameter names
2339
2340	============= ========= ======== =====================================================
2341	keyword required type Description
2342	============= ========= ======== =====================================================
2343	filename yes str or generates the file name prefix for the matching image
2344	list file (MyImage001 for file /tmp/MyImage001.tif) or
2345	a list of file names.
2346	polarization no float generates the polarization expected based on the
2347	monochromator angle, defaults to 0.99.
2348	center no list of generates the approximate beam center on the detector
2349	2 floats in mm, such as [204.8, 204.8].
2350	distance yes float generates the distance from the sample to the detector
2351	in mm
2352	pixelSize no list of generates the size of the pixels in microns such as
2353	2 floats [200.0, 200.0].
2354	wavelength yes float generates the wavelength in Angstroms
2355	============= ========= ======== =====================================================
2356
2357	'''
2358	dir,fil = os.path.split(os.path.abspath(imagefile))
2359	imageName,ext = os.path.splitext(fil)
2360	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'): return
2361	parfiles = glob.glob(os.path.join(GSASIIpath.GetConfigValue('Column_Metadata_directory'),'*.par'))
2362	if len(parfiles) == 0:
2363	print('Sorry, No Column metadata (.par) file found in '+
2364	GSASIIpath.GetConfigValue('Column_Metadata_directory'))
2365	return {}
2366	for parFil in parfiles: # loop over all .par files (hope just 1) in image dir until image is found
2367	parRoot = os.path.splitext(parFil)[0]
2368	for e in (ext+'_lbls','.lbls'):
2369	if os.path.exists(parRoot+e):
2370	lblFil = parRoot+e
2371	break
2372	else:
2373	print('Warning: No labels definitions found for '+parFil)
2374	continue
2375	labels,lbldict,keyCols,keyExp,errors = readColMetadataLabels(lblFil)
2376	if errors:
2377	print('Errors in labels file '+lblFil)
2378	for i in errors: print(' '+i)
2379	continue
2380	else:
2381	print('Read '+lblFil)
2382	# scan through each line in this .par file, looking for the matching image rootname
2383	fp = open(parFil,'Ur')
2384	for iline,line in enumerate(fp):
2385	items = line.strip().split(' ')
2386	nameList = keyExp['filename'](*[items[j] for j in keyCols['filename']])
2387	if type(nameList) is str:
2388	if nameList != imageName: continue
2389	name = nameList
2390	else:
2391	for name in nameList:
2392	if name == imageName: break # got a match
2393	else:
2394	continue
2395	# parse the line and finish
2396	metadata = evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp)
2397	metadata['par file'] = parFil
2398	metadata['lbls file'] = lblFil
2399	print("Metadata read from {} line {}".format(parFil,iline+1))
2400	fp.close()
2401	return metadata
2402	else:
2403	print("Image {} not found in {}".format(imageName,parFil))
2404	fp.close()
2405	continue
2406	fp.close()
2407	else:
2408	print("Warning: No .par metadata for image {}".format(imageName))
2409	return {}
2410
2411	def readColMetadataLabels(lblFil):
2412	'''Read the .*lbls file and setup for metadata assignments
2413	'''
2414	lbldict = {}
2415	keyExp = {}
2416	keyCols = {}
2417	labels = {}
2418	errors = []
2419	fp = open(lblFil,'Ur') # read column labels
2420	for iline,line in enumerate(fp): # read label definitions
2421	line = line.strip()
2422	if not line or line[0] == '#': continue # comments
2423	items = line.split(':')
2424	if len(items) < 2: continue # lines with no colon are also comments
2425	# does this line a definition for a named parameter?
2426	key = items[0]
2427	try:
2428	int(key)
2429	except ValueError: # try as named parameter since not a valid number
2430	items = line.split(':',1)[1].split('\|')
2431	try:
2432	f = eval(items[0]) # compile the expression
2433	if not callable(f):
2434	errors += ['Expression "{}" for key {} is not a function (line {})'.
2435	format(items[0],key,iline)]
2436	continue
2437	keyExp[key] = f
2438	except Exception as msg:
2439	errors += ['Expression "{}" for key {} is not valid (line {})'.
2440	format(items[0],key,iline)]
2441	errors += [str(msg)]
2442	continue
2443	keyCols[key] = [int(i) for i in items[1].strip().split(',')]
2444	if key.lower().startswith('freeprm') and len(items) > 2:
2445	labels[key] = items[2]
2446	continue
2447	if len(items) == 2: # simple column definition
2448	lbldict[int(items[0])] = items[1]
2449	fp.close()
2450	if 'filename' not in keyExp:
2451	errors += ["File {} is invalid. No valid filename expression.".format(lblFil)]
2452	return labels,lbldict,keyCols,keyExp,errors
2453
2454	def evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp,ShowError=False):
2455	'''Evaluate the metadata for a line in the .par file
2456	'''
2457	metadata = {lbldict[j]:items[j] for j in lbldict}
2458	named = {}
2459	for key in keyExp:
2460	try:
2461	res = keyExp[key](*[items[j] for j in keyCols[key]])
2462	except:
2463	if ShowError:
2464	res = "* error *"
2465	else:
2466	continue
2467	named[key] = res
2468	metadata.update(named)
2469	for lbl in labels: # add labels for FreePrm's
2470	metadata['label_'+lbl[4:].lower()] = labels[lbl]
2471	return metadata
2472
2473	def GetColumnMetadata(reader):
2474	'''Add metadata to an image from a column-type metadata file
2475	using :func:`readColMetadata`
2476
2477	:param reader: a reader object from reading an image
2478
2479	'''
2480	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'): return
2481	parParms = readColMetadata(reader.readfilename)
2482	if not parParms: return # check for read failure
2483	specialKeys = ('filename',"polarization", "center", "distance", "pixelSize", "wavelength",)
2484	reader.Comments = ['Metadata from {} assigned by {}'.format(parParms['par file'],parParms['lbls file'])]
2485	for key in parParms:
2486	if key in specialKeys+('par file','lbls file'): continue
2487	reader.Comments += ["{} = {}".format(key,parParms[key])]
2488	if "polarization" in parParms:
2489	reader.Data['PolaVal'][0] = parParms["polarization"]
2490	else:
2491	reader.Data['PolaVal'][0] = 0.99
2492	if "center" in parParms:
2493	reader.Data['center'] = parParms["center"]
2494	if "pixelSize" in parParms:
2495	reader.Data['pixelSize'] = parParms["pixelSize"]
2496	if "wavelength" in parParms:
2497	reader.Data['wavelength'] = parParms['wavelength']
2498	else:
2499	print('Error: wavelength not defined in {}'.format(parParms['lbls file']))
2500	if "distance" in parParms:
2501	reader.Data['distance'] = parParms['distance']
2502	reader.Data['setdist'] = parParms['distance']
2503	else:
2504	print('Error: distance not defined in {}'.format(parParms['lbls file']))
2505
2506	def testColumnMetadata(G2frame):
2507	'''Test the column-oriented metadata parsing, as implemented at 1-ID, by showing results
2508	when using a .par and .lbls pair.
2509
2510	* Select a .par file, if more than one in selected dir.
2511	* Select the .*lbls file, if more than one matching .par file.
2512	* Parse the .lbls file, showing errors if encountered; loop until errors are fixed.
2513	* Search for an image or a line in the .par file and show the results when interpreted
2514
2515	See :func:`readColMetadata` for more details.
2516	'''
2517	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'):
2518	G2G.G2MessageBox(G2frame,'The configuration option for I-ID Metadata is not set.\n'+
2519	'Please use the File/Preferences menu to set Column_Metadata_directory',
2520	'Warning')
2521	return
2522	parFiles = glob.glob(os.path.join(GSASIIpath.GetConfigValue('Column_Metadata_directory'),'*.par'))
2523	if not parFiles:
2524	G2G.G2MessageBox(G2frame,'No .par files found in directory {}. '
2525	.format(GSASIIpath.GetConfigValue('Column_Metadata_directory'))+
2526	'\nThis is set by config variable Column_Metadata_directory '+
2527	'(Set in File/Preferences menu).',
2528	'Warning')
2529	return
2530	parList = []
2531	for parFile in parFiles:
2532	lblList = []
2533	parRoot = os.path.splitext(parFile)[0]
2534	for f in glob.glob(parRoot+'.*lbls'):
2535	if os.path.exists(f): lblList.append(f)
2536	if not len(lblList):
2537	continue
2538	parList.append(parFile)
2539	if len(parList) == 0:
2540	G2G.G2MessageBox(G2frame,'No .lbls or .EXT_lbls file found for .par file(s) in directory {}. '
2541	.format(GSASIIpath.GetConfigValue('Column_Metadata_directory'))+
2542	'\nThis is set by config variable Column_Metadata_directory '+
2543	'(Set in File/Preferences menu).',
2544	'Warning')
2545	return
2546	elif len(parList) == 1:
2547	parFile = parList[0]
2548	else:
2549	dlg = G2G.G2SingleChoiceDialog(G2frame,
2550	'More than 1 .par file found. (Better if only 1!). Choose the one to test in '+
2551	GSASIIpath.GetConfigValue('Column_Metadata_directory'),
2552	'Choose .par file', [os.path.split(i)[1] for i in parList])
2553	if dlg.ShowModal() == wx.ID_OK:
2554	parFile = parList[dlg.GetSelection()]
2555	dlg.Destroy()
2556	else:
2557	dlg.Destroy()
2558	return
2559	# got .par file; now work on .*lbls file
2560	lblList = []
2561	parRoot = os.path.splitext(parFile)[0]
2562	for f in glob.glob(parRoot+'.*lbls'):
2563	if os.path.exists(f): lblList.append(f)
2564	if not len(lblList):
2565	raise Exception('How did this happen! No .*lbls files for '+parFile)
2566	elif len(lblList) == 1:
2567	lblFile = lblList[0]
2568	else:
2569	dlg = G2G.G2SingleChoiceDialog(G2frame,
2570	'Select label file for .par file '+parFile,
2571	'Choose label file', [os.path.split(i)[1] for i in lblList])
2572	if dlg.ShowModal() == wx.ID_OK:
2573	lblFile = lblList[dlg.GetSelection()]
2574	dlg.Destroy()
2575	else:
2576	dlg.Destroy()
2577	return
2578	# parse the labels file
2579	errors = True
2580	while errors:
2581	labels,lbldict,keyCols,keyExp,errors = readColMetadataLabels(lblFile)
2582	if errors:
2583	t = "Error reading file "+lblFile
2584	for l in errors:
2585	t += '\n'
2586	t += l
2587	t += "\n\nPlease edit the file and press OK (or Cancel to quit)"
2588	dlg = wx.MessageDialog(G2frame,message=t,
2589	caption="Read Error",style=wx.ICON_ERROR\| wx.OK\|wx.STAY_ON_TOP\|wx.CANCEL)
2590	if dlg.ShowModal() != wx.ID_OK: return
2591	# request a line number, read that line
2592	dlg = G2G.SingleStringDialog(G2frame,'Read what',
2593	'Enter a line number or an image file name (-1=last line)',
2594	'-1',size=(400,-1))
2595	if dlg.Show():
2596	fileorline = dlg.GetValue()
2597	dlg.Destroy()
2598	else:
2599	dlg.Destroy()
2600	return
2601	# and report the generated key pairs in metadata dict
2602	linenum = None
2603	try:
2604	linenum = int(fileorline)
2605	except:
2606	imageName = os.path.splitext(os.path.split(fileorline)[1])[0]
2607
2608	fp = open(parFile,'Ur')
2609	for iline,line in enumerate(fp):
2610	if linenum is not None:
2611	if iline == linenum:
2612	items = line.strip().split(' ')
2613	n = "Line {}".format(iline)
2614	break
2615	else:
2616	continue
2617	else:
2618	items = line.strip().split(' ')
2619	nameList = keyExp['filename'](*[items[j] for j in keyCols['filename']])
2620	if type(nameList) is str:
2621	if nameList != imageName: continue
2622	name = nameList
2623	break
2624	else:
2625	for name in nameList:
2626	print (name,name == imageName)
2627	if name == imageName:
2628	n = "Image {} found in line {}".format(imageName,iline)
2629	break # got a match
2630	else:
2631	continue
2632	break
2633	else:
2634	if linenum is not None:
2635	n = "Line {}".format(iline)
2636	else:
2637	n = "Image {} not found. Reporting line {}".format(imageName,iline)
2638	items = line.strip().split(' ')
2639	fp.close()
2640	metadata = evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp,True)
2641	title = "Results: ("+n+")"
2642	t = ['Files: '+parFile,lblFile,' ']
2643	n = ["Named parameters:"]
2644	l = ['',"Labeled columns:"]
2645	for key in sorted(metadata):
2646	if key == "filename" or key.startswith('label_prm'): continue
2647	if key in keyCols:
2648	n += [" {} = {}".format(key,metadata[key])]
2649	elif key in lbldict.values():
2650	l += [" {} = {}".format(key,metadata[key])]
2651	else:
2652	t += ["** Unexpected: {}".format(key,metadata[key])]
2653	if type(metadata['filename']) is str:
2654	l += ["","Filename: "+ metadata['filename']]
2655	else:
2656	l += ["","Filename(s): "]
2657	for i,j in enumerate(metadata['filename']):
2658	if i: l[-1] += ', '
2659	l[-1] += j
2660	t += n + l + ['','Unused columns:']
2661	usedCols = lbldict.keys()
2662	for i in keyCols.values(): usedCols += i
2663	for i in range(len(items)):
2664	if i in usedCols: continue
2665	t += [" {}: {}".format(i,items[i])]
2666	dlg = G2G.G2SingleChoiceDialog(None,title,'Column metadata parse results',t,
2667	monoFont=True,filterBox=False,size=(400,600),
2668	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.CENTRE\|wx.OK)
2669	dlg.ShowModal()
2670
2671	if __name__ == '__main__':
2672	import GSASIIdataGUI
2673	application = GSASIIdataGUI.GSASIImain(0)
2674	G2frame = application.main
2675	#app = wx.PySimpleApp()
2676	#G2frame = wx.Frame(None) # create a frame
2677	#frm.Show(True)
2678	#filename = '/tmp/notzip.zip'
2679	#filename = '/tmp/all.zip'
2680	#filename = '/tmp/11bmb_7652.zip'
2681
2682	#selection=None, confirmoverwrite=True, parent=None
2683	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2684	#print ExtractFileFromZip(filename,multipleselect=True)
2685	# #confirmread=False, confirmoverwrite=False)
2686
2687	# choicelist=[ ('a','b','c'),
2688	# ('test1','test2'),('no choice',)]
2689	# titles = [ 'a, b or c', 'tests', 'No option here']
2690	# dlg = MultipleChoicesDialog(
2691	# choicelist,titles,
2692	# parent=frm)
2693	# if dlg.ShowModal() == wx.ID_OK:
2694	# print 'Got OK'
2695	imagefile = '/tmp/NDC5_00237_3.ge3'
2696	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2697
2698	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2699
2700	GSASIIpath.IPyBreak_base()

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