Context Navigation

source: trunk/GSASIIIO.py @ 4539

Last change on this file since 4539 was 4539, checked in by vondreele, 3 years ago
remove commented old/bad code in G2IO fix Instrument parameters plots for pink patterns
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
File size: 90.6 KB

Line
1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2020-08-07 13:50:02 +0000 (Fri, 07 Aug 2020) $
4	# $Author: vondreele $
5	# $Revision: 4539 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 4539 2020-08-07 13:50:02Z vondreele $
8	########### SVN repository information ###################
9	'''
10	GSASIIIO: Misc I/O routines
11	=============================
12
13	Module with miscellaneous routines for input and output. Many
14	are GUI routines to interact with user.
15
16	Includes support for image reading.
17
18	Also includes base 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: 4539 $")
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['outAzimuths'] > 1:
854	dazm = np.min(np.abs(np.diff(azms)))/2.
855	G2frame.IntgOutList = []
856	for i,azm in enumerate(azms[:-1]):
857	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
858	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
859	# if Overwrite delete any duplicate
860	if Overwrite and G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname):
861	print('Replacing '+Aname)
862	item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname)
863	G2frame.GPXtree.Delete(item)
864	else:
865	nOcc = 0
866	while item:
867	Name = G2frame.GPXtree.GetItemText(item)
868	if Aname in Name:
869	nOcc += 1
870	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
871	if nOcc:
872	Aname += '(%d)'%(nOcc)
873	Sample = G2obj.SetDefaultSample() #set as Debye-Scherrer
874	Sample['Gonio. radius'] = data['distance']
875	Sample['Omega'] = data['GonioAngles'][0]
876	Sample['Chi'] = data['GonioAngles'][1]
877	Sample['Phi'] = data['GonioAngles'][2]
878	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
879	polariz = data['PolaVal'][0]
880	for item in Comments:
881	for key in ('Temperature','Pressure','Time','FreePrm1','FreePrm2','FreePrm3','Omega',
882	'Chi','Phi'):
883	if key.lower() in item.lower():
884	try:
885	Sample[key] = float(item.split('=')[1])
886	except:
887	pass
888	if 'label_prm' in item.lower():
889	for num in ('1','2','3'):
890	if 'label_prm'+num in item.lower():
891	Controls['FreePrm'+num] = item.split('=')[1].strip()
892	if 'PWDR' in Aname:
893	if 'target' in data: #from lab x-ray 2D imaging data
894	wave1,wave2 = waves[data['target']]
895	parms = ['PXC',wave1,wave2,0.5,0.0,polariz,290.,-40.,30.,6.,-14.,0.0,0.0001,Azms[i]]
896	else:
897	parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0,0.0001,Azms[i]]
898	elif 'SASD' in Aname:
899	Sample['Trans'] = data['SampleAbs'][0]
900	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
901	Y = G2frame.Integrate[0][i]
902	Ymin = np.min(Y)
903	Ymax = np.max(Y)
904	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
905	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=Aname)
906	G2frame.IntgOutList.append(Id)
907	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
908	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Limits'),copy.deepcopy([tuple(Xminmax),Xminmax]))
909	if 'PWDR' in Aname:
910	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Background'),[['chebyschev-1',1,3,1.0,0.0,0.0],
911	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
912	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
913	for item in inst[0]:
914	inst[0][item] = list(inst[0][item])
915	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),inst)
916	if 'PWDR' in Aname:
917	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
918	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
919	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Index Peak List'),[[],[]])
920	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Unit Cells List'),[])
921	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection Lists'),{})
922	elif 'SASD' in Aname:
923	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
924	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
925	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
926	valuesdict = {
927	'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxsize),'Offset':[0.0,0.0],'delOffset':0.02*Ymax,
928	'refOffset':-0.1Ymax,'refDelt':0.1Ymax,'Yminmax':[Ymin,Ymax]}
929	G2frame.GPXtree.SetItemPyData(Id,[valuesdict,
930	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
931	return Id #last powder pattern generated
932
933	def XYsave(G2frame,XY,labelX='X',labelY='Y',names=[]):
934	'Save XY table data'
935	pth = G2G.GetExportPath(G2frame)
936	dlg = wx.FileDialog(
937	G2frame, 'Enter csv filename for XY table', pth, '',
938	'XY table file (.csv)\|.csv',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
939	try:
940	if dlg.ShowModal() == wx.ID_OK:
941	filename = dlg.GetPath()
942	filename = os.path.splitext(filename)[0]+'.csv'
943	File = open(filename,'w')
944	else:
945	filename = None
946	finally:
947	dlg.Destroy()
948	if not filename:
949	return
950	for i in range(len(XY)):
951	if len(names):
952	header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
953	else:
954	header = '%s,%s(%d)\n'%(labelX,labelY,i)
955	File.write(header)
956	for x,y in XY[i].T:
957	File.write('%.3f,%.3f\n'%(x,y))
958	File.close()
959	print (' XY data saved to: '+filename)
960
961	def PeakListSave(G2frame,file,peaks):
962	'Save powder peaks to a data file'
963	print ('save peak list to file: '+G2frame.peaklistfile)
964	if not peaks:
965	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
966	try:
967	dlg.ShowModal()
968	finally:
969	dlg.Destroy()
970	return
971	for peak in peaks:
972	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
973	(peak[0],peak[2],peak[4],peak[6]))
974	print ('peak list saved')
975
976	def IndexPeakListSave(G2frame,peaks):
977	'Save powder peaks from the indexing list'
978	file = open(G2frame.peaklistfile,'wa')
979	print ('save index peak list to file: '+G2frame.peaklistfile)
980	wx.BeginBusyCursor()
981	try:
982	if not peaks:
983	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
984	try:
985	dlg.ShowModal()
986	finally:
987	dlg.Destroy()
988	return
989	for peak in peaks:
990	file.write("%12.6f\n" % (peak[7]))
991	file.close()
992	finally:
993	wx.EndBusyCursor()
994	print ('index peak list saved')
995
996	def ExtractFileFromZip(filename, selection=None, confirmread=True,
997	confirmoverwrite=True, parent=None,
998	multipleselect=False):
999	'''If the filename is a zip file, extract a file from that
1000	archive.
1001
1002	:param list Selection: used to predefine the name of the file
1003	to be extracted. Filename case and zip directory name are
1004	ignored in selection; the first matching file is used.
1005
1006	:param bool confirmread: if True asks the user to confirm before expanding
1007	the only file in a zip
1008
1009	:param bool confirmoverwrite: if True asks the user to confirm
1010	before overwriting if the extracted file already exists
1011
1012	:param bool multipleselect: if True allows more than one zip
1013	file to be extracted, a list of file(s) is returned.
1014	If only one file is present, do not ask which one, otherwise
1015	offer a list of choices (unless selection is used).
1016
1017	:returns: the name of the file that has been created or a
1018	list of files (see multipleselect)
1019
1020	If the file is not a zipfile, return the name of the input file.
1021	If the zipfile is empty or no file has been selected, return None
1022	'''
1023	import zipfile # do this now, since we can save startup time by doing this only on need
1024	import shutil
1025	zloc = os.path.split(filename)[0]
1026	if not zipfile.is_zipfile(filename):
1027	#print("not zip")
1028	return filename
1029
1030	z = zipfile.ZipFile(filename,'r')
1031	zinfo = z.infolist()
1032
1033	if len(zinfo) == 0:
1034	#print('Zip has no files!')
1035	zlist = [-1]
1036	if selection:
1037	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1038	if selection.lower() in choices:
1039	zlist = [choices.index(selection.lower())]
1040	else:
1041	print('debug: file '+str(selection)+' was not found in '+str(filename))
1042	zlist = [-1]
1043	elif len(zinfo) == 1 and confirmread:
1044	result = wx.ID_NO
1045	dlg = wx.MessageDialog(
1046	parent,
1047	'Is file '+str(zinfo[0].filename)+
1048	' what you want to extract from '+
1049	str(os.path.split(filename)[1])+'?',
1050	'Confirm file',
1051	wx.YES_NO \| wx.ICON_QUESTION)
1052	try:
1053	result = dlg.ShowModal()
1054	finally:
1055	dlg.Destroy()
1056	if result == wx.ID_NO:
1057	zlist = [-1]
1058	else:
1059	zlist = [0]
1060	elif len(zinfo) == 1:
1061	zlist = [0]
1062	elif multipleselect:
1063	# select one or more from a from list
1064	choices = [i.filename for i in zinfo]
1065	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1066	'Choose file(s)',choices)
1067	if dlg.ShowModal() == wx.ID_OK:
1068	zlist = dlg.GetSelections()
1069	else:
1070	zlist = []
1071	dlg.Destroy()
1072	else:
1073	# select one from a from list
1074	choices = [i.filename for i in zinfo]
1075	dlg = wx.SingleChoiceDialog(parent,
1076	'Select file to extract from zip file'+str(filename),'Choose file',
1077	choices,)
1078	if dlg.ShowModal() == wx.ID_OK:
1079	zlist = [dlg.GetSelection()]
1080	else:
1081	zlist = [-1]
1082	dlg.Destroy()
1083
1084	outlist = []
1085	for zindex in zlist:
1086	if zindex >= 0:
1087	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1088	if os.path.exists(efil) and confirmoverwrite:
1089	result = wx.ID_NO
1090	dlg = wx.MessageDialog(parent,
1091	'File '+str(efil)+' already exists. OK to overwrite it?',
1092	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1093	try:
1094	result = dlg.ShowModal()
1095	finally:
1096	dlg.Destroy()
1097	if result == wx.ID_NO:
1098	zindex = -1
1099	if zindex >= 0:
1100	# extract the file to the current directory, regardless of it's original path
1101	#z.extract(zinfo[zindex],zloc)
1102	eloc,efil = os.path.split(zinfo[zindex].filename)
1103	outfile = os.path.join(zloc, efil)
1104	fpin = z.open(zinfo[zindex])
1105	fpout = open(outfile, "wb")
1106	shutil.copyfileobj(fpin, fpout)
1107	fpin.close()
1108	fpout.close()
1109	outlist.append(outfile)
1110	z.close()
1111	if multipleselect and len(outlist) >= 1:
1112	return outlist
1113	elif len(outlist) == 1:
1114	return outlist[0]
1115	else:
1116	return None
1117
1118	def striphist(var,insChar=''):
1119	'strip a histogram number from a var name'
1120	sv = var.split(':')
1121	if len(sv) <= 1: return var
1122	if sv[1]:
1123	sv[1] = insChar
1124	return ':'.join(sv)
1125
1126	######################################################################
1127	# base classes for reading various types of data files
1128	# not used directly, only by subclassing
1129	######################################################################
1130	class ExportBaseclass(object):
1131	'''Defines a base class for the exporting of GSAS-II results.
1132
1133	This class is subclassed in the various exports/G2export_*.py files. Those files
1134	are imported in :meth:`GSASIIdataGUI.GSASII._init_Exports` which defines the
1135	appropriate menu items for each one and the .Exporter method is called
1136	directly from the menu item.
1137
1138	Routines may also define a .Writer method, which is used to write a single
1139	file without invoking any GUI objects.
1140	'''
1141	# TODO: review exporters producing exceptions where .Writer can't be used where G2frame is None (see CIF)
1142	# TODO: review conflicting uses of .Writer with mode (SeqRef) & elsewhere
1143	# TODO: move this class to G2fil
1144	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1145	self.G2frame = G2frame
1146	self.formatName = formatName # short string naming file type
1147	self.extension = extension
1148	if longFormatName: # longer string naming file type
1149	self.longFormatName = longFormatName
1150	else:
1151	self.longFormatName = formatName
1152	self.OverallParms = {}
1153	self.Phases = {}
1154	self.Histograms = {}
1155	self.powderDict = {}
1156	self.sasdDict = {}
1157	self.xtalDict = {}
1158	self.parmDict = {}
1159	self.sigDict = {}
1160	# updated in InitExport:
1161	self.currentExportType = None # type of export that has been requested
1162	# updated in ExportSelect (when used):
1163	self.phasenam = None # a list of selected phases
1164	self.histnam = None # a list of selected histograms
1165	self.filename = None # name of file to be written (single export) or template (multiple files)
1166	self.dirname = '' # name of directory where file(s) will be written
1167	self.fullpath = '' # name of file being written -- full path
1168
1169	# items that should be defined in a subclass of this class
1170	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1171	# The following types are defined: 'project', "phase", "powder", "single"
1172	self.multiple = False # set as True if the class can export multiple phases or histograms
1173	# self.multiple is ignored for "project" exports
1174
1175	def InitExport(self,event):
1176	'''Determines the type of menu that called the Exporter and
1177	misc initialization.
1178	'''
1179	self.filename = None # name of file to be written (single export)
1180	self.dirname = '' # name of file to be written (multiple export)
1181	if event:
1182	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1183
1184	def MakePWDRfilename(self,hist):
1185	'''Make a filename root (no extension) from a PWDR histogram name
1186
1187	:param str hist: the histogram name in data tree (starts with "PWDR ")
1188	'''
1189	file0 = ''
1190	file1 = hist[5:]
1191	# replace repeated blanks
1192	while file1 != file0:
1193	file0 = file1
1194	file1 = file0.replace(' ',' ').strip()
1195	file0 = file1.replace('Azm= ','A')
1196	# if angle has unneeded decimal places on aziumuth, remove them
1197	if file0[-3:] == '.00': file0 = file0[:-3]
1198	file0 = file0.replace('.','_')
1199	file0 = file0.replace(' ','_')
1200	return file0
1201
1202	def ExportSelect(self,AskFile='ask'):
1203	'''Selects histograms or phases when needed. Sets a default file name when
1204	requested into self.filename; always sets a default directory in self.dirname.
1205
1206	:param bool AskFile: Determines how this routine processes getting a
1207	location to store the current export(s).
1208
1209	* if AskFile is 'ask' (default option), get the name of the file to be written;
1210	self.filename and self.dirname are always set. In the case where
1211	multiple files must be generated, the export routine should do this
1212	based on self.filename as a template.
1213	* if AskFile is 'dir', get the name of the directory to be used;
1214	self.filename is not used, but self.dirname is always set. The export routine
1215	will always generate the file name.
1216	* if AskFile is 'single', get only the name of the directory to be used when
1217	multiple items will be written (as multiple files) are used
1218	or a complete file name is requested when a single file
1219	name is selected. self.dirname is always set and self.filename used
1220	only when a single file is selected.
1221	* if AskFile is 'default', creates a name of the file to be used from
1222	the name of the project (.gpx) file. If the project has not been saved,
1223	then the name of file is requested.
1224	self.filename and self.dirname are always set. In the case where
1225	multiple file names must be generated, the export routine should do this
1226	based on self.filename.
1227	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1228	file. If the project has not been saved, then a directory is requested.
1229	self.filename is not used.
1230
1231	:returns: True in case of an error
1232	'''
1233
1234	numselected = 1
1235	if self.currentExportType == 'phase':
1236	if len(self.Phases) == 0:
1237	self.G2frame.ErrorDialog(
1238	'Empty project',
1239	'Project does not contain any phases.')
1240	return True
1241	elif len(self.Phases) == 1:
1242	self.phasenam = list(self.Phases.keys())
1243	elif self.multiple:
1244	choices = sorted(self.Phases.keys())
1245	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1246	if phasenum is None: return True
1247	self.phasenam = [choices[i] for i in phasenum]
1248	if not self.phasenam: return True
1249	numselected = len(self.phasenam)
1250	else:
1251	choices = sorted(self.Phases.keys())
1252	phasenum = G2G.ItemSelector(choices,self.G2frame)
1253	if phasenum is None: return True
1254	self.phasenam = [choices[phasenum]]
1255	numselected = len(self.phasenam)
1256	elif self.currentExportType == 'single':
1257	if len(self.xtalDict) == 0:
1258	self.G2frame.ErrorDialog(
1259	'Empty project',
1260	'Project does not contain any single crystal data.')
1261	return True
1262	elif len(self.xtalDict) == 1:
1263	self.histnam = self.xtalDict.values()
1264	elif self.multiple:
1265	choices = sorted(self.xtalDict.values())
1266	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1267	if not hnum: return True
1268	self.histnam = [choices[i] for i in hnum]
1269	numselected = len(self.histnam)
1270	else:
1271	choices = sorted(self.xtalDict.values())
1272	hnum = G2G.ItemSelector(choices,self.G2frame)
1273	if hnum is None: return True
1274	self.histnam = [choices[hnum]]
1275	numselected = len(self.histnam)
1276	elif self.currentExportType == 'powder':
1277	if len(self.powderDict) == 0:
1278	self.G2frame.ErrorDialog(
1279	'Empty project',
1280	'Project does not contain any powder data.')
1281	return True
1282	elif len(self.powderDict) == 1:
1283	self.histnam = list(self.powderDict.values())
1284	elif self.multiple:
1285	choices = sorted(self.powderDict.values())
1286	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1287	if not hnum: return True
1288	self.histnam = [choices[i] for i in hnum]
1289	numselected = len(self.histnam)
1290	else:
1291	choices = sorted(self.powderDict.values())
1292	hnum = G2G.ItemSelector(choices,self.G2frame)
1293	if hnum is None: return True
1294	self.histnam = [choices[hnum]]
1295	numselected = len(self.histnam)
1296	elif self.currentExportType == 'sasd':
1297	if len(self.sasdDict) == 0:
1298	self.G2frame.ErrorDialog(
1299	'Empty project',
1300	'Project does not contain any small angle data.')
1301	return True
1302	elif len(self.sasdDict) == 1:
1303	self.histnam = self.sasdDict.values()
1304	elif self.multiple:
1305	choices = sorted(self.sasdDict.values())
1306	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1307	if not hnum: return True
1308	self.histnam = [choices[i] for i in hnum]
1309	numselected = len(self.histnam)
1310	else:
1311	choices = sorted(self.sasdDict.values())
1312	hnum = G2G.ItemSelector(choices,self.G2frame)
1313	if hnum is None: return True
1314	self.histnam = [choices[hnum]]
1315	numselected = len(self.histnam)
1316	elif self.currentExportType == 'image':
1317	if len(self.Histograms) == 0:
1318	self.G2frame.ErrorDialog(
1319	'Empty project',
1320	'Project does not contain any images.')
1321	return True
1322	elif len(self.Histograms) == 1:
1323	self.histnam = list(self.Histograms.keys())
1324	else:
1325	choices = sorted(self.Histograms.keys())
1326	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1327	if self.multiple:
1328	if not hnum: return True
1329	self.histnam = [choices[i] for i in hnum]
1330	else:
1331	if hnum is None: return True
1332	self.histnam = [choices[hnum]]
1333	numselected = len(self.histnam)
1334	if self.currentExportType == 'map':
1335	# search for phases with maps
1336	mapPhases = []
1337	choices = []
1338	for phasenam in sorted(self.Phases):
1339	phasedict = self.Phases[phasenam] # pointer to current phase info
1340	if len(phasedict['General']['Map'].get('rho',[])):
1341	mapPhases.append(phasenam)
1342	if phasedict['General']['Map'].get('Flip'):
1343	choices.append('Charge flip map: '+str(phasenam))
1344	elif phasedict['General']['Map'].get('MapType'):
1345	choices.append(
1346	str(phasedict['General']['Map'].get('MapType'))
1347	+ ' map: ' + str(phasenam))
1348	else:
1349	choices.append('unknown map: '+str(phasenam))
1350	# select a map if needed
1351	if len(mapPhases) == 0:
1352	self.G2frame.ErrorDialog(
1353	'Empty project',
1354	'Project does not contain any maps.')
1355	return True
1356	elif len(mapPhases) == 1:
1357	self.phasenam = mapPhases
1358	else:
1359	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1360	if self.multiple:
1361	if not phasenum: return True
1362	self.phasenam = [mapPhases[i] for i in phasenum]
1363	else:
1364	if phasenum is None: return True
1365	self.phasenam = [mapPhases[phasenum]]
1366	numselected = len(self.phasenam)
1367
1368	# items selected, now set self.dirname and usually self.filename
1369	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1370	AskFile == 'default' and not self.G2frame.GSASprojectfile
1371	):
1372	filename = self.askSaveFile()
1373	if not filename: return True
1374	self.dirname,self.filename = os.path.split(filename)
1375	elif AskFile == 'dir' or AskFile == 'single' or (
1376	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1377	):
1378	self.dirname = self.askSaveDirectory()
1379	if not self.dirname: return True
1380	elif AskFile == 'default-dir' or AskFile == 'default':
1381	self.dirname,self.filename = os.path.split(
1382	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1383	)
1384	else:
1385	raise Exception('This should not happen!')
1386
1387	def loadParmDict(self):
1388	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1389	refined values to those from the last cycle and set the uncertainties for the
1390	refined parameters in another dict (self.sigDict).
1391
1392	Expands the parm & sig dicts to include values derived from constraints.
1393
1394	This could be made faster for sequential fits by reducing the histogram list to only
1395	the active histogram being exported.
1396	'''
1397	self.G2frame.CheckNotebook()
1398	self.parmDict = {}
1399	self.sigDict = {}
1400	rigidbodyDict = {}
1401	covDict = {}
1402	consDict = {}
1403	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1404	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1405	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1406	while item:
1407	name = self.G2frame.GPXtree.GetItemText(item)
1408	if name == 'Rigid bodies':
1409	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(item)
1410	elif name == 'Covariance':
1411	covDict = self.G2frame.GPXtree.GetItemPyData(item)
1412	elif name == 'Constraints':
1413	consDict = self.G2frame.GPXtree.GetItemPyData(item)
1414	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1415	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1416	self.parmDict.update(rbDict)
1417	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1418	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1419	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1420	self.parmDict.update(phaseDict)
1421	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
1422	Phases,Histograms,Print=False,resetRefList=False)
1423	self.parmDict.update(hapDict)
1424	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1425	self.parmDict.update(histDict)
1426	self.parmDict.update(zip(
1427	covDict.get('varyList',[]),
1428	covDict.get('variables',[])))
1429	self.sigDict = dict(zip(
1430	covDict.get('varyList',[]),
1431	covDict.get('sig',[])))
1432	# expand to include constraints: first compile a list of constraints
1433	constList = []
1434	for item in consDict:
1435	if item.startswith('_'): continue
1436	constList += consDict[item]
1437	# now process the constraints
1438	G2mv.InitVars()
1439	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
1440	varyList = covDict.get('varyListStart')
1441	if varyList is None and len(constDict) == 0:
1442	# no constraints can use varyList
1443	varyList = covDict.get('varyList')
1444	elif varyList is None:
1445	# old GPX file from before pre-constraint varyList is saved
1446	print (' * Old refinement: Please use Calculate/Refine to redo *')
1447	raise Exception(' * Export aborted *')
1448	else:
1449	varyList = list(varyList)
1450	# add symmetry-generated constraints
1451	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(
1452	G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Rigid bodies'))
1453	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1454	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1455	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1456	Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints
1457	msg = G2mv.EvaluateMultipliers(constDict,phaseDict)
1458	if msg:
1459	print('Unable to interpret multiplier(s): '+msg)
1460	raise Exception(' * CIF creation aborted *')
1461	try:
1462	G2mv.GenerateConstraints(varyList,constDict,fixedList,self.parmDict)
1463	#print(G2mv.VarRemapShow(varyList))
1464	except:
1465	# this really should not happen
1466	print (' * ERROR - constraints are internally inconsistent *')
1467	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
1468	print ('Errors'+errmsg)
1469	if warnmsg: print ('Warnings'+warnmsg)
1470	raise Exception(' * CIF creation aborted *')
1471	# add the constrained values to the parameter dictionary
1472	G2mv.Dict2Map(self.parmDict,varyList)
1473	# and add their uncertainties into the esd dictionary (sigDict)
1474	if covDict.get('covMatrix') is not None:
1475	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
1476
1477	def loadTree(self):
1478	'''Load the contents of the data tree into a set of dicts
1479	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
1480	& self.xtalDict)
1481
1482	* The childrenless data tree items are overall parameters/controls for the
1483	entire project and are placed in self.OverallParms
1484	* Phase items are placed in self.Phases
1485	* Data items are placed in self.Histogram. The key for these data items
1486	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
1487	'''
1488	self.OverallParms = {}
1489	self.powderDict = {}
1490	self.sasdDict = {}
1491	self.xtalDict = {}
1492	self.Phases = {}
1493	self.Histograms = {}
1494	self.SeqRefdata = None
1495	self.SeqRefhist = None
1496	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1497	histType = None
1498	if self.currentExportType == 'phase':
1499	# if exporting phases load them here
1500	sub = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Phases')
1501	if not sub:
1502	print ('no phases found')
1503	return True
1504	item, cookie = self.G2frame.GPXtree.GetFirstChild(sub)
1505	while item:
1506	phaseName = self.G2frame.GPXtree.GetItemText(item)
1507	self.Phases[phaseName] = self.G2frame.GPXtree.GetItemPyData(item)
1508	item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie)
1509	return
1510	elif self.currentExportType == 'single':
1511	histType = 'HKLF'
1512	elif self.currentExportType == 'powder':
1513	histType = 'PWDR'
1514	elif self.currentExportType == 'image':
1515	histType = 'IMG'
1516	elif self.currentExportType == 'sasd':
1517	histType = 'SASD'
1518
1519	if histType: # Loading just one kind of tree entry
1520	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1521	while item:
1522	name = self.G2frame.GPXtree.GetItemText(item)
1523	if name.startswith(histType):
1524	if self.Histograms.get(name): # there is already an item with this name
1525	print('Histogram name '+str(name)+' is repeated. Renaming')
1526	if name[-1] == '9':
1527	name = name[:-1] + '10'
1528	elif name[-1] in '012345678':
1529	name = name[:-1] + str(int(name[-1])+1)
1530	else:
1531	name += '-1'
1532	self.Histograms[name] = {}
1533	# the main info goes into Data, but the 0th
1534	# element contains refinement results, carry
1535	# that over too now.
1536	self.Histograms[name]['Data'] = self.G2frame.GPXtree.GetItemPyData(item)[1]
1537	self.Histograms[name][0] = self.G2frame.GPXtree.GetItemPyData(item)[0]
1538	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1539	while item2:
1540	child = self.G2frame.GPXtree.GetItemText(item2)
1541	self.Histograms[name][child] = self.G2frame.GPXtree.GetItemPyData(item2)
1542	item2, cookie2 = self.G2frame.GPXtree.GetNextChild(item, cookie2)
1543	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1544	# index powder and single crystal histograms by number
1545	for hist in self.Histograms:
1546	if hist.startswith("PWDR"):
1547	d = self.powderDict
1548	elif hist.startswith("HKLF"):
1549	d = self.xtalDict
1550	elif hist.startswith("SASD"):
1551	d = self.sasdDict
1552	else:
1553	return
1554	i = self.Histograms[hist].get('hId')
1555	if i is None and not d.keys():
1556	i = 0
1557	elif i is None or i in d.keys():
1558	i = max(d.keys())+1
1559	d[i] = hist
1560	return
1561	# else standard load: using all interlinked phases and histograms
1562	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1563	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1564	while item:
1565	name = self.G2frame.GPXtree.GetItemText(item)
1566	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1567	if not item2:
1568	self.OverallParms[name] = self.G2frame.GPXtree.GetItemPyData(item)
1569	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1570	# index powder and single crystal histograms
1571	for hist in self.Histograms:
1572	i = self.Histograms[hist]['hId']
1573	if hist.startswith("PWDR"):
1574	self.powderDict[i] = hist
1575	elif hist.startswith("HKLF"):
1576	self.xtalDict[i] = hist
1577	elif hist.startswith("SASD"):
1578	self.sasdDict[i] = hist
1579
1580	def dumpTree(self,mode='type'):
1581	'''Print out information on the data tree dicts loaded in loadTree.
1582	Used for testing only.
1583	'''
1584	if self.SeqRefdata and self.SeqRefhist:
1585	print('Note that dumpTree does not show sequential results')
1586	print ('\nOverall')
1587	if mode == 'type':
1588	def Show(arg): return type(arg)
1589	else:
1590	def Show(arg): return arg
1591	for key in self.OverallParms:
1592	print (' '+key+Show(self.OverallParms[key]))
1593	print ('Phases')
1594	for key1 in self.Phases:
1595	print (' '+key1+Show(self.Phases[key1]))
1596	print ('Histogram')
1597	for key1 in self.Histograms:
1598	print (' '+key1+Show(self.Histograms[key1]))
1599	for key2 in self.Histograms[key1]:
1600	print (' '+key2+Show(self.Histograms[key1][key2]))
1601
1602	def defaultSaveFile(self):
1603	return os.path.abspath(
1604	os.path.splitext(self.G2frame.GSASprojectfile
1605	)[0]+self.extension)
1606
1607	def askSaveFile(self):
1608	'''Ask the user to supply a file name
1609
1610	:returns: a file name (str) or None if Cancel is pressed
1611
1612	'''
1613	#pth = G2G.GetExportPath(self.G2frame)
1614	if self.G2frame.GSASprojectfile:
1615	defnam = os.path.splitext(
1616	os.path.split(self.G2frame.GSASprojectfile)[1]
1617	)[0]+self.extension
1618	else:
1619	defnam = 'default' + self.extension
1620	return G2G.askSaveFile(self.G2frame,defnam,self.extension,self.longFormatName)
1621
1622	def askSaveDirectory(self):
1623	'''Ask the user to supply a directory name. Path name is used as the
1624	starting point for the next export path search.
1625
1626	:returns: a directory name (str) or None if Cancel is pressed
1627
1628	TODO: Can this be replaced with G2G.askSaveDirectory?
1629	'''
1630	pth = G2G.GetExportPath(self.G2frame)
1631	dlg = wx.DirDialog(
1632	self.G2frame, 'Input directory where file(s) will be written', pth,
1633	wx.DD_DEFAULT_STYLE)
1634	dlg.CenterOnParent()
1635	try:
1636	if dlg.ShowModal() == wx.ID_OK:
1637	filename = dlg.GetPath()
1638	self.G2frame.LastExportDir = filename
1639	else:
1640	filename = None
1641	finally:
1642	dlg.Destroy()
1643	return filename
1644
1645	# Tools for file writing.
1646	def OpenFile(self,fil=None,mode='w'):
1647	'''Open the output file
1648
1649	:param str fil: The name of the file to open. If None (default)
1650	the name defaults to self.dirname + self.filename.
1651	If an extension is supplied, it is not overridded,
1652	but if not, the default extension is used.
1653	:returns: the file object opened by the routine which is also
1654	saved as self.fp
1655	'''
1656	if mode == 'd': # debug mode
1657	self.fullpath = '(stdout)'
1658	self.fp = sys.stdout
1659	return
1660	if not fil:
1661	if not os.path.splitext(self.filename)[1]:
1662	self.filename += self.extension
1663	fil = os.path.join(self.dirname,self.filename)
1664	self.fullpath = os.path.abspath(fil)
1665	self.fp = open(self.fullpath,mode)
1666	return self.fp
1667
1668	def Write(self,line):
1669	'''write a line of output, attaching a line-end character
1670
1671	:param str line: the text to be written.
1672	'''
1673	self.fp.write(line+'\n')
1674
1675	def CloseFile(self,fp=None):
1676	'''Close a file opened in OpenFile
1677
1678	:param file fp: the file object to be closed. If None (default)
1679	file object self.fp is closed.
1680	'''
1681	if self.fp == sys.stdout: return # debug mode
1682	if fp is None:
1683	fp = self.fp
1684	self.fp = None
1685	if fp is not None: fp.close()
1686
1687	def SetSeqRef(self,data,hist):
1688	'''Set the exporter to retrieve results from a sequential refinement
1689	rather than the main tree
1690	'''
1691	self.SeqRefdata = data
1692	self.SeqRefhist = hist
1693	data_name = data[hist]
1694	for i,val in zip(data_name['varyList'],data_name['sig']):
1695	self.sigDict[i] = val
1696	self.sigDict[striphist(i)] = val
1697	for i in data_name['parmDict']:
1698	self.parmDict[striphist(i)] = data_name['parmDict'][i]
1699	self.parmDict[i] = data_name['parmDict'][i]
1700	# zero out the dA[xyz] terms, they would only bring confusion
1701	key = i.split(':')
1702	if len(key) < 3: continue
1703	if key[2].startswith('dA'):
1704	self.parmDict[i] = 0.0
1705	for i,(val,sig) in data_name.get('depParmDict',{}).items():
1706	self.parmDict[i] = val
1707	self.sigDict[i] = sig
1708	#GSASIIpath.IPyBreak()
1709
1710	# Tools to pull information out of the data arrays
1711	def GetCell(self,phasenam):
1712	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1713
1714	:param str phasenam: the name for the selected phase
1715	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1716	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1717	cell values and `cellSig` has their uncertainties.
1718	"""
1719	if self.SeqRefdata and self.SeqRefhist:
1720	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
1721	phasedict = self.Phases[phasenam] # pointer to current phase info
1722	try:
1723	pfx = str(phasedict['pId'])+'::'
1724	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
1725	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
1726	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
1727	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
1728	return cellList,cellSig
1729	except KeyError:
1730	cell = phasedict['General']['Cell'][1:]
1731	return cell,7*[0]
1732
1733	def GetSeqCell(self,phasenam,data_name):
1734	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1735	and histogram in a sequential fit
1736
1737	:param str phasenam: the name for the selected phase
1738	:param dict data_name: the sequential refinement parameters for the selected histogram
1739	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1740	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1741	cell values and `cellSig` has their uncertainties.
1742	"""
1743	phasedict = self.Phases[phasenam]
1744	SGdata = phasedict['General']['SGData']
1745	pId = phasedict['pId']
1746	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
1747	ESDlookup = {}
1748	Dlookup = {}
1749	varied = [striphist(i) for i in data_name['varyList']]
1750	for item,val in data_name['newCellDict'].items():
1751	if item in varied:
1752	ESDlookup[val[0]] = item
1753	Dlookup[item] = val[0]
1754	A = RecpCellTerms[:]
1755	for i in range(6):
1756	var = str(pId)+'::A'+str(i)
1757	if var in ESDlookup:
1758	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
1759	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
1760	zeroDict = {i:0.0 for i in cellDict}
1761	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
1762	covData = {
1763	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
1764	'covMatrix': data_name['covMatrix']
1765	}
1766	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
1767
1768	def GetAtoms(self,phasenam):
1769	"""Gets the atoms associated with a phase. Can be used with standard
1770	or macromolecular phases
1771
1772	:param str phasenam: the name for the selected phase
1773	:returns: a list of items for eac atom where each item is a list containing:
1774	label, typ, mult, xyz, and td, where
1775
1776	* label and typ are the atom label and the scattering factor type (str)
1777	* mult is the site multiplicity (int)
1778	* xyz is contains a list with four pairs of numbers:
1779	x, y, z and fractional occupancy and
1780	their standard uncertainty (or a negative value)
1781	* td is contains a list with either one or six pairs of numbers:
1782	if one number it is U\ :sub:`iso` and with six numbers it is
1783	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
1784	paired with their standard uncertainty (or a negative value)
1785	"""
1786	phasedict = self.Phases[phasenam] # pointer to current phase info
1787	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1788	cfrac = cx+3
1789	fpfx = str(phasedict['pId'])+'::Afrac:'
1790	atomslist = []
1791	for i,at in enumerate(phasedict['Atoms']):
1792	if phasedict['General']['Type'] == 'macromolecular':
1793	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1794	else:
1795	label = at[ct-1]
1796	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
1797	fsig = self.sigDict.get(fpfx+str(i),-0.009)
1798	mult = at[cs+1]
1799	typ = at[ct]
1800	xyz = []
1801	for j,v in enumerate(('x','y','z')):
1802	val = at[cx+j]
1803	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
1804	val = self.parmDict.get(pfx, val)
1805	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
1806	sig = self.sigDict.get(dpfx,-0.000009)
1807	xyz.append((val,sig))
1808	xyz.append((fval,fsig))
1809	td = []
1810	if at[cia] == 'I':
1811	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
1812	val = self.parmDict.get(pfx,at[cia+1])
1813	sig = self.sigDict.get(pfx,-0.0009)
1814	td.append((val,sig))
1815	else:
1816	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
1817	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
1818	val = self.parmDict.get(pfx,at[cia+2+i])
1819	sig = self.sigDict.get(pfx,-0.0009)
1820	td.append((val,sig))
1821	atomslist.append((label,typ,mult,xyz,td))
1822	return atomslist
1823	######################################################################
1824	def ExportPowderList(G2frame):
1825	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
1826	along with their descriptions (note that a extension may be repeated
1827	but descriptions are unique).
1828	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1829
1830	:param wx.Frame G2frame: the GSAS-II main data tree window
1831	'''
1832	extList = []
1833	extLabel = []
1834	for obj in G2frame.exporterlist:
1835	if 'powder' in obj.exporttype:
1836	try:
1837	obj.Writer
1838	extList.append(obj.extension)
1839	extLabel.append(obj.formatName)
1840	except AttributeError:
1841	pass
1842	return extList,extLabel
1843
1844	def ExportPowder(G2frame,TreeName,fileroot,extension,hint=''):
1845	'''Writes a single powder histogram using the Export routines.
1846	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1847
1848	:param wx.Frame G2frame: the GSAS-II main data tree window
1849	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
1850	:param str fileroot: name for file to be written, extension ignored
1851	:param str extension: extension for file to be written (start with '.'). Must
1852	match a powder export routine that has a Writer object.
1853	:param str hint: a string that must match the export's format
1854	'''
1855	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
1856	for obj in G2frame.exporterlist:
1857	if obj.extension == extension and 'powder' in obj.exporttype:
1858	if hint and hint not in obj.formatName: continue
1859	obj.currentExportType = 'powder'
1860	obj.InitExport(None)
1861	obj.loadTree() # load all histograms in tree into dicts
1862	if TreeName not in obj.Histograms:
1863	raise Exception('Histogram not found: '+str(TreeName))
1864	try:
1865	obj.Writer
1866	except AttributeError:
1867	continue
1868	try:
1869	obj.Writer(TreeName,filename)
1870	print('wrote file '+filename)
1871	return
1872	except Exception:
1873	print('Export Routine for '+extension+' failed.')
1874	else:
1875	print('No Export routine supports extension '+extension)
1876
1877	def ExportSequential(G2frame,data,obj,exporttype):
1878	'''
1879	Used to export from every phase/dataset in a sequential refinement using
1880	a .Writer method for either projects or phases. Prompts to select histograms
1881	and for phase exports, which phase(s).
1882
1883	:param wx.Frame G2frame: the GSAS-II main data tree window
1884	:param dict data: the sequential refinement data object
1885	:param str exporttype: indicates the type of export ('project' or 'phase')
1886	'''
1887	if len(data['histNames']) == 0:
1888	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
1889	obj.InitExport(None)
1890	obj.loadTree()
1891	obj.loadParmDict()
1892	if len(data['histNames']) == 1:
1893	histlist = data['histNames']
1894	else:
1895	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
1896	'Select histograms',data['histNames'])
1897	if dlg.ShowModal() == wx.ID_OK:
1898	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
1899	dlg.Destroy()
1900	else:
1901	dlg.Destroy()
1902	return
1903	if exporttype == 'Phase':
1904	phaselist = list(obj.Phases.keys())
1905	if len(obj.Phases) == 0:
1906	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
1907	return
1908	elif len(obj.Phases) > 1:
1909	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
1910	'Select phases', phaselist)
1911	if dlg.ShowModal() == wx.ID_OK:
1912	phaselist = [phaselist[l] for l in dlg.GetSelections()]
1913	dlg.Destroy()
1914	else:
1915	dlg.Destroy()
1916	return
1917	filename = obj.askSaveFile()
1918	if not filename: return True
1919	obj.dirname,obj.filename = os.path.split(filename)
1920	print('Writing output to file '+str(obj.filename)+"...")
1921	mode = 'w'
1922	for p in phaselist:
1923	for h in histlist:
1924	obj.SetSeqRef(data,h)
1925	#GSASIIpath.IPyBreak()
1926	obj.Writer(h,phasenam=p,mode=mode)
1927	mode = 'a'
1928	print('...done')
1929	elif exporttype == 'Project': # note that the CIF exporter is not yet ready for this
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 h in histlist:
1936	obj.SetSeqRef(data,h)
1937	obj.Writer(h,mode=mode)
1938	print('\t'+str(h)+' written')
1939	mode = 'a'
1940	print('...done')
1941	elif exporttype == 'Powder':
1942	filename = obj.askSaveFile()
1943	if not filename: return True
1944	obj.dirname,obj.filename = os.path.split(filename)
1945	print('Writing output to file '+str(obj.filename)+"...")
1946	mode = 'w'
1947	for h in histlist:
1948	obj.SetSeqRef(data,h)
1949	obj.Writer(h,mode=mode)
1950	print('\t'+str(h)+' written')
1951	mode = 'a'
1952	print('...done')
1953
1954	def ReadDIFFaX(DIFFaXfile):
1955	print ('read '+DIFFaXfile)
1956	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
1957	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
1958	df = open(DIFFaXfile,'r')
1959	lines = df.readlines()
1960	df.close()
1961	struct = False
1962	Struct = []
1963	stack = False
1964	Stack = []
1965	trans = False
1966	Trans = []
1967	for diff in lines:
1968	diff = diff[:-1].lower()
1969	if '!' in diff:
1970	continue
1971	while '}' in diff: #strip comments
1972	iB = diff.index('{')
1973	iF = diff.index('}')+1
1974	if iB:
1975	diff = diff[:iB]
1976	else:
1977	diff = diff[iF:]
1978	if not diff:
1979	continue
1980	if diff.strip() == 'instrumental':
1981	continue
1982	if diff.strip() == 'structural':
1983	struct = True
1984	continue
1985	elif diff.strip() == 'stacking':
1986	struct = False
1987	stack = True
1988	continue
1989	elif diff.strip() == 'transitions':
1990	stack = False
1991	trans = True
1992	continue
1993	diff = diff.strip()
1994	if struct:
1995	if diff:
1996	Struct.append(diff)
1997	elif stack:
1998	if diff:
1999	Stack.append(diff)
2000	elif trans:
2001	if diff:
2002	Trans.append(diff)
2003
2004	#STRUCTURE records
2005	laueRec = Struct[1].split()
2006	Layer['Laue'] = laueRec[0]
2007	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2008	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2009	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2010	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2011	cell = Struct[0].split()
2012	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2013	nLayers = int(Struct[2])
2014	N = 3
2015	if 'layer' not in Struct[3]:
2016	N = 4
2017	if Struct[3] != 'infinite':
2018	width = Struct[3].split()
2019	Layer['Width'][0] = [float(width[0]),float(width[1])]
2020	for nL in range(nLayers):
2021	if '=' in Struct[N]:
2022	name = Struct[N].split('=')
2023	sameas = int(name[1])-1
2024	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2025	N += 1
2026	continue
2027	Symm = 'None'
2028	if 'centro' in Struct[N+1]: Symm = '-1'
2029	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2030	N += 2
2031	while 'layer' not in Struct[N]:
2032	atom = Struct[N][4:].split()
2033	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2034	if atomType not in Layer['AtInfo']:
2035	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2036	atomName = '%s(%s)'%(atomType,atom[0])
2037	newVals = []
2038	for val in atom[1:6]:
2039	if '/' in val:
2040	newVals.append(eval(val+'.'))
2041	else:
2042	newVals.append(float(val))
2043	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2044	Layer['Layers'][-1]['Atoms'].append(atomRec)
2045	N += 1
2046	if N > len(Struct)-1:
2047	break
2048	#TRANSITIONS records
2049	transArray = []
2050	N = 0
2051	for i in range(nLayers):
2052	transArray.append([])
2053	for j in range(nLayers):
2054	vals = Trans[N].split()
2055	newVals = []
2056	for val in vals[:4]:
2057	if '/' in val:
2058	newVals.append(eval(val+'.'))
2059	else:
2060	newVals.append(float(val))
2061	transArray[-1].append(newVals+['',False])
2062	N += 1
2063	Layer['Transitions'] = transArray
2064	#STACKING records
2065	Layer['Stacking'] = [Stack[0],'']
2066	if Stack[0] == 'recursive':
2067	Layer['Stacking'][1] = Stack[1]
2068	elif Stack[0] == 'explicit':
2069	if Stack[1] == 'random':
2070	Layer['Stacking'][1] = Stack[1]
2071	else:
2072	Layer['Stacking'][1] = 'list'
2073	Layer['Stacking'].append('')
2074	for stack in Stack[2:]:
2075	Layer['Stacking'][2] += ' '+stack
2076	return Layer
2077
2078	def postURL(URL,postdict):
2079	'''Posts a set of values as from a web form. If access fails to an https
2080	site the access is retried with http.
2081
2082	:param str URL: the URL to post; typically something
2083	like 'http://www.../dir/page?'
2084	:param dict postdict: contains keywords and values, such
2085	as {'centrosymmetry': '0', 'crystalsystem': '0', ...}
2086	:returns: a string with the response from the web server or None
2087	if access fails.
2088	'''
2089	try:
2090	import requests # delay this until now, since rarely needed
2091	except:
2092	# this import seems to fail with the Anaconda pythonw on
2093	# macs; it should not!
2094	print('Warning: failed to import requests. Python config error')
2095	return None
2096
2097	repeat = True
2098	while repeat:
2099	r = None
2100	repeat = False
2101	try:
2102	r = requests.get(URL,params=postdict)
2103	if r.status_code == 200:
2104	print('request OK')
2105	page = r.text
2106	return page # success
2107	else:
2108	print('request to {} failed. Reason={}'.format(URL,r.reason))
2109	except Exception as msg: #ConnectionError?
2110	print('connection error - not on internet?')
2111	if GSASIIpath.GetConfigValue('debug'): print(msg)
2112	finally:
2113	if r: r.close()
2114	if URL.startswith('https:'):
2115	repeat = True
2116	URL = URL.replace('https:','http:')
2117	else:
2118	return None
2119
2120	if __name__ == '__main__':
2121	import GSASIIdataGUI
2122	application = GSASIIdataGUI.GSASIImain(0)
2123	G2frame = application.main
2124	#app = wx.PySimpleApp()
2125	#G2frame = wx.Frame(None) # create a frame
2126	#frm.Show(True)
2127	#filename = '/tmp/notzip.zip'
2128	#filename = '/tmp/all.zip'
2129	#filename = '/tmp/11bmb_7652.zip'
2130
2131	#selection=None, confirmoverwrite=True, parent=None
2132	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2133	#print ExtractFileFromZip(filename,multipleselect=True)
2134	# #confirmread=False, confirmoverwrite=False)
2135
2136	# choicelist=[ ('a','b','c'),
2137	# ('test1','test2'),('no choice',)]
2138	# titles = [ 'a, b or c', 'tests', 'No option here']
2139	# dlg = MultipleChoicesDialog(
2140	# choicelist,titles,
2141	# parent=frm)
2142	# if dlg.ShowModal() == wx.ID_OK:
2143	# print 'Got OK'
2144	imagefile = '/tmp/NDC5_00237_3.ge3'
2145	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2146
2147	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2148
2149	GSASIIpath.IPyBreak_base()

Note: See TracBrowser for help on using the repository browser.

Download in other formats: