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source: trunk/GSASIIIO.py

Last change on this file was 5663, checked in by vondreele, 2 days ago

Implement 1st draft of atom deformation refinement - functions from Phil Coppens. Functions apparently correct; derivatives need work. GUI interface done, constraints available for all deformation parameters.
New ORBtables available for orbital form factor coefficients
Add factor sizer to bond (only) control - was only for bond & angle control
new routine GetHistogramTypes? - from tree in G2dataGUI

Add optional comment line to G2ScrolledGrid - shows below table
Move Parameter Impact menu item to be under Compute partials

Property svn:eol-style set to native
Property svn:keywords set to Date Author Revision URL Id

File size: 96.3 KB

Line
1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2023-09-29 20:47:55 +0000 (Fri, 29 Sep 2023) $
4	# $Author: vondreele $
5	# $Revision: 5663 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 5663 2023-09-29 20:47:55Z vondreele $
8	########### SVN repository information ###################
9	'''
10	Misc routines for input and output, including image reading follow.
11
12	TODO: This module needs some work to separate wx from non-wx routines. GUI
13	routines should probably move to GSASIIctrlGUI.
14	'''
15
16	from __future__ import division, print_function
17
18	# Allow this to be imported without wx present. Was needed for G2scriptable, but is
19	# likely not needed anymore
20	try:
21	import wx
22	except ImportError:
23	# was needed by sphinx, but probably not anymore
24	class Placeholder(object):
25	def __init__(self):
26	self.Dialog = object
27	wx = Placeholder()
28	import math
29	import numpy as np
30	import numpy.ma as ma
31
32	import copy
33	import platform
34	if '2' in platform.python_version_tuple()[0]:
35	import cPickle
36	else:
37	import pickle as cPickle
38	import sys
39	import re
40	import random as ran
41	import GSASIIpath
42	GSASIIpath.SetVersionNumber("$Revision: 5663 $")
43	try:
44	import GSASIIdataGUI as G2gd
45	except ImportError:
46	pass
47	import GSASIIobj as G2obj
48	import GSASIIlattice as G2lat
49	try:
50	import GSASIIpwdGUI as G2pdG
51	import GSASIIimgGUI as G2imG
52	except ImportError:
53	pass
54	import GSASIIElem as G2el
55	import GSASIIstrIO as G2stIO
56	import GSASIImapvars as G2mv
57	import GSASIIfiles as G2fil
58	try:
59	import GSASIIctrlGUI as G2G
60	except ImportError:
61	pass
62	import os
63	import os.path as ospath
64
65	DEBUG = False #=True for various prints
66	TRANSP = False #=true to transpose images for testing
67	if GSASIIpath.GetConfigValue('Transpose'): TRANSP = True
68	npsind = lambda x: np.sin(x*np.pi/180.)
69
70	def sfloat(S):
71	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
72	if S.strip():
73	try:
74	return float(S)
75	except ValueError:
76	pass
77	return 0.0
78
79	def sint(S):
80	'Convert a string to int. An empty field is treated as zero'
81	if S.strip():
82	return int(S)
83	else:
84	return 0
85
86	def trim(val):
87	'''Simplify a string containing leading and trailing spaces
88	as well as newlines, tabs, repeated spaces etc. into a shorter and
89	more simple string, by replacing all ranges of whitespace
90	characters with a single space.
91
92	:param str val: the string to be simplified
93
94	:returns: the (usually) shortened version of the string
95	'''
96	return re.sub('\\s+', ' ', val).strip()
97
98	def FileDlgFixExt(dlg,file):
99	'this is needed to fix a problem in linux wx.FileDialog'
100	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
101	if ext not in file:
102	file += ext
103	return file
104
105	def GetPowderPeaks(fileName):
106	'Read powder peaks from a file'
107	sind = lambda x: math.sin(x*math.pi/180.)
108	asind = lambda x: 180.*math.asin(x)/math.pi
109	wave = 1.54052
110	File = open(fileName,'r')
111	Comments = []
112	peaks = []
113	S = File.readline()
114	while S:
115	if S[:1] == '#':
116	Comments.append(S[:-1])
117	else:
118	item = S.split()
119	if len(item) == 1:
120	peaks.append([float(item[0]),1.0])
121	elif len(item) > 1:
122	peaks.append([float(item[0]),float(item[1])])
123	S = File.readline()
124	File.close()
125	if Comments:
126	print ('Comments on file:')
127	for Comment in Comments:
128	print (Comment)
129	if 'wavelength' in Comment:
130	wave = float(Comment.split('=')[1])
131	Peaks = []
132	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
133	for peak in peaks:
134	dsp = peak[0]
135	sth = wave/(2.0*dsp)
136	if sth < 1.0:
137	tth = 2.0*asind(sth)
138	else:
139	break
140	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
141	else: #2-thetas - assume Cuka (for now)
142	for peak in peaks:
143	tth = peak[0]
144	dsp = wave/(2.0*sind(tth/2.0))
145	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
146	limits = [1000.,0.]
147	for peak in Peaks:
148	limits[0] = min(limits[0],peak[0])
149	limits[1] = max(limits[1],peak[0])
150	limits[0] = max(1.,(int(limits[0]-1.)/5)*5.)
151	limits[1] = min(170.,(int(limits[1]+1.)/5)*5.)
152	return Comments,Peaks,limits,wave
153
154	def GetCheckImageFile(G2frame,treeId):
155	'''Try to locate an image file if the project and image have been moved
156	together. If the image file cannot be found, request the location from
157	the user.
158
159	:param wx.Frame G2frame: main GSAS-II Frame and data object
160	:param wx.Id treeId: Id for the main tree item for the image
161	:returns: Npix,imagefile,imagetag with (Npix) number of pixels,
162	imagefile, if it exists, or the name of a file that does exist or False if the user presses Cancel
163	and (imagetag) an optional image number
164
165	'''
166	Npix,Imagefile,imagetag = G2frame.GPXtree.GetImageLoc(treeId)
167	if isinstance(Imagefile,list):
168	imagefile,imagetag = Imagefile
169	else:
170	imagefile = Imagefile
171	if not os.path.exists(imagefile):
172	print ('Image file '+imagefile+' not found')
173	fil = imagefile.replace('\\','/') # windows?!
174	# see if we can find a file with same name or in a similarly named sub-dir
175	pth,fil = os.path.split(fil)
176	prevpth = None
177	while pth and pth != prevpth:
178	prevpth = pth
179	if os.path.exists(os.path.join(G2frame.dirname,fil)):
180	print ('found image file '+os.path.join(G2frame.dirname,fil))
181	imagefile = os.path.join(G2frame.dirname,fil)
182	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
183	return Npix,imagefile,imagetag
184	pth,enddir = os.path.split(pth)
185	fil = os.path.join(enddir,fil)
186	# not found as a subdirectory, drop common parts of path for last saved & image file names
187	# if image was .../A/B/C/imgs/ima.ge
188	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
189	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
190	Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
191	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
192	imgPath = imagefile.replace('\\','/').split('/')
193	for p1,p2 in zip(gpxPath,imgPath):
194	if p1 == p2:
195	gpxPath.pop(0),imgPath.pop(0)
196	else:
197	break
198	fil = os.path.join(*imgPath) # file with non-common prefix elements
199	prevpth = None
200	pth = os.path.abspath(G2frame.dirname)
201	while pth and pth != prevpth:
202	prevpth = pth
203	if os.path.exists(os.path.join(pth,fil)):
204	print ('found image file '+os.path.join(pth,fil))
205	imagefile = os.path.join(pth,fil)
206	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
207	return Npix,imagefile,imagetag
208	pth,enddir = os.path.split(pth)
209	#GSASIIpath.IPyBreak()
210
211	if not os.path.exists(imagefile):
212	# note that this fails (at least on Mac) to get an image during the GUI initialization
213	prevnam = os.path.split(imagefile)[1]
214	prevext = os.path.splitext(imagefile)[1]
215	wildcard = 'Image format ('+prevext+')\|'+prevext
216	dlg = wx.FileDialog(G2frame, 'Previous image file ('+prevnam+') not found; open here', '.', prevnam,
217	wildcard,wx.FD_OPEN)
218	try:
219	dlg.SetFilename(''+ospath.split(imagefile)[1])
220	if dlg.ShowModal() == wx.ID_OK:
221	imagefile = dlg.GetPath()
222	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
223	else:
224	imagefile = None # was False
225	finally:
226	dlg.Destroy()
227	return Npix,imagefile,imagetag
228
229	def EditImageParms(parent,Data,Comments,Image,filename):
230	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
231	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
232	def onClose(event):
233	dlg.EndModal(wx.ID_OK)
234	mainsizer = wx.BoxSizer(wx.VERTICAL)
235	h,w = Image.size[:2]
236	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
237	0,wx.ALIGN_LEFT\|wx.ALL, 2)
238
239	vsizer = wx.BoxSizer(wx.HORIZONTAL)
240	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
241	0,wx.ALIGN_LEFT\|wx.ALL, 2)
242	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
243	vsizer.Add(wdgt)
244	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
245
246	vsizer = wx.BoxSizer(wx.HORIZONTAL)
247	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
248	0,wx.ALIGN_LEFT\|wx.ALL, 2)
249	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,size=(50,-1))
250	vsizer.Add(wdgt)
251	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),wx.ALIGN_LEFT\|wx.ALL, 2)
252	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,size=(50,-1))
253	vsizer.Add(wdgt)
254	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
255
256	vsizer = wx.BoxSizer(wx.HORIZONTAL)
257	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
258	0,wx.ALIGN_LEFT\|wx.ALL, 2)
259	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
260	vsizer.Add(wdgt)
261	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
262
263	vsizer = wx.BoxSizer(wx.HORIZONTAL)
264	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
265	0,wx.ALIGN_LEFT\|wx.ALL, 2)
266	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,size=(75,-1))
267	vsizer.Add(wdgt)
268	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),wx.ALIGN_LEFT\|wx.ALL, 2)
269	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,size=(75,-1))
270	vsizer.Add(wdgt)
271	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
272
273	vsizer = wx.BoxSizer(wx.HORIZONTAL)
274	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
275	0,wx.ALIGN_LEFT\|wx.ALL, 2)
276	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
277	vsizer.Add(wdgt)
278	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
279
280	btnsizer = wx.StdDialogButtonSizer()
281	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
282	OKbtn.SetDefault()
283	OKbtn.Bind(wx.EVT_BUTTON,onClose)
284	btnsizer.AddButton(OKbtn) # not sure why this is needed
285	btnsizer.Realize()
286	mainsizer.Add(btnsizer, 1, wx.ALL\|wx.EXPAND, 5)
287	dlg.SetSizer(mainsizer)
288	dlg.CenterOnParent()
289	dlg.ShowModal()
290
291	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
292	'''Load an image into the tree. Saves the location of the image, as well as the
293	ImageTag (where there is more than one image in the file), if defined.
294	'''
295	ImgNames = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
296	TreeLbl = 'IMG '+os.path.basename(imagefile)
297	ImageTag = Data.get('ImageTag')
298	if ImageTag:
299	TreeLbl += ' #'+'%04d'%(ImageTag)
300	imageInfo = (imagefile,ImageTag)
301	else:
302	imageInfo = imagefile
303	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
304	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=TreeName)
305	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
306	Imax = np.amax(Image)
307	if G2frame.imageDefault:
308	Data.update(copy.deepcopy(G2frame.imageDefault))
309	Data['showLines'] = True
310	Data['ring'] = []
311	Data['rings'] = []
312	Data['cutoff'] = 10.
313	Data['pixLimit'] = 20
314	Data['edgemin'] = 100000000
315	Data['calibdmin'] = 0.5
316	Data['calibskip'] = 0
317	Data['ellipses'] = []
318	Data['calibrant'] = ''
319	Data['GonioAngles'] = [0.,0.,0.]
320	Data['DetDepthRef'] = False
321	else:
322	Data['type'] = 'PWDR'
323	Data['color'] = GSASIIpath.GetConfigValue('Contour_color','Paired')
324	if 'tilt' not in Data: #defaults if not preset in e.g. Bruker importer
325	Data['tilt'] = 0.0
326	Data['rotation'] = 0.0
327	Data['pixLimit'] = 20
328	Data['calibdmin'] = 0.5
329	Data['cutoff'] = 10.
330	Data['showLines'] = False
331	Data['calibskip'] = 0
332	Data['ring'] = []
333	Data['rings'] = []
334	Data['edgemin'] = 100000000
335	Data['ellipses'] = []
336	Data['GonioAngles'] = [0.,0.,0.]
337	Data['DetDepth'] = 0.
338	Data['DetDepthRef'] = False
339	Data['calibrant'] = ''
340	Data['IOtth'] = [5.0,50.0]
341	if GSASIIpath.GetConfigValue('Image_2theta_min'):
342	try:
343	Data['IOtth'][0] = float(GSASIIpath.GetConfigValue('Image_2theta_min'))
344	except:
345	pass
346	if GSASIIpath.GetConfigValue('Image_2theta_max'):
347	try:
348	Data['IOtth'][1] = float(GSASIIpath.GetConfigValue('Image_2theta_max'))
349	except:
350	pass
351	Data['LRazimuth'] = [0.,180.]
352	Data['azmthOff'] = 0.0
353	Data['outChannels'] = 2500
354	Data['outAzimuths'] = 1
355	Data['centerAzm'] = False
356	Data['fullIntegrate'] = GSASIIpath.GetConfigValue('fullIntegrate',True)
357	Data['setRings'] = False
358	Data['background image'] = ['',-1.0]
359	Data['dark image'] = ['',-1.0]
360	Data['Flat Bkg'] = 0.0
361	Data['Oblique'] = [0.5,False]
362	Data['setDefault'] = False
363	Data['range'] = [(0,Imax),[0,Imax]]
364	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Image Controls'),Data)
365	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],
366	'Thresholds':[(0,Imax),[0,Imax]],
367	'SpotMask':{'esdMul':3.,'spotMask':None}}
368	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Masks'),Masks)
369	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Stress/Strain'),
370	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
371	G2frame.GPXtree.SetItemPyData(Id,[Npix,imageInfo])
372	G2frame.PickId = Id
373	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
374	G2frame.Image = Id
375
376	def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None,FormatName=''):
377	'''Read a single image with an image importer. This is called to reread an image
378	after it has already been imported with :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
379	(or :func:`ReadImages` in Auto Integration) so it is not necessary to reload metadata.
380
381	:param wx.Frame G2frame: main GSAS-II Frame and data object.
382	:param str imagefile: name of image file
383	:param bool imageOnly: If True return only the image,
384	otherwise (default) return more (see below)
385	:param int/str ImageTag: specifies a particular image to be read from a file.
386	First image is read if None (default).
387	:param str formatName: the image reader formatName
388
389	:returns: an image as a numpy array or a list of four items:
390	Comments, Data, Npix and the Image, as selected by imageOnly
391
392	'''
393	# determine which formats are compatible with this file
394	primaryReaders = []
395	secondaryReaders = []
396	for rd in G2frame.ImportImageReaderlist:
397	flag = rd.ExtensionValidator(imagefile)
398	if flag is None:
399	secondaryReaders.append(rd)
400	elif flag:
401	if not FormatName:
402	primaryReaders.append(rd)
403	elif FormatName in rd.formatName: #This is a kluge because the rd.formatName was changed!
404	primaryReaders.append(rd)
405	if len(secondaryReaders) + len(primaryReaders) == 0:
406	print('Error: No matching format for file '+imagefile)
407	raise Exception('No image read')
408	errorReport = ''
409	if not imagefile:
410	return
411	for rd in primaryReaders+secondaryReaders:
412	rd.ReInitialize() # purge anything from a previous read
413	rd.errors = "" # clear out any old errors
414	if not rd.ContentsValidator(imagefile): # rejected on cursory check
415	errorReport += "\n "+rd.formatName + ' validator error'
416	if rd.errors:
417	errorReport += ': '+rd.errors
418	continue
419	if imageOnly:
420	ParentFrame = None # prevent GUI access on reread
421	else:
422	ParentFrame = G2frame
423	if GSASIIpath.GetConfigValue('debug'):
424	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
425	else:
426	flag = False
427	try:
428	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
429	except rd.ImportException as detail:
430	rd.errors += "\n Read exception: "+str(detail)
431	except Exception as detail:
432	import traceback
433	rd.errors += "\n Unhandled read exception: "+str(detail)
434	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
435	if flag: # this read succeeded
436	if rd.Image is None:
437	raise Exception('No image read. Strange!')
438	if GSASIIpath.GetConfigValue('Transpose'):
439	print ('Transposing Image!')
440	rd.Image = rd.Image.T
441	#rd.readfilename = imagefile
442	if imageOnly:
443	return rd.Image
444	else:
445	return rd.Comments,rd.Data,rd.Npix,rd.Image
446	else:
447	print('Error reading file '+imagefile)
448	print('Error messages(s)\n'+errorReport)
449	raise Exception('No image read')
450
451	def ReadImages(G2frame,imagefile):
452	'''Read one or more images from a file and put them into the Tree
453	using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
454
455	ToDo: Images are most commonly read in :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
456	which is called from :meth:`GSASIIdataGUI.GSASII.OnImportImage`
457	it would be good if these routines used a common code core so that changes need to
458	be made in only one place.
459
460	:param wx.Frame G2frame: main GSAS-II Frame and data object.
461	:param str imagefile: name of image file
462
463	:returns: a list of the id's of the IMG tree items created
464	'''
465	# determine which formats are compatible with this file
466	primaryReaders = []
467	secondaryReaders = []
468	for rd in G2frame.ImportImageReaderlist:
469	flag = rd.ExtensionValidator(imagefile)
470	if flag is None:
471	secondaryReaders.append(rd)
472	elif flag:
473	primaryReaders.append(rd)
474	if len(secondaryReaders) + len(primaryReaders) == 0:
475	print('Error: No matching format for file '+imagefile)
476	raise Exception('No image read')
477	errorReport = ''
478	rdbuffer = {} # create temporary storage for file reader
479	for rd in primaryReaders+secondaryReaders:
480	rd.ReInitialize() # purge anything from a previous read
481	rd.errors = "" # clear out any old errors
482	if not rd.ContentsValidator(imagefile): # rejected on cursory check
483	errorReport += "\n "+rd.formatName + ' validator error'
484	if rd.errors:
485	errorReport += ': '+rd.errors
486	continue
487	ParentFrame = G2frame
488	block = 0
489	repeat = True
490	CreatedIMGitems = []
491	while repeat: # loop if the reader asks for another pass on the file
492	block += 1
493	repeat = False
494	if GSASIIpath.GetConfigValue('debug'):
495	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
496	else:
497	flag = False
498	try:
499	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
500	except rd.ImportException as detail:
501	rd.errors += "\n Read exception: "+str(detail)
502	except Exception as detail:
503	import traceback
504	rd.errors += "\n Unhandled read exception: "+str(detail)
505	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
506	if flag: # this read succeeded
507	if rd.Image is None:
508	raise Exception('No image read. Strange!')
509	if GSASIIpath.GetConfigValue('Transpose'):
510	print ('Transposing Image!')
511	rd.Image = rd.Image.T
512	rd.Data['ImageTag'] = rd.repeatcount
513	rd.readfilename = imagefile
514	# Load generic metadata, as configured
515	G2fil.GetColumnMetadata(rd)
516	LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
517	repeat = rd.repeat
518	CreatedIMGitems.append(G2frame.Image)
519	if CreatedIMGitems: return CreatedIMGitems
520	else:
521	print('Error reading file '+imagefile)
522	print('Error messages(s)\n'+errorReport)
523	return []
524	#raise Exception('No image read')
525
526	def SaveMultipleImg(G2frame):
527	if not G2frame.GPXtree.GetCount():
528	print ('no images!')
529	return
530	choices = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
531	if len(choices) == 1:
532	names = choices
533	else:
534	dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices)
535	dlg.SetSelections([])
536	names = []
537	if dlg.ShowModal() == wx.ID_OK:
538	names = [choices[sel] for sel in dlg.GetSelections()]
539	dlg.Destroy()
540	if not names: return
541	for name in names:
542	Id = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, name)
543	Npix,imagefile,imagetag = G2frame.GPXtree.GetImageLoc(Id)
544	imroot = os.path.splitext(imagefile)[0]
545	if imagetag:
546	imroot += '_' + str(imagetag)
547	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Image Controls'))
548	print('Writing '+imroot+'.imctrl')
549	File = open(imroot+'.imctrl','w')
550	keys = ['type','wavelength','calibrant','distance','center',
551	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth',
552	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
553	'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg',
554	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image']
555	for key in keys:
556	if key not in Data: continue #uncalibrated!
557	File.write(key+':'+str(Data[key])+'\n')
558	File.close()
559	mask = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Masks'))
560	G2imG.CleanupMasks(mask)
561	print('Writing '+imroot+'.immask')
562	File = open(imroot+'.immask','w')
563	for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
564	File.write(key+':'+str(mask[key])+'\n')
565	File.close()
566
567	def PutG2Image(filename,Comments,Data,Npix,image):
568	'Write an image as a python pickle - might be better as an .edf file?'
569	File = open(filename,'wb')
570	cPickle.dump([Comments,Data,Npix,image],File,2)
571	File.close()
572	return
573
574	objectScanIgnore = [int,bool,float,str,np.float64,np.float32,np.int32,np.int64,np.ndarray,G2obj.G2VarObj,G2obj.ExpressionObj,np.bool_]
575	try:
576	objectScanIgnore += [ma.MaskedArray] # fails in doc builds
577	except AttributeError:
578	pass
579
580	if '2' in platform.python_version_tuple()[0]:
581	objectScanIgnore += [unicode,long,]
582
583	def objectScan(data,tag,indexStack=[]):
584	'''Recursively scan an object looking for unexpected data types.
585	This is used in debug mode to scan .gpx files for objects we did not
586	intend to be there.
587	'''
588	if type(data) is list or type(data) is tuple:
589	for i in range(len(data)):
590	val = objectScan(data[i],tag,indexStack+[i])
591	if val:
592	data[i] = val
593	print('...fixed')
594	elif type(data) is dict:
595	for key in data:
596	val = objectScan(data[key],tag,indexStack+[key])
597	if val:
598	data[key] = val
599	print('...fixed')
600	elif data is None:
601	return None
602	elif type(data) in objectScanIgnore:
603	return None
604	else:
605	s = 'unexpected object in '+tag
606	for i in indexStack:
607	s += "[{}]".format(i)
608	#print(s,data.__class__.__name__) # loses full name of class
609	print(s,type(data))
610	global unexpectedObject
611	unexpectedObject = True
612	# fix bad objects
613	if "gdi.Colour" in str(type(data)):
614	return tuple(data)
615	return
616
617	def cPickleLoad(fp):
618	if '2' in platform.python_version_tuple()[0]:
619	return cPickle.load(fp)
620	else:
621	return cPickle.load(fp,encoding='latin-1')
622
623	def ProjFileOpen(G2frame,showProvenance=True):
624	'Read a GSAS-II project file and load into the G2 data tree'
625	if not os.path.exists(G2frame.GSASprojectfile):
626	print ('\n*** Error attempt to open project file that does not exist:\n '+
627	str(G2frame.GSASprojectfile))
628	return
629	LastSavedUsing = None
630	filep = open(G2frame.GSASprojectfile,'rb')
631	if showProvenance: print ('loading from file: '+G2frame.GSASprojectfile)
632	GPXphase = os.path.splitext(G2frame.GSASprojectfile)[0]+'.seqPhase'
633	GPXhist = os.path.splitext(G2frame.GSASprojectfile)[0]+'.seqHist'
634	deleteSeq = False
635	hist = None
636	tmpHistIndex = {}
637	updateFromSeq = False
638	if os.path.exists(GPXphase) and os.path.exists(GPXhist):
639	dlg = wx.MessageDialog(G2frame,
640	'Load results from crashed sequential fit?\nNo deletes the files!', 'Recover partial sequential fit?', wx.YES \| wx.NO \| wx.CANCEL)
641	dlg.CenterOnParent()
642	try:
643	result = dlg.ShowModal()
644	deleteSeq = result != wx.ID_CANCEL
645	if result == wx.ID_YES:
646	updateFromSeq = True
647	fp = open(GPXphase,'rb')
648	data = cPickleLoad(fp) # first block in file should be Phases
649	if data[0][0] != 'Phases':
650	raise Exception('Unexpected block in {} file. How did this happen?'
651	.format(GPXphase))
652	Phases = {}
653	for name,vals in data[1:]:
654	Phases[name] = vals
655	name,CovData = cPickleLoad(fp)[0] # 2nd block in file should be Covariance
656	name,RigidBodies = cPickleLoad(fp)[0] # 3rd block in file should be Rigid Bodies
657	fp.close()
658	# index the histogram updates
659	hist = open(GPXhist,'rb')
660	try:
661	while True:
662	loc = hist.tell()
663	datum = cPickleLoad(hist)[0]
664	tmpHistIndex[datum[0]] = loc
665	except EOFError:
666	pass
667	finally:
668	dlg.Destroy()
669	wx.BeginBusyCursor()
670	try:
671	if GSASIIpath.GetConfigValue('show_gpxSize'):
672	posPrev = 0
673	sizeList = {}
674	while True:
675	try:
676	data = cPickleLoad(filep)
677	except EOFError:
678	break
679	datum = data[0]
680	if GSASIIpath.GetConfigValue('show_gpxSize'):
681	sizeList[datum[0]] = filep.tell()-posPrev
682	posPrev = filep.tell()
683	# scan the GPX file for unexpected objects
684	if GSASIIpath.GetConfigValue('debug'):
685	global unexpectedObject
686	unexpectedObject = False
687	objectScan(data,'tree item "{}" entry '.format(datum[0]))
688	#if unexpectedObject:
689	# print(datum[0])
690	# GSASIIpath.IPyBreak()
691	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=datum[0])
692	if datum[0] == 'Phases' and GSASIIpath.GetConfigValue('SeparateHistPhaseTreeItem',False):
693	G2frame.GPXtree.AppendItem(parent=G2frame.root,text='Hist/Phase')
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	G2frame.imageDefault['setDefault'] = False
760	if 'formatName' in G2frame.imageDefault: del G2frame.imageDefault['formatName']
761	if LastSavedUsing:
762	print('GPX load successful. Last saved with GSAS-II revision '+LastSavedUsing)
763	else:
764	print('project load successful')
765	if GSASIIpath.GetConfigValue('show_gpxSize'):
766	print(50*'=')
767	print('File section sizes (Kb)')
768	for item in sizeList:
769	print(' {:20s} {:10.3f}'.format(
770	item[:20],sizeList[item]/1024.))
771	print(50*'=')
772	G2frame.NewPlot = True
773	except Exception as errmsg:
774	if GSASIIpath.GetConfigValue('debug'):
775	print('\nError reading GPX file:',errmsg)
776	import traceback
777	print (traceback.format_exc())
778	msg = wx.MessageDialog(G2frame,message="Error reading file "+
779	str(G2frame.GSASprojectfile)+". This is not a current GSAS-II .gpx file",
780	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
781	msg.ShowModal()
782	finally:
783	filep.close()
784	wx.EndBusyCursor()
785	G2frame.Status.SetStatusText('Mouse RB drag/drop to reorder',0)
786	if deleteSeq:
787	if hist: hist.close()
788	try:
789	os.remove(GPXphase)
790	except:
791	print('Warning: unable to delete {}'.format(GPXphase))
792	try:
793	os.remove(GPXhist)
794	except:
795	print('Warning: unable to delete {}'.format(GPXhist))
796	G2frame.SetTitleByGPX()
797	if LastSavedUsing:
798	try:
799	G2G.updateNotifier(G2frame,int(LastSavedUsing))
800	except:
801	pass
802
803	def ProjFileSave(G2frame):
804	'Save a GSAS-II project file'
805	if not G2frame.GPXtree.IsEmpty():
806	try:
807	file = open(G2frame.GSASprojectfile,'wb')
808	except PermissionError:
809	G2G.G2MessageBox(G2frame,'Read only file','Project cannot be saved; change permission & try again')
810	return
811	print ('save to file: '+G2frame.GSASprojectfile)
812	# stick the file name into the tree and version info into tree so they are saved.
813	# (Controls should always be created at this point)
814	try:
815	Controls = G2frame.GPXtree.GetItemPyData(
816	G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
817	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
818	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
819	Controls['PythonVersions'] = G2frame.PackageVersions
820	except:
821	pass
822	wx.BeginBusyCursor()
823	try:
824	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
825	while item:
826	data = []
827	name = G2frame.GPXtree.GetItemText(item)
828	if name.startswith('Hist/Phase'): # skip over this
829	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
830	continue
831	data.append([name,G2frame.GPXtree.GetItemPyData(item)])
832	item2, cookie2 = G2frame.GPXtree.GetFirstChild(item)
833	while item2:
834	name = G2frame.GPXtree.GetItemText(item2)
835	data.append([name,G2frame.GPXtree.GetItemPyData(item2)])
836	item2, cookie2 = G2frame.GPXtree.GetNextChild(item, cookie2)
837	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
838	cPickle.dump(data,file,2)
839	file.close()
840	pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
841	if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
842	G2frame.LastGPXdir = pth
843	finally:
844	wx.EndBusyCursor()
845	print('project save successful')
846
847	def SaveIntegration(G2frame,PickId,data,Overwrite=False):
848	'Save image integration results as powder pattern(s)'
849	waves = {'Cu':[1.54051,1.54433],'Ti':[2.74841,2.75207],'Cr':[2.28962,2.29351],
850	'Fe':[1.93597,1.93991],'Co':[1.78892,1.79278],'Mo':[0.70926,0.713543],
851	'Ag':[0.559363,0.563775]}
852	azms = G2frame.Integrate[1]
853	X = G2frame.Integrate[2][:-1]
854	N = len(X)
855	Id = G2frame.GPXtree.GetItemParent(PickId)
856	name = G2frame.GPXtree.GetItemText(Id)
857	name = name.replace('IMG ',data['type']+' ')
858	Comments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Comments'))
859	Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
860	Comments.append('Dark image = %s\n'%str(data['dark image']))
861	Comments.append('Background image = %s\n'%str(data['background image']))
862	Comments.append('Gain map = %s\n'%str(data['Gain map']))
863
864	if 'PWDR' in name:
865	if 'target' in data:
866	names = ['Type','Lam1','Lam2','I(L2)/I(L1)','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
867	codes = [0 for i in range(14)]
868	else:
869	if data.get('IfPink',False):
870	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','alpha-0','alpha-1','beta-0','beta-1','Azimuth']
871	codes = [0 for i in range(15)]
872	else:
873	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
874	codes = [0 for i in range(12)]
875	elif 'SASD' in name:
876	names = ['Type','Lam','Zero','Azimuth']
877	codes = [0 for i in range(4)]
878	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
879	Xminmax = [X[0],X[-1]]
880	Azms = np.zeros(data['outAzimuths'])
881	dazm = 0.
882	if data['outAzimuths'] > 1:
883	dazm = np.min(np.abs(np.diff(azms)))/2.
884	G2frame.IntgOutList = []
885	for i,azm in enumerate(azms[:-1]):
886	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
887	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
888	# if Overwrite delete any duplicate
889	if Overwrite and G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname):
890	print('Replacing '+Aname)
891	item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname)
892	G2frame.GPXtree.Delete(item)
893	else:
894	nOcc = 0
895	while item:
896	Name = G2frame.GPXtree.GetItemText(item)
897	if Aname in Name:
898	nOcc += 1
899	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
900	if nOcc:
901	Aname += '(%d)'%(nOcc)
902	Sample = G2obj.SetDefaultSample() #set as Debye-Scherrer
903	Sample['Gonio. radius'] = data['distance']
904	Sample['Omega'] = data['GonioAngles'][0]
905	Sample['Chi'] = data['GonioAngles'][1]
906	Sample['Phi'] = data['GonioAngles'][2]
907	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
908	polariz = data['PolaVal'][0]
909	for item in Comments:
910	for key in ('Temperature','Pressure','Time','FreePrm1','FreePrm2','FreePrm3','Omega',
911	'Chi','Phi'):
912	if key.lower() in item.lower():
913	try:
914	Sample[key] = float(item.split('=')[1])
915	except:
916	pass
917	if 'label_prm' in item.lower():
918	for num in ('1','2','3'):
919	if 'label_prm'+num in item.lower():
920	Controls['FreePrm'+num] = item.split('=')[1].strip()
921	if 'PWDR' in Aname:
922	if 'target' in data: #from lab x-ray 2D imaging data
923	wave1,wave2 = waves[data['target']]
924	parms = ['PXC',wave1,wave2,0.5,0.0,polariz,290.,-40.,30.,6.,-14.,0.0,0.0001,Azms[i]]
925	else:
926	if data.get('IfPink',False):
927	parms = ['PXB',data['wavelength'],0.0,polariz,0.,8000.,-150.,-24.,0.,0.,0.,13.,-1300.,3.,-7.,Azms[i]] #from Sect 35 LSS
928	else:
929	parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0,0.0001,Azms[i]]
930	elif 'SASD' in Aname:
931	Sample['Trans'] = data['SampleAbs'][0]
932	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
933	Y = G2frame.Integrate[0][i]
934	Ymin = np.min(Y)
935	Ymax = np.max(Y)
936	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
937	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=Aname)
938	G2frame.IntgOutList.append(Id)
939	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
940	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Limits'),copy.deepcopy([tuple(Xminmax),Xminmax]))
941	if 'PWDR' in Aname:
942	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Background'),[['chebyschev-1',1,3,1.0,0.0,0.0],
943	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[],'background PWDR':['',1.0,False]}])
944	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
945	for item in inst[0]:
946	inst[0][item] = list(inst[0][item])
947	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),inst)
948	if 'PWDR' in Aname:
949	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
950	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
951	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Index Peak List'),[[],[]])
952	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Unit Cells List'),[])
953	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection Lists'),{})
954	elif 'SASD' in Aname:
955	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
956	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
957	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
958	valuesdict = {
959	'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxsize),'Offset':[0.0,0.0],'delOffset':0.02*Ymax,
960	'refOffset':-0.1Ymax,'refDelt':0.1Ymax,'Yminmax':[Ymin,Ymax]}
961	G2frame.GPXtree.SetItemPyData(Id,[valuesdict,
962	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
963	return Id #last powder pattern generated
964
965	def XYsave(G2frame,XY,labelX='X',labelY='Y',names=[]):
966	'Save XY table data'
967	pth = G2G.GetExportPath(G2frame)
968	dlg = wx.FileDialog(
969	G2frame, 'Enter csv filename for XY table', pth, '',
970	'XY table file (.csv)\|.csv',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
971	try:
972	if dlg.ShowModal() == wx.ID_OK:
973	filename = dlg.GetPath()
974	filename = os.path.splitext(filename)[0]+'.csv'
975	File = open(filename,'w')
976	else:
977	filename = None
978	finally:
979	dlg.Destroy()
980	if not filename:
981	return
982	for i in range(len(XY)):
983	if len(names):
984	header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
985	else:
986	header = '%s,%s(%d)\n'%(labelX,labelY,i)
987	File.write(header)
988	for x,y in XY[i].T:
989	File.write('%.3f,%.3f\n'%(x,y))
990	File.close()
991	print (' XY data saved to: '+filename)
992
993	def PeakListSave(G2frame,file,peaks):
994	'Save powder peaks to a data file'
995	print ('save peak list to file: '+G2frame.peaklistfile)
996	if not peaks:
997	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
998	try:
999	dlg.ShowModal()
1000	finally:
1001	dlg.Destroy()
1002	return
1003	for peak in peaks:
1004	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1005	(peak[0],peak[2],peak[4],peak[6]))
1006	print ('peak list saved')
1007
1008	def IndexPeakListSave(G2frame,peaks):
1009	'Save powder peaks from the indexing list'
1010	file = open(G2frame.peaklistfile,'wa')
1011	print ('save index peak list to file: '+G2frame.peaklistfile)
1012	wx.BeginBusyCursor()
1013	try:
1014	if not peaks:
1015	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1016	try:
1017	dlg.ShowModal()
1018	finally:
1019	dlg.Destroy()
1020	return
1021	for peak in peaks:
1022	file.write("%12.6f\n" % (peak[7]))
1023	file.close()
1024	finally:
1025	wx.EndBusyCursor()
1026	print ('index peak list saved')
1027
1028	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1029	confirmoverwrite=True, parent=None,
1030	multipleselect=False):
1031	'''If the filename is a zip file, extract a file from that
1032	archive.
1033
1034	:param list Selection: used to predefine the name of the file
1035	to be extracted. Filename case and zip directory name are
1036	ignored in selection; the first matching file is used.
1037
1038	:param bool confirmread: if True asks the user to confirm before expanding
1039	the only file in a zip
1040
1041	:param bool confirmoverwrite: if True asks the user to confirm
1042	before overwriting if the extracted file already exists
1043
1044	:param bool multipleselect: if True allows more than one zip
1045	file to be extracted, a list of file(s) is returned.
1046	If only one file is present, do not ask which one, otherwise
1047	offer a list of choices (unless selection is used).
1048
1049	:returns: the name of the file that has been created or a
1050	list of files (see multipleselect)
1051
1052	If the file is not a zipfile, return the name of the input file.
1053	If the zipfile is empty or no file has been selected, return None
1054	'''
1055	import zipfile # do this now, since we can save startup time by doing this only on need
1056	import shutil
1057	zloc = os.path.split(filename)[0]
1058	if not zipfile.is_zipfile(filename):
1059	#print("not zip")
1060	return filename
1061
1062	z = zipfile.ZipFile(filename,'r')
1063	zinfo = z.infolist()
1064
1065	if len(zinfo) == 0:
1066	#print('Zip has no files!')
1067	zlist = [-1]
1068	if selection:
1069	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1070	if selection.lower() in choices:
1071	zlist = [choices.index(selection.lower())]
1072	else:
1073	print('debug: file '+str(selection)+' was not found in '+str(filename))
1074	zlist = [-1]
1075	elif len(zinfo) == 1 and confirmread:
1076	result = wx.ID_NO
1077	dlg = wx.MessageDialog(
1078	parent,
1079	'Is file '+str(zinfo[0].filename)+
1080	' what you want to extract from '+
1081	str(os.path.split(filename)[1])+'?',
1082	'Confirm file',
1083	wx.YES_NO \| wx.ICON_QUESTION)
1084	try:
1085	result = dlg.ShowModal()
1086	finally:
1087	dlg.Destroy()
1088	if result == wx.ID_NO:
1089	zlist = [-1]
1090	else:
1091	zlist = [0]
1092	elif len(zinfo) == 1:
1093	zlist = [0]
1094	elif multipleselect:
1095	# select one or more from a from list
1096	choices = [i.filename for i in zinfo]
1097	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1098	'Choose file(s)',choices)
1099	if dlg.ShowModal() == wx.ID_OK:
1100	zlist = dlg.GetSelections()
1101	else:
1102	zlist = []
1103	dlg.Destroy()
1104	else:
1105	# select one from a from list
1106	choices = [i.filename for i in zinfo]
1107	dlg = wx.SingleChoiceDialog(parent,
1108	'Select file to extract from zip file'+str(filename),'Choose file',
1109	choices,)
1110	if dlg.ShowModal() == wx.ID_OK:
1111	zlist = [dlg.GetSelection()]
1112	else:
1113	zlist = [-1]
1114	dlg.Destroy()
1115
1116	outlist = []
1117	for zindex in zlist:
1118	if zindex >= 0:
1119	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1120	if os.path.exists(efil) and confirmoverwrite:
1121	result = wx.ID_NO
1122	dlg = wx.MessageDialog(parent,
1123	'File '+str(efil)+' already exists. OK to overwrite it?',
1124	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1125	try:
1126	result = dlg.ShowModal()
1127	finally:
1128	dlg.Destroy()
1129	if result == wx.ID_NO:
1130	zindex = -1
1131	if zindex >= 0:
1132	# extract the file to the current directory, regardless of it's original path
1133	#z.extract(zinfo[zindex],zloc)
1134	eloc,efil = os.path.split(zinfo[zindex].filename)
1135	outfile = os.path.join(zloc, efil)
1136	fpin = z.open(zinfo[zindex])
1137	fpout = open(outfile, "wb")
1138	shutil.copyfileobj(fpin, fpout)
1139	fpin.close()
1140	fpout.close()
1141	outlist.append(outfile)
1142	z.close()
1143	if multipleselect and len(outlist) >= 1:
1144	return outlist
1145	elif len(outlist) == 1:
1146	return outlist[0]
1147	else:
1148	return None
1149
1150	def striphist(var,insChar=''):
1151	'strip a histogram number from a var name'
1152	sv = var.split(':')
1153	if len(sv) <= 1: return var
1154	if sv[1]:
1155	sv[1] = insChar
1156	return ':'.join(sv)
1157
1158	######################################################################
1159	# base classes for reading various types of data files
1160	# not used directly, only by subclassing
1161	######################################################################
1162	class ExportBaseclass(object):
1163	'''Defines a base class for the exporting of GSAS-II results.
1164
1165	This class is subclassed in the various exports/G2export_*.py files. Those files
1166	are imported in :meth:`GSASIIdataGUI.GSASII._init_Exports` which defines the
1167	appropriate menu items for each one and the .Exporter method is called
1168	directly from the menu item.
1169
1170	Routines may also define a .Writer method, which is used to write a single
1171	file without invoking any GUI objects.
1172	'''
1173	# TODO: review exporters producing exceptions where .Writer can't be used where G2frame is None (see CIF)
1174	# TODO: review conflicting uses of .Writer with mode (SeqRef) & elsewhere
1175	# TODO: move this class to G2fil
1176	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1177	self.G2frame = G2frame
1178	self.formatName = formatName # short string naming file type
1179	self.extension = extension
1180	if longFormatName: # longer string naming file type
1181	self.longFormatName = longFormatName
1182	else:
1183	self.longFormatName = formatName
1184	self.OverallParms = {}
1185	self.Phases = {}
1186	self.Histograms = {}
1187	self.powderDict = {}
1188	self.sasdDict = {}
1189	self.refdDict = {}
1190	self.xtalDict = {}
1191	self.parmDict = {}
1192	self.sigDict = {}
1193	self.fp = None
1194	# updated in InitExport:
1195	self.currentExportType = None # type of export that has been requested
1196	# updated in ExportSelect (when used):
1197	self.phasenam = None # a list of selected phases
1198	self.histnam = None # a list of selected histograms
1199	self.filename = None # name of file to be written (single export) or template (multiple files)
1200	self.dirname = '' # name of directory where file(s) will be written
1201	self.fullpath = '' # name of file being written -- full path
1202
1203	# items that should be defined in a subclass of this class
1204	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1205	# The following types are defined: 'project', "phase", "powder", "single"
1206	self.multiple = False # set as True if the class can export multiple phases or histograms
1207	# self.multiple is ignored for "project" exports
1208
1209	def InitExport(self,event):
1210	'''Determines the type of menu that called the Exporter and
1211	misc initialization.
1212	'''
1213	self.filename = None # name of file to be written (single export)
1214	self.dirname = '' # name of file to be written (multiple export)
1215	if event:
1216	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1217
1218	def MakePWDRfilename(self,hist):
1219	'''Make a filename root (no extension) from a PWDR histogram name
1220
1221	:param str hist: the histogram name in data tree (starts with "PWDR ")
1222	'''
1223	file0 = ''
1224	file1 = hist[5:]
1225	# replace repeated blanks
1226	while file1 != file0:
1227	file0 = file1
1228	file1 = file0.replace(' ',' ').strip()
1229	file0 = file1.replace('Azm= ','A')
1230	# if angle has unneeded decimal places on aziumuth, remove them
1231	if file0[-3:] == '.00': file0 = file0[:-3]
1232	file0 = file0.replace('.','_')
1233	file0 = file0.replace(' ','_')
1234	return file0
1235
1236	def ExportSelect(self,AskFile='ask'):
1237	'''Selects histograms or phases when needed. Sets a default file name when
1238	requested into self.filename; always sets a default directory in self.dirname.
1239
1240	:param bool AskFile: Determines how this routine processes getting a
1241	location to store the current export(s).
1242
1243	* if AskFile is 'ask' (default option), get the name of the file to be written;
1244	self.filename and self.dirname are always set. In the case where
1245	multiple files must be generated, the export routine should do this
1246	based on self.filename as a template.
1247	* if AskFile is 'dir', get the name of the directory to be used;
1248	self.filename is not used, but self.dirname is always set. The export routine
1249	will always generate the file name.
1250	* if AskFile is 'single', get only the name of the directory to be used when
1251	multiple items will be written (as multiple files) are used
1252	or a complete file name is requested when a single file
1253	name is selected. self.dirname is always set and self.filename used
1254	only when a single file is selected.
1255	* if AskFile is 'default', creates a name of the file to be used from
1256	the name of the project (.gpx) file. If the project has not been saved,
1257	then the name of file is requested.
1258	self.filename and self.dirname are always set. In the case where
1259	multiple file names must be generated, the export routine should do this
1260	based on self.filename.
1261	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1262	file. If the project has not been saved, then a directory is requested.
1263	self.filename is not used.
1264
1265	:returns: True in case of an error
1266	'''
1267
1268	numselected = 1
1269	if self.currentExportType == 'phase':
1270	if len(self.Phases) == 0:
1271	self.G2frame.ErrorDialog(
1272	'Empty project',
1273	'Project does not contain any phases.')
1274	return True
1275	elif len(self.Phases) == 1:
1276	self.phasenam = list(self.Phases.keys())
1277	elif self.multiple:
1278	choices = sorted(self.Phases.keys())
1279	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1280	if phasenum is None: return True
1281	self.phasenam = [choices[i] for i in phasenum]
1282	if not self.phasenam: return True
1283	numselected = len(self.phasenam)
1284	else:
1285	choices = sorted(self.Phases.keys())
1286	phasenum = G2G.ItemSelector(choices,self.G2frame)
1287	if phasenum is None: return True
1288	self.phasenam = [choices[phasenum]]
1289	numselected = len(self.phasenam)
1290	elif self.currentExportType == 'single':
1291	if len(self.xtalDict) == 0:
1292	self.G2frame.ErrorDialog(
1293	'Empty project',
1294	'Project does not contain any single crystal data.')
1295	return True
1296	elif len(self.xtalDict) == 1:
1297	self.histnam = self.xtalDict.values()
1298	elif self.multiple:
1299	choices = sorted(self.xtalDict.values())
1300	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1301	if not hnum: return True
1302	self.histnam = [choices[i] for i in hnum]
1303	numselected = len(self.histnam)
1304	else:
1305	choices = sorted(self.xtalDict.values())
1306	hnum = G2G.ItemSelector(choices,self.G2frame)
1307	if hnum is None: return True
1308	self.histnam = [choices[hnum]]
1309	numselected = len(self.histnam)
1310	elif self.currentExportType == 'powder':
1311	if len(self.powderDict) == 0:
1312	self.G2frame.ErrorDialog(
1313	'Empty project',
1314	'Project does not contain any powder data.')
1315	return True
1316	elif len(self.powderDict) == 1:
1317	self.histnam = list(self.powderDict.values())
1318	elif self.multiple:
1319	choices = sorted(self.powderDict.values())
1320	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1321	if not hnum: return True
1322	self.histnam = [choices[i] for i in hnum]
1323	numselected = len(self.histnam)
1324	else:
1325	choices = sorted(self.powderDict.values())
1326	hnum = G2G.ItemSelector(choices,self.G2frame)
1327	if hnum is None: return True
1328	self.histnam = [choices[hnum]]
1329	numselected = len(self.histnam)
1330	elif self.currentExportType == 'sasd':
1331	if len(self.sasdDict) == 0:
1332	self.G2frame.ErrorDialog(
1333	'Empty project',
1334	'Project does not contain any small angle data.')
1335	return True
1336	elif len(self.sasdDict) == 1:
1337	self.histnam = self.sasdDict.values()
1338	elif self.multiple:
1339	choices = sorted(self.sasdDict.values())
1340	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1341	if not hnum: return True
1342	self.histnam = [choices[i] for i in hnum]
1343	numselected = len(self.histnam)
1344	else:
1345	choices = sorted(self.sasdDict.values())
1346	hnum = G2G.ItemSelector(choices,self.G2frame)
1347	if hnum is None: return True
1348	self.histnam = [choices[hnum]]
1349	numselected = len(self.histnam)
1350	elif self.currentExportType == 'refd':
1351	if len(self.refdDict) == 0:
1352	self.G2frame.ErrorDialog(
1353	'Empty project',
1354	'Project does not contain any reflectivity data.')
1355	return True
1356	elif len(self.refdDict) == 1:
1357	self.histnam = self.refdDict.values()
1358	elif self.multiple:
1359	choices = sorted(self.refdDict.values())
1360	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1361	if not hnum: return True
1362	self.histnam = [choices[i] for i in hnum]
1363	numselected = len(self.histnam)
1364	else:
1365	choices = sorted(self.refdDict.values())
1366	hnum = G2G.ItemSelector(choices,self.G2frame)
1367	if hnum is None: return True
1368	self.histnam = [choices[hnum]]
1369	numselected = len(self.histnam)
1370	elif self.currentExportType == 'image':
1371	if len(self.Histograms) == 0:
1372	self.G2frame.ErrorDialog(
1373	'Empty project',
1374	'Project does not contain any images.')
1375	return True
1376	elif len(self.Histograms) == 1:
1377	self.histnam = list(self.Histograms.keys())
1378	else:
1379	choices = sorted(self.Histograms.keys())
1380	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1381	if self.multiple:
1382	if not hnum: return True
1383	self.histnam = [choices[i] for i in hnum]
1384	else:
1385	if hnum is None: return True
1386	self.histnam = [choices[hnum]]
1387	numselected = len(self.histnam)
1388	if self.currentExportType == 'map':
1389	# search for phases with maps
1390	mapPhases = []
1391	choices = []
1392	for phasenam in sorted(self.Phases):
1393	phasedict = self.Phases[phasenam] # pointer to current phase info
1394	if len(phasedict['General']['Map'].get('rho',[])):
1395	mapPhases.append(phasenam)
1396	if phasedict['General']['Map'].get('Flip'):
1397	choices.append('Charge flip map: '+str(phasenam))
1398	elif phasedict['General']['Map'].get('MapType'):
1399	choices.append(
1400	str(phasedict['General']['Map'].get('MapType'))
1401	+ ' map: ' + str(phasenam))
1402	else:
1403	choices.append('unknown map: '+str(phasenam))
1404	# select a map if needed
1405	if len(mapPhases) == 0:
1406	self.G2frame.ErrorDialog(
1407	'Empty project',
1408	'Project does not contain any maps.')
1409	return True
1410	elif len(mapPhases) == 1:
1411	self.phasenam = mapPhases
1412	else:
1413	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1414	if self.multiple:
1415	if not phasenum: return True
1416	self.phasenam = [mapPhases[i] for i in phasenum]
1417	else:
1418	if phasenum is None: return True
1419	self.phasenam = [mapPhases[phasenum]]
1420	numselected = len(self.phasenam)
1421
1422	# items selected, now set self.dirname and usually self.filename
1423	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1424	AskFile == 'default' and not self.G2frame.GSASprojectfile
1425	):
1426	filename = self.askSaveFile()
1427	if not filename: return True
1428	self.dirname,self.filename = os.path.split(filename)
1429	elif AskFile == 'dir' or AskFile == 'single' or (
1430	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1431	):
1432	self.dirname = self.askSaveDirectory()
1433	if not self.dirname: return True
1434	elif AskFile == 'default-dir' or AskFile == 'default':
1435	self.dirname,self.filename = os.path.split(
1436	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1437	)
1438	else:
1439	raise Exception('This should not happen!')
1440
1441	def loadParmDict(self):
1442	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1443	refined values to those from the last cycle and set the uncertainties for the
1444	refined parameters in another dict (self.sigDict).
1445
1446	Expands the parm & sig dicts to include values derived from constraints.
1447
1448	This could be made faster for sequential fits by reducing the histogram list to only
1449	the active histogram being exported.
1450	'''
1451	# TODO: this does not expand wild-card constraints properly for sequential fits.
1452	# this needs revisiting for sequential exports if constraints need to be generated correctly.
1453
1454	self.G2frame.CheckNotebook()
1455	self.parmDict = {}
1456	self.sigDict = {} # dict with s.u. values, currently used only for CIF & Bracket exports
1457	rigidbodyDict = {}
1458	covDict = {}
1459	consDict = {}
1460	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1461	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1462	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1463	while item:
1464	name = self.G2frame.GPXtree.GetItemText(item)
1465	if name == 'Rigid bodies':
1466	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(item)
1467	elif name == 'Covariance':
1468	covDict = self.G2frame.GPXtree.GetItemPyData(item)
1469	elif name == 'Constraints':
1470	consDict = self.G2frame.GPXtree.GetItemPyData(item)
1471	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1472	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1473	self.parmDict.update(rbDict)
1474	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1475	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,EFtables,ORBtables,BLtables,MFtables,maxSSwave = \
1476	G2stIO.GetPhaseData(Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1477	self.parmDict.update(phaseDict)
1478	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(Phases,Histograms,Print=False,resetRefList=False)
1479	self.parmDict.update(hapDict)
1480	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1481	self.parmDict.update(histDict)
1482	self.parmDict.update(zip(
1483	covDict.get('varyList',[]),
1484	covDict.get('variables',[])))
1485	self.sigDict = dict(zip(
1486	covDict.get('varyList',[]),
1487	covDict.get('sig',[])))
1488	# expand to include constraints: first compile a list of constraints
1489	constList = []
1490	for item in consDict:
1491	if item.startswith('_'): continue
1492	constList += consDict[item]
1493	# now process the constraints
1494	G2mv.InitVars()
1495	constrDict,fixedList,ignored = G2mv.ProcessConstraints(constList)
1496	varyList = covDict.get('varyListStart')
1497	if varyList is None and len(constrDict) == 0:
1498	# no constraints can use varyList
1499	varyList = covDict.get('varyList')
1500	elif varyList is None:
1501	varyList = []
1502	# # old GPX file from before pre-constraint varyList is saved
1503	# print (' * Old refinement: Please use Calculate/Refine to redo *')
1504	# raise Exception(' * Export aborted *')
1505	else:
1506	varyList = list(varyList)
1507	# add symmetry-generated constraints
1508	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(
1509	G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Rigid bodies'))
1510	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1511	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False) # done twice, needed?
1512	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,EFtables,ORBtables,BLtables,MFtables,maxSSwave = \
1513	G2stIO.GetPhaseData(Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints
1514	msg = G2mv.EvaluateMultipliers(constrDict,phaseDict)
1515	if msg:
1516	print('Unable to interpret multiplier(s): '+msg)
1517	raise Exception(' * CIF creation aborted *')
1518	errmsg,warnmsg,groups,parmlist = G2mv.GenerateConstraints(varyList,constrDict,fixedList,self.parmDict)
1519	if errmsg:
1520	# this really should not happen
1521	print (' * ERROR - constraints are internally inconsistent *')
1522	print ('Errors: ',errmsg)
1523	if warnmsg: print ('Warnings'+warnmsg)
1524	raise Exception(' * CIF creation aborted *')
1525	G2mv.Map2Dict(self.parmDict,varyList) # changes varyList
1526	G2mv.Dict2Map(self.parmDict) # add the constrained values to the parameter dictionary
1527	# and add their uncertainties into the esd dictionary (sigDict)
1528	if covDict.get('covMatrix') is not None:
1529	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],noSym=True))
1530	if 'depSigDict' in self.OverallParms['Covariance']:
1531	self.sigDict.update(
1532	{i:v[1] for i,v in self.OverallParms['Covariance']['depSigDict'].items()})
1533
1534	def loadTree(self):
1535	'''Load the contents of the data tree into a set of dicts
1536	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
1537	& self.xtalDict)
1538
1539	* The childrenless data tree items are overall parameters/controls for the
1540	entire project and are placed in self.OverallParms
1541	* Phase items are placed in self.Phases
1542	* Data items are placed in self.Histogram. The key for these data items
1543	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
1544	'''
1545	self.OverallParms = {}
1546	self.powderDict = {}
1547	self.sasdDict = {}
1548	self.refdDict = {}
1549	self.xtalDict = {}
1550	self.Phases = {}
1551	self.Histograms = {}
1552	self.SeqRefdata = None
1553	self.SeqRefhist = None
1554	self.DelayOpen = False
1555	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1556	histType = None
1557	if self.currentExportType == 'phase':
1558	# if exporting phases load them here
1559	sub = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Phases')
1560	if not sub:
1561	print ('no phases found')
1562	return True
1563	item, cookie = self.G2frame.GPXtree.GetFirstChild(sub)
1564	while item:
1565	phaseName = self.G2frame.GPXtree.GetItemText(item)
1566	self.Phases[phaseName] = self.G2frame.GPXtree.GetItemPyData(item)
1567	item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie)
1568	# Get rigid body info into self.OverallParms
1569	for key in ('Rigid bodies','Covariance'):
1570	item = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,key)
1571	if item:
1572	self.OverallParms[key] = self.G2frame.GPXtree.GetItemPyData(item)
1573	item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie)
1574	return
1575	elif self.currentExportType == 'single':
1576	histType = 'HKLF'
1577	elif self.currentExportType == 'powder':
1578	histType = 'PWDR'
1579	elif self.currentExportType == 'image':
1580	histType = 'IMG'
1581	elif self.currentExportType == 'sasd':
1582	histType = 'SASD'
1583	elif self.currentExportType == 'refd':
1584	histType = 'REFD'
1585
1586	if histType: # Loading just one kind of tree entry
1587	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1588	while item:
1589	name = self.G2frame.GPXtree.GetItemText(item)
1590	if name.startswith(histType):
1591	if self.Histograms.get(name): # there is already an item with this name
1592	print('Histogram name '+str(name)+' is repeated. Renaming')
1593	if name[-1] == '9':
1594	name = name[:-1] + '10'
1595	elif name[-1] in '012345678':
1596	name = name[:-1] + str(int(name[-1])+1)
1597	else:
1598	name += '-1'
1599	self.Histograms[name] = {}
1600	# the main info goes into Data, but the 0th
1601	# element contains refinement results, carry
1602	# that over too now.
1603	self.Histograms[name]['Data'] = self.G2frame.GPXtree.GetItemPyData(item)[1]
1604	self.Histograms[name][0] = self.G2frame.GPXtree.GetItemPyData(item)[0]
1605	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1606	while item2:
1607	child = self.G2frame.GPXtree.GetItemText(item2)
1608	self.Histograms[name][child] = self.G2frame.GPXtree.GetItemPyData(item2)
1609	item2, cookie2 = self.G2frame.GPXtree.GetNextChild(item, cookie2)
1610	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1611	# index powder and single crystal histograms by number
1612	for hist in self.Histograms:
1613	if hist.startswith("PWDR"):
1614	d = self.powderDict
1615	elif hist.startswith("HKLF"):
1616	d = self.xtalDict
1617	elif hist.startswith("SASD"):
1618	d = self.sasdDict
1619	elif hist.startswith("REFD"):
1620	d = self.refdDict
1621	else:
1622	return
1623	i = self.Histograms[hist].get('hId')
1624	if i is None and not d.keys():
1625	i = 0
1626	elif i is None or i in d.keys():
1627	i = max(d.keys())+1
1628	d[i] = hist
1629	return
1630	# else standard load: using all interlinked phases and histograms
1631	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1632	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1633	while item:
1634	name = self.G2frame.GPXtree.GetItemText(item)
1635	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1636	if not item2:
1637	self.OverallParms[name] = self.G2frame.GPXtree.GetItemPyData(item)
1638	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1639	# index powder and single crystal histograms
1640	for hist in self.Histograms:
1641	i = self.Histograms[hist]['hId']
1642	if hist.startswith("PWDR"):
1643	self.powderDict[i] = hist
1644	elif hist.startswith("HKLF"):
1645	self.xtalDict[i] = hist
1646	elif hist.startswith("SASD"):
1647	self.sasdDict[i] = hist
1648	elif hist.startswith("REFD"):
1649	self.refdDict[i] = hist
1650
1651	def dumpTree(self,mode='type'):
1652	'''Print out information on the data tree dicts loaded in loadTree.
1653	Used for testing only.
1654	'''
1655	if self.SeqRefdata and self.SeqRefhist:
1656	print('Note that dumpTree does not show sequential results')
1657	print ('\nOverall')
1658	if mode == 'type':
1659	def Show(arg): return type(arg)
1660	else:
1661	def Show(arg): return arg
1662	for key in self.OverallParms:
1663	print (' '+key+Show(self.OverallParms[key]))
1664	print ('Phases')
1665	for key1 in self.Phases:
1666	print (' '+key1+Show(self.Phases[key1]))
1667	print ('Histogram')
1668	for key1 in self.Histograms:
1669	print (' '+key1+Show(self.Histograms[key1]))
1670	for key2 in self.Histograms[key1]:
1671	print (' '+key2+Show(self.Histograms[key1][key2]))
1672
1673	def defaultSaveFile(self):
1674	return os.path.abspath(
1675	os.path.splitext(self.G2frame.GSASprojectfile
1676	)[0]+self.extension)
1677
1678	def askSaveFile(self):
1679	'''Ask the user to supply a file name
1680
1681	:returns: a file name (str) or None if Cancel is pressed
1682
1683	'''
1684	#pth = G2G.GetExportPath(self.G2frame)
1685	if self.G2frame.GSASprojectfile:
1686	defnam = os.path.splitext(
1687	os.path.split(self.G2frame.GSASprojectfile)[1]
1688	)[0]+self.extension
1689	else:
1690	defnam = 'default' + self.extension
1691	return G2G.askSaveFile(self.G2frame,defnam,self.extension,self.longFormatName)
1692
1693	def askSaveDirectory(self):
1694	'''Ask the user to supply a directory name. Path name is used as the
1695	starting point for the next export path search.
1696
1697	:returns: a directory name (str) or None if Cancel is pressed
1698
1699	TODO: Can this be replaced with G2G.askSaveDirectory?
1700	'''
1701	pth = G2G.GetExportPath(self.G2frame)
1702	dlg = wx.DirDialog(
1703	self.G2frame, 'Input directory where file(s) will be written', pth,
1704	wx.DD_DEFAULT_STYLE)
1705	dlg.CenterOnParent()
1706	try:
1707	if dlg.ShowModal() == wx.ID_OK:
1708	filename = dlg.GetPath()
1709	self.G2frame.LastExportDir = filename
1710	else:
1711	filename = None
1712	finally:
1713	dlg.Destroy()
1714	return filename
1715
1716	# Tools for file writing.
1717	def OpenFile(self,fil=None,mode='w',delayOpen=False):
1718	'''Open the output file
1719
1720	:param str fil: The name of the file to open. If None (default)
1721	the name defaults to self.dirname + self.filename.
1722	If an extension is supplied, it is not overridded,
1723	but if not, the default extension is used.
1724	:param str mode: The mode can 'w' to write a file, or 'a' to append to it. If
1725	the mode is 'd' (for debug), output is displayed on the console.
1726	:returns: the file object opened by the routine which is also
1727	saved as self.fp
1728	'''
1729	if mode == 'd': # debug mode
1730	self.fullpath = '(stdout)'
1731	self.fp = sys.stdout
1732	return
1733	if not fil:
1734	if not os.path.splitext(self.filename)[1]:
1735	self.filename += self.extension
1736	fil = os.path.join(self.dirname,self.filename)
1737	self.fullpath = os.path.abspath(fil)
1738	self.DelayOpen = False
1739	if delayOpen:
1740	self.DelayOpen = True
1741	self.fp = None
1742	return
1743	self.fp = open(self.fullpath,mode)
1744	return self.fp
1745
1746	def openDelayed(self,mode='w'):
1747	self.DelayOpen = False
1748	self.fp = open(self.fullpath,mode)
1749	return self.fp
1750
1751	def Write(self,line):
1752	'''write a line of output, attaching a line-end character
1753
1754	:param str line: the text to be written.
1755	'''
1756	if self.fp is None:
1757	raise Exception('Attempt to Write without use of OpenFile')
1758	self.fp.write(line+'\n')
1759
1760	def CloseFile(self,fp=None):
1761	'''Close a file opened in OpenFile
1762
1763	:param file fp: the file object to be closed. If None (default)
1764	file object self.fp is closed.
1765	'''
1766	if self.fp is None and self.DelayOpen:
1767	if GSASIIpath.GetConfigValue('debug'):
1768	print('Delayed open: close before file not created')
1769	return
1770	if self.fp is None:
1771	if GSASIIpath.GetConfigValue('debug'):
1772	raise Exception('Attempt to CloseFile without use of OpenFile')
1773	else:
1774	print('Attempt to CloseFile without use of OpenFile')
1775	return
1776	if self.fp == sys.stdout: return # debug mode
1777	if fp is None:
1778	fp = self.fp
1779	self.fp = None
1780	if fp is not None: fp.close()
1781
1782	def SetSeqRef(self,data,hist):
1783	'''Set the exporter to retrieve results from a sequential refinement
1784	rather than the main tree
1785	'''
1786	self.SeqRefdata = data
1787	self.SeqRefhist = hist
1788	data_name = data[hist]
1789	for i,val in zip(data_name['varyList'],data_name['sig']):
1790	self.sigDict[i] = val
1791	self.sigDict[striphist(i)] = val
1792	for i in data_name['parmDict']:
1793	self.parmDict[striphist(i)] = data_name['parmDict'][i]
1794	self.parmDict[i] = data_name['parmDict'][i]
1795	# zero out the dA[xyz] terms, they would only bring confusion
1796	key = i.split(':')
1797	if len(key) < 3: continue
1798	if key[2].startswith('dA'):
1799	self.parmDict[i] = 0.0
1800	for i,(val,sig) in data_name.get('depParmDict',{}).items():
1801	self.parmDict[i] = val
1802	self.sigDict[i] = sig
1803	#GSASIIpath.IPyBreak()
1804
1805	# Tools to pull information out of the data arrays
1806	def GetCell(self,phasenam,unique=False):
1807	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1808
1809	:param str phasenam: the name for the selected phase
1810	:param bool unique: when True, only directly refined parameters
1811	(a in cubic, a & alpha in rhombohedral cells) are assigned
1812	positive s.u. values. Used as True for CIF generation.
1813	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1814	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1815	cell values and `cellSig` has their uncertainties.
1816	"""
1817	if self.SeqRefdata and self.SeqRefhist:
1818	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
1819	phasedict = self.Phases[phasenam] # pointer to current phase info
1820	try:
1821	pfx = str(phasedict['pId'])+'::'
1822	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
1823	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
1824	self.OverallParms['Covariance'],unique=unique) # returns 7 vals, includes sigVol
1825	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
1826	return cellList,cellSig
1827	except KeyError:
1828	cell = phasedict['General']['Cell'][1:]
1829	return cell,7*[0]
1830
1831	def GetSeqCell(self,phasenam,data_name):
1832	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1833	and histogram in a sequential fit
1834
1835	:param str phasenam: the name for the selected phase
1836	:param dict data_name: the sequential refinement parameters for the selected histogram
1837	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1838	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1839	cell values and `cellSig` has their uncertainties.
1840	"""
1841	phasedict = self.Phases[phasenam]
1842	SGdata = phasedict['General']['SGData']
1843	pId = phasedict['pId']
1844	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
1845	ESDlookup = {}
1846	Dlookup = {}
1847	varied = [striphist(i) for i in data_name['varyList']]
1848	for item,val in data_name['newCellDict'].items():
1849	if item in varied:
1850	ESDlookup[val[0]] = item
1851	Dlookup[item] = val[0]
1852	A = RecpCellTerms[:]
1853	for i in range(6):
1854	var = str(pId)+'::A'+str(i)
1855	if var in ESDlookup:
1856	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
1857	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
1858	zeroDict = {i:0.0 for i in cellDict}
1859	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
1860	covData = {
1861	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
1862	'covMatrix': data_name['covMatrix']
1863	}
1864	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
1865
1866	def GetAtoms(self,phasenam):
1867	"""Gets the atoms associated with a phase. Can be used with standard
1868	or macromolecular phases
1869
1870	:param str phasenam: the name for the selected phase
1871	:returns: a list of items for eac atom where each item is a list containing:
1872	label, typ, mult, xyz, and td, where
1873
1874	* label and typ are the atom label and the scattering factor type (str)
1875	* mult is the site multiplicity (int)
1876	* xyz is contains a list with four pairs of numbers:
1877	x, y, z and fractional occupancy and
1878	their standard uncertainty (or a negative value)
1879	* td is contains a list with either one or six pairs of numbers:
1880	if one number it is U\\ :sub:`iso` and with six numbers it is
1881	U\\ :sub:`11`, U\\ :sub:`22`, U\\ :sub:`33`, U\\ :sub:`12`, U\\ :sub:`13` & U\\ :sub:`23`
1882	paired with their standard uncertainty (or a negative value)
1883	"""
1884	phasedict = self.Phases[phasenam] # pointer to current phase info
1885	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1886	cfrac = cx+3
1887	fpfx = str(phasedict['pId'])+'::Afrac:'
1888	atomslist = []
1889	for i,at in enumerate(phasedict['Atoms']):
1890	if phasedict['General']['Type'] == 'macromolecular':
1891	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1892	else:
1893	label = at[ct-1]
1894	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
1895	fsig = self.sigDict.get(fpfx+str(i),-0.009)
1896	mult = at[cs+1]
1897	typ = at[ct]
1898	xyz = []
1899	for j,v in enumerate(('x','y','z')):
1900	val = at[cx+j]
1901	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
1902	val = self.parmDict.get(pfx, val)
1903	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
1904	sig = self.sigDict.get(dpfx,-0.000009)
1905	xyz.append((val,sig))
1906	xyz.append((fval,fsig))
1907	td = []
1908	if at[cia] == 'I':
1909	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
1910	val = self.parmDict.get(pfx,at[cia+1])
1911	sig = self.sigDict.get(pfx,-0.0009)
1912	td.append((val,sig))
1913	else:
1914	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
1915	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
1916	val = self.parmDict.get(pfx,at[cia+2+i])
1917	sig = self.sigDict.get(pfx,-0.0009)
1918	td.append((val,sig))
1919	atomslist.append((label,typ,mult,xyz,td))
1920	return atomslist
1921	######################################################################
1922	def ExportPowderList(G2frame):
1923	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
1924	along with their descriptions (note that a extension may be repeated
1925	but descriptions are unique).
1926	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1927
1928	:param wx.Frame G2frame: the GSAS-II main data tree window
1929	'''
1930	extList = []
1931	extLabel = []
1932	for obj in G2frame.exporterlist:
1933	if 'powder' in obj.exporttype:
1934	try:
1935	obj.Writer
1936	extList.append(obj.extension)
1937	extLabel.append(obj.formatName)
1938	except AttributeError:
1939	pass
1940	return extList,extLabel
1941
1942	def ExportPowder(G2frame,TreeName,fileroot,extension,hint=''):
1943	'''Writes a single powder histogram using the Export routines.
1944	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1945
1946	:param wx.Frame G2frame: the GSAS-II main data tree window
1947	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
1948	:param str fileroot: name for file to be written, extension ignored
1949	:param str extension: extension for file to be written (start with '.'). Must
1950	match a powder export routine that has a Writer object.
1951	:param str hint: a string that must match the export's format
1952	'''
1953	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
1954	for obj in G2frame.exporterlist:
1955	if obj.extension == extension and 'powder' in obj.exporttype:
1956	if hint and hint not in obj.formatName: continue
1957	obj.currentExportType = 'powder'
1958	obj.InitExport(None)
1959	obj.loadTree() # load all histograms in tree into dicts
1960	if TreeName not in obj.Histograms:
1961	raise Exception('Histogram not found: '+str(TreeName))
1962	try:
1963	obj.Writer
1964	except AttributeError:
1965	continue
1966	try:
1967	obj.Writer(TreeName,filename)
1968	print('wrote file '+filename)
1969	return
1970	except Exception:
1971	print('Export Routine for '+extension+' failed.')
1972	else:
1973	print('No Export routine supports extension '+extension)
1974
1975	def ExportSequentialFullCIF(G2frame,seqData,Controls):
1976	'''Handles access to CIF exporter a bit differently for sequential fits, as this is
1977	not accessed via the usual export menus
1978	'''
1979	import G2export_CIF
1980	#import imp
1981	#imp.reload(G2export_CIF) #TODO for debug
1982	#print('reload G2export_CIF')
1983	obj = G2export_CIF.ExportProjectCIF(G2frame)
1984	obj.Exporter(None,seqData=seqData,Controls=Controls)
1985
1986	def ExportSequential(G2frame,data,obj,exporttype):
1987	'''
1988	Used to export from every phase/dataset in a sequential refinement using
1989	a .Writer method for either projects or phases. Prompts to select histograms
1990	and for phase exports, which phase(s).
1991
1992	:param wx.Frame G2frame: the GSAS-II main data tree window
1993	:param dict data: the sequential refinement data object
1994	:param exporter obj: an exporter object
1995	:param str exporttype: indicates the type of export ('project' or 'phase')
1996	'''
1997	if len(data['histNames']) == 0:
1998	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
1999	obj.InitExport(None)
2000	obj.loadTree()
2001	obj.loadParmDict()
2002	if len(data['histNames']) == 1:
2003	histlist = data['histNames']
2004	else:
2005	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
2006	'Select histograms',data['histNames'])
2007	if dlg.ShowModal() == wx.ID_OK:
2008	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
2009	dlg.Destroy()
2010	else:
2011	dlg.Destroy()
2012	return
2013	if exporttype == 'Phase':
2014	phaselist = list(obj.Phases.keys())
2015	if len(obj.Phases) == 0:
2016	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
2017	return
2018	elif len(obj.Phases) > 1:
2019	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
2020	'Select phases', phaselist)
2021	if dlg.ShowModal() == wx.ID_OK:
2022	phaselist = [phaselist[l] for l in dlg.GetSelections()]
2023	dlg.Destroy()
2024	else:
2025	dlg.Destroy()
2026	return
2027	filename = obj.askSaveFile()
2028	if not filename: return True
2029	obj.dirname,obj.filename = os.path.split(filename)
2030	print('Writing output to file '+str(obj.filename)+"...")
2031	mode = 'w'
2032	for p in phaselist:
2033	for h in histlist:
2034	obj.SetSeqRef(data,h)
2035	#GSASIIpath.IPyBreak()
2036	obj.Writer(h,phasenam=p,mode=mode)
2037	mode = 'a'
2038	print('...done')
2039	elif exporttype == 'Project': # note that the CIF exporter is not yet ready for this
2040	filename = obj.askSaveFile()
2041	if not filename: return True
2042	obj.dirname,obj.filename = os.path.split(filename)
2043	print('Writing output to file '+str(obj.filename)+"...")
2044	mode = 'w'
2045	for h in histlist:
2046	obj.SetSeqRef(data,h)
2047	obj.Writer(h,mode=mode)
2048	print('\t'+str(h)+' written')
2049	mode = 'a'
2050	print('...done')
2051	elif exporttype == 'Powder':
2052	filename = obj.askSaveFile()
2053	if not filename: return True
2054	obj.dirname,obj.filename = os.path.split(filename)
2055	print('Writing output to file '+str(obj.filename)+"...")
2056	mode = 'w'
2057	for h in histlist:
2058	obj.SetSeqRef(data,h)
2059	obj.Writer(h,mode=mode)
2060	print('\t'+str(h)+' written')
2061	mode = 'a'
2062	print('...done')
2063
2064	def ReadDIFFaX(DIFFaXfile):
2065	print ('read '+DIFFaXfile)
2066	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
2067	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
2068	df = open(DIFFaXfile,'r')
2069	lines = df.readlines()
2070	df.close()
2071	struct = False
2072	Struct = []
2073	stack = False
2074	Stack = []
2075	trans = False
2076	Trans = []
2077	for diff in lines:
2078	diff = diff[:-1].lower()
2079	if '!' in diff:
2080	continue
2081	while '}' in diff: #strip comments
2082	iB = diff.index('{')
2083	iF = diff.index('}')+1
2084	if iB:
2085	diff = diff[:iB]
2086	else:
2087	diff = diff[iF:]
2088	if not diff:
2089	continue
2090	if diff.strip() == 'instrumental':
2091	continue
2092	if diff.strip() == 'structural':
2093	struct = True
2094	continue
2095	elif diff.strip() == 'stacking':
2096	struct = False
2097	stack = True
2098	continue
2099	elif diff.strip() == 'transitions':
2100	stack = False
2101	trans = True
2102	continue
2103	diff = diff.strip()
2104	if struct:
2105	if diff:
2106	Struct.append(diff)
2107	elif stack:
2108	if diff:
2109	Stack.append(diff)
2110	elif trans:
2111	if diff:
2112	Trans.append(diff)
2113
2114	#STRUCTURE records
2115	laueRec = Struct[1].split()
2116	Layer['Laue'] = laueRec[0]
2117	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2118	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2119	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2120	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2121	cell = Struct[0].split()
2122	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2123	nLayers = int(Struct[2])
2124	N = 3
2125	if 'layer' not in Struct[3]:
2126	N = 4
2127	if Struct[3] != 'infinite':
2128	width = Struct[3].split()
2129	Layer['Width'][0] = [float(width[0]),float(width[1])]
2130	for nL in range(nLayers):
2131	if '=' in Struct[N]:
2132	name = Struct[N].split('=')
2133	sameas = int(name[1])-1
2134	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2135	N += 1
2136	continue
2137	Symm = 'None'
2138	if 'centro' in Struct[N+1]: Symm = '-1'
2139	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2140	N += 2
2141	while 'layer' not in Struct[N]:
2142	atom = Struct[N][4:].split()
2143	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2144	if atomType not in Layer['AtInfo']:
2145	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2146	atomName = '%s(%s)'%(atomType,atom[0])
2147	newVals = []
2148	for val in atom[1:6]:
2149	if '/' in val:
2150	newVals.append(eval(val+'.'))
2151	else:
2152	newVals.append(float(val))
2153	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2154	Layer['Layers'][-1]['Atoms'].append(atomRec)
2155	N += 1
2156	if N > len(Struct)-1:
2157	break
2158	#TRANSITIONS records
2159	transArray = []
2160	N = 0
2161	for i in range(nLayers):
2162	transArray.append([])
2163	for j in range(nLayers):
2164	vals = Trans[N].split()
2165	newVals = []
2166	for val in vals[:4]:
2167	if '/' in val:
2168	newVals.append(eval(val+'.'))
2169	else:
2170	newVals.append(float(val))
2171	transArray[-1].append(newVals+['',False])
2172	N += 1
2173	Layer['Transitions'] = transArray
2174	#STACKING records
2175	Layer['Stacking'] = [Stack[0],'']
2176	if Stack[0] == 'recursive':
2177	Layer['Stacking'][1] = Stack[1]
2178	elif Stack[0] == 'explicit':
2179	if Stack[1] == 'random':
2180	Layer['Stacking'][1] = Stack[1]
2181	else:
2182	Layer['Stacking'][1] = 'list'
2183	Layer['Stacking'].append('')
2184	for stack in Stack[2:]:
2185	Layer['Stacking'][2] += ' '+stack
2186	return Layer
2187
2188	def postURL(URL,postdict):
2189	'''Posts a set of values as from a web form. If access fails to an https
2190	site the access is retried with http.
2191
2192	:param str URL: the URL to post; typically something
2193	like 'http://www.../dir/page?'
2194	:param dict postdict: contains keywords and values, such
2195	as {'centrosymmetry': '0', 'crystalsystem': '0', ...}
2196	:returns: a string with the response from the web server or None
2197	if access fails.
2198	'''
2199	try:
2200	import requests # delay this until now, since rarely needed
2201	except:
2202	# this import seems to fail with the Anaconda pythonw on
2203	# macs; it should not!
2204	print('Warning: failed to import requests. Python config error')
2205	return None
2206
2207	repeat = True
2208	while repeat:
2209	r = None
2210	repeat = False
2211	try:
2212	r = requests.get(URL,params=postdict)
2213	if r.status_code == 200:
2214	print('request OK')
2215	page = r.text
2216	return page # success
2217	else:
2218	print('request to {} failed. Reason={}'.format(URL,r.reason))
2219	except Exception as msg: #ConnectionError?
2220	print('connection error - not on internet?')
2221	if GSASIIpath.GetConfigValue('debug'): print(msg)
2222	finally:
2223	if r: r.close()
2224	if URL.startswith('https:'):
2225	repeat = True
2226	URL = URL.replace('https:','http:')
2227	else:
2228	return None
2229
2230	if __name__ == '__main__':
2231	import GSASIIdataGUI
2232	application = GSASIIdataGUI.GSASIImain(0)
2233	G2frame = application.main
2234	#app = wx.PySimpleApp()
2235	#G2frame = wx.Frame(None) # create a frame
2236	#frm.Show(True)
2237	#filename = '/tmp/notzip.zip'
2238	#filename = '/tmp/all.zip'
2239	#filename = '/tmp/11bmb_7652.zip'
2240
2241	#selection=None, confirmoverwrite=True, parent=None
2242	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2243	#print ExtractFileFromZip(filename,multipleselect=True)
2244	# #confirmread=False, confirmoverwrite=False)
2245
2246	# choicelist=[ ('a','b','c'),
2247	# ('test1','test2'),('no choice',)]
2248	# titles = [ 'a, b or c', 'tests', 'No option here']
2249	# dlg = MultipleChoicesDialog(
2250	# choicelist,titles,
2251	# parent=frm)
2252	# if dlg.ShowModal() == wx.ID_OK:
2253	# print 'Got OK'
2254	imagefile = '/tmp/NDC5_00237_3.ge3'
2255	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2256
2257	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2258
2259	GSASIIpath.IPyBreak_base()

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source: trunk/GSASIIIO.py

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