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source: trunk/GSASIIIO.py @ 3195

Last change on this file since 3195 was 3195, checked in by toby, 6 years ago
generalize 1ID metadata import to column-oriented; add routine to test .lbls file; recognize Dexala in either orientation
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2017-12-18 21:18:15 +0000 (Mon, 18 Dec 2017) $
4	# $Author: toby $
5	# $Revision: 3195 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 3195 2017-12-18 21:18:15Z toby $
8	########### SVN repository information ###################
9	'''
10	GSASIIIO: Misc I/O routines
11	=============================
12
13	Module with miscellaneous routines for input and output. Many
14	are GUI routines to interact with user.
15
16	Includes support for image reading.
17
18	Also includes base classes for data import routines.
19
20	This module needs some work to separate wx from non-wx routines
21	'''
22	# If this is being used for GSASIIscriptable, don't depend on wx
23	from __future__ import division, print_function
24	try:
25	import wx
26	except ImportError:
27	class Placeholder(object):
28	def __init__(self):
29	self.Dialog = object
30	wx = Placeholder()
31	import math
32	import numpy as np
33	import copy
34	import platform
35	if '2' in platform.python_version_tuple()[0]:
36	import cPickle
37	else:
38	import _pickle as cPickle
39	import sys
40	import re
41	import glob
42	import random as ran
43	import GSASIIpath
44	GSASIIpath.SetVersionNumber("$Revision: 3195 $")
45	try:
46	import GSASIIdataGUI as G2gd
47	except ImportError:
48	pass
49	import GSASIIobj as G2obj
50	import GSASIIlattice as G2lat
51	import GSASIImath as G2mth
52	try:
53	import GSASIIpwdGUI as G2pdG
54	import GSASIIimgGUI as G2imG
55	except ImportError:
56	pass
57	import GSASIIimage as G2img
58	import GSASIIElem as G2el
59	import GSASIIstrIO as G2stIO
60	import GSASIImapvars as G2mv
61	try:
62	import GSASIIctrlGUI as G2G
63	except ImportError:
64	pass
65	import os
66	import os.path as ospath
67
68	DEBUG = False #=True for various prints
69	TRANSP = False #=true to transpose images for testing
70	if GSASIIpath.GetConfigValue('Transpose'): TRANSP = True
71	npsind = lambda x: np.sin(x*np.pi/180.)
72
73	def sfloat(S):
74	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
75	if S.strip():
76	try:
77	return float(S)
78	except ValueError:
79	pass
80	return 0.0
81
82	def sint(S):
83	'Convert a string to int. An empty field is treated as zero'
84	if S.strip():
85	return int(S)
86	else:
87	return 0
88
89	def trim(val):
90	'''Simplify a string containing leading and trailing spaces
91	as well as newlines, tabs, repeated spaces etc. into a shorter and
92	more simple string, by replacing all ranges of whitespace
93	characters with a single space.
94
95	:param str val: the string to be simplified
96
97	:returns: the (usually) shortened version of the string
98	'''
99	return re.sub('\s+', ' ', val).strip()
100
101	def FileDlgFixExt(dlg,file):
102	'this is needed to fix a problem in linux wx.FileDialog'
103	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
104	if ext not in file:
105	file += ext
106	return file
107
108	def GetPowderPeaks(fileName):
109	'Read powder peaks from a file'
110	sind = lambda x: math.sin(x*math.pi/180.)
111	asind = lambda x: 180.*math.asin(x)/math.pi
112	wave = 1.54052
113	File = open(fileName,'Ur')
114	Comments = []
115	peaks = []
116	S = File.readline()
117	while S:
118	if S[:1] == '#':
119	Comments.append(S[:-1])
120	else:
121	item = S.split()
122	if len(item) == 1:
123	peaks.append([float(item[0]),1.0])
124	elif len(item) > 1:
125	peaks.append([float(item[0]),float(item[0])])
126	S = File.readline()
127	File.close()
128	if Comments:
129	print ('Comments on file:')
130	for Comment in Comments:
131	print (Comment)
132	if 'wavelength' in Comment:
133	wave = float(Comment.split('=')[1])
134	Peaks = []
135	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
136	for peak in peaks:
137	dsp = peak[0]
138	sth = wave/(2.0*dsp)
139	if sth < 1.0:
140	tth = 2.0*asind(sth)
141	else:
142	break
143	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
144	else: #2-thetas - assume Cuka (for now)
145	for peak in peaks:
146	tth = peak[0]
147	dsp = wave/(2.0*sind(tth/2.0))
148	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
149	limits = [1000.,0.]
150	for peak in Peaks:
151	limits[0] = min(limits[0],peak[0])
152	limits[1] = max(limits[1],peak[0])
153	limits[0] = max(1.,(int(limits[0]-1.)/5)*5.)
154	limits[1] = min(170.,(int(limits[1]+1.)/5)*5.)
155	return Comments,Peaks,limits,wave
156
157	def GetCheckImageFile(G2frame,treeId):
158	'''Try to locate an image file if the project and image have been moved
159	together. If the image file cannot be found, request the location from
160	the user.
161
162	:param wx.Frame G2frame: main GSAS-II Frame and data object
163	:param wx.Id treeId: Id for the main tree item for the image
164	:returns: Npix,imagefile,imagetag with (Npix) number of pixels,
165	imagefile, if it exists, or the name of a file that does exist or False if the user presses Cancel
166	and (imagetag) an optional image number
167
168	'''
169	Npix,Imagefile,imagetag = G2frame.GPXtree.GetImageLoc(treeId)
170	if isinstance(Imagefile,list):
171	imagefile,imagetag = Imagefile
172	else:
173	imagefile = Imagefile
174	if not os.path.exists(imagefile):
175	print ('Image file '+imagefile+' not found')
176	fil = imagefile.replace('\\','/') # windows?!
177	# see if we can find a file with same name or in a similarly named sub-dir
178	pth,fil = os.path.split(fil)
179	prevpth = None
180	while pth and pth != prevpth:
181	prevpth = pth
182	if os.path.exists(os.path.join(G2frame.dirname,fil)):
183	print ('found image file '+os.path.join(G2frame.dirname,fil))
184	imagefile = os.path.join(G2frame.dirname,fil)
185	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
186	return Npix,imagefile,imagetag
187	pth,enddir = os.path.split(pth)
188	fil = os.path.join(enddir,fil)
189	# not found as a subdirectory, drop common parts of path for last saved & image file names
190	# if image was .../A/B/C/imgs/ima.ge
191	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
192	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
193	Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
194	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
195	imgPath = imagefile.replace('\\','/').split('/')
196	for p1,p2 in zip(gpxPath,imgPath):
197	if p1 == p2:
198	gpxPath.pop(0),imgPath.pop(0)
199	else:
200	break
201	fil = os.path.join(*imgPath) # file with non-common prefix elements
202	prevpth = None
203	pth = os.path.abspath(G2frame.dirname)
204	while pth and pth != prevpth:
205	prevpth = pth
206	if os.path.exists(os.path.join(pth,fil)):
207	print ('found image file '+os.path.join(pth,fil))
208	imagefile = os.path.join(pth,fil)
209	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
210	return Npix,imagefile,imagetag
211	pth,enddir = os.path.split(pth)
212	#GSASIIpath.IPyBreak()
213
214	if not os.path.exists(imagefile):
215	prevnam = os.path.split(imagefile)[1]
216	prevext = os.path.splitext(imagefile)[1]
217	wildcard = 'Image format ('+prevext+')\|'+prevext
218	dlg = wx.FileDialog(G2frame, 'Previous image file ('+prevnam+') not found; open here', '.', prevnam,
219	wildcard,wx.FD_OPEN)
220	try:
221	dlg.SetFilename(''+ospath.split(imagefile)[1])
222	if dlg.ShowModal() == wx.ID_OK:
223	imagefile = dlg.GetPath()
224	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
225	else:
226	imagefile = False
227	finally:
228	dlg.Destroy()
229	return Npix,imagefile,imagetag
230
231	def EditImageParms(parent,Data,Comments,Image,filename):
232	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
233	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
234	def onClose(event):
235	dlg.EndModal(wx.ID_OK)
236	mainsizer = wx.BoxSizer(wx.VERTICAL)
237	h,w = Image.shape[:2]
238	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
239	0,wx.ALIGN_LEFT\|wx.ALL, 2)
240
241	vsizer = wx.BoxSizer(wx.HORIZONTAL)
242	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
243	0,wx.ALIGN_LEFT\|wx.ALL, 2)
244	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
245	vsizer.Add(wdgt)
246	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
247
248	vsizer = wx.BoxSizer(wx.HORIZONTAL)
249	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
250	0,wx.ALIGN_LEFT\|wx.ALL, 2)
251	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
252	size=(50,-1))
253	vsizer.Add(wdgt)
254	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),wx.ALIGN_LEFT\|wx.ALL, 2)
255	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,size=(50,-1))
256	vsizer.Add(wdgt)
257	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
258
259	vsizer = wx.BoxSizer(wx.HORIZONTAL)
260	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
261	0,wx.ALIGN_LEFT\|wx.ALL, 2)
262	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
263	vsizer.Add(wdgt)
264	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
265
266	vsizer = wx.BoxSizer(wx.HORIZONTAL)
267	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
268	0,wx.ALIGN_LEFT\|wx.ALL, 2)
269	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,size=(75,-1))
270	vsizer.Add(wdgt)
271	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),wx.ALIGN_LEFT\|wx.ALL, 2)
272	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,size=(75,-1))
273	vsizer.Add(wdgt)
274	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
275
276	vsizer = wx.BoxSizer(wx.HORIZONTAL)
277	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
278	0,wx.ALIGN_LEFT\|wx.ALL, 2)
279	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
280	vsizer.Add(wdgt)
281	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
282
283	btnsizer = wx.StdDialogButtonSizer()
284	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
285	OKbtn.SetDefault()
286	OKbtn.Bind(wx.EVT_BUTTON,onClose)
287	btnsizer.AddButton(OKbtn) # not sure why this is needed
288	btnsizer.Realize()
289	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
290	dlg.SetSizer(mainsizer)
291	dlg.CenterOnParent()
292	dlg.ShowModal()
293
294	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
295	'''Load an image into the tree. Saves the location of the image, as well as the
296	ImageTag (where there is more than one image in the file), if defined.
297	'''
298	ImgNames = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
299	TreeLbl = 'IMG '+os.path.basename(imagefile)
300	ImageTag = Data.get('ImageTag')
301	if ImageTag:
302	TreeLbl += ' #'+'%04d'%(ImageTag)
303	imageInfo = (imagefile,ImageTag)
304	else:
305	imageInfo = imagefile
306	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
307	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=TreeName)
308	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
309	Imax = np.amax(Image)
310	if G2frame.imageDefault:
311	Data = copy.copy(G2frame.imageDefault)
312	Data['showLines'] = True
313	Data['ring'] = []
314	Data['rings'] = []
315	Data['cutoff'] = 10
316	Data['pixLimit'] = 20
317	Data['edgemin'] = 100000000
318	Data['calibdmin'] = 0.5
319	Data['calibskip'] = 0
320	Data['ellipses'] = []
321	Data['calibrant'] = ''
322	Data['GonioAngles'] = [0.,0.,0.]
323	Data['DetDepthRef'] = False
324	else:
325	Data['type'] = 'PWDR'
326	Data['color'] = GSASIIpath.GetConfigValue('Contour_color','Paired')
327	Data['tilt'] = 0.0
328	Data['rotation'] = 0.0
329	Data['showLines'] = False
330	Data['ring'] = []
331	Data['rings'] = []
332	Data['cutoff'] = 10
333	Data['pixLimit'] = 20
334	Data['calibdmin'] = 0.5
335	Data['calibskip'] = 0
336	Data['edgemin'] = 100000000
337	Data['ellipses'] = []
338	Data['GonioAngles'] = [0.,0.,0.]
339	Data['DetDepth'] = 0.
340	Data['DetDepthRef'] = False
341	Data['calibrant'] = ''
342	Data['IOtth'] = [2.0,5.0]
343	Data['LRazimuth'] = [0.,180.]
344	Data['azmthOff'] = 0.0
345	Data['outChannels'] = 2500
346	Data['outAzimuths'] = 1
347	Data['centerAzm'] = False
348	Data['fullIntegrate'] = False
349	Data['setRings'] = False
350	Data['background image'] = ['',-1.0]
351	Data['dark image'] = ['',-1.0]
352	Data['Flat Bkg'] = 0.0
353	Data['setDefault'] = False
354	Data['range'] = [(0,Imax),[0,Imax]]
355	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Image Controls'),Data)
356	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(0,Imax),[0,Imax]]}
357	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Masks'),Masks)
358	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Stress/Strain'),
359	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
360	G2frame.GPXtree.SetItemPyData(Id,[Npix,imageInfo])
361	G2frame.PickId = Id
362	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
363	G2frame.Image = Id
364
365	def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None,FormatName=''):
366	'''Read a single image with an image importer. This is called to reread an image
367	after it has already been imported with :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
368	(or :func:`ReadImages` in Auto Integration) so it is not necessary to reload metadata.
369
370	:param wx.Frame G2frame: main GSAS-II Frame and data object.
371	:param str imagefile: name of image file
372	:param bool imageOnly: If True return only the image,
373	otherwise (default) return more (see below)
374	:param int/str ImageTag: specifies a particular image to be read from a file.
375	First image is read if None (default).
376	:param str formatName: the image reader formatName
377
378	:returns: an image as a numpy array or a list of four items:
379	Comments, Data, Npix and the Image, as selected by imageOnly
380
381	'''
382	# determine which formats are compatible with this file
383	primaryReaders = []
384	secondaryReaders = []
385	for rd in G2frame.ImportImageReaderlist:
386	flag = rd.ExtensionValidator(imagefile)
387	if flag is None:
388	secondaryReaders.append(rd)
389	elif flag:
390	if not FormatName:
391	primaryReaders.append(rd)
392	elif FormatName == rd.formatName:
393	primaryReaders.append(rd)
394	if len(secondaryReaders) + len(primaryReaders) == 0:
395	print('Error: No matching format for file '+imagefile)
396	raise Exception('No image read')
397	errorReport = ''
398	if not imagefile:
399	return
400	for rd in primaryReaders+secondaryReaders:
401	rd.ReInitialize() # purge anything from a previous read
402	rd.errors = "" # clear out any old errors
403	if not rd.ContentsValidator(imagefile): # rejected on cursory check
404	errorReport += "\n "+rd.formatName + ' validator error'
405	if rd.errors:
406	errorReport += ': '+rd.errors
407	continue
408	if imageOnly:
409	ParentFrame = None # prevent GUI access on reread
410	else:
411	ParentFrame = G2frame
412	if GSASIIpath.GetConfigValue('debug'):
413	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
414	else:
415	flag = False
416	try:
417	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
418	except rd.ImportException as detail:
419	rd.errors += "\n Read exception: "+str(detail)
420	except Exception as detail:
421	import traceback
422	rd.errors += "\n Unhandled read exception: "+str(detail)
423	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
424	if flag: # this read succeeded
425	if rd.Image is None:
426	raise Exception('No image read. Strange!')
427	if GSASIIpath.GetConfigValue('Transpose'):
428	print ('Transposing Image!')
429	rd.Image = rd.Image.T
430	#rd.readfilename = imagefile
431	if imageOnly:
432	return rd.Image
433	else:
434	return rd.Comments,rd.Data,rd.Npix,rd.Image
435	else:
436	print('Error reading file '+imagefile)
437	print('Error messages(s)\n'+errorReport)
438	raise Exception('No image read')
439
440	def ReadImages(G2frame,imagefile):
441	'''Read one or more images from a file and put them into the Tree
442	using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
443
444	ToDo: Images are most commonly read in :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
445	which is called from :meth:`GSASIIdataGUI.GSASII.OnImportImage`
446	it would be good if these routines used a common code core so that changes need to
447	be made in only one place.
448
449	:param wx.Frame G2frame: main GSAS-II Frame and data object.
450	:param str imagefile: name of image file
451
452	:returns: a list of the id's of the IMG tree items created
453	'''
454	# determine which formats are compatible with this file
455	primaryReaders = []
456	secondaryReaders = []
457	for rd in G2frame.ImportImageReaderlist:
458	flag = rd.ExtensionValidator(imagefile)
459	if flag is None:
460	secondaryReaders.append(rd)
461	elif flag:
462	primaryReaders.append(rd)
463	if len(secondaryReaders) + len(primaryReaders) == 0:
464	print('Error: No matching format for file '+imagefile)
465	raise Exception('No image read')
466	errorReport = ''
467	rdbuffer = {} # create temporary storage for file reader
468	for rd in primaryReaders+secondaryReaders:
469	rd.ReInitialize() # purge anything from a previous read
470	rd.errors = "" # clear out any old errors
471	if not rd.ContentsValidator(imagefile): # rejected on cursory check
472	errorReport += "\n "+rd.formatName + ' validator error'
473	if rd.errors:
474	errorReport += ': '+rd.errors
475	continue
476	ParentFrame = G2frame
477	block = 0
478	repeat = True
479	CreatedIMGitems = []
480	while repeat: # loop if the reader asks for another pass on the file
481	block += 1
482	repeat = False
483	if GSASIIpath.GetConfigValue('debug'):
484	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
485	else:
486	flag = False
487	try:
488	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
489	except rd.ImportException as detail:
490	rd.errors += "\n Read exception: "+str(detail)
491	except Exception as detail:
492	import traceback
493	rd.errors += "\n Unhandled read exception: "+str(detail)
494	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
495	if flag: # this read succeeded
496	if rd.Image is None:
497	raise Exception('No image read. Strange!')
498	if GSASIIpath.GetConfigValue('Transpose'):
499	print ('Transposing Image!')
500	rd.Image = rd.Image.T
501	rd.Data['ImageTag'] = rd.repeatcount
502	rd.readfilename = imagefile
503	# Load generic metadata, as configured
504	GetColumnMetadata(rd)
505	LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
506	repeat = rd.repeat
507	CreatedIMGitems.append(G2frame.Image)
508	if CreatedIMGitems: return CreatedIMGitems
509	else:
510	print('Error reading file '+imagefile)
511	print('Error messages(s)\n'+errorReport)
512	return []
513	#raise Exception('No image read')
514
515	def SaveMultipleImg(G2frame):
516	if not G2frame.GPXtree.GetCount():
517	print ('no images!')
518	return
519	choices = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
520	if len(choices) == 1:
521	names = choices
522	else:
523	dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices)
524	dlg.SetSelections([])
525	names = []
526	if dlg.ShowModal() == wx.ID_OK:
527	names = [choices[sel] for sel in dlg.GetSelections()]
528	dlg.Destroy()
529	if not names: return
530	for name in names:
531	Id = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, name)
532	Npix,imagefile,imagetag = G2frame.GPXtree.GetImageLoc(Id)
533	imroot = os.path.splitext(imagefile)[0]
534	if imagetag:
535	imroot += '_' + str(imagetag)
536	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Image Controls'))
537	print('Writing '+imroot+'.imctrl')
538	File = open(imroot+'.imctrl','w')
539	keys = ['type','wavelength','calibrant','distance','center',
540	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth',
541	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
542	'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg',
543	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image']
544	for key in keys:
545	if key not in Data: continue #uncalibrated!
546	File.write(key+':'+str(Data[key])+'\n')
547	File.close()
548	mask = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Masks'))
549	G2imG.CleanupMasks(mask)
550	print('Writing '+imroot+'.immask')
551	File = open(imroot+'.immask','w')
552	for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
553	File.write(key+':'+str(mask[key])+'\n')
554	File.close()
555
556	def PutG2Image(filename,Comments,Data,Npix,image):
557	'Write an image as a python pickle - might be better as an .edf file?'
558	File = open(filename,'wb')
559	cPickle.dump([Comments,Data,Npix,image],File,2)
560	File.close()
561	return
562
563	def ProjFileOpen(G2frame,showProvenance=True):
564	'Read a GSAS-II project file and load into the G2 data tree'
565	if not os.path.exists(G2frame.GSASprojectfile):
566	print ('\n*** Error attempt to open project file that does not exist:\n '+
567	str(G2frame.GSASprojectfile))
568	return
569	LastSavedUsing = None
570	file = open(G2frame.GSASprojectfile,'rb')
571	if showProvenance: print ('loading from file: '+G2frame.GSASprojectfile)
572	#G2frame.SetTitle("GSAS-II data tree: "+
573	# os.path.split(G2frame.GSASprojectfile)[1])
574	G2frame.SetTitle("GSAS-II data tree: "+
575	os.path.split(G2frame.GSASprojectfile)[1],1)
576	wx.BeginBusyCursor()
577	try:
578	while True:
579	try:
580	if '2' in platform.python_version_tuple()[0]:
581	data = cPickle.load(file)
582	else:
583	data = cPickle.load(file,encoding='latin-1')
584	except EOFError:
585	break
586	datum = data[0]
587
588	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=datum[0])
589	if datum[0].startswith('PWDR'):
590	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
591	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
592	G2frame.GPXtree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
593	elif datum[0].startswith('HKLF'):
594	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
595	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
596	G2frame.GPXtree.SetItemPyData(Id,datum[1])
597	else:
598	G2frame.GPXtree.SetItemPyData(Id,datum[1])
599	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
600	LastSavedUsing = datum[1]['LastSavedUsing']
601	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance:
602	print('Packages used to create .GPX file:')
603	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
604	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
605	print(" {:<14s}: {:s}".format(p[0],p[1]))
606	else:
607	for p in datum[1]['PythonVersions']:
608	print(" {:<12s} {:s}".format(p[0]+':',p[1]))
609	oldPDF = False
610	for datus in data[1:]:
611	#patch - 1/23/17 PDF cleanup
612	if datus[0][:4] in ['I(Q)','S(Q)','F(Q)','G(R)']:
613	oldPDF = True
614	data[1][1][datus[0][:4]] = copy.deepcopy(datus[1][:2])
615	continue
616	#end PDF cleanup
617	sub = G2frame.GPXtree.AppendItem(Id,datus[0])
618	#patch
619	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
620	if datum[0].startswith('PWDR'):
621	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
622	else:
623	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
624	for item in datus[1][0]: #zip makes tuples - now make lists!
625	datus[1][0][item] = list(datus[1][0][item])
626	#end patch
627	G2frame.GPXtree.SetItemPyData(sub,datus[1])
628	if 'PDF ' in datum[0][:4] and oldPDF:
629	sub = G2frame.GPXtree.AppendItem(Id,'PDF Peaks')
630	G2frame.GPXtree.SetItemPyData(sub,{'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
631	if datum[0].startswith('IMG'): #retrieve image default flag & data if set
632	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls'))
633	if Data['setDefault']:
634	G2frame.imageDefault = Data
635	file.close()
636	if LastSavedUsing:
637	print('GPX load successful. Last saved with GSAS-II revision '+LastSavedUsing)
638	else:
639	print('project load successful')
640	G2frame.NewPlot = True
641	except:
642	msg = wx.MessageDialog(G2frame,message="Error reading file "+
643	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
644	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
645	msg.ShowModal()
646	finally:
647	wx.EndBusyCursor()
648	G2frame.Status.SetStatusText('Mouse RB drag/drop to reorder',0)
649
650	def ProjFileSave(G2frame):
651	'Save a GSAS-II project file'
652	if not G2frame.GPXtree.IsEmpty():
653	file = open(G2frame.GSASprojectfile,'wb')
654	print ('save to file: '+G2frame.GSASprojectfile)
655	# stick the file name into the tree and version info into tree so they are saved.
656	# (Controls should always be created at this point)
657	try:
658	Controls = G2frame.GPXtree.GetItemPyData(
659	G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
660	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
661	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
662	Controls['PythonVersions'] = G2frame.PackageVersions
663	except:
664	pass
665	wx.BeginBusyCursor()
666	try:
667	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
668	while item:
669	data = []
670	name = G2frame.GPXtree.GetItemText(item)
671	data.append([name,G2frame.GPXtree.GetItemPyData(item)])
672	item2, cookie2 = G2frame.GPXtree.GetFirstChild(item)
673	while item2:
674	name = G2frame.GPXtree.GetItemText(item2)
675	data.append([name,G2frame.GPXtree.GetItemPyData(item2)])
676	item2, cookie2 = G2frame.GPXtree.GetNextChild(item, cookie2)
677	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
678	cPickle.dump(data,file,2)
679	file.close()
680	pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
681	if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
682	G2frame.LastGPXdir = pth
683	finally:
684	wx.EndBusyCursor()
685	print('project save successful')
686
687	def SaveIntegration(G2frame,PickId,data,Overwrite=False):
688	'Save image integration results as powder pattern(s)'
689	azms = G2frame.Integrate[1]
690	X = G2frame.Integrate[2][:-1]
691	N = len(X)
692	Id = G2frame.GPXtree.GetItemParent(PickId)
693	name = G2frame.GPXtree.GetItemText(Id)
694	name = name.replace('IMG ',data['type']+' ')
695	Comments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Comments'))
696	Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
697	if 'PWDR' in name:
698	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
699	codes = [0 for i in range(12)]
700	elif 'SASD' in name:
701	names = ['Type','Lam','Zero','Azimuth']
702	codes = [0 for i in range(4)]
703	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
704	Xminmax = [X[0],X[-1]]
705	Azms = []
706	dazm = 0.
707	if data['fullIntegrate'] and data['outAzimuths'] == 1:
708	Azms = [45.0,] #a poor man's average?
709	else:
710	for i,azm in enumerate(azms[:-1]):
711	if azm > 360. and azms[i+1] > 360.:
712	Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
713	else:
714	Azms.append(G2img.meanAzm(azm,azms[i+1]))
715	dazm = np.min(np.abs(np.diff(azms)))/2.
716	G2frame.IntgOutList = []
717	for i,azm in enumerate(azms[:-1]):
718	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
719	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
720	# if Overwrite delete any duplicate
721	if Overwrite and G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname):
722	print('Replacing '+Aname)
723	item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname)
724	G2frame.GPXtree.Delete(item)
725	else:
726	nOcc = 0
727	while item:
728	Name = G2frame.GPXtree.GetItemText(item)
729	if Aname in Name:
730	nOcc += 1
731	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
732	if nOcc:
733	Aname += '(%d)'%(nOcc)
734	Sample = G2obj.SetDefaultSample() #set as Debye-Scherrer
735	Sample['Gonio. radius'] = data['distance']
736	Sample['Omega'] = data['GonioAngles'][0]
737	Sample['Chi'] = data['GonioAngles'][1]
738	Sample['Phi'] = data['GonioAngles'][2]
739	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
740	polariz = 0.99 #set default polarization for synchrotron radiation!
741	for item in Comments:
742	if 'polariz' in item:
743	try:
744	polariz = float(item.split('=')[1])
745	except:
746	polariz = 0.99
747	for key in ('Temperature','Pressure','Time','FreePrm1','FreePrm2','FreePrm3','Omega',
748	'Chi','Phi'):
749	if key.lower() in item.lower():
750	try:
751	Sample[key] = float(item.split('=')[1])
752	except:
753	pass
754	if 'label_prm' in item.lower():
755	for num in ('1','2','3'):
756	if 'label_prm'+num in item.lower():
757	Controls['FreePrm'+num] = item.split('=')[1].strip()
758	if 'PWDR' in Aname:
759	parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0,0.0001,Azms[i]]
760	elif 'SASD' in Aname:
761	Sample['Trans'] = data['SampleAbs'][0]
762	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
763	Y = G2frame.Integrate[0][i]
764	Ymin = np.min(Y)
765	Ymax = np.max(Y)
766	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
767	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=Aname)
768	G2frame.IntgOutList.append(Id)
769	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
770	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Limits'),copy.deepcopy([tuple(Xminmax),Xminmax]))
771	if 'PWDR' in Aname:
772	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
773	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
774	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
775	for item in inst[0]:
776	inst[0][item] = list(inst[0][item])
777	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),inst)
778	if 'PWDR' in Aname:
779	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
780	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
781	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Index Peak List'),[[],[]])
782	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Unit Cells List'),[])
783	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection Lists'),{})
784	elif 'SASD' in Aname:
785	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
786	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
787	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
788	valuesdict = {
789	'wtFactor':1.0,
790	'Dummy':False,
791	'ranId':ran.randint(0,sys.maxsize),
792	'Offset':[0.0,0.0],'delOffset':0.02Ymax,'refOffset':-0.1Ymax,'refDelt':0.1*Ymax,
793	'qPlot':False,'dPlot':False,'sqrtPlot':False,'Yminmax':[Ymin,Ymax]
794	}
795	G2frame.GPXtree.SetItemPyData(
796	Id,[valuesdict,
797	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
798	return Id #last powder pattern generated
799
800	def XYsave(G2frame,XY,labelX='X',labelY='Y',names=None):
801	'Save XY table data'
802	pth = G2G.GetExportPath(G2frame)
803	dlg = wx.FileDialog(
804	G2frame, 'Enter csv filename for XY table', pth, '',
805	'XY table file (.csv)\|.csv',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
806	try:
807	if dlg.ShowModal() == wx.ID_OK:
808	filename = dlg.GetPath()
809	filename = os.path.splitext(filename)[0]+'.csv'
810	File = open(filename,'w')
811	else:
812	filename = None
813	finally:
814	dlg.Destroy()
815	if not filename:
816	return
817	for i in range(len(XY)):
818	if names != None:
819	header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
820	else:
821	header = '%s,%s(%d)\n'%(labelX,labelY,i)
822	File.write(header)
823	for x,y in XY[i].T:
824	File.write('%.3f,%.3f\n'%(x,y))
825	File.close()
826	print (' XY data saved to: '+filename)
827
828	def PDFSave(G2frame,exports,PDFsaves):
829	'Save a PDF I(Q), S(Q), F(Q) and G(r) in column formats'
830	import scipy.interpolate as scintp
831	for export in exports:
832	PickId = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, export)
833	PDFControls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame, PickId,'PDF Controls'))
834	if PDFsaves[0]: #I(Q)
835	iqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.iq')
836	iqdata = PDFControls['I(Q)'][0]
837	iqfxn = scintp.interp1d(iqdata[0],iqdata[1],kind='linear')
838	iqfile = open(iqfilename,'w')
839	iqfile.write('#T I(Q) %s\n'%(export))
840	iqfile.write('#L Q I(Q)\n')
841	qnew = np.arange(iqdata[0][0],iqdata[0][-1],0.005)
842	iqnew = zip(qnew,iqfxn(qnew))
843	for q,iq in iqnew:
844	iqfile.write("%15.6g %15.6g\n" % (q,iq))
845	iqfile.close()
846	print (' I(Q) saved to: '+iqfilename)
847
848	if PDFsaves[1]: #S(Q)
849	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
850	sqdata = PDFControls['S(Q)'][1]
851	sqfxn = scintp.interp1d(sqdata[0],sqdata[1],kind='linear')
852	sqfile = open(sqfilename,'w')
853	sqfile.write('#T S(Q) %s\n'%(export))
854	sqfile.write('#L Q S(Q)\n')
855	qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
856	sqnew = zip(qnew,sqfxn(qnew))
857	for q,sq in sqnew:
858	sqfile.write("%15.6g %15.6g\n" % (q,sq))
859	sqfile.close()
860	print (' S(Q) saved to: '+sqfilename)
861
862	if PDFsaves[2]: #F(Q)
863	fqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.fq')
864	fqdata = PDFControls['F(Q)'][1]
865	fqfxn = scintp.interp1d(fqdata[0],fqdata[1],kind='linear')
866	fqfile = open(sqfilename,'w')
867	fqfile.write('#T F(Q) %s\n'%(export))
868	fqfile.write('#L Q F(Q)\n')
869	qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
870	fqnew = zip(qnew,fqfxn(qnew))
871	for q,fq in fqnew:
872	fqfile.write("%15.6g %15.6g\n" % (q,fq))
873	fqfile.close()
874	print (' F(Q) saved to: '+fqfilename)
875
876	if PDFsaves[3]: #G(R)
877	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
878	grdata = PDFControls['G(R)'][1]
879	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
880	grfile = open(grfilename,'w')
881	grfile.write('#T G(R) %s\n'%(export))
882	grfile.write('#L R G(R)\n')
883	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
884	grnew = zip(rnew,grfxn(rnew))
885	for r,gr in grnew:
886	grfile.write("%15.6g %15.6g\n" % (r,gr))
887	grfile.close()
888	print (' G(R) saved to: '+grfilename)
889
890	if PDFsaves[4]: #pdfGUI file for G(R)
891	pId = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, 'PWDR'+export[4:])
892	Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame, pId,'Instrument Parameters'))[0]
893	Limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame, pId,'Limits'))
894	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
895	grdata = PDFControls['G(R)'][1]
896	qdata = PDFControls['I(Q)'][1][0]
897	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
898	grfile = open(grfilename,'w')
899	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
900	grnew = zip(rnew,grfxn(rnew))
901
902	grfile.write('[DEFAULT]\n')
903	grfile.write('\n')
904	grfile.write('version = GSAS-II-v'+str(GSASIIpath.GetVersionNumber())+'\n')
905	grfile.write('\n')
906	grfile.write('# input and output specifications\n')
907	grfile.write('dataformat = Qnm\n')
908	grfile.write('inputfile = %s\n'%(PDFControls['Sample']['Name']))
909	grfile.write('backgroundfile = %s\n'%(PDFControls['Sample Bkg.']['Name']))
910	grfile.write('outputtype = gr\n')
911	grfile.write('\n')
912	grfile.write('# PDF calculation setup\n')
913	if 'x' in Inst['Type']:
914	grfile.write('mode = %s\n'%('xray'))
915	elif 'N' in Inst['Type']:
916	grfile.write('mode = %s\n'%('neutron'))
917	wave = G2mth.getMeanWave(Inst)
918	grfile.write('wavelength = %.5f\n'%(wave))
919	formula = ''
920	for el in PDFControls['ElList']:
921	formula += el
922	num = PDFControls['ElList'][el]['FormulaNo']
923	if num == round(num):
924	formula += '%d'%(int(num))
925	else:
926	formula += '%.2f'%(num)
927	grfile.write('composition = %s\n'%(formula))
928	grfile.write('bgscale = %.3f\n'%(-PDFControls['Sample Bkg.']['Mult']))
929	highQ = 2.*np.pi/G2lat.Pos2dsp(Inst,Limits[1][1])
930	grfile.write('qmaxinst = %.2f\n'%(highQ))
931	grfile.write('qmin = %.5f\n'%(qdata[0]))
932	grfile.write('qmax = %.4f\n'%(qdata[-1]))
933	grfile.write('rmin = %.2f\n'%(PDFControls['Rmin']))
934	grfile.write('rmax = %.2f\n'%(PDFControls['Rmax']))
935	grfile.write('rstep = 0.01\n')
936
937
938	grfile.write('\n')
939	grfile.write('# End of config '+63*'-')
940	grfile.write('\n')
941	grfile.write('#### start data\n')
942	grfile.write('#S 1\n')
943	grfile.write('#L r($\AA$) G($\AA^{-2}$)\n')
944	for r,gr in grnew:
945	grfile.write("%15.2F %15.6F\n" % (r,gr))
946	grfile.close()
947	print (' G(R) saved to: '+grfilename)
948
949	def PeakListSave(G2frame,file,peaks):
950	'Save powder peaks to a data file'
951	print ('save peak list to file: '+G2frame.peaklistfile)
952	if not peaks:
953	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
954	try:
955	dlg.ShowModal()
956	finally:
957	dlg.Destroy()
958	return
959	for peak in peaks:
960	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
961	(peak[0],peak[2],peak[4],peak[6]))
962	print ('peak list saved')
963
964	def IndexPeakListSave(G2frame,peaks):
965	'Save powder peaks from the indexing list'
966	file = open(G2frame.peaklistfile,'wa')
967	print ('save index peak list to file: '+G2frame.peaklistfile)
968	wx.BeginBusyCursor()
969	try:
970	if not peaks:
971	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
972	try:
973	dlg.ShowModal()
974	finally:
975	dlg.Destroy()
976	return
977	for peak in peaks:
978	file.write("%12.6f\n" % (peak[7]))
979	file.close()
980	finally:
981	wx.EndBusyCursor()
982	print ('index peak list saved')
983
984	class MultipleChoicesDialog(wx.Dialog):
985	'''A dialog that offers a series of choices, each with a
986	title and a wx.Choice widget. Intended to be used Modally.
987	typical input:
988
989	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
990	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
991
992	selections are placed in self.chosen when OK is pressed
993
994	Also see GSASIIctrlGUI
995	'''
996	def __init__(self,choicelist,headinglist,
997	head='Select options',
998	title='Please select from options below',
999	parent=None):
1000	self.chosen = []
1001	wx.Dialog.__init__(
1002	self,parent,wx.ID_ANY,head,
1003	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1004	panel = wx.Panel(self)
1005	mainSizer = wx.BoxSizer(wx.VERTICAL)
1006	mainSizer.Add((10,10),1)
1007	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1008	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1009	self.ChItems = []
1010	for choice,lbl in zip(choicelist,headinglist):
1011	mainSizer.Add((10,10),1)
1012	self.chosen.append(0)
1013	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1014	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1015	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1016	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1017
1018	OkBtn = wx.Button(panel,-1,"Ok")
1019	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1020	cancelBtn = wx.Button(panel,-1,"Cancel")
1021	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1022	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1023	btnSizer.Add((20,20),1)
1024	btnSizer.Add(OkBtn)
1025	btnSizer.Add((20,20),1)
1026	btnSizer.Add(cancelBtn)
1027	btnSizer.Add((20,20),1)
1028	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1029	panel.SetSizer(mainSizer)
1030	panel.Fit()
1031	self.Fit()
1032
1033	def OnOk(self,event):
1034	parent = self.GetParent()
1035	if parent is not None: parent.Raise()
1036	# save the results from the choice widgets
1037	self.chosen = []
1038	for w in self.ChItems:
1039	self.chosen.append(w.GetSelection())
1040	self.EndModal(wx.ID_OK)
1041
1042	def OnCancel(self,event):
1043	parent = self.GetParent()
1044	if parent is not None: parent.Raise()
1045	self.chosen = []
1046	self.EndModal(wx.ID_CANCEL)
1047
1048	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1049	confirmoverwrite=True, parent=None,
1050	multipleselect=False):
1051	'''If the filename is a zip file, extract a file from that
1052	archive.
1053
1054	:param list Selection: used to predefine the name of the file
1055	to be extracted. Filename case and zip directory name are
1056	ignored in selection; the first matching file is used.
1057
1058	:param bool confirmread: if True asks the user to confirm before expanding
1059	the only file in a zip
1060
1061	:param bool confirmoverwrite: if True asks the user to confirm
1062	before overwriting if the extracted file already exists
1063
1064	:param bool multipleselect: if True allows more than one zip
1065	file to be extracted, a list of file(s) is returned.
1066	If only one file is present, do not ask which one, otherwise
1067	offer a list of choices (unless selection is used).
1068
1069	:returns: the name of the file that has been created or a
1070	list of files (see multipleselect)
1071
1072	If the file is not a zipfile, return the name of the input file.
1073	If the zipfile is empty or no file has been selected, return None
1074	'''
1075	import zipfile # do this now, since we can save startup time by doing this only on need
1076	import shutil
1077	zloc = os.path.split(filename)[0]
1078	if not zipfile.is_zipfile(filename):
1079	#print("not zip")
1080	return filename
1081
1082	z = zipfile.ZipFile(filename,'r')
1083	zinfo = z.infolist()
1084
1085	if len(zinfo) == 0:
1086	#print('Zip has no files!')
1087	zlist = [-1]
1088	if selection:
1089	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1090	if selection.lower() in choices:
1091	zlist = [choices.index(selection.lower())]
1092	else:
1093	print('debug: file '+str(selection)+' was not found in '+str(filename))
1094	zlist = [-1]
1095	elif len(zinfo) == 1 and confirmread:
1096	result = wx.ID_NO
1097	dlg = wx.MessageDialog(
1098	parent,
1099	'Is file '+str(zinfo[0].filename)+
1100	' what you want to extract from '+
1101	str(os.path.split(filename)[1])+'?',
1102	'Confirm file',
1103	wx.YES_NO \| wx.ICON_QUESTION)
1104	try:
1105	result = dlg.ShowModal()
1106	finally:
1107	dlg.Destroy()
1108	if result == wx.ID_NO:
1109	zlist = [-1]
1110	else:
1111	zlist = [0]
1112	elif len(zinfo) == 1:
1113	zlist = [0]
1114	elif multipleselect:
1115	# select one or more from a from list
1116	choices = [i.filename for i in zinfo]
1117	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1118	'Choose file(s)',choices)
1119	if dlg.ShowModal() == wx.ID_OK:
1120	zlist = dlg.GetSelections()
1121	else:
1122	zlist = []
1123	dlg.Destroy()
1124	else:
1125	# select one from a from list
1126	choices = [i.filename for i in zinfo]
1127	dlg = wx.SingleChoiceDialog(parent,
1128	'Select file to extract from zip file'+str(filename),'Choose file',
1129	choices,)
1130	if dlg.ShowModal() == wx.ID_OK:
1131	zlist = [dlg.GetSelection()]
1132	else:
1133	zlist = [-1]
1134	dlg.Destroy()
1135
1136	outlist = []
1137	for zindex in zlist:
1138	if zindex >= 0:
1139	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1140	if os.path.exists(efil) and confirmoverwrite:
1141	result = wx.ID_NO
1142	dlg = wx.MessageDialog(parent,
1143	'File '+str(efil)+' already exists. OK to overwrite it?',
1144	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1145	try:
1146	result = dlg.ShowModal()
1147	finally:
1148	dlg.Destroy()
1149	if result == wx.ID_NO:
1150	zindex = -1
1151	if zindex >= 0:
1152	# extract the file to the current directory, regardless of it's original path
1153	#z.extract(zinfo[zindex],zloc)
1154	eloc,efil = os.path.split(zinfo[zindex].filename)
1155	outfile = os.path.join(zloc, efil)
1156	fpin = z.open(zinfo[zindex])
1157	fpout = file(outfile, "wb")
1158	shutil.copyfileobj(fpin, fpout)
1159	fpin.close()
1160	fpout.close()
1161	outlist.append(outfile)
1162	z.close()
1163	if multipleselect and len(outlist) >= 1:
1164	return outlist
1165	elif len(outlist) == 1:
1166	return outlist[0]
1167	else:
1168	return None
1169
1170	######################################################################
1171	# base classes for reading various types of data files
1172	# not used directly, only by subclassing
1173	######################################################################
1174	def BlockSelector(ChoiceList, ParentFrame=None,title='Select a block',
1175	size=None, header='Block Selector',useCancel=True):
1176	''' Provide a wx dialog to select a block if the file contains more
1177	than one set of data and one must be selected
1178	'''
1179	if useCancel:
1180	dlg = wx.SingleChoiceDialog(
1181	ParentFrame,title, header,ChoiceList)
1182	else:
1183	dlg = wx.SingleChoiceDialog(
1184	ParentFrame,title, header,ChoiceList,
1185	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1186	if size: dlg.SetSize(size)
1187	dlg.CenterOnParent()
1188	if dlg.ShowModal() == wx.ID_OK:
1189	sel = dlg.GetSelection()
1190	return sel
1191	else:
1192	return None
1193	dlg.Destroy()
1194
1195	def MultipleBlockSelector(ChoiceList, ParentFrame=None,
1196	title='Select a block',size=None, header='Block Selector'):
1197	'''Provide a wx dialog to select a block of data if the
1198	file contains more than one set of data and one must be
1199	selected.
1200
1201	:returns: a list of the selected blocks
1202	'''
1203	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1204	wx.CHOICEDLG_STYLE)
1205	dlg.CenterOnScreen()
1206	if size: dlg.SetSize(size)
1207	if dlg.ShowModal() == wx.ID_OK:
1208	sel = dlg.GetSelections()
1209	else:
1210	return []
1211	dlg.Destroy()
1212	selected = []
1213	if len(ChoiceList) in sel:
1214	return range(len(ChoiceList))
1215	else:
1216	return sel
1217	return selected
1218
1219	def MultipleChoicesSelector(choicelist, headinglist, ParentFrame=None, **kwargs):
1220	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1221	widget. Typical input:
1222
1223	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1224
1225	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1226
1227	optional keyword parameters are: head (window title) and title
1228	returns a list of selected indicies for each choice (or None)
1229	'''
1230	result = None
1231	dlg = MultipleChoicesDialog(choicelist,headinglist,
1232	parent=ParentFrame, **kwargs)
1233	dlg.CenterOnParent()
1234	if dlg.ShowModal() == wx.ID_OK:
1235	result = dlg.chosen
1236	dlg.Destroy()
1237	return result
1238
1239	def PhaseSelector(ChoiceList, ParentFrame=None,
1240	title='Select a phase', size=None,header='Phase Selector'):
1241	''' Provide a wx dialog to select a phase if the file contains more
1242	than one phase
1243	'''
1244	return BlockSelector(ChoiceList,ParentFrame,title,
1245	size,header)
1246
1247	######################################################################
1248	def striphist(var,insChar=''):
1249	'strip a histogram number from a var name'
1250	sv = var.split(':')
1251	if len(sv) <= 1: return var
1252	if sv[1]:
1253	sv[1] = insChar
1254	return ':'.join(sv)
1255	class ExportBaseclass(object):
1256	'''Defines a base class for the exporting of GSAS-II results.
1257
1258	This class is subclassed in the various exports/G2export_*.py files. Those files
1259	are imported in :meth:`GSASIIdataGUI.GSASII._init_Exports` which defines the
1260	appropriate menu items for each one and the .Exporter method is called
1261	directly from the menu item.
1262
1263	Routines may also define a .Writer method, which is used to write a single
1264	file without invoking any GUI objects.
1265	'''
1266	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1267	self.G2frame = G2frame
1268	self.formatName = formatName # short string naming file type
1269	self.extension = extension
1270	if longFormatName: # longer string naming file type
1271	self.longFormatName = longFormatName
1272	else:
1273	self.longFormatName = formatName
1274	self.OverallParms = {}
1275	self.Phases = {}
1276	self.Histograms = {}
1277	self.powderDict = {}
1278	self.xtalDict = {}
1279	self.parmDict = {}
1280	self.sigDict = {}
1281	# updated in InitExport:
1282	self.currentExportType = None # type of export that has been requested
1283	# updated in ExportSelect (when used):
1284	self.phasenam = None # a list of selected phases
1285	self.histnam = None # a list of selected histograms
1286	self.filename = None # name of file to be written (single export) or template (multiple files)
1287	self.dirname = '' # name of directory where file(s) will be written
1288	self.fullpath = '' # name of file being written -- full path
1289
1290	# items that should be defined in a subclass of this class
1291	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1292	# The following types are defined: 'project', "phase", "powder", "single"
1293	self.multiple = False # set as True if the class can export multiple phases or histograms
1294	# self.multiple is ignored for "project" exports
1295
1296	def InitExport(self,event):
1297	'''Determines the type of menu that called the Exporter and
1298	misc initialization.
1299	'''
1300	self.filename = None # name of file to be written (single export)
1301	self.dirname = '' # name of file to be written (multiple export)
1302	if event:
1303	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1304
1305	def MakePWDRfilename(self,hist):
1306	'''Make a filename root (no extension) from a PWDR histogram name
1307
1308	:param str hist: the histogram name in data tree (starts with "PWDR ")
1309	'''
1310	file0 = ''
1311	file1 = hist[5:]
1312	# replace repeated blanks
1313	while file1 != file0:
1314	file0 = file1
1315	file1 = file0.replace(' ',' ').strip()
1316	file0 = file1.replace('Azm= ','A')
1317	# if angle has unneeded decimal places on aziumuth, remove them
1318	if file0[-3:] == '.00': file0 = file0[:-3]
1319	file0 = file0.replace('.','_')
1320	file0 = file0.replace(' ','_')
1321	return file0
1322
1323	def ExportSelect(self,AskFile='ask'):
1324	'''Selects histograms or phases when needed. Sets a default file name when
1325	requested into self.filename; always sets a default directory in self.dirname.
1326
1327	:param bool AskFile: Determines how this routine processes getting a
1328	location to store the current export(s).
1329
1330	* if AskFile is 'ask' (default option), get the name of the file to be written;
1331	self.filename and self.dirname are always set. In the case where
1332	multiple files must be generated, the export routine should do this
1333	based on self.filename as a template.
1334	* if AskFile is 'dir', get the name of the directory to be used;
1335	self.filename is not used, but self.dirname is always set. The export routine
1336	will always generate the file name.
1337	* if AskFile is 'single', get only the name of the directory to be used when
1338	multiple items will be written (as multiple files) are used
1339	or a complete file name is requested when a single file
1340	name is selected. self.dirname is always set and self.filename used
1341	only when a single file is selected.
1342	* if AskFile is 'default', creates a name of the file to be used from
1343	the name of the project (.gpx) file. If the project has not been saved,
1344	then the name of file is requested.
1345	self.filename and self.dirname are always set. In the case where
1346	multiple file names must be generated, the export routine should do this
1347	based on self.filename.
1348	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1349	file. If the project has not been saved, then a directory is requested.
1350	self.filename is not used.
1351
1352	:returns: True in case of an error
1353	'''
1354
1355	numselected = 1
1356	if self.currentExportType == 'phase':
1357	if len(self.Phases) == 0:
1358	self.G2frame.ErrorDialog(
1359	'Empty project',
1360	'Project does not contain any phases.')
1361	return True
1362	elif len(self.Phases) == 1:
1363	self.phasenam = self.Phases.keys()
1364	elif self.multiple:
1365	choices = sorted(self.Phases.keys())
1366	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1367	if phasenum is None: return True
1368	self.phasenam = [choices[i] for i in phasenum]
1369	if not self.phasenam: return True
1370	numselected = len(self.phasenam)
1371	else:
1372	choices = sorted(self.Phases.keys())
1373	phasenum = G2G.ItemSelector(choices,self.G2frame)
1374	if phasenum is None: return True
1375	self.phasenam = [choices[phasenum]]
1376	numselected = len(self.phasenam)
1377	elif self.currentExportType == 'single':
1378	if len(self.xtalDict) == 0:
1379	self.G2frame.ErrorDialog(
1380	'Empty project',
1381	'Project does not contain any single crystal data.')
1382	return True
1383	elif len(self.xtalDict) == 1:
1384	self.histnam = self.xtalDict.values()
1385	elif self.multiple:
1386	choices = sorted(self.xtalDict.values())
1387	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1388	if not hnum: return True
1389	self.histnam = [choices[i] for i in hnum]
1390	numselected = len(self.histnam)
1391	else:
1392	choices = sorted(self.xtalDict.values())
1393	hnum = G2G.ItemSelector(choices,self.G2frame)
1394	if hnum is None: return True
1395	self.histnam = [choices[hnum]]
1396	numselected = len(self.histnam)
1397	elif self.currentExportType == 'powder':
1398	if len(self.powderDict) == 0:
1399	self.G2frame.ErrorDialog(
1400	'Empty project',
1401	'Project does not contain any powder data.')
1402	return True
1403	elif len(self.powderDict) == 1:
1404	self.histnam = self.powderDict.values()
1405	elif self.multiple:
1406	choices = sorted(self.powderDict.values())
1407	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1408	if not hnum: return True
1409	self.histnam = [choices[i] for i in hnum]
1410	numselected = len(self.histnam)
1411	else:
1412	choices = sorted(self.powderDict.values())
1413	hnum = G2G.ItemSelector(choices,self.G2frame)
1414	if hnum is None: return True
1415	self.histnam = [choices[hnum]]
1416	numselected = len(self.histnam)
1417	elif self.currentExportType == 'image':
1418	if len(self.Histograms) == 0:
1419	self.G2frame.ErrorDialog(
1420	'Empty project',
1421	'Project does not contain any images.')
1422	return True
1423	elif len(self.Histograms) == 1:
1424	self.histnam = self.Histograms.keys()
1425	else:
1426	choices = sorted(self.Histograms.keys())
1427	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1428	if self.multiple:
1429	if not hnum: return True
1430	self.histnam = [choices[i] for i in hnum]
1431	else:
1432	if hnum is None: return True
1433	self.histnam = [choices[hnum]]
1434	numselected = len(self.histnam)
1435	if self.currentExportType == 'map':
1436	# search for phases with maps
1437	mapPhases = []
1438	choices = []
1439	for phasenam in sorted(self.Phases):
1440	phasedict = self.Phases[phasenam] # pointer to current phase info
1441	if len(phasedict['General']['Map'].get('rho',[])):
1442	mapPhases.append(phasenam)
1443	if phasedict['General']['Map'].get('Flip'):
1444	choices.append('Charge flip map: '+str(phasenam))
1445	elif phasedict['General']['Map'].get('MapType'):
1446	choices.append(
1447	str(phasedict['General']['Map'].get('MapType'))
1448	+ ' map: ' + str(phasenam))
1449	else:
1450	choices.append('unknown map: '+str(phasenam))
1451	# select a map if needed
1452	if len(mapPhases) == 0:
1453	self.G2frame.ErrorDialog(
1454	'Empty project',
1455	'Project does not contain any maps.')
1456	return True
1457	elif len(mapPhases) == 1:
1458	self.phasenam = mapPhases
1459	else:
1460	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1461	if self.multiple:
1462	if not phasenum: return True
1463	self.phasenam = [mapPhases[i] for i in phasenum]
1464	else:
1465	if phasenum is None: return True
1466	self.phasenam = [mapPhases[phasenum]]
1467	numselected = len(self.phasenam)
1468
1469	# items selected, now set self.dirname and usually self.filename
1470	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1471	AskFile == 'default' and not self.G2frame.GSASprojectfile
1472	):
1473	filename = self.askSaveFile()
1474	if not filename: return True
1475	self.dirname,self.filename = os.path.split(filename)
1476	elif AskFile == 'dir' or AskFile == 'single' or (
1477	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1478	):
1479	self.dirname = self.askSaveDirectory()
1480	if not self.dirname: return True
1481	elif AskFile == 'default-dir' or AskFile == 'default':
1482	self.dirname,self.filename = os.path.split(
1483	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1484	)
1485	else:
1486	raise Exception('This should not happen!')
1487
1488	def loadParmDict(self):
1489	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1490	refined values to those from the last cycle and set the uncertainties for the
1491	refined parameters in another dict (self.sigDict).
1492
1493	Expands the parm & sig dicts to include values derived from constraints.
1494	'''
1495	self.parmDict = {}
1496	self.sigDict = {}
1497	rigidbodyDict = {}
1498	covDict = {}
1499	consDict = {}
1500	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1501	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1502	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1503	while item:
1504	name = self.G2frame.GPXtree.GetItemText(item)
1505	if name == 'Rigid bodies':
1506	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(item)
1507	elif name == 'Covariance':
1508	covDict = self.G2frame.GPXtree.GetItemPyData(item)
1509	elif name == 'Constraints':
1510	consDict = self.G2frame.GPXtree.GetItemPyData(item)
1511	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1512	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1513	self.parmDict.update(rbDict)
1514	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1515	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1516	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1517	self.parmDict.update(phaseDict)
1518	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
1519	Phases,Histograms,Print=False,resetRefList=False)
1520	self.parmDict.update(hapDict)
1521	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1522	self.parmDict.update(histDict)
1523	self.parmDict.update(zip(
1524	covDict.get('varyList',[]),
1525	covDict.get('variables',[])))
1526	self.sigDict = dict(zip(
1527	covDict.get('varyList',[]),
1528	covDict.get('sig',[])))
1529	# expand to include constraints: first compile a list of constraints
1530	constList = []
1531	for item in consDict:
1532	if item.startswith('_'): continue
1533	constList += consDict[item]
1534	# now process the constraints
1535	G2mv.InitVars()
1536	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
1537	varyList = covDict.get('varyListStart')
1538	if varyList is None and len(constDict) == 0:
1539	# no constraints can use varyList
1540	varyList = covDict.get('varyList')
1541	elif varyList is None:
1542	# old GPX file from before pre-constraint varyList is saved
1543	print (' * Old refinement: Please use Calculate/Refine to redo *')
1544	raise Exception(' * Export aborted *')
1545	else:
1546	varyList = list(varyList)
1547	try:
1548	groups,parmlist = G2mv.GroupConstraints(constDict)
1549	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
1550	except:
1551	# this really should not happen
1552	print (' * ERROR - constraints are internally inconsistent *')
1553	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
1554	print ('Errors'+errmsg)
1555	if warnmsg: print ('Warnings'+warnmsg)
1556	raise Exception(' * CIF creation aborted *')
1557	# add the constrained values to the parameter dictionary
1558	G2mv.Dict2Map(self.parmDict,varyList)
1559	# and add their uncertainties into the esd dictionary (sigDict)
1560	if covDict.get('covMatrix') is not None:
1561	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
1562
1563	def loadTree(self):
1564	'''Load the contents of the data tree into a set of dicts
1565	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
1566	& self.xtalDict)
1567
1568	* The childrenless data tree items are overall parameters/controls for the
1569	entire project and are placed in self.OverallParms
1570	* Phase items are placed in self.Phases
1571	* Data items are placed in self.Histogram. The key for these data items
1572	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
1573	'''
1574	self.OverallParms = {}
1575	self.powderDict = {}
1576	self.xtalDict = {}
1577	self.Phases = {}
1578	self.Histograms = {}
1579	self.SeqRefdata = None
1580	self.SeqRefhist = None
1581	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1582	histType = None
1583	if self.currentExportType == 'phase':
1584	# if exporting phases load them here
1585	sub = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Phases')
1586	if not sub:
1587	print ('no phases found')
1588	return True
1589	item, cookie = self.G2frame.GPXtree.GetFirstChild(sub)
1590	while item:
1591	phaseName = self.G2frame.GPXtree.GetItemText(item)
1592	self.Phases[phaseName] = self.G2frame.GPXtree.GetItemPyData(item)
1593	item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie)
1594	return
1595	elif self.currentExportType == 'single':
1596	histType = 'HKLF'
1597	elif self.currentExportType == 'powder':
1598	histType = 'PWDR'
1599	elif self.currentExportType == 'image':
1600	histType = 'IMG'
1601
1602	if histType: # Loading just one kind of tree entry
1603	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1604	while item:
1605	name = self.G2frame.GPXtree.GetItemText(item)
1606	if name.startswith(histType):
1607	if self.Histograms.get(name): # there is already an item with this name
1608	print('Histogram name '+str(name)+' is repeated. Renaming')
1609	if name[-1] == '9':
1610	name = name[:-1] + '10'
1611	elif name[-1] in '012345678':
1612	name = name[:-1] + str(int(name[-1])+1)
1613	else:
1614	name += '-1'
1615	self.Histograms[name] = {}
1616	# the main info goes into Data, but the 0th
1617	# element contains refinement results, carry
1618	# that over too now.
1619	self.Histograms[name]['Data'] = self.G2frame.GPXtree.GetItemPyData(item)[1]
1620	self.Histograms[name][0] = self.G2frame.GPXtree.GetItemPyData(item)[0]
1621	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1622	while item2:
1623	child = self.G2frame.GPXtree.GetItemText(item2)
1624	self.Histograms[name][child] = self.G2frame.GPXtree.GetItemPyData(item2)
1625	item2, cookie2 = self.G2frame.GPXtree.GetNextChild(item, cookie2)
1626	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1627	# index powder and single crystal histograms by number
1628	for hist in self.Histograms:
1629	if hist.startswith("PWDR"):
1630	d = self.powderDict
1631	elif hist.startswith("HKLF"):
1632	d = self.xtalDict
1633	else:
1634	return
1635	i = self.Histograms[hist].get('hId')
1636	if i is None and not d.keys():
1637	i = 0
1638	elif i is None or i in d.keys():
1639	i = max(d.keys())+1
1640	d[i] = hist
1641	return
1642	# else standard load: using all interlinked phases and histograms
1643	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1644	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1645	while item:
1646	name = self.G2frame.GPXtree.GetItemText(item)
1647	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1648	if not item2:
1649	self.OverallParms[name] = self.G2frame.GPXtree.GetItemPyData(item)
1650	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1651	# index powder and single crystal histograms
1652	for hist in self.Histograms:
1653	i = self.Histograms[hist]['hId']
1654	if hist.startswith("PWDR"):
1655	self.powderDict[i] = hist
1656	elif hist.startswith("HKLF"):
1657	self.xtalDict[i] = hist
1658
1659	def dumpTree(self,mode='type'):
1660	'''Print out information on the data tree dicts loaded in loadTree.
1661	Used for testing only.
1662	'''
1663	if self.SeqRefdata and self.SeqRefhist:
1664	print('Note that dumpTree does not show sequential results')
1665	print ('\nOverall')
1666	if mode == 'type':
1667	def Show(arg): return type(arg)
1668	else:
1669	def Show(arg): return arg
1670	for key in self.OverallParms:
1671	print (' '+key+Show(self.OverallParms[key]))
1672	print ('Phases')
1673	for key1 in self.Phases:
1674	print (' '+key1+Show(self.Phases[key1]))
1675	print ('Histogram')
1676	for key1 in self.Histograms:
1677	print (' '+key1+Show(self.Histograms[key1]))
1678	for key2 in self.Histograms[key1]:
1679	print (' '+key2+Show(self.Histograms[key1][key2]))
1680
1681	def defaultSaveFile(self):
1682	return os.path.abspath(
1683	os.path.splitext(self.G2frame.GSASprojectfile
1684	)[0]+self.extension)
1685
1686	def askSaveFile(self):
1687	'''Ask the user to supply a file name
1688
1689	:returns: a file name (str) or None if Cancel is pressed
1690	'''
1691
1692	pth = G2G.GetExportPath(self.G2frame)
1693	defnam = os.path.splitext(
1694	os.path.split(self.G2frame.GSASprojectfile)[1]
1695	)[0]+self.extension
1696	dlg = wx.FileDialog(
1697	self.G2frame, 'Input name for file to write', pth, defnam,
1698	self.longFormatName+' ('+self.extension+')\|'+self.extension,
1699	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
1700	dlg.CenterOnParent()
1701	try:
1702	if dlg.ShowModal() == wx.ID_OK:
1703	filename = dlg.GetPath()
1704	self.G2frame.LastExportDir = os.path.split(filename)[0]
1705	filename = os.path.splitext(filename)[0]+self.extension # make sure extension is correct
1706	else:
1707	filename = None
1708	finally:
1709	dlg.Destroy()
1710	return filename
1711
1712	def askSaveDirectory(self):
1713	'''Ask the user to supply a directory name. Path name is used as the
1714	starting point for the next export path search.
1715
1716	:returns: a directory name (str) or None if Cancel is pressed
1717	'''
1718	pth = G2G.GetExportPath(self.G2frame)
1719	dlg = wx.DirDialog(
1720	self.G2frame, 'Input directory where file(s) will be written', pth,
1721	wx.DD_DEFAULT_STYLE)
1722	dlg.CenterOnParent()
1723	try:
1724	if dlg.ShowModal() == wx.ID_OK:
1725	filename = dlg.GetPath()
1726	self.G2frame.LastExportDir = filename
1727	else:
1728	filename = None
1729	finally:
1730	dlg.Destroy()
1731	return filename
1732
1733	# Tools for file writing.
1734	def OpenFile(self,fil=None,mode='w'):
1735	'''Open the output file
1736
1737	:param str fil: The name of the file to open. If None (default)
1738	the name defaults to self.dirname + self.filename.
1739	If an extension is supplied, it is not overridded,
1740	but if not, the default extension is used.
1741	:returns: the file object opened by the routine which is also
1742	saved as self.fp
1743	'''
1744	if mode == 'd': # debug mode
1745	self.fullpath = '(stdout)'
1746	self.fp = sys.stdout
1747	return
1748	if not fil:
1749	if not os.path.splitext(self.filename)[1]:
1750	self.filename += self.extension
1751	fil = os.path.join(self.dirname,self.filename)
1752	self.fullpath = os.path.abspath(fil)
1753	self.fp = open(self.fullpath,mode)
1754	return self.fp
1755
1756	def Write(self,line):
1757	'''write a line of output, attaching a line-end character
1758
1759	:param str line: the text to be written.
1760	'''
1761	self.fp.write(line+'\n')
1762
1763	def CloseFile(self,fp=None):
1764	'''Close a file opened in OpenFile
1765
1766	:param file fp: the file object to be closed. If None (default)
1767	file object self.fp is closed.
1768	'''
1769	if self.fp == sys.stdout: return # debug mode
1770	if fp is None:
1771	fp = self.fp
1772	self.fp = None
1773	if fp is not None: fp.close()
1774
1775	def SetSeqRef(self,data,hist):
1776	'''Set the exporter to retrieve results from a sequential refinement
1777	rather than the main tree
1778	'''
1779	self.SeqRefdata = data
1780	self.SeqRefhist = hist
1781	data_name = data[hist]
1782	for i,val in zip(data_name['varyList'],data_name['sig']):
1783	self.sigDict[i] = val
1784	self.sigDict[striphist(i)] = val
1785	for i in data_name['parmDict']:
1786	self.parmDict[striphist(i)] = data_name['parmDict'][i]
1787	self.parmDict[i] = data_name['parmDict'][i]
1788	# zero out the dA[xyz] terms, they would only bring confusion
1789	key = i.split(':')
1790	if len(key) < 3: continue
1791	if key[2].startswith('dA'):
1792	self.parmDict[i] = 0.0
1793	for i,(val,sig) in data_name.get('depParmDict',{}).iteritems():
1794	self.parmDict[i] = val
1795	self.sigDict[i] = sig
1796	#GSASIIpath.IPyBreak()
1797
1798	# Tools to pull information out of the data arrays
1799	def GetCell(self,phasenam):
1800	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1801
1802	:param str phasenam: the name for the selected phase
1803	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1804	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1805	cell values and `cellSig` has their uncertainties.
1806	"""
1807	if self.SeqRefdata and self.SeqRefhist:
1808	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
1809	phasedict = self.Phases[phasenam] # pointer to current phase info
1810	try:
1811	pfx = str(phasedict['pId'])+'::'
1812	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
1813	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
1814	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
1815	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
1816	return cellList,cellSig
1817	except KeyError:
1818	cell = phasedict['General']['Cell'][1:]
1819	return cell,7*[0]
1820
1821	def GetSeqCell(self,phasenam,data_name):
1822	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1823	and histogram in a sequential fit
1824
1825	:param str phasenam: the name for the selected phase
1826	:param dict data_name: the sequential refinement parameters for the selected histogram
1827	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1828	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1829	cell values and `cellSig` has their uncertainties.
1830	"""
1831	phasedict = self.Phases[phasenam]
1832	SGdata = phasedict['General']['SGData']
1833	pId = phasedict['pId']
1834	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
1835	ESDlookup = {}
1836	Dlookup = {}
1837	varied = [striphist(i) for i in data_name['varyList']]
1838	for item,val in data_name['newCellDict'].iteritems():
1839	if item in varied:
1840	ESDlookup[val[0]] = item
1841	Dlookup[item] = val[0]
1842	A = RecpCellTerms[:]
1843	for i in range(6):
1844	var = str(pId)+'::A'+str(i)
1845	if var in ESDlookup:
1846	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
1847	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
1848	zeroDict = {i:0.0 for i in cellDict}
1849	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
1850	covData = {
1851	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
1852	'covMatrix': data_name['covMatrix']
1853	}
1854	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
1855
1856	def GetAtoms(self,phasenam):
1857	"""Gets the atoms associated with a phase. Can be used with standard
1858	or macromolecular phases
1859
1860	:param str phasenam: the name for the selected phase
1861	:returns: a list of items for eac atom where each item is a list containing:
1862	label, typ, mult, xyz, and td, where
1863
1864	* label and typ are the atom label and the scattering factor type (str)
1865	* mult is the site multiplicity (int)
1866	* xyz is contains a list with four pairs of numbers:
1867	x, y, z and fractional occupancy and
1868	their standard uncertainty (or a negative value)
1869	* td is contains a list with either one or six pairs of numbers:
1870	if one number it is U\ :sub:`iso` and with six numbers it is
1871	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
1872	paired with their standard uncertainty (or a negative value)
1873	"""
1874	phasedict = self.Phases[phasenam] # pointer to current phase info
1875	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1876	cfrac = cx+3
1877	fpfx = str(phasedict['pId'])+'::Afrac:'
1878	atomslist = []
1879	for i,at in enumerate(phasedict['Atoms']):
1880	if phasedict['General']['Type'] == 'macromolecular':
1881	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1882	else:
1883	label = at[ct-1]
1884	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
1885	fsig = self.sigDict.get(fpfx+str(i),-0.009)
1886	mult = at[cs+1]
1887	typ = at[ct]
1888	xyz = []
1889	for j,v in enumerate(('x','y','z')):
1890	val = at[cx+j]
1891	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
1892	val = self.parmDict.get(pfx, val)
1893	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
1894	sig = self.sigDict.get(dpfx,-0.000009)
1895	xyz.append((val,sig))
1896	xyz.append((fval,fsig))
1897	td = []
1898	if at[cia] == 'I':
1899	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
1900	val = self.parmDict.get(pfx,at[cia+1])
1901	sig = self.sigDict.get(pfx,-0.0009)
1902	td.append((val,sig))
1903	else:
1904	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
1905	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
1906	val = self.parmDict.get(pfx,at[cia+2+i])
1907	sig = self.sigDict.get(pfx,-0.0009)
1908	td.append((val,sig))
1909	atomslist.append((label,typ,mult,xyz,td))
1910	return atomslist
1911	######################################################################
1912	def ExportPowderList(G2frame):
1913	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
1914	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1915
1916	:param wx.Frame G2frame: the GSAS-II main data tree window
1917	'''
1918	extList = []
1919	for obj in G2frame.exporterlist:
1920	if 'powder' in obj.exporttype:
1921	try:
1922	obj.Writer
1923	extList.append(obj.extension)
1924	except AttributeError:
1925	pass
1926	return extList
1927
1928	def ExportPowder(G2frame,TreeName,fileroot,extension):
1929	'''Writes a single powder histogram using the Export routines.
1930	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1931
1932	:param wx.Frame G2frame: the GSAS-II main data tree window
1933	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
1934	:param str fileroot: name for file to be written, extension ignored
1935	:param str extension: extension for file to be written (start with '.'). Must
1936	match a powder export routine that has a Writer object.
1937	'''
1938	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
1939	for obj in G2frame.exporterlist:
1940	if obj.extension == extension and 'powder' in obj.exporttype:
1941	obj.currentExportType = 'powder'
1942	obj.InitExport(None)
1943	obj.loadTree() # load all histograms in tree into dicts
1944	if TreeName not in obj.Histograms:
1945	raise Exception('Histogram not found: '+str(TreeName))
1946	try:
1947	obj.Writer
1948	except AttributeError:
1949	continue
1950	try:
1951	obj.Writer(TreeName,filename)
1952	print('wrote file '+filename)
1953	return
1954	except Exception:
1955	print('Export Routine for '+extension+' failed.')
1956	else:
1957	print('No Export routine supports extension '+extension)
1958
1959	def ExportSequential(G2frame,data,obj,exporttype):
1960	'''
1961	Used to export from every phase/dataset in a sequential refinement using
1962	a .Writer method for either projects or phases. Prompts to select histograms
1963	and for phase exports, which phase(s).
1964
1965	:param wx.Frame G2frame: the GSAS-II main data tree window
1966	:param dict data: the sequential refinement data object
1967	:param str exporttype: indicates the type of export ('project' or 'phase')
1968	'''
1969	if len(data['histNames']) == 0:
1970	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
1971	obj.InitExport(None)
1972	obj.loadTree()
1973	obj.loadParmDict()
1974	if len(data['histNames']) == 1:
1975	histlist = data['histNames']
1976	else:
1977	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
1978	'Select histograms',data['histNames'])
1979	if dlg.ShowModal() == wx.ID_OK:
1980	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
1981	dlg.Destroy()
1982	else:
1983	dlg.Destroy()
1984	return
1985	if exporttype == 'Phase':
1986	phaselist = list(obj.Phases.keys())
1987	if len(obj.Phases) == 0:
1988	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
1989	return
1990	elif len(obj.Phases) > 1:
1991	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
1992	'Select phases', phaselist)
1993	if dlg.ShowModal() == wx.ID_OK:
1994	phaselist = [phaselist[l] for l in dlg.GetSelections()]
1995	dlg.Destroy()
1996	else:
1997	dlg.Destroy()
1998	return
1999	filename = obj.askSaveFile()
2000	if not filename: return True
2001	obj.dirname,obj.filename = os.path.split(filename)
2002	print('Writing output to file '+str(obj.filename)+"...")
2003	mode = 'w'
2004	for p in phaselist:
2005	for h in histlist:
2006	obj.SetSeqRef(data,h)
2007	#GSASIIpath.IPyBreak()
2008	obj.Writer(h,phasenam=p,mode=mode)
2009	mode = 'a'
2010	print('...done')
2011	elif exporttype == 'Project': # note that the CIF exporter is not yet ready for this
2012	filename = obj.askSaveFile()
2013	if not filename: return True
2014	obj.dirname,obj.filename = os.path.split(filename)
2015	print('Writing output to file '+str(obj.filename)+"...")
2016	mode = 'w'
2017	for h in histlist:
2018	obj.SetSeqRef(data,h)
2019	obj.Writer(h,mode=mode)
2020	print('\t'+str(h)+' written')
2021	mode = 'a'
2022	print('...done')
2023	elif exporttype == 'Powder':
2024	filename = obj.askSaveFile()
2025	if not filename: return True
2026	obj.dirname,obj.filename = os.path.split(filename)
2027	print('Writing output to file '+str(obj.filename)+"...")
2028	mode = 'w'
2029	for h in histlist:
2030	obj.SetSeqRef(data,h)
2031	obj.Writer(h,mode=mode)
2032	print('\t'+str(h)+' written')
2033	mode = 'a'
2034	print('...done')
2035
2036	def ReadDIFFaX(DIFFaXfile):
2037	print ('read '+DIFFaXfile)
2038	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
2039	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
2040	df = open(DIFFaXfile,'r')
2041	lines = df.readlines()
2042	df.close()
2043	struct = False
2044	Struct = []
2045	stack = False
2046	Stack = []
2047	trans = False
2048	Trans = []
2049	for diff in lines:
2050	diff = diff[:-1].lower()
2051	if '!' in diff:
2052	continue
2053	while '}' in diff: #strip comments
2054	iB = diff.index('{')
2055	iF = diff.index('}')+1
2056	if iB:
2057	diff = diff[:iB]
2058	else:
2059	diff = diff[iF:]
2060	if not diff:
2061	continue
2062	if diff.strip() == 'instrumental':
2063	continue
2064	if diff.strip() == 'structural':
2065	struct = True
2066	continue
2067	elif diff.strip() == 'stacking':
2068	struct = False
2069	stack = True
2070	continue
2071	elif diff.strip() == 'transitions':
2072	stack = False
2073	trans = True
2074	continue
2075	diff = diff.strip()
2076	if struct:
2077	if diff:
2078	Struct.append(diff)
2079	elif stack:
2080	if diff:
2081	Stack.append(diff)
2082	elif trans:
2083	if diff:
2084	Trans.append(diff)
2085
2086	#STRUCTURE records
2087	laueRec = Struct[1].split()
2088	Layer['Laue'] = laueRec[0]
2089	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2090	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2091	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2092	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2093	cell = Struct[0].split()
2094	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2095	nLayers = int(Struct[2])
2096	N = 3
2097	if 'layer' not in Struct[3]:
2098	N = 4
2099	if Struct[3] != 'infinite':
2100	width = Struct[3].split()
2101	Layer['Width'][0] = [float(width[0]),float(width[1])]
2102	for nL in range(nLayers):
2103	if '=' in Struct[N]:
2104	name = Struct[N].split('=')
2105	sameas = int(name[1])-1
2106	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2107	N += 1
2108	continue
2109	Symm = 'None'
2110	if 'centro' in Struct[N+1]: Symm = '-1'
2111	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2112	N += 2
2113	while 'layer' not in Struct[N]:
2114	atom = Struct[N][4:].split()
2115	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2116	if atomType not in Layer['AtInfo']:
2117	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2118	atomName = '%s(%s)'%(atomType,atom[0])
2119	newVals = []
2120	for val in atom[1:6]:
2121	if '/' in val:
2122	newVals.append(eval(val+'.'))
2123	else:
2124	newVals.append(float(val))
2125	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2126	Layer['Layers'][-1]['Atoms'].append(atomRec)
2127	N += 1
2128	if N > len(Struct)-1:
2129	break
2130	#TRANSITIONS records
2131	transArray = []
2132	N = 0
2133	for i in range(nLayers):
2134	transArray.append([])
2135	for j in range(nLayers):
2136	vals = Trans[N].split()
2137	newVals = []
2138	for val in vals[:4]:
2139	if '/' in val:
2140	newVals.append(eval(val+'.'))
2141	else:
2142	newVals.append(float(val))
2143	transArray[-1].append(newVals+['',False])
2144	N += 1
2145	Layer['Transitions'] = transArray
2146	#STACKING records
2147	Layer['Stacking'] = [Stack[0],'']
2148	if Stack[0] == 'recursive':
2149	Layer['Stacking'][1] = Stack[1]
2150	elif Stack[0] == 'explicit':
2151	if Stack[1] == 'random':
2152	Layer['Stacking'][1] = Stack[1]
2153	else:
2154	Layer['Stacking'][1] = 'list'
2155	Layer['Stacking'].append('')
2156	for stack in Stack[2:]:
2157	Layer['Stacking'][2] += ' '+stack
2158	return Layer
2159
2160	def readColMetadata(imagefile):
2161	'''Reads image metadata from a column-oriented metadata table
2162	(1-ID style .par file). Called by :func:`GetColumnMetadata`
2163
2164	The .par file has any number of columns separated by spaces.
2165	The directory for the file must be specified in
2166	Config variable ``Column_Metadata_directory``.
2167	As an index to the .par file a second "label file" must be specified with the
2168	same file root name as the .par file but the extension must be .XXX_lbls (where
2169	.XXX is the extension of the image) or if that is not present extension
2170	.lbls.
2171
2172	:param str imagefile: the full name of the image file (with extension, directory optional)
2173
2174	:returns: a dict with parameter values. Named parameters will have the type based on
2175	the specified Python function, named columns will be character strings
2176
2177	The contents of the label file will look like this::
2178
2179	# define keywords
2180	filename:lambda x,y: "{}_{:0>6}".format(x,y)\|33,34
2181	distance: float \| 75
2182	wavelength:lambda keV: 12.398425/float(keV)\|9
2183	pixelSize:lambda x: [74.8, 74.8]\|0
2184	ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)\|0,1,2,3,4
2185	Temperature: float\|53
2186	FreePrm2: int \| 34 \| Free Parm2 Label
2187	# define other variables
2188	0:day
2189	1:month
2190	2:date
2191	3:time
2192	4:year
2193	7:I_ring
2194
2195	This file contains three types of lines in any order.
2196	* Named parameters are evaluated with user-supplied Python code (see
2197	subsequent information). Specific named parameters are used
2198	to determine values that are used for image interpretation (see table,
2199	below). Any others are copied to the Comments subsection of the Image
2200	tree item.
2201	* Column labels are defined with a column number (integer) followed by
2202	a colon (:) and a label to be assigned to that column. All labeled
2203	columns are copied to the Image's Comments subsection.
2204	* Comments are any line that does not contain a colon.
2205
2206	Note that columns are numbered starting at zero.
2207
2208	Any named parameter may be defined provided it is not a valid integer,
2209	but the named parameters in the table have special meanings, as descibed.
2210	The parameter name is followed by a colon. After the colon, specify
2211	Python code that defines or specifies a function that will be called to
2212	generate a value for that parameter.
2213
2214	Note that several keywords, if defined in the Comments, will be found and
2215	placed in the appropriate section of the powder histogram(s)'s Sample
2216	Parameters after an integration: 'Temperature','Pressure','Time',
2217	'FreePrm1','FreePrm2','FreePrm3','Omega','Chi', and 'Phi'.
2218
2219	After the Python code, supply a vertical bar (\|) and then a list of one
2220	more more columns that will be supplied as arguments to that function.
2221
2222	Note that the labels for the three FreePrm items can be changed by
2223	including that label as a third item with an additional vertical bar. Labels
2224	will be ignored for any other named parameters.
2225
2226	The examples above are discussed here:
2227
2228	``filename:lambda x,y: "{}_{:0>6}".format(x,y)\|33,34``
2229	Here the function to be used is defined with a lambda statement::
2230
2231	lambda x,y: "{}_{:0>6}".format(x,y)
2232
2233	This function will use the format function to create a file name from the
2234	contents of columns 33 and 34. The first parameter (x, col. 33) is inserted directly into
2235	the file name, followed by a underscore (_), followed by the second parameter (y, col. 34),
2236	which will be left-padded with zeros to six characters (format directive ``:0>6``).
2237
2238	When there will be more than one image generated per line in the .par file, an alternate way to
2239	generate list of file names takes into account the number of images generated::
2240
2241	lambda x,y,z: ["{}_{:0>6}".format(x,int(y)+i) for i in range(int(z))]
2242
2243	Here a third parameter is used to specify the number of images generated, where
2244	the image number is incremented for each image.
2245
2246	``distance: float \| 75``
2247	Here the contents of column 75 will be converted to a floating point number
2248	by calling float on it. Note that the spaces here are ignored.
2249
2250	``wavelength:lambda keV: 12.398425/float(keV)\|9``
2251	Here we define an algebraic expression to convert an energy in keV to a
2252	wavelength and pass the contents of column 9 as that input energy
2253
2254	``pixelSize:lambda x: [74.8, 74.8]\|0``
2255	In this case the pixel size is a constant (a list of two numbers). The first
2256	column is passed as an argument as at least one argument is required, but that
2257	value is not used in the expression.
2258
2259	``ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)\|0,1,2,3,4``
2260	This example defines a parameter that takes items in the first five columns
2261	and formats them in a different way. This parameter is not one of the pre-defined
2262	parameter names below. Some external code could be used to change the month string
2263	(argument ``m``) to a integer from 1 to 12.
2264
2265	``FreePrm2: int \| 34 \| Free Parm2 Label``
2266	In this example, the contents of column 34 will be converted to an integer and
2267	placed as the second free-named parameter in the Sample Parameters after an
2268	integration. The label for this parameter will be changed to "Free Parm2 Label".
2269
2270	Pre-defined parameter names
2271
2272	============= ========= ======== =====================================================
2273	keyword required type Description
2274	============= ========= ======== =====================================================
2275	filename yes str or generates the file name prefix for the matching image
2276	list file (MyImage001 for file /tmp/MyImage001.tif) or
2277	a list of file names.
2278	polarization no float generates the polarization expected based on the
2279	monochromator angle, defaults to 0.99.
2280	center no list of generates the approximate beam center on the detector
2281	2 floats in mm, such as [204.8, 204.8].
2282	distance yes float generates the distance from the sample to the detector
2283	in mm
2284	pixelSize no list of generates the size of the pixels in microns such as
2285	2 floats [200.0, 200.0].
2286	wavelength yes float generates the wavelength in Angstroms
2287	============= ========= ======== =====================================================
2288
2289	'''
2290	dir,fil = os.path.split(os.path.abspath(imagefile))
2291	imageName,ext = os.path.splitext(fil)
2292	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'): return
2293	parfiles = glob.glob(os.path.join(GSASIIpath.GetConfigValue('Column_Metadata_directory'),'*.par'))
2294	if len(parfiles) == 0:
2295	print('Sorry, No Column metadata (.par) file found in '+
2296	GSASIIpath.GetConfigValue('Column_Metadata_directory'))
2297	return {}
2298	for parFil in parfiles: # loop over all .par files (hope just 1) in image dir until image is found
2299	parRoot = os.path.splitext(parFil)[0]
2300	for e in (ext+'_lbls','.lbls'):
2301	if os.path.exists(parRoot+e):
2302	lblFil = parRoot+e
2303	break
2304	else:
2305	print('Warning: No labels definitions found for '+parFil)
2306	continue
2307	labels,lbldict,keyCols,keyExp,errors = readColMetadataLabels(lblFil)
2308	if errors:
2309	print('Errors in labels file '+lblFil)
2310	for i in errors: print(' '+i)
2311	continue
2312	else:
2313	print('Read '+lblFil)
2314	# scan through each line in this .par file, looking for the matching image rootname
2315	fp = open(parFil,'Ur')
2316	for iline,line in enumerate(fp):
2317	items = line.strip().split(' ')
2318	nameList = keyExp['filename'](*[items[j] for j in keyCols['filename']])
2319	if type(nameList) is str:
2320	if nameList != imageName: continue
2321	name = nameList
2322	else:
2323	for name in nameList:
2324	if name == imageName: break # got a match
2325	else:
2326	continue
2327	# parse the line and finish
2328	metadata = evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp)
2329	metadata['par file'] = parFil
2330	metadata['lbls file'] = lblFil
2331	print("Metadata read from {} line {}".format(parFil,iline+1))
2332	fp.close()
2333	return metadata
2334	else:
2335	print("Image {} not found in {}".format(imageName,parFil))
2336	fp.close()
2337	continue
2338	fp.close()
2339	else:
2340	print("Warning: No .par metadata for image {}".format(imageName))
2341	return {}
2342
2343	def readColMetadataLabels(lblFil):
2344	'''Read the .*lbls file and setup for metadata assignments
2345	'''
2346	lbldict = {}
2347	keyExp = {}
2348	keyCols = {}
2349	labels = {}
2350	errors = []
2351	fp = open(lblFil,'Ur') # read column labels
2352	for iline,line in enumerate(fp): # read label definitions
2353	line = line.strip()
2354	if not line or line[0] == '#': continue # comments
2355	items = line.split(':')
2356	if len(items) < 2: continue # lines with no colon are also comments
2357	# does this line a definition for a named parameter?
2358	key = items[0]
2359	try:
2360	int(key)
2361	except ValueError: # try as named parameter since not a valid number
2362	items = line.split(':',1)[1].split('\|')
2363	try:
2364	f = eval(items[0]) # compile the expression
2365	if not callable(f):
2366	errors += ['Expression "{}" for key {} is not a function (line {})'.
2367	format(items[0],key,iline)]
2368	continue
2369	keyExp[key] = f
2370	except Exception as msg:
2371	errors += ['Expression "{}" for key {} is not valid (line {})'.
2372	format(items[0],key,iline)]
2373	errors += [str(msg)]
2374	continue
2375	keyCols[key] = [int(i) for i in items[1].strip().split(',')]
2376	if key.lower().startswith('freeprm') and len(items) > 2:
2377	labels[key] = items[2]
2378	continue
2379	if len(items) == 2: # simple column definition
2380	lbldict[int(items[0])] = items[1]
2381	fp.close()
2382	if 'filename' not in keyExp:
2383	errors += ["File {} is invalid. No valid filename expression.".format(lblFil)]
2384	return labels,lbldict,keyCols,keyExp,errors
2385
2386	def evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp,ShowError=False):
2387	'''Evaluate the metadata for a line in the .par file
2388	'''
2389	metadata = {lbldict[j]:items[j] for j in lbldict}
2390	named = {}
2391	for key in keyExp:
2392	try:
2393	res = keyExp[key](*[items[j] for j in keyCols[key]])
2394	except:
2395	if ShowError:
2396	res = "* error *"
2397	else:
2398	continue
2399	named[key] = res
2400	metadata.update(named)
2401	for lbl in labels: # add labels for FreePrm's
2402	metadata['label_'+lbl[4:].lower()] = labels[lbl]
2403	return metadata
2404
2405	def GetColumnMetadata(reader):
2406	'''Add metadata to an image from a column-type metadata file
2407	using :func:`readColMetadata`
2408
2409	:param reader: a reader object from reading an image
2410
2411	'''
2412	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'): return
2413	parParms = readColMetadata(reader.readfilename)
2414	if not parParms: return # check for read failure
2415	specialKeys = ('filename',"polarization", "center", "distance", "pixelSize", "wavelength",)
2416	reader.Comments = ['Metadata from {} assigned by {}'.format(parParms['par file'],parParms['lbls file'])]
2417	for key in parParms:
2418	if key in specialKeys+('par file','lbls file'): continue
2419	reader.Comments += ["{} = {}".format(key,parParms[key])]
2420	if "polarization" in parParms:
2421	reader.Data['PolaVal'][0] = parParms["polarization"]
2422	else:
2423	reader.Data['PolaVal'][0] = 0.99
2424	if "center" in parParms:
2425	reader.Data['center'] = parParms["center"]
2426	if "pixelSize" in parParms:
2427	reader.Data['pixelSize'] = parParms["pixelSize"]
2428	if "wavelength" in parParms:
2429	reader.Data['wavelength'] = parParms['wavelength']
2430	else:
2431	print('Error: wavelength not defined in {}'.format(parParms['lbls file']))
2432	if "distance" in parParms:
2433	reader.Data['distance'] = parParms['distance']
2434	reader.Data['setdist'] = parParms['distance']
2435	else:
2436	print('Error: distance not defined in {}'.format(parParms['lbls file']))
2437
2438	def testColumnMetadata(G2frame):
2439	'''Test the column-oriented metadata parsing, as implemented at 1-ID, by showing results
2440	when using a .par and .lbls pair.
2441
2442	* Select a .par file, if more than one in selected dir.
2443	* Select the .*lbls file, if more than one matching .par file.
2444	* Parse the .lbls file, showing errors if encountered; loop until errors are fixed.
2445	* Search for an image or a line in the .par file and show the results when interpreted
2446
2447	See :func:`readColMetadata` for more details.
2448	'''
2449	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'):
2450	G2G.G2MessageBox(G2frame,'The configuration option for I-ID Metadata is not set.\n'+
2451	'Please use the File/Preferences menu to set Column_Metadata_directory',
2452	'Warning')
2453	return
2454	parFiles = glob.glob(os.path.join(GSASIIpath.GetConfigValue('Column_Metadata_directory'),'*.par'))
2455	if not parFiles:
2456	G2G.G2MessageBox(G2frame,'No .par files found in directory {}. '
2457	.format(GSASIIpath.GetConfigValue('Column_Metadata_directory'))+
2458	'\nThis is set by config variable Column_Metadata_directory '+
2459	'(Set in File/Preferences menu).',
2460	'Warning')
2461	return
2462	parList = []
2463	for parFile in parFiles:
2464	lblList = []
2465	parRoot = os.path.splitext(parFile)[0]
2466	for f in glob.glob(parRoot+'.*lbls'):
2467	if os.path.exists(f): lblList.append(f)
2468	if not len(lblList):
2469	continue
2470	parList.append(parFile)
2471	if len(parList) == 0:
2472	G2G.G2MessageBox(G2frame,'No .lbls or .EXT_lbls file found for .par file(s) in directory {}. '
2473	.format(GSASIIpath.GetConfigValue('Column_Metadata_directory'))+
2474	'\nThis is set by config variable Column_Metadata_directory '+
2475	'(Set in File/Preferences menu).',
2476	'Warning')
2477	return
2478	elif len(parList) == 1:
2479	parFile = parList[0]
2480	else:
2481	dlg = G2G.G2SingleChoiceDialog(G2frame,
2482	'More than 1 .par file found. (Better if only 1!). Choose the one to test in '+
2483	GSASIIpath.GetConfigValue('Column_Metadata_directory'),
2484	'Choose .par file', [os.path.split(i)[1] for i in parList])
2485	if dlg.ShowModal() == wx.ID_OK:
2486	parFile = parList[dlg.GetSelection()]
2487	dlg.Destroy()
2488	else:
2489	dlg.Destroy()
2490	return
2491	# got .par file; now work on .*lbls file
2492	lblList = []
2493	parRoot = os.path.splitext(parFile)[0]
2494	for f in glob.glob(parRoot+'.*lbls'):
2495	if os.path.exists(f): lblList.append(f)
2496	if not len(lblList):
2497	raise Exception('How did this happen! No .*lbls files for '+parFile)
2498	elif len(lblList) == 1:
2499	lblFile = lblList[0]
2500	else:
2501	dlg = G2G.G2SingleChoiceDialog(G2frame,
2502	'Select label file for .par file '+parFile,
2503	'Choose label file', [os.path.split(i)[1] for i in lblList])
2504	if dlg.ShowModal() == wx.ID_OK:
2505	lblFile = lblList[dlg.GetSelection()]
2506	dlg.Destroy()
2507	else:
2508	dlg.Destroy()
2509	return
2510	# parse the labels file
2511	errors = True
2512	while errors:
2513	labels,lbldict,keyCols,keyExp,errors = readColMetadataLabels(lblFile)
2514	if errors:
2515	t = "Error reading file "+lblFile
2516	for l in errors:
2517	t += '\n'
2518	t += l
2519	t += "\n\nPlease edit the file and press OK (or Cancel to quit)"
2520	dlg = wx.MessageDialog(G2frame,message=t,
2521	caption="Read Error",style=wx.ICON_ERROR\| wx.OK\|wx.STAY_ON_TOP\|wx.CANCEL)
2522	if dlg.ShowModal() != wx.ID_OK: return
2523	# request a line number, read that line
2524	dlg = G2G.SingleStringDialog(G2frame,'Read what',
2525	'Enter a line number or an image file name (-1=last line)',
2526	'-1',size=(400,-1))
2527	if dlg.Show():
2528	fileorline = dlg.GetValue()
2529	dlg.Destroy()
2530	else:
2531	dlg.Destroy()
2532	return
2533	# and report the generated key pairs in metadata dict
2534	linenum = None
2535	try:
2536	linenum = int(fileorline)
2537	except:
2538	imageName = os.path.splitext(os.path.split(fileorline)[1])[0]
2539
2540	fp = open(parFile,'Ur')
2541	for iline,line in enumerate(fp):
2542	if linenum is not None:
2543	if iline == linenum:
2544	items = line.strip().split(' ')
2545	n = "Line {}".format(iline)
2546	break
2547	else:
2548	continue
2549	else:
2550	items = line.strip().split(' ')
2551	nameList = keyExp['filename'](*[items[j] for j in keyCols['filename']])
2552	if type(nameList) is str:
2553	if nameList != imageName: continue
2554	name = nameList
2555	break
2556	else:
2557	for name in nameList:
2558	print (name,name == imageName)
2559	if name == imageName:
2560	n = "Image {} found in line {}".format(imageName,iline)
2561	break # got a match
2562	else:
2563	continue
2564	break
2565	else:
2566	if linenum is not None:
2567	n = "Line {}".format(iline)
2568	else:
2569	n = "Image {} not found. Reporting line {}".format(imageName,iline)
2570	items = line.strip().split(' ')
2571	fp.close()
2572	metadata = evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp,True)
2573	title = "Results: ("+n+")"
2574	t = []
2575	n = ["Named parameters:"]
2576	l = ['',"Labeled columns:"]
2577	for key in sorted(metadata):
2578	if key == "filename" or key.startswith('label_prm'): continue
2579	if key in keyCols:
2580	n += [" {} = {}".format(key,metadata[key])]
2581	elif key in lbldict.values():
2582	l += [" {} = {}".format(key,metadata[key])]
2583	else:
2584	t += ["** Unexpected: {}".format(key,metadata[key])]
2585	if type(metadata['filename']) is str:
2586	l += ["","Filename: "+ metadata['filename']]
2587	else:
2588	l += ["","Filename(s): "]
2589	for i,j in enumerate(metadata['filename']):
2590	if i: l[-1] += ', '
2591	l[-1] += j
2592	t += n + l + ['','Unused columns:']
2593	usedCols = lbldict.keys()
2594	for i in keyCols.values(): usedCols += i
2595	for i in range(len(items)):
2596	if i in usedCols: continue
2597	t += [" {}: {}".format(i,items[i])]
2598	dlg = G2G.G2SingleChoiceDialog(None,title,'Column metadata parse results',t,
2599	monoFont=True,filterBox=False,size=(400,600),
2600	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.CENTRE\|wx.OK)
2601	dlg.ShowModal()
2602
2603	if __name__ == '__main__':
2604	import GSASIIdataGUI
2605	application = GSASIIdataGUI.GSASIImain(0)
2606	G2frame = application.main
2607	#app = wx.PySimpleApp()
2608	#G2frame = wx.Frame(None) # create a frame
2609	#frm.Show(True)
2610	#filename = '/tmp/notzip.zip'
2611	#filename = '/tmp/all.zip'
2612	#filename = '/tmp/11bmb_7652.zip'
2613
2614	#selection=None, confirmoverwrite=True, parent=None
2615	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2616	#print ExtractFileFromZip(filename,multipleselect=True)
2617	# #confirmread=False, confirmoverwrite=False)
2618
2619	# choicelist=[ ('a','b','c'),
2620	# ('test1','test2'),('no choice',)]
2621	# titles = [ 'a, b or c', 'tests', 'No option here']
2622	# dlg = MultipleChoicesDialog(
2623	# choicelist,titles,
2624	# parent=frm)
2625	# if dlg.ShowModal() == wx.ID_OK:
2626	# print 'Got OK'
2627	imagefile = '/tmp/NDC5_00237_3.ge3'
2628	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2629
2630	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2631
2632	GSASIIpath.IPyBreak_base()

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