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source: trunk/GSASIIIO.py @ 3216

Last change on this file since 3216 was 3216, checked in by toby, 6 years ago
add data & parameter access in scripting
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2018-01-08 03:06:19 +0000 (Mon, 08 Jan 2018) $
4	# $Author: toby $
5	# $Revision: 3216 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 3216 2018-01-08 03:06:19Z 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: 3216 $")
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	# TODO: review exporters producing exceptions where .Writer can't be used where G2frame is None (see CIF)
1267	# TODO: review conflicting uses of .Writer with mode (SeqRef) & elsewhere
1268	# TODO: move this class to G2fil
1269	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1270	self.G2frame = G2frame
1271	self.formatName = formatName # short string naming file type
1272	self.extension = extension
1273	if longFormatName: # longer string naming file type
1274	self.longFormatName = longFormatName
1275	else:
1276	self.longFormatName = formatName
1277	self.OverallParms = {}
1278	self.Phases = {}
1279	self.Histograms = {}
1280	self.powderDict = {}
1281	self.xtalDict = {}
1282	self.parmDict = {}
1283	self.sigDict = {}
1284	# updated in InitExport:
1285	self.currentExportType = None # type of export that has been requested
1286	# updated in ExportSelect (when used):
1287	self.phasenam = None # a list of selected phases
1288	self.histnam = None # a list of selected histograms
1289	self.filename = None # name of file to be written (single export) or template (multiple files)
1290	self.dirname = '' # name of directory where file(s) will be written
1291	self.fullpath = '' # name of file being written -- full path
1292
1293	# items that should be defined in a subclass of this class
1294	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1295	# The following types are defined: 'project', "phase", "powder", "single"
1296	self.multiple = False # set as True if the class can export multiple phases or histograms
1297	# self.multiple is ignored for "project" exports
1298
1299	def InitExport(self,event):
1300	'''Determines the type of menu that called the Exporter and
1301	misc initialization.
1302	'''
1303	self.filename = None # name of file to be written (single export)
1304	self.dirname = '' # name of file to be written (multiple export)
1305	if event:
1306	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1307
1308	def MakePWDRfilename(self,hist):
1309	'''Make a filename root (no extension) from a PWDR histogram name
1310
1311	:param str hist: the histogram name in data tree (starts with "PWDR ")
1312	'''
1313	file0 = ''
1314	file1 = hist[5:]
1315	# replace repeated blanks
1316	while file1 != file0:
1317	file0 = file1
1318	file1 = file0.replace(' ',' ').strip()
1319	file0 = file1.replace('Azm= ','A')
1320	# if angle has unneeded decimal places on aziumuth, remove them
1321	if file0[-3:] == '.00': file0 = file0[:-3]
1322	file0 = file0.replace('.','_')
1323	file0 = file0.replace(' ','_')
1324	return file0
1325
1326	def ExportSelect(self,AskFile='ask'):
1327	'''Selects histograms or phases when needed. Sets a default file name when
1328	requested into self.filename; always sets a default directory in self.dirname.
1329
1330	:param bool AskFile: Determines how this routine processes getting a
1331	location to store the current export(s).
1332
1333	* if AskFile is 'ask' (default option), get the name of the file to be written;
1334	self.filename and self.dirname are always set. In the case where
1335	multiple files must be generated, the export routine should do this
1336	based on self.filename as a template.
1337	* if AskFile is 'dir', get the name of the directory to be used;
1338	self.filename is not used, but self.dirname is always set. The export routine
1339	will always generate the file name.
1340	* if AskFile is 'single', get only the name of the directory to be used when
1341	multiple items will be written (as multiple files) are used
1342	or a complete file name is requested when a single file
1343	name is selected. self.dirname is always set and self.filename used
1344	only when a single file is selected.
1345	* if AskFile is 'default', creates a name of the file to be used from
1346	the name of the project (.gpx) file. If the project has not been saved,
1347	then the name of file is requested.
1348	self.filename and self.dirname are always set. In the case where
1349	multiple file names must be generated, the export routine should do this
1350	based on self.filename.
1351	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1352	file. If the project has not been saved, then a directory is requested.
1353	self.filename is not used.
1354
1355	:returns: True in case of an error
1356	'''
1357
1358	numselected = 1
1359	if self.currentExportType == 'phase':
1360	if len(self.Phases) == 0:
1361	self.G2frame.ErrorDialog(
1362	'Empty project',
1363	'Project does not contain any phases.')
1364	return True
1365	elif len(self.Phases) == 1:
1366	self.phasenam = self.Phases.keys()
1367	elif self.multiple:
1368	choices = sorted(self.Phases.keys())
1369	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1370	if phasenum is None: return True
1371	self.phasenam = [choices[i] for i in phasenum]
1372	if not self.phasenam: return True
1373	numselected = len(self.phasenam)
1374	else:
1375	choices = sorted(self.Phases.keys())
1376	phasenum = G2G.ItemSelector(choices,self.G2frame)
1377	if phasenum is None: return True
1378	self.phasenam = [choices[phasenum]]
1379	numselected = len(self.phasenam)
1380	elif self.currentExportType == 'single':
1381	if len(self.xtalDict) == 0:
1382	self.G2frame.ErrorDialog(
1383	'Empty project',
1384	'Project does not contain any single crystal data.')
1385	return True
1386	elif len(self.xtalDict) == 1:
1387	self.histnam = self.xtalDict.values()
1388	elif self.multiple:
1389	choices = sorted(self.xtalDict.values())
1390	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1391	if not hnum: return True
1392	self.histnam = [choices[i] for i in hnum]
1393	numselected = len(self.histnam)
1394	else:
1395	choices = sorted(self.xtalDict.values())
1396	hnum = G2G.ItemSelector(choices,self.G2frame)
1397	if hnum is None: return True
1398	self.histnam = [choices[hnum]]
1399	numselected = len(self.histnam)
1400	elif self.currentExportType == 'powder':
1401	if len(self.powderDict) == 0:
1402	self.G2frame.ErrorDialog(
1403	'Empty project',
1404	'Project does not contain any powder data.')
1405	return True
1406	elif len(self.powderDict) == 1:
1407	self.histnam = self.powderDict.values()
1408	elif self.multiple:
1409	choices = sorted(self.powderDict.values())
1410	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1411	if not hnum: return True
1412	self.histnam = [choices[i] for i in hnum]
1413	numselected = len(self.histnam)
1414	else:
1415	choices = sorted(self.powderDict.values())
1416	hnum = G2G.ItemSelector(choices,self.G2frame)
1417	if hnum is None: return True
1418	self.histnam = [choices[hnum]]
1419	numselected = len(self.histnam)
1420	elif self.currentExportType == 'image':
1421	if len(self.Histograms) == 0:
1422	self.G2frame.ErrorDialog(
1423	'Empty project',
1424	'Project does not contain any images.')
1425	return True
1426	elif len(self.Histograms) == 1:
1427	self.histnam = self.Histograms.keys()
1428	else:
1429	choices = sorted(self.Histograms.keys())
1430	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1431	if self.multiple:
1432	if not hnum: return True
1433	self.histnam = [choices[i] for i in hnum]
1434	else:
1435	if hnum is None: return True
1436	self.histnam = [choices[hnum]]
1437	numselected = len(self.histnam)
1438	if self.currentExportType == 'map':
1439	# search for phases with maps
1440	mapPhases = []
1441	choices = []
1442	for phasenam in sorted(self.Phases):
1443	phasedict = self.Phases[phasenam] # pointer to current phase info
1444	if len(phasedict['General']['Map'].get('rho',[])):
1445	mapPhases.append(phasenam)
1446	if phasedict['General']['Map'].get('Flip'):
1447	choices.append('Charge flip map: '+str(phasenam))
1448	elif phasedict['General']['Map'].get('MapType'):
1449	choices.append(
1450	str(phasedict['General']['Map'].get('MapType'))
1451	+ ' map: ' + str(phasenam))
1452	else:
1453	choices.append('unknown map: '+str(phasenam))
1454	# select a map if needed
1455	if len(mapPhases) == 0:
1456	self.G2frame.ErrorDialog(
1457	'Empty project',
1458	'Project does not contain any maps.')
1459	return True
1460	elif len(mapPhases) == 1:
1461	self.phasenam = mapPhases
1462	else:
1463	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1464	if self.multiple:
1465	if not phasenum: return True
1466	self.phasenam = [mapPhases[i] for i in phasenum]
1467	else:
1468	if phasenum is None: return True
1469	self.phasenam = [mapPhases[phasenum]]
1470	numselected = len(self.phasenam)
1471
1472	# items selected, now set self.dirname and usually self.filename
1473	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1474	AskFile == 'default' and not self.G2frame.GSASprojectfile
1475	):
1476	filename = self.askSaveFile()
1477	if not filename: return True
1478	self.dirname,self.filename = os.path.split(filename)
1479	elif AskFile == 'dir' or AskFile == 'single' or (
1480	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1481	):
1482	self.dirname = self.askSaveDirectory()
1483	if not self.dirname: return True
1484	elif AskFile == 'default-dir' or AskFile == 'default':
1485	self.dirname,self.filename = os.path.split(
1486	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1487	)
1488	else:
1489	raise Exception('This should not happen!')
1490
1491	def loadParmDict(self):
1492	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1493	refined values to those from the last cycle and set the uncertainties for the
1494	refined parameters in another dict (self.sigDict).
1495
1496	Expands the parm & sig dicts to include values derived from constraints.
1497	'''
1498	self.parmDict = {}
1499	self.sigDict = {}
1500	rigidbodyDict = {}
1501	covDict = {}
1502	consDict = {}
1503	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1504	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1505	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1506	while item:
1507	name = self.G2frame.GPXtree.GetItemText(item)
1508	if name == 'Rigid bodies':
1509	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(item)
1510	elif name == 'Covariance':
1511	covDict = self.G2frame.GPXtree.GetItemPyData(item)
1512	elif name == 'Constraints':
1513	consDict = self.G2frame.GPXtree.GetItemPyData(item)
1514	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1515	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1516	self.parmDict.update(rbDict)
1517	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1518	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1519	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1520	self.parmDict.update(phaseDict)
1521	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
1522	Phases,Histograms,Print=False,resetRefList=False)
1523	self.parmDict.update(hapDict)
1524	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1525	self.parmDict.update(histDict)
1526	self.parmDict.update(zip(
1527	covDict.get('varyList',[]),
1528	covDict.get('variables',[])))
1529	self.sigDict = dict(zip(
1530	covDict.get('varyList',[]),
1531	covDict.get('sig',[])))
1532	# expand to include constraints: first compile a list of constraints
1533	constList = []
1534	for item in consDict:
1535	if item.startswith('_'): continue
1536	constList += consDict[item]
1537	# now process the constraints
1538	G2mv.InitVars()
1539	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
1540	varyList = covDict.get('varyListStart')
1541	if varyList is None and len(constDict) == 0:
1542	# no constraints can use varyList
1543	varyList = covDict.get('varyList')
1544	elif varyList is None:
1545	# old GPX file from before pre-constraint varyList is saved
1546	print (' * Old refinement: Please use Calculate/Refine to redo *')
1547	raise Exception(' * Export aborted *')
1548	else:
1549	varyList = list(varyList)
1550	try:
1551	groups,parmlist = G2mv.GroupConstraints(constDict)
1552	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
1553	except:
1554	# this really should not happen
1555	print (' * ERROR - constraints are internally inconsistent *')
1556	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
1557	print ('Errors'+errmsg)
1558	if warnmsg: print ('Warnings'+warnmsg)
1559	raise Exception(' * CIF creation aborted *')
1560	# add the constrained values to the parameter dictionary
1561	G2mv.Dict2Map(self.parmDict,varyList)
1562	# and add their uncertainties into the esd dictionary (sigDict)
1563	if covDict.get('covMatrix') is not None:
1564	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
1565
1566	def loadTree(self):
1567	'''Load the contents of the data tree into a set of dicts
1568	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
1569	& self.xtalDict)
1570
1571	* The childrenless data tree items are overall parameters/controls for the
1572	entire project and are placed in self.OverallParms
1573	* Phase items are placed in self.Phases
1574	* Data items are placed in self.Histogram. The key for these data items
1575	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
1576	'''
1577	self.OverallParms = {}
1578	self.powderDict = {}
1579	self.xtalDict = {}
1580	self.Phases = {}
1581	self.Histograms = {}
1582	self.SeqRefdata = None
1583	self.SeqRefhist = None
1584	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1585	histType = None
1586	if self.currentExportType == 'phase':
1587	# if exporting phases load them here
1588	sub = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Phases')
1589	if not sub:
1590	print ('no phases found')
1591	return True
1592	item, cookie = self.G2frame.GPXtree.GetFirstChild(sub)
1593	while item:
1594	phaseName = self.G2frame.GPXtree.GetItemText(item)
1595	self.Phases[phaseName] = self.G2frame.GPXtree.GetItemPyData(item)
1596	item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie)
1597	return
1598	elif self.currentExportType == 'single':
1599	histType = 'HKLF'
1600	elif self.currentExportType == 'powder':
1601	histType = 'PWDR'
1602	elif self.currentExportType == 'image':
1603	histType = 'IMG'
1604
1605	if histType: # Loading just one kind of tree entry
1606	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1607	while item:
1608	name = self.G2frame.GPXtree.GetItemText(item)
1609	if name.startswith(histType):
1610	if self.Histograms.get(name): # there is already an item with this name
1611	print('Histogram name '+str(name)+' is repeated. Renaming')
1612	if name[-1] == '9':
1613	name = name[:-1] + '10'
1614	elif name[-1] in '012345678':
1615	name = name[:-1] + str(int(name[-1])+1)
1616	else:
1617	name += '-1'
1618	self.Histograms[name] = {}
1619	# the main info goes into Data, but the 0th
1620	# element contains refinement results, carry
1621	# that over too now.
1622	self.Histograms[name]['Data'] = self.G2frame.GPXtree.GetItemPyData(item)[1]
1623	self.Histograms[name][0] = self.G2frame.GPXtree.GetItemPyData(item)[0]
1624	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1625	while item2:
1626	child = self.G2frame.GPXtree.GetItemText(item2)
1627	self.Histograms[name][child] = self.G2frame.GPXtree.GetItemPyData(item2)
1628	item2, cookie2 = self.G2frame.GPXtree.GetNextChild(item, cookie2)
1629	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1630	# index powder and single crystal histograms by number
1631	for hist in self.Histograms:
1632	if hist.startswith("PWDR"):
1633	d = self.powderDict
1634	elif hist.startswith("HKLF"):
1635	d = self.xtalDict
1636	else:
1637	return
1638	i = self.Histograms[hist].get('hId')
1639	if i is None and not d.keys():
1640	i = 0
1641	elif i is None or i in d.keys():
1642	i = max(d.keys())+1
1643	d[i] = hist
1644	return
1645	# else standard load: using all interlinked phases and histograms
1646	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1647	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1648	while item:
1649	name = self.G2frame.GPXtree.GetItemText(item)
1650	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1651	if not item2:
1652	self.OverallParms[name] = self.G2frame.GPXtree.GetItemPyData(item)
1653	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1654	# index powder and single crystal histograms
1655	for hist in self.Histograms:
1656	i = self.Histograms[hist]['hId']
1657	if hist.startswith("PWDR"):
1658	self.powderDict[i] = hist
1659	elif hist.startswith("HKLF"):
1660	self.xtalDict[i] = hist
1661
1662	def dumpTree(self,mode='type'):
1663	'''Print out information on the data tree dicts loaded in loadTree.
1664	Used for testing only.
1665	'''
1666	if self.SeqRefdata and self.SeqRefhist:
1667	print('Note that dumpTree does not show sequential results')
1668	print ('\nOverall')
1669	if mode == 'type':
1670	def Show(arg): return type(arg)
1671	else:
1672	def Show(arg): return arg
1673	for key in self.OverallParms:
1674	print (' '+key+Show(self.OverallParms[key]))
1675	print ('Phases')
1676	for key1 in self.Phases:
1677	print (' '+key1+Show(self.Phases[key1]))
1678	print ('Histogram')
1679	for key1 in self.Histograms:
1680	print (' '+key1+Show(self.Histograms[key1]))
1681	for key2 in self.Histograms[key1]:
1682	print (' '+key2+Show(self.Histograms[key1][key2]))
1683
1684	def defaultSaveFile(self):
1685	return os.path.abspath(
1686	os.path.splitext(self.G2frame.GSASprojectfile
1687	)[0]+self.extension)
1688
1689	def askSaveFile(self):
1690	'''Ask the user to supply a file name
1691
1692	:returns: a file name (str) or None if Cancel is pressed
1693	'''
1694
1695	pth = G2G.GetExportPath(self.G2frame)
1696	defnam = os.path.splitext(
1697	os.path.split(self.G2frame.GSASprojectfile)[1]
1698	)[0]+self.extension
1699	dlg = wx.FileDialog(
1700	self.G2frame, 'Input name for file to write', pth, defnam,
1701	self.longFormatName+' ('+self.extension+')\|'+self.extension,
1702	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
1703	dlg.CenterOnParent()
1704	try:
1705	if dlg.ShowModal() == wx.ID_OK:
1706	filename = dlg.GetPath()
1707	self.G2frame.LastExportDir = os.path.split(filename)[0]
1708	filename = os.path.splitext(filename)[0]+self.extension # make sure extension is correct
1709	else:
1710	filename = None
1711	finally:
1712	dlg.Destroy()
1713	return filename
1714
1715	def askSaveDirectory(self):
1716	'''Ask the user to supply a directory name. Path name is used as the
1717	starting point for the next export path search.
1718
1719	:returns: a directory name (str) or None if Cancel is pressed
1720	'''
1721	pth = G2G.GetExportPath(self.G2frame)
1722	dlg = wx.DirDialog(
1723	self.G2frame, 'Input directory where file(s) will be written', pth,
1724	wx.DD_DEFAULT_STYLE)
1725	dlg.CenterOnParent()
1726	try:
1727	if dlg.ShowModal() == wx.ID_OK:
1728	filename = dlg.GetPath()
1729	self.G2frame.LastExportDir = filename
1730	else:
1731	filename = None
1732	finally:
1733	dlg.Destroy()
1734	return filename
1735
1736	# Tools for file writing.
1737	def OpenFile(self,fil=None,mode='w'):
1738	'''Open the output file
1739
1740	:param str fil: The name of the file to open. If None (default)
1741	the name defaults to self.dirname + self.filename.
1742	If an extension is supplied, it is not overridded,
1743	but if not, the default extension is used.
1744	:returns: the file object opened by the routine which is also
1745	saved as self.fp
1746	'''
1747	if mode == 'd': # debug mode
1748	self.fullpath = '(stdout)'
1749	self.fp = sys.stdout
1750	return
1751	if not fil:
1752	if not os.path.splitext(self.filename)[1]:
1753	self.filename += self.extension
1754	fil = os.path.join(self.dirname,self.filename)
1755	self.fullpath = os.path.abspath(fil)
1756	self.fp = open(self.fullpath,mode)
1757	return self.fp
1758
1759	def Write(self,line):
1760	'''write a line of output, attaching a line-end character
1761
1762	:param str line: the text to be written.
1763	'''
1764	self.fp.write(line+'\n')
1765
1766	def CloseFile(self,fp=None):
1767	'''Close a file opened in OpenFile
1768
1769	:param file fp: the file object to be closed. If None (default)
1770	file object self.fp is closed.
1771	'''
1772	if self.fp == sys.stdout: return # debug mode
1773	if fp is None:
1774	fp = self.fp
1775	self.fp = None
1776	if fp is not None: fp.close()
1777
1778	def SetSeqRef(self,data,hist):
1779	'''Set the exporter to retrieve results from a sequential refinement
1780	rather than the main tree
1781	'''
1782	self.SeqRefdata = data
1783	self.SeqRefhist = hist
1784	data_name = data[hist]
1785	for i,val in zip(data_name['varyList'],data_name['sig']):
1786	self.sigDict[i] = val
1787	self.sigDict[striphist(i)] = val
1788	for i in data_name['parmDict']:
1789	self.parmDict[striphist(i)] = data_name['parmDict'][i]
1790	self.parmDict[i] = data_name['parmDict'][i]
1791	# zero out the dA[xyz] terms, they would only bring confusion
1792	key = i.split(':')
1793	if len(key) < 3: continue
1794	if key[2].startswith('dA'):
1795	self.parmDict[i] = 0.0
1796	for i,(val,sig) in data_name.get('depParmDict',{}).iteritems():
1797	self.parmDict[i] = val
1798	self.sigDict[i] = sig
1799	#GSASIIpath.IPyBreak()
1800
1801	def SetFromArray(self,hist,histname):
1802	'''Load a histogram into the exporter in preparation for use of the .Writer
1803	rather than the main tree. This is used in GSASIIscriptable when wx
1804	is not present.
1805	'''
1806	self.Histograms[histname] = {}
1807	self.Histograms[histname]['Data'] = hist['data'][1]
1808	self.Histograms[histname]['Instrument Parameters'] = hist['Instrument Parameters']
1809	self.Histograms[histname]['Sample Parameters'] = hist['Sample Parameters']
1810
1811	# Tools to pull information out of the data arrays
1812	def GetCell(self,phasenam):
1813	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1814
1815	:param str phasenam: the name for the selected phase
1816	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1817	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1818	cell values and `cellSig` has their uncertainties.
1819	"""
1820	if self.SeqRefdata and self.SeqRefhist:
1821	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
1822	phasedict = self.Phases[phasenam] # pointer to current phase info
1823	try:
1824	pfx = str(phasedict['pId'])+'::'
1825	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
1826	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
1827	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
1828	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
1829	return cellList,cellSig
1830	except KeyError:
1831	cell = phasedict['General']['Cell'][1:]
1832	return cell,7*[0]
1833
1834	def GetSeqCell(self,phasenam,data_name):
1835	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1836	and histogram in a sequential fit
1837
1838	:param str phasenam: the name for the selected phase
1839	:param dict data_name: the sequential refinement parameters for the selected histogram
1840	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1841	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1842	cell values and `cellSig` has their uncertainties.
1843	"""
1844	phasedict = self.Phases[phasenam]
1845	SGdata = phasedict['General']['SGData']
1846	pId = phasedict['pId']
1847	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
1848	ESDlookup = {}
1849	Dlookup = {}
1850	varied = [striphist(i) for i in data_name['varyList']]
1851	for item,val in data_name['newCellDict'].iteritems():
1852	if item in varied:
1853	ESDlookup[val[0]] = item
1854	Dlookup[item] = val[0]
1855	A = RecpCellTerms[:]
1856	for i in range(6):
1857	var = str(pId)+'::A'+str(i)
1858	if var in ESDlookup:
1859	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
1860	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
1861	zeroDict = {i:0.0 for i in cellDict}
1862	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
1863	covData = {
1864	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
1865	'covMatrix': data_name['covMatrix']
1866	}
1867	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
1868
1869	def GetAtoms(self,phasenam):
1870	"""Gets the atoms associated with a phase. Can be used with standard
1871	or macromolecular phases
1872
1873	:param str phasenam: the name for the selected phase
1874	:returns: a list of items for eac atom where each item is a list containing:
1875	label, typ, mult, xyz, and td, where
1876
1877	* label and typ are the atom label and the scattering factor type (str)
1878	* mult is the site multiplicity (int)
1879	* xyz is contains a list with four pairs of numbers:
1880	x, y, z and fractional occupancy and
1881	their standard uncertainty (or a negative value)
1882	* td is contains a list with either one or six pairs of numbers:
1883	if one number it is U\ :sub:`iso` and with six numbers it is
1884	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
1885	paired with their standard uncertainty (or a negative value)
1886	"""
1887	phasedict = self.Phases[phasenam] # pointer to current phase info
1888	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1889	cfrac = cx+3
1890	fpfx = str(phasedict['pId'])+'::Afrac:'
1891	atomslist = []
1892	for i,at in enumerate(phasedict['Atoms']):
1893	if phasedict['General']['Type'] == 'macromolecular':
1894	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1895	else:
1896	label = at[ct-1]
1897	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
1898	fsig = self.sigDict.get(fpfx+str(i),-0.009)
1899	mult = at[cs+1]
1900	typ = at[ct]
1901	xyz = []
1902	for j,v in enumerate(('x','y','z')):
1903	val = at[cx+j]
1904	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
1905	val = self.parmDict.get(pfx, val)
1906	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
1907	sig = self.sigDict.get(dpfx,-0.000009)
1908	xyz.append((val,sig))
1909	xyz.append((fval,fsig))
1910	td = []
1911	if at[cia] == 'I':
1912	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
1913	val = self.parmDict.get(pfx,at[cia+1])
1914	sig = self.sigDict.get(pfx,-0.0009)
1915	td.append((val,sig))
1916	else:
1917	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
1918	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
1919	val = self.parmDict.get(pfx,at[cia+2+i])
1920	sig = self.sigDict.get(pfx,-0.0009)
1921	td.append((val,sig))
1922	atomslist.append((label,typ,mult,xyz,td))
1923	return atomslist
1924	######################################################################
1925	def ExportPowderList(G2frame):
1926	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
1927	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1928
1929	:param wx.Frame G2frame: the GSAS-II main data tree window
1930	'''
1931	extList = []
1932	for obj in G2frame.exporterlist:
1933	if 'powder' in obj.exporttype:
1934	try:
1935	obj.Writer
1936	extList.append(obj.extension)
1937	except AttributeError:
1938	pass
1939	return extList
1940
1941	def ExportPowder(G2frame,TreeName,fileroot,extension):
1942	'''Writes a single powder histogram using the Export routines.
1943	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1944
1945	:param wx.Frame G2frame: the GSAS-II main data tree window
1946	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
1947	:param str fileroot: name for file to be written, extension ignored
1948	:param str extension: extension for file to be written (start with '.'). Must
1949	match a powder export routine that has a Writer object.
1950	'''
1951	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
1952	for obj in G2frame.exporterlist:
1953	if obj.extension == extension and 'powder' in obj.exporttype:
1954	obj.currentExportType = 'powder'
1955	obj.InitExport(None)
1956	obj.loadTree() # load all histograms in tree into dicts
1957	if TreeName not in obj.Histograms:
1958	raise Exception('Histogram not found: '+str(TreeName))
1959	try:
1960	obj.Writer
1961	except AttributeError:
1962	continue
1963	try:
1964	obj.Writer(TreeName,filename)
1965	print('wrote file '+filename)
1966	return
1967	except Exception:
1968	print('Export Routine for '+extension+' failed.')
1969	else:
1970	print('No Export routine supports extension '+extension)
1971
1972	def ExportSequential(G2frame,data,obj,exporttype):
1973	'''
1974	Used to export from every phase/dataset in a sequential refinement using
1975	a .Writer method for either projects or phases. Prompts to select histograms
1976	and for phase exports, which phase(s).
1977
1978	:param wx.Frame G2frame: the GSAS-II main data tree window
1979	:param dict data: the sequential refinement data object
1980	:param str exporttype: indicates the type of export ('project' or 'phase')
1981	'''
1982	if len(data['histNames']) == 0:
1983	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
1984	obj.InitExport(None)
1985	obj.loadTree()
1986	obj.loadParmDict()
1987	if len(data['histNames']) == 1:
1988	histlist = data['histNames']
1989	else:
1990	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
1991	'Select histograms',data['histNames'])
1992	if dlg.ShowModal() == wx.ID_OK:
1993	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
1994	dlg.Destroy()
1995	else:
1996	dlg.Destroy()
1997	return
1998	if exporttype == 'Phase':
1999	phaselist = list(obj.Phases.keys())
2000	if len(obj.Phases) == 0:
2001	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
2002	return
2003	elif len(obj.Phases) > 1:
2004	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
2005	'Select phases', phaselist)
2006	if dlg.ShowModal() == wx.ID_OK:
2007	phaselist = [phaselist[l] for l in dlg.GetSelections()]
2008	dlg.Destroy()
2009	else:
2010	dlg.Destroy()
2011	return
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 p in phaselist:
2018	for h in histlist:
2019	obj.SetSeqRef(data,h)
2020	#GSASIIpath.IPyBreak()
2021	obj.Writer(h,phasenam=p,mode=mode)
2022	mode = 'a'
2023	print('...done')
2024	elif exporttype == 'Project': # note that the CIF exporter is not yet ready for this
2025	filename = obj.askSaveFile()
2026	if not filename: return True
2027	obj.dirname,obj.filename = os.path.split(filename)
2028	print('Writing output to file '+str(obj.filename)+"...")
2029	mode = 'w'
2030	for h in histlist:
2031	obj.SetSeqRef(data,h)
2032	obj.Writer(h,mode=mode)
2033	print('\t'+str(h)+' written')
2034	mode = 'a'
2035	print('...done')
2036	elif exporttype == 'Powder':
2037	filename = obj.askSaveFile()
2038	if not filename: return True
2039	obj.dirname,obj.filename = os.path.split(filename)
2040	print('Writing output to file '+str(obj.filename)+"...")
2041	mode = 'w'
2042	for h in histlist:
2043	obj.SetSeqRef(data,h)
2044	obj.Writer(h,mode=mode)
2045	print('\t'+str(h)+' written')
2046	mode = 'a'
2047	print('...done')
2048
2049	def ReadDIFFaX(DIFFaXfile):
2050	print ('read '+DIFFaXfile)
2051	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
2052	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
2053	df = open(DIFFaXfile,'r')
2054	lines = df.readlines()
2055	df.close()
2056	struct = False
2057	Struct = []
2058	stack = False
2059	Stack = []
2060	trans = False
2061	Trans = []
2062	for diff in lines:
2063	diff = diff[:-1].lower()
2064	if '!' in diff:
2065	continue
2066	while '}' in diff: #strip comments
2067	iB = diff.index('{')
2068	iF = diff.index('}')+1
2069	if iB:
2070	diff = diff[:iB]
2071	else:
2072	diff = diff[iF:]
2073	if not diff:
2074	continue
2075	if diff.strip() == 'instrumental':
2076	continue
2077	if diff.strip() == 'structural':
2078	struct = True
2079	continue
2080	elif diff.strip() == 'stacking':
2081	struct = False
2082	stack = True
2083	continue
2084	elif diff.strip() == 'transitions':
2085	stack = False
2086	trans = True
2087	continue
2088	diff = diff.strip()
2089	if struct:
2090	if diff:
2091	Struct.append(diff)
2092	elif stack:
2093	if diff:
2094	Stack.append(diff)
2095	elif trans:
2096	if diff:
2097	Trans.append(diff)
2098
2099	#STRUCTURE records
2100	laueRec = Struct[1].split()
2101	Layer['Laue'] = laueRec[0]
2102	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2103	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2104	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2105	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2106	cell = Struct[0].split()
2107	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2108	nLayers = int(Struct[2])
2109	N = 3
2110	if 'layer' not in Struct[3]:
2111	N = 4
2112	if Struct[3] != 'infinite':
2113	width = Struct[3].split()
2114	Layer['Width'][0] = [float(width[0]),float(width[1])]
2115	for nL in range(nLayers):
2116	if '=' in Struct[N]:
2117	name = Struct[N].split('=')
2118	sameas = int(name[1])-1
2119	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2120	N += 1
2121	continue
2122	Symm = 'None'
2123	if 'centro' in Struct[N+1]: Symm = '-1'
2124	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2125	N += 2
2126	while 'layer' not in Struct[N]:
2127	atom = Struct[N][4:].split()
2128	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2129	if atomType not in Layer['AtInfo']:
2130	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2131	atomName = '%s(%s)'%(atomType,atom[0])
2132	newVals = []
2133	for val in atom[1:6]:
2134	if '/' in val:
2135	newVals.append(eval(val+'.'))
2136	else:
2137	newVals.append(float(val))
2138	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2139	Layer['Layers'][-1]['Atoms'].append(atomRec)
2140	N += 1
2141	if N > len(Struct)-1:
2142	break
2143	#TRANSITIONS records
2144	transArray = []
2145	N = 0
2146	for i in range(nLayers):
2147	transArray.append([])
2148	for j in range(nLayers):
2149	vals = Trans[N].split()
2150	newVals = []
2151	for val in vals[:4]:
2152	if '/' in val:
2153	newVals.append(eval(val+'.'))
2154	else:
2155	newVals.append(float(val))
2156	transArray[-1].append(newVals+['',False])
2157	N += 1
2158	Layer['Transitions'] = transArray
2159	#STACKING records
2160	Layer['Stacking'] = [Stack[0],'']
2161	if Stack[0] == 'recursive':
2162	Layer['Stacking'][1] = Stack[1]
2163	elif Stack[0] == 'explicit':
2164	if Stack[1] == 'random':
2165	Layer['Stacking'][1] = Stack[1]
2166	else:
2167	Layer['Stacking'][1] = 'list'
2168	Layer['Stacking'].append('')
2169	for stack in Stack[2:]:
2170	Layer['Stacking'][2] += ' '+stack
2171	return Layer
2172
2173	def readColMetadata(imagefile):
2174	'''Reads image metadata from a column-oriented metadata table
2175	(1-ID style .par file). Called by :func:`GetColumnMetadata`
2176
2177	The .par file has any number of columns separated by spaces.
2178	The directory for the file must be specified in
2179	Config variable ``Column_Metadata_directory``.
2180	As an index to the .par file a second "label file" must be specified with the
2181	same file root name as the .par file but the extension must be .XXX_lbls (where
2182	.XXX is the extension of the image) or if that is not present extension
2183	.lbls.
2184
2185	:param str imagefile: the full name of the image file (with extension, directory optional)
2186
2187	:returns: a dict with parameter values. Named parameters will have the type based on
2188	the specified Python function, named columns will be character strings
2189
2190	The contents of the label file will look like this::
2191
2192	# define keywords
2193	filename:lambda x,y: "{}_{:0>6}".format(x,y)\|33,34
2194	distance: float \| 75
2195	wavelength:lambda keV: 12.398425/float(keV)\|9
2196	pixelSize:lambda x: [74.8, 74.8]\|0
2197	ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)\|0,1,2,3,4
2198	Temperature: float\|53
2199	FreePrm2: int \| 34 \| Free Parm2 Label
2200	# define other variables
2201	0:day
2202	1:month
2203	2:date
2204	3:time
2205	4:year
2206	7:I_ring
2207
2208	This file contains three types of lines in any order.
2209	* Named parameters are evaluated with user-supplied Python code (see
2210	subsequent information). Specific named parameters are used
2211	to determine values that are used for image interpretation (see table,
2212	below). Any others are copied to the Comments subsection of the Image
2213	tree item.
2214	* Column labels are defined with a column number (integer) followed by
2215	a colon (:) and a label to be assigned to that column. All labeled
2216	columns are copied to the Image's Comments subsection.
2217	* Comments are any line that does not contain a colon.
2218
2219	Note that columns are numbered starting at zero.
2220
2221	Any named parameter may be defined provided it is not a valid integer,
2222	but the named parameters in the table have special meanings, as descibed.
2223	The parameter name is followed by a colon. After the colon, specify
2224	Python code that defines or specifies a function that will be called to
2225	generate a value for that parameter.
2226
2227	Note that several keywords, if defined in the Comments, will be found and
2228	placed in the appropriate section of the powder histogram(s)'s Sample
2229	Parameters after an integration: ``Temperature``,``Pressure``,``Time``,
2230	``FreePrm1``,``FreePrm2``,``FreePrm3``,``Omega``,``Chi``, and ``Phi``.
2231
2232	After the Python code, supply a vertical bar (\|) and then a list of one
2233	more more columns that will be supplied as arguments to that function.
2234
2235	Note that the labels for the three FreePrm items can be changed by
2236	including that label as a third item with an additional vertical bar. Labels
2237	will be ignored for any other named parameters.
2238
2239	The examples above are discussed here:
2240
2241	``filename:lambda x,y: "{}_{:0>6}".format(x,y)\|33,34``
2242	Here the function to be used is defined with a lambda statement::
2243
2244	lambda x,y: "{}_{:0>6}".format(x,y)
2245
2246	This function will use the format function to create a file name from the
2247	contents of columns 33 and 34. The first parameter (x, col. 33) is inserted directly into
2248	the file name, followed by a underscore (_), followed by the second parameter (y, col. 34),
2249	which will be left-padded with zeros to six characters (format directive ``:0>6``).
2250
2251	When there will be more than one image generated per line in the .par file, an alternate way to
2252	generate list of file names takes into account the number of images generated::
2253
2254	lambda x,y,z: ["{}_{:0>6}".format(x,int(y)+i) for i in range(int(z))]
2255
2256	Here a third parameter is used to specify the number of images generated, where
2257	the image number is incremented for each image.
2258
2259	``distance: float \| 75``
2260	Here the contents of column 75 will be converted to a floating point number
2261	by calling float on it. Note that the spaces here are ignored.
2262
2263	``wavelength:lambda keV: 12.398425/float(keV)\|9``
2264	Here we define an algebraic expression to convert an energy in keV to a
2265	wavelength and pass the contents of column 9 as that input energy
2266
2267	``pixelSize:lambda x: [74.8, 74.8]\|0``
2268	In this case the pixel size is a constant (a list of two numbers). The first
2269	column is passed as an argument as at least one argument is required, but that
2270	value is not used in the expression.
2271
2272	``ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)\|0,1,2,3,4``
2273	This example defines a parameter that takes items in the first five columns
2274	and formats them in a different way. This parameter is not one of the pre-defined
2275	parameter names below. Some external code could be used to change the month string
2276	(argument ``m``) to a integer from 1 to 12.
2277
2278	``FreePrm2: int \| 34 \| Free Parm2 Label``
2279	In this example, the contents of column 34 will be converted to an integer and
2280	placed as the second free-named parameter in the Sample Parameters after an
2281	integration. The label for this parameter will be changed to "Free Parm2 Label".
2282
2283	Pre-defined parameter names
2284
2285	============= ========= ======== =====================================================
2286	keyword required type Description
2287	============= ========= ======== =====================================================
2288	filename yes str or generates the file name prefix for the matching image
2289	list file (MyImage001 for file /tmp/MyImage001.tif) or
2290	a list of file names.
2291	polarization no float generates the polarization expected based on the
2292	monochromator angle, defaults to 0.99.
2293	center no list of generates the approximate beam center on the detector
2294	2 floats in mm, such as [204.8, 204.8].
2295	distance yes float generates the distance from the sample to the detector
2296	in mm
2297	pixelSize no list of generates the size of the pixels in microns such as
2298	2 floats [200.0, 200.0].
2299	wavelength yes float generates the wavelength in Angstroms
2300	============= ========= ======== =====================================================
2301
2302	'''
2303	dir,fil = os.path.split(os.path.abspath(imagefile))
2304	imageName,ext = os.path.splitext(fil)
2305	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'): return
2306	parfiles = glob.glob(os.path.join(GSASIIpath.GetConfigValue('Column_Metadata_directory'),'*.par'))
2307	if len(parfiles) == 0:
2308	print('Sorry, No Column metadata (.par) file found in '+
2309	GSASIIpath.GetConfigValue('Column_Metadata_directory'))
2310	return {}
2311	for parFil in parfiles: # loop over all .par files (hope just 1) in image dir until image is found
2312	parRoot = os.path.splitext(parFil)[0]
2313	for e in (ext+'_lbls','.lbls'):
2314	if os.path.exists(parRoot+e):
2315	lblFil = parRoot+e
2316	break
2317	else:
2318	print('Warning: No labels definitions found for '+parFil)
2319	continue
2320	labels,lbldict,keyCols,keyExp,errors = readColMetadataLabels(lblFil)
2321	if errors:
2322	print('Errors in labels file '+lblFil)
2323	for i in errors: print(' '+i)
2324	continue
2325	else:
2326	print('Read '+lblFil)
2327	# scan through each line in this .par file, looking for the matching image rootname
2328	fp = open(parFil,'Ur')
2329	for iline,line in enumerate(fp):
2330	items = line.strip().split(' ')
2331	nameList = keyExp['filename'](*[items[j] for j in keyCols['filename']])
2332	if type(nameList) is str:
2333	if nameList != imageName: continue
2334	name = nameList
2335	else:
2336	for name in nameList:
2337	if name == imageName: break # got a match
2338	else:
2339	continue
2340	# parse the line and finish
2341	metadata = evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp)
2342	metadata['par file'] = parFil
2343	metadata['lbls file'] = lblFil
2344	print("Metadata read from {} line {}".format(parFil,iline+1))
2345	fp.close()
2346	return metadata
2347	else:
2348	print("Image {} not found in {}".format(imageName,parFil))
2349	fp.close()
2350	continue
2351	fp.close()
2352	else:
2353	print("Warning: No .par metadata for image {}".format(imageName))
2354	return {}
2355
2356	def readColMetadataLabels(lblFil):
2357	'''Read the .*lbls file and setup for metadata assignments
2358	'''
2359	lbldict = {}
2360	keyExp = {}
2361	keyCols = {}
2362	labels = {}
2363	errors = []
2364	fp = open(lblFil,'Ur') # read column labels
2365	for iline,line in enumerate(fp): # read label definitions
2366	line = line.strip()
2367	if not line or line[0] == '#': continue # comments
2368	items = line.split(':')
2369	if len(items) < 2: continue # lines with no colon are also comments
2370	# does this line a definition for a named parameter?
2371	key = items[0]
2372	try:
2373	int(key)
2374	except ValueError: # try as named parameter since not a valid number
2375	items = line.split(':',1)[1].split('\|')
2376	try:
2377	f = eval(items[0]) # compile the expression
2378	if not callable(f):
2379	errors += ['Expression "{}" for key {} is not a function (line {})'.
2380	format(items[0],key,iline)]
2381	continue
2382	keyExp[key] = f
2383	except Exception as msg:
2384	errors += ['Expression "{}" for key {} is not valid (line {})'.
2385	format(items[0],key,iline)]
2386	errors += [str(msg)]
2387	continue
2388	keyCols[key] = [int(i) for i in items[1].strip().split(',')]
2389	if key.lower().startswith('freeprm') and len(items) > 2:
2390	labels[key] = items[2]
2391	continue
2392	if len(items) == 2: # simple column definition
2393	lbldict[int(items[0])] = items[1]
2394	fp.close()
2395	if 'filename' not in keyExp:
2396	errors += ["File {} is invalid. No valid filename expression.".format(lblFil)]
2397	return labels,lbldict,keyCols,keyExp,errors
2398
2399	def evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp,ShowError=False):
2400	'''Evaluate the metadata for a line in the .par file
2401	'''
2402	metadata = {lbldict[j]:items[j] for j in lbldict}
2403	named = {}
2404	for key in keyExp:
2405	try:
2406	res = keyExp[key](*[items[j] for j in keyCols[key]])
2407	except:
2408	if ShowError:
2409	res = "* error *"
2410	else:
2411	continue
2412	named[key] = res
2413	metadata.update(named)
2414	for lbl in labels: # add labels for FreePrm's
2415	metadata['label_'+lbl[4:].lower()] = labels[lbl]
2416	return metadata
2417
2418	def GetColumnMetadata(reader):
2419	'''Add metadata to an image from a column-type metadata file
2420	using :func:`readColMetadata`
2421
2422	:param reader: a reader object from reading an image
2423
2424	'''
2425	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'): return
2426	parParms = readColMetadata(reader.readfilename)
2427	if not parParms: return # check for read failure
2428	specialKeys = ('filename',"polarization", "center", "distance", "pixelSize", "wavelength",)
2429	reader.Comments = ['Metadata from {} assigned by {}'.format(parParms['par file'],parParms['lbls file'])]
2430	for key in parParms:
2431	if key in specialKeys+('par file','lbls file'): continue
2432	reader.Comments += ["{} = {}".format(key,parParms[key])]
2433	if "polarization" in parParms:
2434	reader.Data['PolaVal'][0] = parParms["polarization"]
2435	else:
2436	reader.Data['PolaVal'][0] = 0.99
2437	if "center" in parParms:
2438	reader.Data['center'] = parParms["center"]
2439	if "pixelSize" in parParms:
2440	reader.Data['pixelSize'] = parParms["pixelSize"]
2441	if "wavelength" in parParms:
2442	reader.Data['wavelength'] = parParms['wavelength']
2443	else:
2444	print('Error: wavelength not defined in {}'.format(parParms['lbls file']))
2445	if "distance" in parParms:
2446	reader.Data['distance'] = parParms['distance']
2447	reader.Data['setdist'] = parParms['distance']
2448	else:
2449	print('Error: distance not defined in {}'.format(parParms['lbls file']))
2450
2451	def testColumnMetadata(G2frame):
2452	'''Test the column-oriented metadata parsing, as implemented at 1-ID, by showing results
2453	when using a .par and .lbls pair.
2454
2455	* Select a .par file, if more than one in selected dir.
2456	* Select the .*lbls file, if more than one matching .par file.
2457	* Parse the .lbls file, showing errors if encountered; loop until errors are fixed.
2458	* Search for an image or a line in the .par file and show the results when interpreted
2459
2460	See :func:`readColMetadata` for more details.
2461	'''
2462	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'):
2463	G2G.G2MessageBox(G2frame,'The configuration option for I-ID Metadata is not set.\n'+
2464	'Please use the File/Preferences menu to set Column_Metadata_directory',
2465	'Warning')
2466	return
2467	parFiles = glob.glob(os.path.join(GSASIIpath.GetConfigValue('Column_Metadata_directory'),'*.par'))
2468	if not parFiles:
2469	G2G.G2MessageBox(G2frame,'No .par files found in directory {}. '
2470	.format(GSASIIpath.GetConfigValue('Column_Metadata_directory'))+
2471	'\nThis is set by config variable Column_Metadata_directory '+
2472	'(Set in File/Preferences menu).',
2473	'Warning')
2474	return
2475	parList = []
2476	for parFile in parFiles:
2477	lblList = []
2478	parRoot = os.path.splitext(parFile)[0]
2479	for f in glob.glob(parRoot+'.*lbls'):
2480	if os.path.exists(f): lblList.append(f)
2481	if not len(lblList):
2482	continue
2483	parList.append(parFile)
2484	if len(parList) == 0:
2485	G2G.G2MessageBox(G2frame,'No .lbls or .EXT_lbls file found for .par file(s) in directory {}. '
2486	.format(GSASIIpath.GetConfigValue('Column_Metadata_directory'))+
2487	'\nThis is set by config variable Column_Metadata_directory '+
2488	'(Set in File/Preferences menu).',
2489	'Warning')
2490	return
2491	elif len(parList) == 1:
2492	parFile = parList[0]
2493	else:
2494	dlg = G2G.G2SingleChoiceDialog(G2frame,
2495	'More than 1 .par file found. (Better if only 1!). Choose the one to test in '+
2496	GSASIIpath.GetConfigValue('Column_Metadata_directory'),
2497	'Choose .par file', [os.path.split(i)[1] for i in parList])
2498	if dlg.ShowModal() == wx.ID_OK:
2499	parFile = parList[dlg.GetSelection()]
2500	dlg.Destroy()
2501	else:
2502	dlg.Destroy()
2503	return
2504	# got .par file; now work on .*lbls file
2505	lblList = []
2506	parRoot = os.path.splitext(parFile)[0]
2507	for f in glob.glob(parRoot+'.*lbls'):
2508	if os.path.exists(f): lblList.append(f)
2509	if not len(lblList):
2510	raise Exception('How did this happen! No .*lbls files for '+parFile)
2511	elif len(lblList) == 1:
2512	lblFile = lblList[0]
2513	else:
2514	dlg = G2G.G2SingleChoiceDialog(G2frame,
2515	'Select label file for .par file '+parFile,
2516	'Choose label file', [os.path.split(i)[1] for i in lblList])
2517	if dlg.ShowModal() == wx.ID_OK:
2518	lblFile = lblList[dlg.GetSelection()]
2519	dlg.Destroy()
2520	else:
2521	dlg.Destroy()
2522	return
2523	# parse the labels file
2524	errors = True
2525	while errors:
2526	labels,lbldict,keyCols,keyExp,errors = readColMetadataLabels(lblFile)
2527	if errors:
2528	t = "Error reading file "+lblFile
2529	for l in errors:
2530	t += '\n'
2531	t += l
2532	t += "\n\nPlease edit the file and press OK (or Cancel to quit)"
2533	dlg = wx.MessageDialog(G2frame,message=t,
2534	caption="Read Error",style=wx.ICON_ERROR\| wx.OK\|wx.STAY_ON_TOP\|wx.CANCEL)
2535	if dlg.ShowModal() != wx.ID_OK: return
2536	# request a line number, read that line
2537	dlg = G2G.SingleStringDialog(G2frame,'Read what',
2538	'Enter a line number or an image file name (-1=last line)',
2539	'-1',size=(400,-1))
2540	if dlg.Show():
2541	fileorline = dlg.GetValue()
2542	dlg.Destroy()
2543	else:
2544	dlg.Destroy()
2545	return
2546	# and report the generated key pairs in metadata dict
2547	linenum = None
2548	try:
2549	linenum = int(fileorline)
2550	except:
2551	imageName = os.path.splitext(os.path.split(fileorline)[1])[0]
2552
2553	fp = open(parFile,'Ur')
2554	for iline,line in enumerate(fp):
2555	if linenum is not None:
2556	if iline == linenum:
2557	items = line.strip().split(' ')
2558	n = "Line {}".format(iline)
2559	break
2560	else:
2561	continue
2562	else:
2563	items = line.strip().split(' ')
2564	nameList = keyExp['filename'](*[items[j] for j in keyCols['filename']])
2565	if type(nameList) is str:
2566	if nameList != imageName: continue
2567	name = nameList
2568	break
2569	else:
2570	for name in nameList:
2571	print (name,name == imageName)
2572	if name == imageName:
2573	n = "Image {} found in line {}".format(imageName,iline)
2574	break # got a match
2575	else:
2576	continue
2577	break
2578	else:
2579	if linenum is not None:
2580	n = "Line {}".format(iline)
2581	else:
2582	n = "Image {} not found. Reporting line {}".format(imageName,iline)
2583	items = line.strip().split(' ')
2584	fp.close()
2585	metadata = evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp,True)
2586	title = "Results: ("+n+")"
2587	t = ['Files: '+parFile,lblFile,' ']
2588	n = ["Named parameters:"]
2589	l = ['',"Labeled columns:"]
2590	for key in sorted(metadata):
2591	if key == "filename" or key.startswith('label_prm'): continue
2592	if key in keyCols:
2593	n += [" {} = {}".format(key,metadata[key])]
2594	elif key in lbldict.values():
2595	l += [" {} = {}".format(key,metadata[key])]
2596	else:
2597	t += ["** Unexpected: {}".format(key,metadata[key])]
2598	if type(metadata['filename']) is str:
2599	l += ["","Filename: "+ metadata['filename']]
2600	else:
2601	l += ["","Filename(s): "]
2602	for i,j in enumerate(metadata['filename']):
2603	if i: l[-1] += ', '
2604	l[-1] += j
2605	t += n + l + ['','Unused columns:']
2606	usedCols = lbldict.keys()
2607	for i in keyCols.values(): usedCols += i
2608	for i in range(len(items)):
2609	if i in usedCols: continue
2610	t += [" {}: {}".format(i,items[i])]
2611	dlg = G2G.G2SingleChoiceDialog(None,title,'Column metadata parse results',t,
2612	monoFont=True,filterBox=False,size=(400,600),
2613	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.CENTRE\|wx.OK)
2614	dlg.ShowModal()
2615
2616	if __name__ == '__main__':
2617	import GSASIIdataGUI
2618	application = GSASIIdataGUI.GSASIImain(0)
2619	G2frame = application.main
2620	#app = wx.PySimpleApp()
2621	#G2frame = wx.Frame(None) # create a frame
2622	#frm.Show(True)
2623	#filename = '/tmp/notzip.zip'
2624	#filename = '/tmp/all.zip'
2625	#filename = '/tmp/11bmb_7652.zip'
2626
2627	#selection=None, confirmoverwrite=True, parent=None
2628	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2629	#print ExtractFileFromZip(filename,multipleselect=True)
2630	# #confirmread=False, confirmoverwrite=False)
2631
2632	# choicelist=[ ('a','b','c'),
2633	# ('test1','test2'),('no choice',)]
2634	# titles = [ 'a, b or c', 'tests', 'No option here']
2635	# dlg = MultipleChoicesDialog(
2636	# choicelist,titles,
2637	# parent=frm)
2638	# if dlg.ShowModal() == wx.ID_OK:
2639	# print 'Got OK'
2640	imagefile = '/tmp/NDC5_00237_3.ge3'
2641	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2642
2643	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2644
2645	GSASIIpath.IPyBreak_base()

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