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source: trunk/GSASIIIO.py @ 4498

Last change on this file since 4498 was 4498, checked in by toby, 3 years ago
cleanup errors and cruft noted in spyder
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2020-06-19 02:32:02 +0000 (Fri, 19 Jun 2020) $
4	# $Author: toby $
5	# $Revision: 4498 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 4498 2020-06-19 02:32:02Z 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 class for data export routines (TODO: should move)
19
20	TODO: This module needs some work to separate wx from non-wx routines. GUI
21	routines should probably move to GSASIIctrlGUI.
22	'''
23
24	from __future__ import division, print_function
25
26	# Allow this to be imported without wx present. Was needed for G2scriptable, but is
27	# likely not needed anymore
28	try:
29	import wx
30	except ImportError:
31	# was needed by sphinx, but probably not anymore
32	class Placeholder(object):
33	def __init__(self):
34	self.Dialog = object
35	wx = Placeholder()
36	import math
37	import numpy as np
38	import numpy.ma as ma
39
40	import copy
41	import platform
42	if '2' in platform.python_version_tuple()[0]:
43	import cPickle
44	else:
45	import pickle as cPickle
46	import sys
47	import re
48	import random as ran
49	import GSASIIpath
50	GSASIIpath.SetVersionNumber("$Revision: 4498 $")
51	try:
52	import GSASIIdataGUI as G2gd
53	except ImportError:
54	pass
55	import GSASIIobj as G2obj
56	import GSASIIlattice as G2lat
57	try:
58	import GSASIIpwdGUI as G2pdG
59	import GSASIIimgGUI as G2imG
60	except ImportError:
61	pass
62	import GSASIIElem as G2el
63	import GSASIIstrIO as G2stIO
64	import GSASIImapvars as G2mv
65	import GSASIIfiles as G2fil
66	try:
67	import GSASIIctrlGUI as G2G
68	except ImportError:
69	pass
70	import os
71	import os.path as ospath
72
73	DEBUG = False #=True for various prints
74	TRANSP = False #=true to transpose images for testing
75	if GSASIIpath.GetConfigValue('Transpose'): TRANSP = True
76	npsind = lambda x: np.sin(x*np.pi/180.)
77
78	def sfloat(S):
79	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
80	if S.strip():
81	try:
82	return float(S)
83	except ValueError:
84	pass
85	return 0.0
86
87	def sint(S):
88	'Convert a string to int. An empty field is treated as zero'
89	if S.strip():
90	return int(S)
91	else:
92	return 0
93
94	def trim(val):
95	'''Simplify a string containing leading and trailing spaces
96	as well as newlines, tabs, repeated spaces etc. into a shorter and
97	more simple string, by replacing all ranges of whitespace
98	characters with a single space.
99
100	:param str val: the string to be simplified
101
102	:returns: the (usually) shortened version of the string
103	'''
104	return re.sub('\s+', ' ', val).strip()
105
106	def FileDlgFixExt(dlg,file):
107	'this is needed to fix a problem in linux wx.FileDialog'
108	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
109	if ext not in file:
110	file += ext
111	return file
112
113	def GetPowderPeaks(fileName):
114	'Read powder peaks from a file'
115	sind = lambda x: math.sin(x*math.pi/180.)
116	asind = lambda x: 180.*math.asin(x)/math.pi
117	wave = 1.54052
118	File = open(fileName,'Ur')
119	Comments = []
120	peaks = []
121	S = File.readline()
122	while S:
123	if S[:1] == '#':
124	Comments.append(S[:-1])
125	else:
126	item = S.split()
127	if len(item) == 1:
128	peaks.append([float(item[0]),1.0])
129	elif len(item) > 1:
130	peaks.append([float(item[0]),float(item[0])])
131	S = File.readline()
132	File.close()
133	if Comments:
134	print ('Comments on file:')
135	for Comment in Comments:
136	print (Comment)
137	if 'wavelength' in Comment:
138	wave = float(Comment.split('=')[1])
139	Peaks = []
140	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
141	for peak in peaks:
142	dsp = peak[0]
143	sth = wave/(2.0*dsp)
144	if sth < 1.0:
145	tth = 2.0*asind(sth)
146	else:
147	break
148	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
149	else: #2-thetas - assume Cuka (for now)
150	for peak in peaks:
151	tth = peak[0]
152	dsp = wave/(2.0*sind(tth/2.0))
153	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
154	limits = [1000.,0.]
155	for peak in Peaks:
156	limits[0] = min(limits[0],peak[0])
157	limits[1] = max(limits[1],peak[0])
158	limits[0] = max(1.,(int(limits[0]-1.)/5)*5.)
159	limits[1] = min(170.,(int(limits[1]+1.)/5)*5.)
160	return Comments,Peaks,limits,wave
161
162	def GetCheckImageFile(G2frame,treeId):
163	'''Try to locate an image file if the project and image have been moved
164	together. If the image file cannot be found, request the location from
165	the user.
166
167	:param wx.Frame G2frame: main GSAS-II Frame and data object
168	:param wx.Id treeId: Id for the main tree item for the image
169	:returns: Npix,imagefile,imagetag with (Npix) number of pixels,
170	imagefile, if it exists, or the name of a file that does exist or False if the user presses Cancel
171	and (imagetag) an optional image number
172
173	'''
174	Npix,Imagefile,imagetag = G2frame.GPXtree.GetImageLoc(treeId)
175	if isinstance(Imagefile,list):
176	imagefile,imagetag = Imagefile
177	else:
178	imagefile = Imagefile
179	if not os.path.exists(imagefile):
180	print ('Image file '+imagefile+' not found')
181	fil = imagefile.replace('\\','/') # windows?!
182	# see if we can find a file with same name or in a similarly named sub-dir
183	pth,fil = os.path.split(fil)
184	prevpth = None
185	while pth and pth != prevpth:
186	prevpth = pth
187	if os.path.exists(os.path.join(G2frame.dirname,fil)):
188	print ('found image file '+os.path.join(G2frame.dirname,fil))
189	imagefile = os.path.join(G2frame.dirname,fil)
190	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
191	return Npix,imagefile,imagetag
192	pth,enddir = os.path.split(pth)
193	fil = os.path.join(enddir,fil)
194	# not found as a subdirectory, drop common parts of path for last saved & image file names
195	# if image was .../A/B/C/imgs/ima.ge
196	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
197	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
198	Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
199	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
200	imgPath = imagefile.replace('\\','/').split('/')
201	for p1,p2 in zip(gpxPath,imgPath):
202	if p1 == p2:
203	gpxPath.pop(0),imgPath.pop(0)
204	else:
205	break
206	fil = os.path.join(*imgPath) # file with non-common prefix elements
207	prevpth = None
208	pth = os.path.abspath(G2frame.dirname)
209	while pth and pth != prevpth:
210	prevpth = pth
211	if os.path.exists(os.path.join(pth,fil)):
212	print ('found image file '+os.path.join(pth,fil))
213	imagefile = os.path.join(pth,fil)
214	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
215	return Npix,imagefile,imagetag
216	pth,enddir = os.path.split(pth)
217	#GSASIIpath.IPyBreak()
218
219	if not os.path.exists(imagefile):
220	# note that this fails (at least on Mac) to get an image during the GUI initialization
221	prevnam = os.path.split(imagefile)[1]
222	prevext = os.path.splitext(imagefile)[1]
223	wildcard = 'Image format ('+prevext+')\|'+prevext
224	dlg = wx.FileDialog(G2frame, 'Previous image file ('+prevnam+') not found; open here', '.', prevnam,
225	wildcard,wx.FD_OPEN)
226	try:
227	dlg.SetFilename(''+ospath.split(imagefile)[1])
228	if dlg.ShowModal() == wx.ID_OK:
229	imagefile = dlg.GetPath()
230	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
231	else:
232	imagefile = None # was False
233	finally:
234	dlg.Destroy()
235	return Npix,imagefile,imagetag
236
237	def EditImageParms(parent,Data,Comments,Image,filename):
238	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
239	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
240	def onClose(event):
241	dlg.EndModal(wx.ID_OK)
242	mainsizer = wx.BoxSizer(wx.VERTICAL)
243	h,w = Image.shape[:2]
244	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
245	0,wx.ALIGN_LEFT\|wx.ALL, 2)
246
247	vsizer = wx.BoxSizer(wx.HORIZONTAL)
248	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
249	0,wx.ALIGN_LEFT\|wx.ALL, 2)
250	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
251	vsizer.Add(wdgt)
252	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
253
254	vsizer = wx.BoxSizer(wx.HORIZONTAL)
255	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
256	0,wx.ALIGN_LEFT\|wx.ALL, 2)
257	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,size=(50,-1))
258	vsizer.Add(wdgt)
259	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),wx.ALIGN_LEFT\|wx.ALL, 2)
260	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,size=(50,-1))
261	vsizer.Add(wdgt)
262	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
263
264	vsizer = wx.BoxSizer(wx.HORIZONTAL)
265	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
266	0,wx.ALIGN_LEFT\|wx.ALL, 2)
267	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
268	vsizer.Add(wdgt)
269	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
270
271	vsizer = wx.BoxSizer(wx.HORIZONTAL)
272	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
273	0,wx.ALIGN_LEFT\|wx.ALL, 2)
274	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,size=(75,-1))
275	vsizer.Add(wdgt)
276	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),wx.ALIGN_LEFT\|wx.ALL, 2)
277	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,size=(75,-1))
278	vsizer.Add(wdgt)
279	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
280
281	vsizer = wx.BoxSizer(wx.HORIZONTAL)
282	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
283	0,wx.ALIGN_LEFT\|wx.ALL, 2)
284	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
285	vsizer.Add(wdgt)
286	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
287
288	btnsizer = wx.StdDialogButtonSizer()
289	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
290	OKbtn.SetDefault()
291	OKbtn.Bind(wx.EVT_BUTTON,onClose)
292	btnsizer.AddButton(OKbtn) # not sure why this is needed
293	btnsizer.Realize()
294	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
295	dlg.SetSizer(mainsizer)
296	dlg.CenterOnParent()
297	dlg.ShowModal()
298
299	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
300	'''Load an image into the tree. Saves the location of the image, as well as the
301	ImageTag (where there is more than one image in the file), if defined.
302	'''
303	ImgNames = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
304	TreeLbl = 'IMG '+os.path.basename(imagefile)
305	ImageTag = Data.get('ImageTag')
306	if ImageTag:
307	TreeLbl += ' #'+'%04d'%(ImageTag)
308	imageInfo = (imagefile,ImageTag)
309	else:
310	imageInfo = imagefile
311	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
312	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=TreeName)
313	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
314	Imax = np.amax(Image)
315	if G2frame.imageDefault:
316	Data = copy.copy(G2frame.imageDefault)
317	Data['showLines'] = True
318	Data['ring'] = []
319	Data['rings'] = []
320	Data['cutoff'] = 10.
321	Data['pixLimit'] = 20
322	Data['edgemin'] = 100000000
323	Data['calibdmin'] = 0.5
324	Data['calibskip'] = 0
325	Data['ellipses'] = []
326	Data['calibrant'] = ''
327	Data['GonioAngles'] = [0.,0.,0.]
328	Data['DetDepthRef'] = False
329	else:
330	Data['type'] = 'PWDR'
331	Data['color'] = GSASIIpath.GetConfigValue('Contour_color','Paired')
332	if 'tilt' not in Data: #defaults if not preset in e.g. Bruker importer
333	Data['tilt'] = 0.0
334	Data['rotation'] = 0.0
335	Data['pixLimit'] = 20
336	Data['calibdmin'] = 0.5
337	Data['cutoff'] = 10.
338	Data['showLines'] = False
339	Data['calibskip'] = 0
340	Data['ring'] = []
341	Data['rings'] = []
342	Data['edgemin'] = 100000000
343	Data['ellipses'] = []
344	Data['GonioAngles'] = [0.,0.,0.]
345	Data['DetDepth'] = 0.
346	Data['DetDepthRef'] = False
347	Data['calibrant'] = ''
348	Data['IOtth'] = [5.0,50.0]
349	if GSASIIpath.GetConfigValue('Image_2theta_min'):
350	try:
351	Data['IOtth'][0] = float(GSASIIpath.GetConfigValue('Image_2theta_min'))
352	except:
353	pass
354	if GSASIIpath.GetConfigValue('Image_2theta_max'):
355	try:
356	Data['IOtth'][1] = float(GSASIIpath.GetConfigValue('Image_2theta_max'))
357	except:
358	pass
359	Data['LRazimuth'] = [0.,180.]
360	Data['azmthOff'] = 0.0
361	Data['outChannels'] = 2500
362	Data['outAzimuths'] = 1
363	Data['centerAzm'] = False
364	Data['fullIntegrate'] = GSASIIpath.GetConfigValue('fullIntegrate',True)
365	Data['setRings'] = False
366	Data['background image'] = ['',-1.0]
367	Data['dark image'] = ['',-1.0]
368	Data['Flat Bkg'] = 0.0
369	Data['Oblique'] = [0.5,False]
370	Data['setDefault'] = False
371	Data['range'] = [(0,Imax),[0,Imax]]
372	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Image Controls'),Data)
373	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],
374	'Thresholds':[(0,Imax),[0,Imax]],
375	'SpotMask':{'esdMul':3.,'spotMask':None}}
376	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Masks'),Masks)
377	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Stress/Strain'),
378	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
379	G2frame.GPXtree.SetItemPyData(Id,[Npix,imageInfo])
380	G2frame.PickId = Id
381	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
382	G2frame.Image = Id
383
384	def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None,FormatName=''):
385	'''Read a single image with an image importer. This is called to reread an image
386	after it has already been imported with :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
387	(or :func:`ReadImages` in Auto Integration) so it is not necessary to reload metadata.
388
389	:param wx.Frame G2frame: main GSAS-II Frame and data object.
390	:param str imagefile: name of image file
391	:param bool imageOnly: If True return only the image,
392	otherwise (default) return more (see below)
393	:param int/str ImageTag: specifies a particular image to be read from a file.
394	First image is read if None (default).
395	:param str formatName: the image reader formatName
396
397	:returns: an image as a numpy array or a list of four items:
398	Comments, Data, Npix and the Image, as selected by imageOnly
399
400	'''
401	# determine which formats are compatible with this file
402	primaryReaders = []
403	secondaryReaders = []
404	for rd in G2frame.ImportImageReaderlist:
405	flag = rd.ExtensionValidator(imagefile)
406	if flag is None:
407	secondaryReaders.append(rd)
408	elif flag:
409	if not FormatName:
410	primaryReaders.append(rd)
411	elif FormatName == rd.formatName:
412	primaryReaders.append(rd)
413	if len(secondaryReaders) + len(primaryReaders) == 0:
414	print('Error: No matching format for file '+imagefile)
415	raise Exception('No image read')
416	errorReport = ''
417	if not imagefile:
418	return
419	for rd in primaryReaders+secondaryReaders:
420	rd.ReInitialize() # purge anything from a previous read
421	rd.errors = "" # clear out any old errors
422	if not rd.ContentsValidator(imagefile): # rejected on cursory check
423	errorReport += "\n "+rd.formatName + ' validator error'
424	if rd.errors:
425	errorReport += ': '+rd.errors
426	continue
427	if imageOnly:
428	ParentFrame = None # prevent GUI access on reread
429	else:
430	ParentFrame = G2frame
431	if GSASIIpath.GetConfigValue('debug'):
432	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
433	else:
434	flag = False
435	try:
436	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
437	except rd.ImportException as detail:
438	rd.errors += "\n Read exception: "+str(detail)
439	except Exception as detail:
440	import traceback
441	rd.errors += "\n Unhandled read exception: "+str(detail)
442	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
443	if flag: # this read succeeded
444	if rd.Image is None:
445	raise Exception('No image read. Strange!')
446	if GSASIIpath.GetConfigValue('Transpose'):
447	print ('Transposing Image!')
448	rd.Image = rd.Image.T
449	#rd.readfilename = imagefile
450	if imageOnly:
451	return rd.Image
452	else:
453	return rd.Comments,rd.Data,rd.Npix,rd.Image
454	else:
455	print('Error reading file '+imagefile)
456	print('Error messages(s)\n'+errorReport)
457	raise Exception('No image read')
458
459	def ReadImages(G2frame,imagefile):
460	'''Read one or more images from a file and put them into the Tree
461	using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
462
463	ToDo: Images are most commonly read in :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
464	which is called from :meth:`GSASIIdataGUI.GSASII.OnImportImage`
465	it would be good if these routines used a common code core so that changes need to
466	be made in only one place.
467
468	:param wx.Frame G2frame: main GSAS-II Frame and data object.
469	:param str imagefile: name of image file
470
471	:returns: a list of the id's of the IMG tree items created
472	'''
473	# determine which formats are compatible with this file
474	primaryReaders = []
475	secondaryReaders = []
476	for rd in G2frame.ImportImageReaderlist:
477	flag = rd.ExtensionValidator(imagefile)
478	if flag is None:
479	secondaryReaders.append(rd)
480	elif flag:
481	primaryReaders.append(rd)
482	if len(secondaryReaders) + len(primaryReaders) == 0:
483	print('Error: No matching format for file '+imagefile)
484	raise Exception('No image read')
485	errorReport = ''
486	rdbuffer = {} # create temporary storage for file reader
487	for rd in primaryReaders+secondaryReaders:
488	rd.ReInitialize() # purge anything from a previous read
489	rd.errors = "" # clear out any old errors
490	if not rd.ContentsValidator(imagefile): # rejected on cursory check
491	errorReport += "\n "+rd.formatName + ' validator error'
492	if rd.errors:
493	errorReport += ': '+rd.errors
494	continue
495	ParentFrame = G2frame
496	block = 0
497	repeat = True
498	CreatedIMGitems = []
499	while repeat: # loop if the reader asks for another pass on the file
500	block += 1
501	repeat = False
502	if GSASIIpath.GetConfigValue('debug'):
503	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
504	else:
505	flag = False
506	try:
507	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
508	except rd.ImportException as detail:
509	rd.errors += "\n Read exception: "+str(detail)
510	except Exception as detail:
511	import traceback
512	rd.errors += "\n Unhandled read exception: "+str(detail)
513	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
514	if flag: # this read succeeded
515	if rd.Image is None:
516	raise Exception('No image read. Strange!')
517	if GSASIIpath.GetConfigValue('Transpose'):
518	print ('Transposing Image!')
519	rd.Image = rd.Image.T
520	rd.Data['ImageTag'] = rd.repeatcount
521	rd.readfilename = imagefile
522	# Load generic metadata, as configured
523	G2fil.GetColumnMetadata(rd)
524	LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
525	repeat = rd.repeat
526	CreatedIMGitems.append(G2frame.Image)
527	if CreatedIMGitems: return CreatedIMGitems
528	else:
529	print('Error reading file '+imagefile)
530	print('Error messages(s)\n'+errorReport)
531	return []
532	#raise Exception('No image read')
533
534	def SaveMultipleImg(G2frame):
535	if not G2frame.GPXtree.GetCount():
536	print ('no images!')
537	return
538	choices = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
539	if len(choices) == 1:
540	names = choices
541	else:
542	dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices)
543	dlg.SetSelections([])
544	names = []
545	if dlg.ShowModal() == wx.ID_OK:
546	names = [choices[sel] for sel in dlg.GetSelections()]
547	dlg.Destroy()
548	if not names: return
549	for name in names:
550	Id = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, name)
551	Npix,imagefile,imagetag = G2frame.GPXtree.GetImageLoc(Id)
552	imroot = os.path.splitext(imagefile)[0]
553	if imagetag:
554	imroot += '_' + str(imagetag)
555	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Image Controls'))
556	print('Writing '+imroot+'.imctrl')
557	File = open(imroot+'.imctrl','w')
558	keys = ['type','wavelength','calibrant','distance','center',
559	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth',
560	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
561	'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg',
562	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image']
563	for key in keys:
564	if key not in Data: continue #uncalibrated!
565	File.write(key+':'+str(Data[key])+'\n')
566	File.close()
567	mask = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Masks'))
568	G2imG.CleanupMasks(mask)
569	print('Writing '+imroot+'.immask')
570	File = open(imroot+'.immask','w')
571	for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
572	File.write(key+':'+str(mask[key])+'\n')
573	File.close()
574
575	def PutG2Image(filename,Comments,Data,Npix,image):
576	'Write an image as a python pickle - might be better as an .edf file?'
577	File = open(filename,'wb')
578	cPickle.dump([Comments,Data,Npix,image],File,2)
579	File.close()
580	return
581
582	objectScanIgnore = [int,bool,float,str,np.float64,np.float32,np.int32,np.int64,np.ndarray,G2obj.G2VarObj,G2obj.ExpressionObj]
583	try:
584	objectScanIgnore += [ma.MaskedArray] # fails in doc builds
585	except AttributeError:
586	pass
587
588	if '2' in platform.python_version_tuple()[0]:
589	objectScanIgnore += [unicode,long,]
590
591	def objectScan(data,tag,indexStack=[]):
592	'''Recursively scan an object looking for unexpected data types.
593	This is used in debug mode to scan .gpx files for objects we did not
594	intend to be there.
595	'''
596	if type(data) is list or type(data) is tuple:
597	for i in range(len(data)):
598	val = objectScan(data[i],tag,indexStack+[i])
599	if val:
600	data[i] = val
601	print('...fixed')
602	elif type(data) is dict:
603	for key in data:
604	val = objectScan(data[key],tag,indexStack+[key])
605	if val:
606	data[key] = val
607	print('...fixed')
608	elif data is None:
609	return None
610	elif type(data) in objectScanIgnore:
611	return None
612	else:
613	s = 'unexpected object in '+tag
614	for i in indexStack:
615	s += "[{}]".format(i)
616	#print(s,data.__class__.__name__) # loses full name of class
617	print(s,type(data))
618	global unexpectedObject
619	unexpectedObject = True
620	# fix bad objects
621	if "gdi.Colour" in str(type(data)):
622	return tuple(data)
623	return
624
625	def cPickleLoad(fp):
626	if '2' in platform.python_version_tuple()[0]:
627	return cPickle.load(fp)
628	else:
629	return cPickle.load(fp,encoding='latin-1')
630
631	def ProjFileOpen(G2frame,showProvenance=True):
632	'Read a GSAS-II project file and load into the G2 data tree'
633	if not os.path.exists(G2frame.GSASprojectfile):
634	print ('\n*** Error attempt to open project file that does not exist:\n '+
635	str(G2frame.GSASprojectfile))
636	return
637	LastSavedUsing = None
638	filep = open(G2frame.GSASprojectfile,'rb')
639	if showProvenance: print ('loading from file: '+G2frame.GSASprojectfile)
640	GPXphase = os.path.splitext(G2frame.GSASprojectfile)[0]+'.seqPhase'
641	GPXhist = os.path.splitext(G2frame.GSASprojectfile)[0]+'.seqHist'
642	deleteSeq = False
643	hist = None
644	tmpHistIndex = {}
645	updateFromSeq = False
646	if os.path.exists(GPXphase) and os.path.exists(GPXhist):
647	dlg = wx.MessageDialog(G2frame,
648	'Load results from crashed sequential fit?\nNo deletes the files!', 'Recover partial sequential fit?', wx.YES \| wx.NO \| wx.CANCEL)
649	dlg.CenterOnParent()
650	try:
651	result = dlg.ShowModal()
652	deleteSeq = result != wx.ID_CANCEL
653	if result == wx.ID_YES:
654	updateFromSeq = True
655	fp = open(GPXphase,'rb')
656	data = cPickleLoad(fp) # first block in file should be Phases
657	if data[0][0] != 'Phases':
658	raise Exception('Unexpected block in {} file. How did this happen?'
659	.format(GPXphase))
660	Phases = {}
661	for name,vals in data[1:]:
662	Phases[name] = vals
663	name,CovData = cPickleLoad(fp)[0] # 2nd block in file should be Covariance
664	name,RigidBodies = cPickleLoad(fp)[0] # 3rd block in file should be Rigid Bodies
665	fp.close()
666	# index the histogram updates
667	hist = open(GPXhist,'rb')
668	try:
669	while True:
670	loc = hist.tell()
671	datum = cPickleLoad(hist)[0]
672	tmpHistIndex[datum[0]] = loc
673	except EOFError:
674	pass
675	finally:
676	dlg.Destroy()
677	wx.BeginBusyCursor()
678	try:
679	while True:
680	try:
681	data = cPickleLoad(filep)
682	except EOFError:
683	break
684	datum = data[0]
685	# scan the GPX file for unexpected objects
686	if GSASIIpath.GetConfigValue('debug'):
687	global unexpectedObject
688	unexpectedObject = False
689	objectScan(data,'tree item "{}" entry '.format(datum[0]))
690	#if unexpectedObject:
691	# print(datum[0])
692	# GSASIIpath.IPyBreak()
693	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=datum[0])
694	if updateFromSeq and datum[0] == 'Phases':
695	for pdata in data[1:]:
696	if pdata[0] in Phases:
697	pdata[1].update(Phases[pdata[0]])
698	elif updateFromSeq and datum[0] == 'Covariance':
699	data[0][1] = CovData
700	elif updateFromSeq and datum[0] == 'Rigid bodies':
701	data[0][1] = RigidBodies
702	elif updateFromSeq and datum[0] in tmpHistIndex:
703	hist.seek(tmpHistIndex[datum[0]])
704	hdata = cPickleLoad(hist)
705	if data[0][0] != hdata[0][0]:
706	print('Error! Updating {} with {}'.format(data[0][0],hdata[0][0]))
707	datum = hdata[0]
708	xferItems = ['Background','Instrument Parameters','Sample Parameters','Reflection Lists']
709	hItems = {name:j+1 for j,(name,val) in enumerate(hdata[1:]) if name in xferItems}
710	for j,(name,val) in enumerate(data[1:]):
711	if name not in xferItems: continue
712	data[j+1][1] = hdata[hItems[name]][1]
713	if datum[0].startswith('PWDR'):
714	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
715	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
716	G2frame.GPXtree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
717	elif datum[0].startswith('HKLF'):
718	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
719	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
720	G2frame.GPXtree.SetItemPyData(Id,datum[1])
721	else:
722	G2frame.GPXtree.SetItemPyData(Id,datum[1])
723	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
724	LastSavedUsing = datum[1]['LastSavedUsing']
725	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance:
726	print('DBG_Packages used to create .GPX file:')
727	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
728	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
729	print(" {:<14s}: {:s}".format(p[0],p[1]))
730	else:
731	for p in datum[1]['PythonVersions']:
732	print(" {:<12s} {:s}".format(p[0]+':',p[1]))
733	oldPDF = False
734	for datus in data[1:]:
735	#patch - 1/23/17 PDF cleanup
736	if datus[0][:4] in ['I(Q)','S(Q)','F(Q)','G(R)']:
737	oldPDF = True
738	data[1][1][datus[0][:4]] = copy.deepcopy(datus[1][:2])
739	continue
740	#end PDF cleanup
741	sub = G2frame.GPXtree.AppendItem(Id,datus[0])
742	#patch
743	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
744	if datum[0].startswith('PWDR'):
745	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
746	else:
747	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
748	for item in datus[1][0]: #zip makes tuples - now make lists!
749	datus[1][0][item] = list(datus[1][0][item])
750	#end patch
751	G2frame.GPXtree.SetItemPyData(sub,datus[1])
752	if 'PDF ' in datum[0][:4] and oldPDF:
753	sub = G2frame.GPXtree.AppendItem(Id,'PDF Peaks')
754	G2frame.GPXtree.SetItemPyData(sub,{'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
755	if datum [0].startswith('IMG'): #retrieve image default flag & data if set
756	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls'))
757	if Data['setDefault']:
758	G2frame.imageDefault = Data
759	if LastSavedUsing:
760	print('GPX load successful. Last saved with GSAS-II revision '+LastSavedUsing)
761	else:
762	print('project load successful')
763	G2frame.NewPlot = True
764	except Exception as errmsg:
765	if GSASIIpath.GetConfigValue('debug'):
766	print('\nError reading GPX file:',errmsg)
767	import traceback
768	print (traceback.format_exc())
769	msg = wx.MessageDialog(G2frame,message="Error reading file "+
770	str(G2frame.GSASprojectfile)+". This is not a current GSAS-II .gpx file",
771	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
772	msg.ShowModal()
773	finally:
774	filep.close()
775	wx.EndBusyCursor()
776	G2frame.Status.SetStatusText('Mouse RB drag/drop to reorder',0)
777	if deleteSeq:
778	if hist: hist.close()
779	try:
780	os.remove(GPXphase)
781	except:
782	print('Warning: unable to delete {}'.format(GPXphase))
783	try:
784	os.remove(GPXhist)
785	except:
786	print('Warning: unable to delete {}'.format(GPXhist))
787	G2frame.SetTitleByGPX()
788
789	def ProjFileSave(G2frame):
790	'Save a GSAS-II project file'
791	if not G2frame.GPXtree.IsEmpty():
792	file = open(G2frame.GSASprojectfile,'wb')
793	print ('save to file: '+G2frame.GSASprojectfile)
794	# stick the file name into the tree and version info into tree so they are saved.
795	# (Controls should always be created at this point)
796	try:
797	Controls = G2frame.GPXtree.GetItemPyData(
798	G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
799	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
800	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
801	Controls['PythonVersions'] = G2frame.PackageVersions
802	except:
803	pass
804	wx.BeginBusyCursor()
805	try:
806	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
807	while item:
808	data = []
809	name = G2frame.GPXtree.GetItemText(item)
810	data.append([name,G2frame.GPXtree.GetItemPyData(item)])
811	item2, cookie2 = G2frame.GPXtree.GetFirstChild(item)
812	while item2:
813	name = G2frame.GPXtree.GetItemText(item2)
814	data.append([name,G2frame.GPXtree.GetItemPyData(item2)])
815	item2, cookie2 = G2frame.GPXtree.GetNextChild(item, cookie2)
816	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
817	cPickle.dump(data,file,2)
818	file.close()
819	pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
820	if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
821	G2frame.LastGPXdir = pth
822	finally:
823	wx.EndBusyCursor()
824	print('project save successful')
825
826	def SaveIntegration(G2frame,PickId,data,Overwrite=False):
827	'Save image integration results as powder pattern(s)'
828	waves = {'Cu':[1.54051,1.54433],'Ti':[2.74841,2.75207],'Cr':[2.28962,2.29351],
829	'Fe':[1.93597,1.93991],'Co':[1.78892,1.79278],'Mo':[0.70926,0.713543],
830	'Ag':[0.559363,0.563775]}
831	azms = G2frame.Integrate[1]
832	X = G2frame.Integrate[2][:-1]
833	N = len(X)
834	Id = G2frame.GPXtree.GetItemParent(PickId)
835	name = G2frame.GPXtree.GetItemText(Id)
836	name = name.replace('IMG ',data['type']+' ')
837	Comments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Comments'))
838	Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
839	if 'PWDR' in name:
840	if 'target' in data:
841	names = ['Type','Lam1','Lam2','I(L2)/I(L1)','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
842	codes = [0 for i in range(14)]
843	else:
844	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
845	codes = [0 for i in range(12)]
846	elif 'SASD' in name:
847	names = ['Type','Lam','Zero','Azimuth']
848	codes = [0 for i in range(4)]
849	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
850	Xminmax = [X[0],X[-1]]
851	Azms = np.zeros(data['outAzimuths'])
852	dazm = 0.
853	# if data['fullIntegrate'] and data['outAzimuths'] == 1:
854	# Azms = [0.0,] #a poor man's average?
855	# else:
856	## for i,azm in enumerate(azms[:-1]):
857	## if azm > 360. and azms[i+1] > 360.:
858	## Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
859	## else:
860	## Azms.append(G2img.meanAzm(azm,azms[i+1]))
861	if data['outAzimuths'] > 1:
862	dazm = np.min(np.abs(np.diff(azms)))/2.
863	G2frame.IntgOutList = []
864	for i,azm in enumerate(azms[:-1]):
865	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
866	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
867	# if Overwrite delete any duplicate
868	if Overwrite and G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname):
869	print('Replacing '+Aname)
870	item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname)
871	G2frame.GPXtree.Delete(item)
872	else:
873	nOcc = 0
874	while item:
875	Name = G2frame.GPXtree.GetItemText(item)
876	if Aname in Name:
877	nOcc += 1
878	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
879	if nOcc:
880	Aname += '(%d)'%(nOcc)
881	Sample = G2obj.SetDefaultSample() #set as Debye-Scherrer
882	Sample['Gonio. radius'] = data['distance']
883	Sample['Omega'] = data['GonioAngles'][0]
884	Sample['Chi'] = data['GonioAngles'][1]
885	Sample['Phi'] = data['GonioAngles'][2]
886	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
887	polariz = 0.99 #set default polarization for synchrotron radiation!
888	for item in Comments:
889	if 'polariz' in item:
890	try:
891	polariz = float(item.split('=')[1])
892	except:
893	polariz = 0.99
894	for key in ('Temperature','Pressure','Time','FreePrm1','FreePrm2','FreePrm3','Omega',
895	'Chi','Phi'):
896	if key.lower() in item.lower():
897	try:
898	Sample[key] = float(item.split('=')[1])
899	except:
900	pass
901	if 'label_prm' in item.lower():
902	for num in ('1','2','3'):
903	if 'label_prm'+num in item.lower():
904	Controls['FreePrm'+num] = item.split('=')[1].strip()
905	if 'PWDR' in Aname:
906	if 'target' in data: #from lab x-ray 2D imaging data
907	wave1,wave2 = waves[data['target']]
908	parms = ['PXC',wave1,wave2,0.5,0.0,polariz,290.,-40.,30.,6.,-14.,0.0,0.0001,Azms[i]]
909	else:
910	parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0,0.0001,Azms[i]]
911	elif 'SASD' in Aname:
912	Sample['Trans'] = data['SampleAbs'][0]
913	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
914	Y = G2frame.Integrate[0][i]
915	Ymin = np.min(Y)
916	Ymax = np.max(Y)
917	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
918	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=Aname)
919	G2frame.IntgOutList.append(Id)
920	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
921	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Limits'),copy.deepcopy([tuple(Xminmax),Xminmax]))
922	if 'PWDR' in Aname:
923	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Background'),[['chebyschev-1',1,3,1.0,0.0,0.0],
924	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
925	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
926	for item in inst[0]:
927	inst[0][item] = list(inst[0][item])
928	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),inst)
929	if 'PWDR' in Aname:
930	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
931	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
932	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Index Peak List'),[[],[]])
933	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Unit Cells List'),[])
934	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection Lists'),{})
935	elif 'SASD' in Aname:
936	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
937	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
938	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
939	valuesdict = {
940	'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxsize),'Offset':[0.0,0.0],'delOffset':0.02*Ymax,
941	'refOffset':-0.1Ymax,'refDelt':0.1Ymax,'Yminmax':[Ymin,Ymax]}
942	G2frame.GPXtree.SetItemPyData(Id,[valuesdict,
943	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
944	return Id #last powder pattern generated
945
946	def XYsave(G2frame,XY,labelX='X',labelY='Y',names=[]):
947	'Save XY table data'
948	pth = G2G.GetExportPath(G2frame)
949	dlg = wx.FileDialog(
950	G2frame, 'Enter csv filename for XY table', pth, '',
951	'XY table file (.csv)\|.csv',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
952	try:
953	if dlg.ShowModal() == wx.ID_OK:
954	filename = dlg.GetPath()
955	filename = os.path.splitext(filename)[0]+'.csv'
956	File = open(filename,'w')
957	else:
958	filename = None
959	finally:
960	dlg.Destroy()
961	if not filename:
962	return
963	for i in range(len(XY)):
964	if len(names):
965	header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
966	else:
967	header = '%s,%s(%d)\n'%(labelX,labelY,i)
968	File.write(header)
969	for x,y in XY[i].T:
970	File.write('%.3f,%.3f\n'%(x,y))
971	File.close()
972	print (' XY data saved to: '+filename)
973
974	def PeakListSave(G2frame,file,peaks):
975	'Save powder peaks to a data file'
976	print ('save peak list to file: '+G2frame.peaklistfile)
977	if not peaks:
978	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
979	try:
980	dlg.ShowModal()
981	finally:
982	dlg.Destroy()
983	return
984	for peak in peaks:
985	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
986	(peak[0],peak[2],peak[4],peak[6]))
987	print ('peak list saved')
988
989	def IndexPeakListSave(G2frame,peaks):
990	'Save powder peaks from the indexing list'
991	file = open(G2frame.peaklistfile,'wa')
992	print ('save index peak list to file: '+G2frame.peaklistfile)
993	wx.BeginBusyCursor()
994	try:
995	if not peaks:
996	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
997	try:
998	dlg.ShowModal()
999	finally:
1000	dlg.Destroy()
1001	return
1002	for peak in peaks:
1003	file.write("%12.6f\n" % (peak[7]))
1004	file.close()
1005	finally:
1006	wx.EndBusyCursor()
1007	print ('index peak list saved')
1008
1009	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1010	confirmoverwrite=True, parent=None,
1011	multipleselect=False):
1012	'''If the filename is a zip file, extract a file from that
1013	archive.
1014
1015	:param list Selection: used to predefine the name of the file
1016	to be extracted. Filename case and zip directory name are
1017	ignored in selection; the first matching file is used.
1018
1019	:param bool confirmread: if True asks the user to confirm before expanding
1020	the only file in a zip
1021
1022	:param bool confirmoverwrite: if True asks the user to confirm
1023	before overwriting if the extracted file already exists
1024
1025	:param bool multipleselect: if True allows more than one zip
1026	file to be extracted, a list of file(s) is returned.
1027	If only one file is present, do not ask which one, otherwise
1028	offer a list of choices (unless selection is used).
1029
1030	:returns: the name of the file that has been created or a
1031	list of files (see multipleselect)
1032
1033	If the file is not a zipfile, return the name of the input file.
1034	If the zipfile is empty or no file has been selected, return None
1035	'''
1036	import zipfile # do this now, since we can save startup time by doing this only on need
1037	import shutil
1038	zloc = os.path.split(filename)[0]
1039	if not zipfile.is_zipfile(filename):
1040	#print("not zip")
1041	return filename
1042
1043	z = zipfile.ZipFile(filename,'r')
1044	zinfo = z.infolist()
1045
1046	if len(zinfo) == 0:
1047	#print('Zip has no files!')
1048	zlist = [-1]
1049	if selection:
1050	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1051	if selection.lower() in choices:
1052	zlist = [choices.index(selection.lower())]
1053	else:
1054	print('debug: file '+str(selection)+' was not found in '+str(filename))
1055	zlist = [-1]
1056	elif len(zinfo) == 1 and confirmread:
1057	result = wx.ID_NO
1058	dlg = wx.MessageDialog(
1059	parent,
1060	'Is file '+str(zinfo[0].filename)+
1061	' what you want to extract from '+
1062	str(os.path.split(filename)[1])+'?',
1063	'Confirm file',
1064	wx.YES_NO \| wx.ICON_QUESTION)
1065	try:
1066	result = dlg.ShowModal()
1067	finally:
1068	dlg.Destroy()
1069	if result == wx.ID_NO:
1070	zlist = [-1]
1071	else:
1072	zlist = [0]
1073	elif len(zinfo) == 1:
1074	zlist = [0]
1075	elif multipleselect:
1076	# select one or more from a from list
1077	choices = [i.filename for i in zinfo]
1078	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1079	'Choose file(s)',choices)
1080	if dlg.ShowModal() == wx.ID_OK:
1081	zlist = dlg.GetSelections()
1082	else:
1083	zlist = []
1084	dlg.Destroy()
1085	else:
1086	# select one from a from list
1087	choices = [i.filename for i in zinfo]
1088	dlg = wx.SingleChoiceDialog(parent,
1089	'Select file to extract from zip file'+str(filename),'Choose file',
1090	choices,)
1091	if dlg.ShowModal() == wx.ID_OK:
1092	zlist = [dlg.GetSelection()]
1093	else:
1094	zlist = [-1]
1095	dlg.Destroy()
1096
1097	outlist = []
1098	for zindex in zlist:
1099	if zindex >= 0:
1100	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1101	if os.path.exists(efil) and confirmoverwrite:
1102	result = wx.ID_NO
1103	dlg = wx.MessageDialog(parent,
1104	'File '+str(efil)+' already exists. OK to overwrite it?',
1105	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1106	try:
1107	result = dlg.ShowModal()
1108	finally:
1109	dlg.Destroy()
1110	if result == wx.ID_NO:
1111	zindex = -1
1112	if zindex >= 0:
1113	# extract the file to the current directory, regardless of it's original path
1114	#z.extract(zinfo[zindex],zloc)
1115	eloc,efil = os.path.split(zinfo[zindex].filename)
1116	outfile = os.path.join(zloc, efil)
1117	fpin = z.open(zinfo[zindex])
1118	fpout = open(outfile, "wb")
1119	shutil.copyfileobj(fpin, fpout)
1120	fpin.close()
1121	fpout.close()
1122	outlist.append(outfile)
1123	z.close()
1124	if multipleselect and len(outlist) >= 1:
1125	return outlist
1126	elif len(outlist) == 1:
1127	return outlist[0]
1128	else:
1129	return None
1130
1131	def striphist(var,insChar=''):
1132	'strip a histogram number from a var name'
1133	sv = var.split(':')
1134	if len(sv) <= 1: return var
1135	if sv[1]:
1136	sv[1] = insChar
1137	return ':'.join(sv)
1138
1139	######################################################################
1140	# base classes for reading various types of data files
1141	# not used directly, only by subclassing
1142	######################################################################
1143	class ExportBaseclass(object):
1144	'''Defines a base class for the exporting of GSAS-II results.
1145
1146	This class is subclassed in the various exports/G2export_*.py files. Those files
1147	are imported in :meth:`GSASIIdataGUI.GSASII._init_Exports` which defines the
1148	appropriate menu items for each one and the .Exporter method is called
1149	directly from the menu item.
1150
1151	Routines may also define a .Writer method, which is used to write a single
1152	file without invoking any GUI objects.
1153	'''
1154	# TODO: review exporters producing exceptions where .Writer can't be used where G2frame is None (see CIF)
1155	# TODO: review conflicting uses of .Writer with mode (SeqRef) & elsewhere
1156	# TODO: move this class to G2fil
1157	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1158	self.G2frame = G2frame
1159	self.formatName = formatName # short string naming file type
1160	self.extension = extension
1161	if longFormatName: # longer string naming file type
1162	self.longFormatName = longFormatName
1163	else:
1164	self.longFormatName = formatName
1165	self.OverallParms = {}
1166	self.Phases = {}
1167	self.Histograms = {}
1168	self.powderDict = {}
1169	self.sasdDict = {}
1170	self.xtalDict = {}
1171	self.parmDict = {}
1172	self.sigDict = {}
1173	# updated in InitExport:
1174	self.currentExportType = None # type of export that has been requested
1175	# updated in ExportSelect (when used):
1176	self.phasenam = None # a list of selected phases
1177	self.histnam = None # a list of selected histograms
1178	self.filename = None # name of file to be written (single export) or template (multiple files)
1179	self.dirname = '' # name of directory where file(s) will be written
1180	self.fullpath = '' # name of file being written -- full path
1181
1182	# items that should be defined in a subclass of this class
1183	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1184	# The following types are defined: 'project', "phase", "powder", "single"
1185	self.multiple = False # set as True if the class can export multiple phases or histograms
1186	# self.multiple is ignored for "project" exports
1187
1188	def InitExport(self,event):
1189	'''Determines the type of menu that called the Exporter and
1190	misc initialization.
1191	'''
1192	self.filename = None # name of file to be written (single export)
1193	self.dirname = '' # name of file to be written (multiple export)
1194	if event:
1195	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1196
1197	def MakePWDRfilename(self,hist):
1198	'''Make a filename root (no extension) from a PWDR histogram name
1199
1200	:param str hist: the histogram name in data tree (starts with "PWDR ")
1201	'''
1202	file0 = ''
1203	file1 = hist[5:]
1204	# replace repeated blanks
1205	while file1 != file0:
1206	file0 = file1
1207	file1 = file0.replace(' ',' ').strip()
1208	file0 = file1.replace('Azm= ','A')
1209	# if angle has unneeded decimal places on aziumuth, remove them
1210	if file0[-3:] == '.00': file0 = file0[:-3]
1211	file0 = file0.replace('.','_')
1212	file0 = file0.replace(' ','_')
1213	return file0
1214
1215	def ExportSelect(self,AskFile='ask'):
1216	'''Selects histograms or phases when needed. Sets a default file name when
1217	requested into self.filename; always sets a default directory in self.dirname.
1218
1219	:param bool AskFile: Determines how this routine processes getting a
1220	location to store the current export(s).
1221
1222	* if AskFile is 'ask' (default option), get the name of the file to be written;
1223	self.filename and self.dirname are always set. In the case where
1224	multiple files must be generated, the export routine should do this
1225	based on self.filename as a template.
1226	* if AskFile is 'dir', get the name of the directory to be used;
1227	self.filename is not used, but self.dirname is always set. The export routine
1228	will always generate the file name.
1229	* if AskFile is 'single', get only the name of the directory to be used when
1230	multiple items will be written (as multiple files) are used
1231	or a complete file name is requested when a single file
1232	name is selected. self.dirname is always set and self.filename used
1233	only when a single file is selected.
1234	* if AskFile is 'default', creates a name of the file to be used from
1235	the name of the project (.gpx) file. If the project has not been saved,
1236	then the name of file is requested.
1237	self.filename and self.dirname are always set. In the case where
1238	multiple file names must be generated, the export routine should do this
1239	based on self.filename.
1240	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1241	file. If the project has not been saved, then a directory is requested.
1242	self.filename is not used.
1243
1244	:returns: True in case of an error
1245	'''
1246
1247	numselected = 1
1248	if self.currentExportType == 'phase':
1249	if len(self.Phases) == 0:
1250	self.G2frame.ErrorDialog(
1251	'Empty project',
1252	'Project does not contain any phases.')
1253	return True
1254	elif len(self.Phases) == 1:
1255	self.phasenam = list(self.Phases.keys())
1256	elif self.multiple:
1257	choices = sorted(self.Phases.keys())
1258	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1259	if phasenum is None: return True
1260	self.phasenam = [choices[i] for i in phasenum]
1261	if not self.phasenam: return True
1262	numselected = len(self.phasenam)
1263	else:
1264	choices = sorted(self.Phases.keys())
1265	phasenum = G2G.ItemSelector(choices,self.G2frame)
1266	if phasenum is None: return True
1267	self.phasenam = [choices[phasenum]]
1268	numselected = len(self.phasenam)
1269	elif self.currentExportType == 'single':
1270	if len(self.xtalDict) == 0:
1271	self.G2frame.ErrorDialog(
1272	'Empty project',
1273	'Project does not contain any single crystal data.')
1274	return True
1275	elif len(self.xtalDict) == 1:
1276	self.histnam = self.xtalDict.values()
1277	elif self.multiple:
1278	choices = sorted(self.xtalDict.values())
1279	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1280	if not hnum: return True
1281	self.histnam = [choices[i] for i in hnum]
1282	numselected = len(self.histnam)
1283	else:
1284	choices = sorted(self.xtalDict.values())
1285	hnum = G2G.ItemSelector(choices,self.G2frame)
1286	if hnum is None: return True
1287	self.histnam = [choices[hnum]]
1288	numselected = len(self.histnam)
1289	elif self.currentExportType == 'powder':
1290	if len(self.powderDict) == 0:
1291	self.G2frame.ErrorDialog(
1292	'Empty project',
1293	'Project does not contain any powder data.')
1294	return True
1295	elif len(self.powderDict) == 1:
1296	self.histnam = list(self.powderDict.values())
1297	elif self.multiple:
1298	choices = sorted(self.powderDict.values())
1299	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1300	if not hnum: return True
1301	self.histnam = [choices[i] for i in hnum]
1302	numselected = len(self.histnam)
1303	else:
1304	choices = sorted(self.powderDict.values())
1305	hnum = G2G.ItemSelector(choices,self.G2frame)
1306	if hnum is None: return True
1307	self.histnam = [choices[hnum]]
1308	numselected = len(self.histnam)
1309	elif self.currentExportType == 'sasd':
1310	if len(self.sasdDict) == 0:
1311	self.G2frame.ErrorDialog(
1312	'Empty project',
1313	'Project does not contain any small angle data.')
1314	return True
1315	elif len(self.sasdDict) == 1:
1316	self.histnam = self.sasdDict.values()
1317	elif self.multiple:
1318	choices = sorted(self.sasdDict.values())
1319	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1320	if not hnum: return True
1321	self.histnam = [choices[i] for i in hnum]
1322	numselected = len(self.histnam)
1323	else:
1324	choices = sorted(self.sasdDict.values())
1325	hnum = G2G.ItemSelector(choices,self.G2frame)
1326	if hnum is None: return True
1327	self.histnam = [choices[hnum]]
1328	numselected = len(self.histnam)
1329	elif self.currentExportType == 'image':
1330	if len(self.Histograms) == 0:
1331	self.G2frame.ErrorDialog(
1332	'Empty project',
1333	'Project does not contain any images.')
1334	return True
1335	elif len(self.Histograms) == 1:
1336	self.histnam = list(self.Histograms.keys())
1337	else:
1338	choices = sorted(self.Histograms.keys())
1339	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1340	if self.multiple:
1341	if not hnum: return True
1342	self.histnam = [choices[i] for i in hnum]
1343	else:
1344	if hnum is None: return True
1345	self.histnam = [choices[hnum]]
1346	numselected = len(self.histnam)
1347	if self.currentExportType == 'map':
1348	# search for phases with maps
1349	mapPhases = []
1350	choices = []
1351	for phasenam in sorted(self.Phases):
1352	phasedict = self.Phases[phasenam] # pointer to current phase info
1353	if len(phasedict['General']['Map'].get('rho',[])):
1354	mapPhases.append(phasenam)
1355	if phasedict['General']['Map'].get('Flip'):
1356	choices.append('Charge flip map: '+str(phasenam))
1357	elif phasedict['General']['Map'].get('MapType'):
1358	choices.append(
1359	str(phasedict['General']['Map'].get('MapType'))
1360	+ ' map: ' + str(phasenam))
1361	else:
1362	choices.append('unknown map: '+str(phasenam))
1363	# select a map if needed
1364	if len(mapPhases) == 0:
1365	self.G2frame.ErrorDialog(
1366	'Empty project',
1367	'Project does not contain any maps.')
1368	return True
1369	elif len(mapPhases) == 1:
1370	self.phasenam = mapPhases
1371	else:
1372	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1373	if self.multiple:
1374	if not phasenum: return True
1375	self.phasenam = [mapPhases[i] for i in phasenum]
1376	else:
1377	if phasenum is None: return True
1378	self.phasenam = [mapPhases[phasenum]]
1379	numselected = len(self.phasenam)
1380
1381	# items selected, now set self.dirname and usually self.filename
1382	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1383	AskFile == 'default' and not self.G2frame.GSASprojectfile
1384	):
1385	filename = self.askSaveFile()
1386	if not filename: return True
1387	self.dirname,self.filename = os.path.split(filename)
1388	elif AskFile == 'dir' or AskFile == 'single' or (
1389	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1390	):
1391	self.dirname = self.askSaveDirectory()
1392	if not self.dirname: return True
1393	elif AskFile == 'default-dir' or AskFile == 'default':
1394	self.dirname,self.filename = os.path.split(
1395	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1396	)
1397	else:
1398	raise Exception('This should not happen!')
1399
1400	def loadParmDict(self):
1401	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1402	refined values to those from the last cycle and set the uncertainties for the
1403	refined parameters in another dict (self.sigDict).
1404
1405	Expands the parm & sig dicts to include values derived from constraints.
1406
1407	This could be made faster for sequential fits by reducing the histogram list to only
1408	the active histogram being exported.
1409	'''
1410	self.G2frame.CheckNotebook()
1411	self.parmDict = {}
1412	self.sigDict = {}
1413	rigidbodyDict = {}
1414	covDict = {}
1415	consDict = {}
1416	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1417	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1418	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1419	while item:
1420	name = self.G2frame.GPXtree.GetItemText(item)
1421	if name == 'Rigid bodies':
1422	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(item)
1423	elif name == 'Covariance':
1424	covDict = self.G2frame.GPXtree.GetItemPyData(item)
1425	elif name == 'Constraints':
1426	consDict = self.G2frame.GPXtree.GetItemPyData(item)
1427	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1428	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1429	self.parmDict.update(rbDict)
1430	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1431	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1432	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1433	self.parmDict.update(phaseDict)
1434	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
1435	Phases,Histograms,Print=False,resetRefList=False)
1436	self.parmDict.update(hapDict)
1437	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1438	self.parmDict.update(histDict)
1439	self.parmDict.update(zip(
1440	covDict.get('varyList',[]),
1441	covDict.get('variables',[])))
1442	self.sigDict = dict(zip(
1443	covDict.get('varyList',[]),
1444	covDict.get('sig',[])))
1445	# expand to include constraints: first compile a list of constraints
1446	constList = []
1447	for item in consDict:
1448	if item.startswith('_'): continue
1449	constList += consDict[item]
1450	# now process the constraints
1451	G2mv.InitVars()
1452	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
1453	varyList = covDict.get('varyListStart')
1454	if varyList is None and len(constDict) == 0:
1455	# no constraints can use varyList
1456	varyList = covDict.get('varyList')
1457	elif varyList is None:
1458	# old GPX file from before pre-constraint varyList is saved
1459	print (' * Old refinement: Please use Calculate/Refine to redo *')
1460	raise Exception(' * Export aborted *')
1461	else:
1462	varyList = list(varyList)
1463	# add symmetry-generated constraints
1464	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(
1465	G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Rigid bodies'))
1466	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1467	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1468	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1469	Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints
1470	msg = G2mv.EvaluateMultipliers(constDict,phaseDict)
1471	if msg:
1472	print('Unable to interpret multiplier(s): '+msg)
1473	raise Exception(' * CIF creation aborted *')
1474	try:
1475	G2mv.GenerateConstraints(varyList,constDict,fixedList,self.parmDict)
1476	#print(G2mv.VarRemapShow(varyList))
1477	except:
1478	# this really should not happen
1479	print (' * ERROR - constraints are internally inconsistent *')
1480	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
1481	print ('Errors'+errmsg)
1482	if warnmsg: print ('Warnings'+warnmsg)
1483	raise Exception(' * CIF creation aborted *')
1484	# add the constrained values to the parameter dictionary
1485	G2mv.Dict2Map(self.parmDict,varyList)
1486	# and add their uncertainties into the esd dictionary (sigDict)
1487	if covDict.get('covMatrix') is not None:
1488	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
1489
1490	def loadTree(self):
1491	'''Load the contents of the data tree into a set of dicts
1492	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
1493	& self.xtalDict)
1494
1495	* The childrenless data tree items are overall parameters/controls for the
1496	entire project and are placed in self.OverallParms
1497	* Phase items are placed in self.Phases
1498	* Data items are placed in self.Histogram. The key for these data items
1499	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
1500	'''
1501	self.OverallParms = {}
1502	self.powderDict = {}
1503	self.sasdDict = {}
1504	self.xtalDict = {}
1505	self.Phases = {}
1506	self.Histograms = {}
1507	self.SeqRefdata = None
1508	self.SeqRefhist = None
1509	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1510	histType = None
1511	if self.currentExportType == 'phase':
1512	# if exporting phases load them here
1513	sub = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Phases')
1514	if not sub:
1515	print ('no phases found')
1516	return True
1517	item, cookie = self.G2frame.GPXtree.GetFirstChild(sub)
1518	while item:
1519	phaseName = self.G2frame.GPXtree.GetItemText(item)
1520	self.Phases[phaseName] = self.G2frame.GPXtree.GetItemPyData(item)
1521	item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie)
1522	return
1523	elif self.currentExportType == 'single':
1524	histType = 'HKLF'
1525	elif self.currentExportType == 'powder':
1526	histType = 'PWDR'
1527	elif self.currentExportType == 'image':
1528	histType = 'IMG'
1529	elif self.currentExportType == 'sasd':
1530	histType = 'SASD'
1531
1532	if histType: # Loading just one kind of tree entry
1533	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1534	while item:
1535	name = self.G2frame.GPXtree.GetItemText(item)
1536	if name.startswith(histType):
1537	if self.Histograms.get(name): # there is already an item with this name
1538	print('Histogram name '+str(name)+' is repeated. Renaming')
1539	if name[-1] == '9':
1540	name = name[:-1] + '10'
1541	elif name[-1] in '012345678':
1542	name = name[:-1] + str(int(name[-1])+1)
1543	else:
1544	name += '-1'
1545	self.Histograms[name] = {}
1546	# the main info goes into Data, but the 0th
1547	# element contains refinement results, carry
1548	# that over too now.
1549	self.Histograms[name]['Data'] = self.G2frame.GPXtree.GetItemPyData(item)[1]
1550	self.Histograms[name][0] = self.G2frame.GPXtree.GetItemPyData(item)[0]
1551	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1552	while item2:
1553	child = self.G2frame.GPXtree.GetItemText(item2)
1554	self.Histograms[name][child] = self.G2frame.GPXtree.GetItemPyData(item2)
1555	item2, cookie2 = self.G2frame.GPXtree.GetNextChild(item, cookie2)
1556	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1557	# index powder and single crystal histograms by number
1558	for hist in self.Histograms:
1559	if hist.startswith("PWDR"):
1560	d = self.powderDict
1561	elif hist.startswith("HKLF"):
1562	d = self.xtalDict
1563	elif hist.startswith("SASD"):
1564	d = self.sasdDict
1565	else:
1566	return
1567	i = self.Histograms[hist].get('hId')
1568	if i is None and not d.keys():
1569	i = 0
1570	elif i is None or i in d.keys():
1571	i = max(d.keys())+1
1572	d[i] = hist
1573	return
1574	# else standard load: using all interlinked phases and histograms
1575	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1576	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1577	while item:
1578	name = self.G2frame.GPXtree.GetItemText(item)
1579	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1580	if not item2:
1581	self.OverallParms[name] = self.G2frame.GPXtree.GetItemPyData(item)
1582	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1583	# index powder and single crystal histograms
1584	for hist in self.Histograms:
1585	i = self.Histograms[hist]['hId']
1586	if hist.startswith("PWDR"):
1587	self.powderDict[i] = hist
1588	elif hist.startswith("HKLF"):
1589	self.xtalDict[i] = hist
1590	elif hist.startswith("SASD"):
1591	self.sasdDict[i] = hist
1592
1593	def dumpTree(self,mode='type'):
1594	'''Print out information on the data tree dicts loaded in loadTree.
1595	Used for testing only.
1596	'''
1597	if self.SeqRefdata and self.SeqRefhist:
1598	print('Note that dumpTree does not show sequential results')
1599	print ('\nOverall')
1600	if mode == 'type':
1601	def Show(arg): return type(arg)
1602	else:
1603	def Show(arg): return arg
1604	for key in self.OverallParms:
1605	print (' '+key+Show(self.OverallParms[key]))
1606	print ('Phases')
1607	for key1 in self.Phases:
1608	print (' '+key1+Show(self.Phases[key1]))
1609	print ('Histogram')
1610	for key1 in self.Histograms:
1611	print (' '+key1+Show(self.Histograms[key1]))
1612	for key2 in self.Histograms[key1]:
1613	print (' '+key2+Show(self.Histograms[key1][key2]))
1614
1615	def defaultSaveFile(self):
1616	return os.path.abspath(
1617	os.path.splitext(self.G2frame.GSASprojectfile
1618	)[0]+self.extension)
1619
1620	def askSaveFile(self):
1621	'''Ask the user to supply a file name
1622
1623	:returns: a file name (str) or None if Cancel is pressed
1624
1625	'''
1626	#pth = G2G.GetExportPath(self.G2frame)
1627	if self.G2frame.GSASprojectfile:
1628	defnam = os.path.splitext(
1629	os.path.split(self.G2frame.GSASprojectfile)[1]
1630	)[0]+self.extension
1631	else:
1632	defnam = 'default' + self.extension
1633	return G2G.askSaveFile(self.G2frame,defnam,self.extension,self.longFormatName)
1634
1635	def askSaveDirectory(self):
1636	'''Ask the user to supply a directory name. Path name is used as the
1637	starting point for the next export path search.
1638
1639	:returns: a directory name (str) or None if Cancel is pressed
1640
1641	TODO: Can this be replaced with G2G.askSaveDirectory?
1642	'''
1643	pth = G2G.GetExportPath(self.G2frame)
1644	dlg = wx.DirDialog(
1645	self.G2frame, 'Input directory where file(s) will be written', pth,
1646	wx.DD_DEFAULT_STYLE)
1647	dlg.CenterOnParent()
1648	try:
1649	if dlg.ShowModal() == wx.ID_OK:
1650	filename = dlg.GetPath()
1651	self.G2frame.LastExportDir = filename
1652	else:
1653	filename = None
1654	finally:
1655	dlg.Destroy()
1656	return filename
1657
1658	# Tools for file writing.
1659	def OpenFile(self,fil=None,mode='w'):
1660	'''Open the output file
1661
1662	:param str fil: The name of the file to open. If None (default)
1663	the name defaults to self.dirname + self.filename.
1664	If an extension is supplied, it is not overridded,
1665	but if not, the default extension is used.
1666	:returns: the file object opened by the routine which is also
1667	saved as self.fp
1668	'''
1669	if mode == 'd': # debug mode
1670	self.fullpath = '(stdout)'
1671	self.fp = sys.stdout
1672	return
1673	if not fil:
1674	if not os.path.splitext(self.filename)[1]:
1675	self.filename += self.extension
1676	fil = os.path.join(self.dirname,self.filename)
1677	self.fullpath = os.path.abspath(fil)
1678	self.fp = open(self.fullpath,mode)
1679	return self.fp
1680
1681	def Write(self,line):
1682	'''write a line of output, attaching a line-end character
1683
1684	:param str line: the text to be written.
1685	'''
1686	self.fp.write(line+'\n')
1687
1688	def CloseFile(self,fp=None):
1689	'''Close a file opened in OpenFile
1690
1691	:param file fp: the file object to be closed. If None (default)
1692	file object self.fp is closed.
1693	'''
1694	if self.fp == sys.stdout: return # debug mode
1695	if fp is None:
1696	fp = self.fp
1697	self.fp = None
1698	if fp is not None: fp.close()
1699
1700	def SetSeqRef(self,data,hist):
1701	'''Set the exporter to retrieve results from a sequential refinement
1702	rather than the main tree
1703	'''
1704	self.SeqRefdata = data
1705	self.SeqRefhist = hist
1706	data_name = data[hist]
1707	for i,val in zip(data_name['varyList'],data_name['sig']):
1708	self.sigDict[i] = val
1709	self.sigDict[striphist(i)] = val
1710	for i in data_name['parmDict']:
1711	self.parmDict[striphist(i)] = data_name['parmDict'][i]
1712	self.parmDict[i] = data_name['parmDict'][i]
1713	# zero out the dA[xyz] terms, they would only bring confusion
1714	key = i.split(':')
1715	if len(key) < 3: continue
1716	if key[2].startswith('dA'):
1717	self.parmDict[i] = 0.0
1718	for i,(val,sig) in data_name.get('depParmDict',{}).items():
1719	self.parmDict[i] = val
1720	self.sigDict[i] = sig
1721	#GSASIIpath.IPyBreak()
1722
1723	# Tools to pull information out of the data arrays
1724	def GetCell(self,phasenam):
1725	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1726
1727	:param str phasenam: the name for the selected phase
1728	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1729	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1730	cell values and `cellSig` has their uncertainties.
1731	"""
1732	if self.SeqRefdata and self.SeqRefhist:
1733	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
1734	phasedict = self.Phases[phasenam] # pointer to current phase info
1735	try:
1736	pfx = str(phasedict['pId'])+'::'
1737	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
1738	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
1739	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
1740	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
1741	return cellList,cellSig
1742	except KeyError:
1743	cell = phasedict['General']['Cell'][1:]
1744	return cell,7*[0]
1745
1746	def GetSeqCell(self,phasenam,data_name):
1747	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1748	and histogram in a sequential fit
1749
1750	:param str phasenam: the name for the selected phase
1751	:param dict data_name: the sequential refinement parameters for the selected histogram
1752	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1753	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1754	cell values and `cellSig` has their uncertainties.
1755	"""
1756	phasedict = self.Phases[phasenam]
1757	SGdata = phasedict['General']['SGData']
1758	pId = phasedict['pId']
1759	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
1760	ESDlookup = {}
1761	Dlookup = {}
1762	varied = [striphist(i) for i in data_name['varyList']]
1763	for item,val in data_name['newCellDict'].items():
1764	if item in varied:
1765	ESDlookup[val[0]] = item
1766	Dlookup[item] = val[0]
1767	A = RecpCellTerms[:]
1768	for i in range(6):
1769	var = str(pId)+'::A'+str(i)
1770	if var in ESDlookup:
1771	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
1772	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
1773	zeroDict = {i:0.0 for i in cellDict}
1774	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
1775	covData = {
1776	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
1777	'covMatrix': data_name['covMatrix']
1778	}
1779	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
1780
1781	def GetAtoms(self,phasenam):
1782	"""Gets the atoms associated with a phase. Can be used with standard
1783	or macromolecular phases
1784
1785	:param str phasenam: the name for the selected phase
1786	:returns: a list of items for eac atom where each item is a list containing:
1787	label, typ, mult, xyz, and td, where
1788
1789	* label and typ are the atom label and the scattering factor type (str)
1790	* mult is the site multiplicity (int)
1791	* xyz is contains a list with four pairs of numbers:
1792	x, y, z and fractional occupancy and
1793	their standard uncertainty (or a negative value)
1794	* td is contains a list with either one or six pairs of numbers:
1795	if one number it is U\ :sub:`iso` and with six numbers it is
1796	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
1797	paired with their standard uncertainty (or a negative value)
1798	"""
1799	phasedict = self.Phases[phasenam] # pointer to current phase info
1800	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1801	cfrac = cx+3
1802	fpfx = str(phasedict['pId'])+'::Afrac:'
1803	atomslist = []
1804	for i,at in enumerate(phasedict['Atoms']):
1805	if phasedict['General']['Type'] == 'macromolecular':
1806	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1807	else:
1808	label = at[ct-1]
1809	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
1810	fsig = self.sigDict.get(fpfx+str(i),-0.009)
1811	mult = at[cs+1]
1812	typ = at[ct]
1813	xyz = []
1814	for j,v in enumerate(('x','y','z')):
1815	val = at[cx+j]
1816	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
1817	val = self.parmDict.get(pfx, val)
1818	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
1819	sig = self.sigDict.get(dpfx,-0.000009)
1820	xyz.append((val,sig))
1821	xyz.append((fval,fsig))
1822	td = []
1823	if at[cia] == 'I':
1824	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
1825	val = self.parmDict.get(pfx,at[cia+1])
1826	sig = self.sigDict.get(pfx,-0.0009)
1827	td.append((val,sig))
1828	else:
1829	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
1830	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
1831	val = self.parmDict.get(pfx,at[cia+2+i])
1832	sig = self.sigDict.get(pfx,-0.0009)
1833	td.append((val,sig))
1834	atomslist.append((label,typ,mult,xyz,td))
1835	return atomslist
1836	######################################################################
1837	def ExportPowderList(G2frame):
1838	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
1839	along with their descriptions (note that a extension may be repeated
1840	but descriptions are unique).
1841	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1842
1843	:param wx.Frame G2frame: the GSAS-II main data tree window
1844	'''
1845	extList = []
1846	extLabel = []
1847	for obj in G2frame.exporterlist:
1848	if 'powder' in obj.exporttype:
1849	try:
1850	obj.Writer
1851	extList.append(obj.extension)
1852	extLabel.append(obj.formatName)
1853	except AttributeError:
1854	pass
1855	return extList,extLabel
1856
1857	def ExportPowder(G2frame,TreeName,fileroot,extension,hint=''):
1858	'''Writes a single powder histogram using the Export routines.
1859	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1860
1861	:param wx.Frame G2frame: the GSAS-II main data tree window
1862	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
1863	:param str fileroot: name for file to be written, extension ignored
1864	:param str extension: extension for file to be written (start with '.'). Must
1865	match a powder export routine that has a Writer object.
1866	:param str hint: a string that must match the export's format
1867	'''
1868	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
1869	for obj in G2frame.exporterlist:
1870	if obj.extension == extension and 'powder' in obj.exporttype:
1871	if hint and hint not in obj.formatName: continue
1872	obj.currentExportType = 'powder'
1873	obj.InitExport(None)
1874	obj.loadTree() # load all histograms in tree into dicts
1875	if TreeName not in obj.Histograms:
1876	raise Exception('Histogram not found: '+str(TreeName))
1877	try:
1878	obj.Writer
1879	except AttributeError:
1880	continue
1881	try:
1882	obj.Writer(TreeName,filename)
1883	print('wrote file '+filename)
1884	return
1885	except Exception:
1886	print('Export Routine for '+extension+' failed.')
1887	else:
1888	print('No Export routine supports extension '+extension)
1889
1890	def ExportSequential(G2frame,data,obj,exporttype):
1891	'''
1892	Used to export from every phase/dataset in a sequential refinement using
1893	a .Writer method for either projects or phases. Prompts to select histograms
1894	and for phase exports, which phase(s).
1895
1896	:param wx.Frame G2frame: the GSAS-II main data tree window
1897	:param dict data: the sequential refinement data object
1898	:param str exporttype: indicates the type of export ('project' or 'phase')
1899	'''
1900	if len(data['histNames']) == 0:
1901	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
1902	obj.InitExport(None)
1903	obj.loadTree()
1904	obj.loadParmDict()
1905	if len(data['histNames']) == 1:
1906	histlist = data['histNames']
1907	else:
1908	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
1909	'Select histograms',data['histNames'])
1910	if dlg.ShowModal() == wx.ID_OK:
1911	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
1912	dlg.Destroy()
1913	else:
1914	dlg.Destroy()
1915	return
1916	if exporttype == 'Phase':
1917	phaselist = list(obj.Phases.keys())
1918	if len(obj.Phases) == 0:
1919	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
1920	return
1921	elif len(obj.Phases) > 1:
1922	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
1923	'Select phases', phaselist)
1924	if dlg.ShowModal() == wx.ID_OK:
1925	phaselist = [phaselist[l] for l in dlg.GetSelections()]
1926	dlg.Destroy()
1927	else:
1928	dlg.Destroy()
1929	return
1930	filename = obj.askSaveFile()
1931	if not filename: return True
1932	obj.dirname,obj.filename = os.path.split(filename)
1933	print('Writing output to file '+str(obj.filename)+"...")
1934	mode = 'w'
1935	for p in phaselist:
1936	for h in histlist:
1937	obj.SetSeqRef(data,h)
1938	#GSASIIpath.IPyBreak()
1939	obj.Writer(h,phasenam=p,mode=mode)
1940	mode = 'a'
1941	print('...done')
1942	elif exporttype == 'Project': # note that the CIF exporter is not yet ready for this
1943	filename = obj.askSaveFile()
1944	if not filename: return True
1945	obj.dirname,obj.filename = os.path.split(filename)
1946	print('Writing output to file '+str(obj.filename)+"...")
1947	mode = 'w'
1948	for h in histlist:
1949	obj.SetSeqRef(data,h)
1950	obj.Writer(h,mode=mode)
1951	print('\t'+str(h)+' written')
1952	mode = 'a'
1953	print('...done')
1954	elif exporttype == 'Powder':
1955	filename = obj.askSaveFile()
1956	if not filename: return True
1957	obj.dirname,obj.filename = os.path.split(filename)
1958	print('Writing output to file '+str(obj.filename)+"...")
1959	mode = 'w'
1960	for h in histlist:
1961	obj.SetSeqRef(data,h)
1962	obj.Writer(h,mode=mode)
1963	print('\t'+str(h)+' written')
1964	mode = 'a'
1965	print('...done')
1966
1967	def ReadDIFFaX(DIFFaXfile):
1968	print ('read '+DIFFaXfile)
1969	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
1970	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
1971	df = open(DIFFaXfile,'r')
1972	lines = df.readlines()
1973	df.close()
1974	struct = False
1975	Struct = []
1976	stack = False
1977	Stack = []
1978	trans = False
1979	Trans = []
1980	for diff in lines:
1981	diff = diff[:-1].lower()
1982	if '!' in diff:
1983	continue
1984	while '}' in diff: #strip comments
1985	iB = diff.index('{')
1986	iF = diff.index('}')+1
1987	if iB:
1988	diff = diff[:iB]
1989	else:
1990	diff = diff[iF:]
1991	if not diff:
1992	continue
1993	if diff.strip() == 'instrumental':
1994	continue
1995	if diff.strip() == 'structural':
1996	struct = True
1997	continue
1998	elif diff.strip() == 'stacking':
1999	struct = False
2000	stack = True
2001	continue
2002	elif diff.strip() == 'transitions':
2003	stack = False
2004	trans = True
2005	continue
2006	diff = diff.strip()
2007	if struct:
2008	if diff:
2009	Struct.append(diff)
2010	elif stack:
2011	if diff:
2012	Stack.append(diff)
2013	elif trans:
2014	if diff:
2015	Trans.append(diff)
2016
2017	#STRUCTURE records
2018	laueRec = Struct[1].split()
2019	Layer['Laue'] = laueRec[0]
2020	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2021	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2022	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2023	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2024	cell = Struct[0].split()
2025	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2026	nLayers = int(Struct[2])
2027	N = 3
2028	if 'layer' not in Struct[3]:
2029	N = 4
2030	if Struct[3] != 'infinite':
2031	width = Struct[3].split()
2032	Layer['Width'][0] = [float(width[0]),float(width[1])]
2033	for nL in range(nLayers):
2034	if '=' in Struct[N]:
2035	name = Struct[N].split('=')
2036	sameas = int(name[1])-1
2037	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2038	N += 1
2039	continue
2040	Symm = 'None'
2041	if 'centro' in Struct[N+1]: Symm = '-1'
2042	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2043	N += 2
2044	while 'layer' not in Struct[N]:
2045	atom = Struct[N][4:].split()
2046	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2047	if atomType not in Layer['AtInfo']:
2048	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2049	atomName = '%s(%s)'%(atomType,atom[0])
2050	newVals = []
2051	for val in atom[1:6]:
2052	if '/' in val:
2053	newVals.append(eval(val+'.'))
2054	else:
2055	newVals.append(float(val))
2056	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2057	Layer['Layers'][-1]['Atoms'].append(atomRec)
2058	N += 1
2059	if N > len(Struct)-1:
2060	break
2061	#TRANSITIONS records
2062	transArray = []
2063	N = 0
2064	for i in range(nLayers):
2065	transArray.append([])
2066	for j in range(nLayers):
2067	vals = Trans[N].split()
2068	newVals = []
2069	for val in vals[:4]:
2070	if '/' in val:
2071	newVals.append(eval(val+'.'))
2072	else:
2073	newVals.append(float(val))
2074	transArray[-1].append(newVals+['',False])
2075	N += 1
2076	Layer['Transitions'] = transArray
2077	#STACKING records
2078	Layer['Stacking'] = [Stack[0],'']
2079	if Stack[0] == 'recursive':
2080	Layer['Stacking'][1] = Stack[1]
2081	elif Stack[0] == 'explicit':
2082	if Stack[1] == 'random':
2083	Layer['Stacking'][1] = Stack[1]
2084	else:
2085	Layer['Stacking'][1] = 'list'
2086	Layer['Stacking'].append('')
2087	for stack in Stack[2:]:
2088	Layer['Stacking'][2] += ' '+stack
2089	return Layer
2090
2091	def postURL(URL,postdict):
2092	'''Posts a set of values as from a web form. If access fails to an https
2093	site the access is retried with http.
2094
2095	:param str URL: the URL to post; typically something
2096	like 'http://www.../dir/page?'
2097	:param dict postdict: contains keywords and values, such
2098	as {'centrosymmetry': '0', 'crystalsystem': '0', ...}
2099	:returns: a string with the response from the web server or None
2100	if access fails.
2101	'''
2102	try:
2103	import requests # delay this until now, since rarely needed
2104	except:
2105	# this import seems to fail with the Anaconda pythonw on
2106	# macs; it should not!
2107	print('Warning: failed to import requests. Python config error')
2108	return None
2109
2110	repeat = True
2111	while repeat:
2112	r = None
2113	repeat = False
2114	try:
2115	r = requests.get(URL,params=postdict)
2116	if r.status_code == 200:
2117	print('request OK')
2118	page = r.text
2119	return page # success
2120	else:
2121	print('request to {} failed. Reason={}'.format(URL,r.reason))
2122	except Exception as msg: #ConnectionError?
2123	print('connection error - not on internet?')
2124	if GSASIIpath.GetConfigValue('debug'): print(msg)
2125	finally:
2126	if r: r.close()
2127	if URL.startswith('https:'):
2128	repeat = True
2129	URL = URL.replace('https:','http:')
2130	else:
2131	return None
2132
2133	if __name__ == '__main__':
2134	import GSASIIdataGUI
2135	application = GSASIIdataGUI.GSASIImain(0)
2136	G2frame = application.main
2137	#app = wx.PySimpleApp()
2138	#G2frame = wx.Frame(None) # create a frame
2139	#frm.Show(True)
2140	#filename = '/tmp/notzip.zip'
2141	#filename = '/tmp/all.zip'
2142	#filename = '/tmp/11bmb_7652.zip'
2143
2144	#selection=None, confirmoverwrite=True, parent=None
2145	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2146	#print ExtractFileFromZip(filename,multipleselect=True)
2147	# #confirmread=False, confirmoverwrite=False)
2148
2149	# choicelist=[ ('a','b','c'),
2150	# ('test1','test2'),('no choice',)]
2151	# titles = [ 'a, b or c', 'tests', 'No option here']
2152	# dlg = MultipleChoicesDialog(
2153	# choicelist,titles,
2154	# parent=frm)
2155	# if dlg.ShowModal() == wx.ID_OK:
2156	# print 'Got OK'
2157	imagefile = '/tmp/NDC5_00237_3.ge3'
2158	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2159
2160	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2161
2162	GSASIIpath.IPyBreak_base()

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