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source: trunk/GSASIIIO.py @ 2436

Last change on this file since 2436 was 2436, checked in by vondreele, 7 years ago
implement decimal azimuth ranges (from integer)
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2016-08-19 14:13:58 +0000 (Fri, 19 Aug 2016) $
4	# $Author: vondreele $
5	# $Revision: 2436 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 2436 2016-08-19 14:13:58Z vondreele $
8	########### SVN repository information ###################
9	'''
10	GSASIIIO: Misc I/O routines
11	=============================
12
13	Module with miscellaneous routines for input and output. Many
14	are GUI routines to interact with user.
15
16	Includes support for image reading.
17
18	Also includes base classes for data import routines.
19
20	'''
21	"""GSASIIIO: functions for IO of data
22	Copyright: 2008, Robert B. Von Dreele (Argonne National Laboratory)
23	"""
24	import wx
25	import math
26	import numpy as np
27	import copy
28	import cPickle
29	import sys
30	import re
31	import random as ran
32	import GSASIIpath
33	GSASIIpath.SetVersionNumber("$Revision: 2436 $")
34	import GSASIIgrid as G2gd
35	import GSASIIspc as G2spc
36	import GSASIIobj as G2obj
37	import GSASIIlattice as G2lat
38	import GSASIIpwdGUI as G2pdG
39	import GSASIIimgGUI as G2imG
40	import GSASIIimage as G2img
41	import GSASIIElem as G2el
42	import GSASIIstrIO as G2stIO
43	import GSASIImapvars as G2mv
44	import GSASIIctrls as G2G
45	import os
46	import os.path as ospath
47
48	DEBUG = False #=True for various prints
49	TRANSP = False #=true to transpose images for testing
50	if GSASIIpath.GetConfigValue('Transpose'): TRANSP = True
51	npsind = lambda x: np.sin(x*np.pi/180.)
52
53	def sfloat(S):
54	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
55	if S.strip():
56	try:
57	return float(S)
58	except ValueError:
59	pass
60	return 0.0
61
62	def sint(S):
63	'Convert a string to int. An empty field is treated as zero'
64	if S.strip():
65	return int(S)
66	else:
67	return 0
68
69	def trim(val):
70	'''Simplify a string containing leading and trailing spaces
71	as well as newlines, tabs, repeated spaces etc. into a shorter and
72	more simple string, by replacing all ranges of whitespace
73	characters with a single space.
74
75	:param str val: the string to be simplified
76
77	:returns: the (usually) shortened version of the string
78	'''
79	return re.sub('\s+', ' ', val).strip()
80
81	def makeInstDict(names,data,codes):
82	inst = dict(zip(names,zip(data,data,codes)))
83	for item in inst:
84	inst[item] = list(inst[item])
85	return inst
86
87	def FileDlgFixExt(dlg,file):
88	'this is needed to fix a problem in linux wx.FileDialog'
89	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
90	if ext not in file:
91	file += ext
92	return file
93
94	def GetPowderPeaks(fileName):
95	'Read powder peaks from a file'
96	sind = lambda x: math.sin(x*math.pi/180.)
97	asind = lambda x: 180.*math.asin(x)/math.pi
98	wave = 1.54052
99	File = open(fileName,'Ur')
100	Comments = []
101	peaks = []
102	S = File.readline()
103	while S:
104	if S[:1] == '#':
105	Comments.append(S[:-1])
106	else:
107	item = S.split()
108	if len(item) == 1:
109	peaks.append([float(item[0]),1.0])
110	elif len(item) > 1:
111	peaks.append([float(item[0]),float(item[0])])
112	S = File.readline()
113	File.close()
114	if Comments:
115	print 'Comments on file:'
116	for Comment in Comments:
117	print Comment
118	if 'wavelength' in Comment:
119	wave = float(Comment.split('=')[1])
120	Peaks = []
121	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
122	for peak in peaks:
123	dsp = peak[0]
124	sth = wave/(2.0*dsp)
125	if sth < 1.0:
126	tth = 2.0*asind(sth)
127	else:
128	break
129	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
130	else: #2-thetas - assume Cuka (for now)
131	for peak in peaks:
132	tth = peak[0]
133	dsp = wave/(2.0*sind(tth/2.0))
134	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
135	limits = [1000.,0.]
136	for peak in Peaks:
137	limits[0] = min(limits[0],peak[0])
138	limits[1] = max(limits[1],peak[0])
139	limits[0] = max(1.,(int(limits[0]-1.)/5)*5.)
140	limits[1] = min(170.,(int(limits[1]+1.)/5)*5.)
141	return Comments,Peaks,limits,wave
142
143	def CheckImageFile(G2frame,imagefile):
144	'''Try to locate an image file if the project and image have been moved
145	together. If the image file cannot be found, request the location from
146	the user.
147
148	:param wx.Frame G2frame: main GSAS-II Frame and data object
149	:param str imagefile: name of image file
150	:returns: imagefile, if it exists, or the name of a file
151	that does exist or False if the user presses Cancel
152
153	'''
154	if not os.path.exists(imagefile):
155	print 'Image file '+imagefile+' not found'
156	fil = imagefile.replace('\\','/') # windows?!
157	# see if we can find a file with same name or in a similarly named sub-dir
158	pth,fil = os.path.split(fil)
159	prevpth = None
160	while pth and pth != prevpth:
161	prevpth = pth
162	if os.path.exists(os.path.join(G2frame.dirname,fil)):
163	print 'found image file '+os.path.join(G2frame.dirname,fil)
164	return os.path.join(G2frame.dirname,fil)
165	pth,enddir = os.path.split(pth)
166	fil = os.path.join(enddir,fil)
167	# not found as a subdirectory, drop common parts of path for last saved & image file names
168	# if image was .../A/B/C/imgs/ima.ge
169	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
170	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
171	Controls = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
172	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
173	imgPath = imagefile.replace('\\','/').split('/')
174	for p1,p2 in zip(gpxPath,imgPath):
175	if p1 == p2:
176	gpxPath.pop(0),imgPath.pop(0)
177	else:
178	break
179	fil = os.path.join(*imgPath) # file with non-common prefix elements
180	prevpth = None
181	pth = os.path.abspath(G2frame.dirname)
182	while pth and pth != prevpth:
183	prevpth = pth
184	if os.path.exists(os.path.join(pth,fil)):
185	print 'found image file '+os.path.join(pth,fil)
186	return os.path.join(pth,fil)
187	pth,enddir = os.path.split(pth)
188	#GSASIIpath.IPyBreak()
189
190	if not os.path.exists(imagefile):
191	prevnam = os.path.split(imagefile)[1]
192	prevext = os.path.splitext(imagefile)[1]
193	wildcard = 'Image format ('+prevext+')\|'+prevext
194	dlg = wx.FileDialog(G2frame, 'Previous image file ('+prevnam+') not found; open here', '.', prevnam,
195	wildcard,wx.OPEN)
196	try:
197	dlg.SetFilename(''+ospath.split(imagefile)[1])
198	if dlg.ShowModal() == wx.ID_OK:
199	imagefile = dlg.GetPath()
200	else:
201	imagefile = False
202	finally:
203	dlg.Destroy()
204	return imagefile
205
206	def EditImageParms(parent,Data,Comments,Image,filename):
207	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
208	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
209	def onClose(event):
210	dlg.EndModal(wx.ID_OK)
211	mainsizer = wx.BoxSizer(wx.VERTICAL)
212	h,w = Image.shape[:2]
213	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,
214	'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
215	0,wx.ALIGN_LEFT\|wx.ALL, 2)
216
217	vsizer = wx.BoxSizer(wx.HORIZONTAL)
218	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
219	0,wx.ALIGN_LEFT\|wx.ALL, 2)
220	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
221	vsizer.Add(wdgt)
222	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
223
224	vsizer = wx.BoxSizer(wx.HORIZONTAL)
225	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
226	0,wx.ALIGN_LEFT\|wx.ALL, 2)
227	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
228	size=(50,-1))
229	vsizer.Add(wdgt)
230	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),
231	wx.ALIGN_LEFT\|wx.ALL, 2)
232	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,
233	size=(50,-1))
234	vsizer.Add(wdgt)
235	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
236
237	vsizer = wx.BoxSizer(wx.HORIZONTAL)
238	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
239	0,wx.ALIGN_LEFT\|wx.ALL, 2)
240	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
241	vsizer.Add(wdgt)
242	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
243
244	vsizer = wx.BoxSizer(wx.HORIZONTAL)
245	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
246	0,wx.ALIGN_LEFT\|wx.ALL, 2)
247	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,
248	size=(75,-1))
249	vsizer.Add(wdgt)
250	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),
251	wx.ALIGN_LEFT\|wx.ALL, 2)
252	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,
253	size=(75,-1))
254	vsizer.Add(wdgt)
255	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
256
257	vsizer = wx.BoxSizer(wx.HORIZONTAL)
258	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
259	0,wx.ALIGN_LEFT\|wx.ALL, 2)
260	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
261	vsizer.Add(wdgt)
262	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
263
264	btnsizer = wx.StdDialogButtonSizer()
265	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
266	OKbtn.SetDefault()
267	OKbtn.Bind(wx.EVT_BUTTON,onClose)
268	btnsizer.AddButton(OKbtn) # not sure why this is needed
269	btnsizer.Realize()
270	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
271	dlg.SetSizer(mainsizer)
272	dlg.CenterOnParent()
273	dlg.ShowModal()
274
275	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
276	'''Load an image into the tree. Saves the location of the image, as well as the
277	ImageTag (where there is more than one image in the file), if defined.
278	'''
279	ImgNames = G2gd.GetPatternTreeDataNames(G2frame,['IMG ',])
280	TreeLbl = 'IMG '+os.path.basename(imagefile)
281	ImageTag = Data.get('ImageTag')
282	if ImageTag:
283	TreeLbl += ' #'+'%04d'%(ImageTag)
284	imageInfo = (imagefile,ImageTag)
285	else:
286	imageInfo = imagefile
287	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
288	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=TreeName)
289	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
290	Imax = np.amax(Image)
291	Imin = max(0.0,np.amin(Image)) #force positive
292	if G2frame.imageDefault:
293	Data = copy.copy(G2frame.imageDefault)
294	Data['showLines'] = True
295	Data['ring'] = []
296	Data['rings'] = []
297	Data['cutoff'] = 10
298	Data['pixLimit'] = 20
299	Data['edgemin'] = 100000000
300	Data['calibdmin'] = 0.5
301	Data['calibskip'] = 0
302	Data['ellipses'] = []
303	Data['calibrant'] = ''
304	Data['GonioAngles'] = [0.,0.,0.]
305	Data['DetDepthRef'] = False
306	else:
307	Data['type'] = 'PWDR'
308	Data['color'] = 'Paired'
309	Data['tilt'] = 0.0
310	Data['rotation'] = 0.0
311	Data['showLines'] = False
312	Data['ring'] = []
313	Data['rings'] = []
314	Data['cutoff'] = 10
315	Data['pixLimit'] = 20
316	Data['calibdmin'] = 0.5
317	Data['calibskip'] = 0
318	Data['edgemin'] = 100000000
319	Data['ellipses'] = []
320	Data['GonioAngles'] = [0.,0.,0.]
321	Data['DetDepth'] = 0.
322	Data['DetDepthRef'] = False
323	Data['calibrant'] = ''
324	Data['IOtth'] = [2.0,5.0]
325	Data['LRazimuth'] = [0.,180.]
326	Data['azmthOff'] = 0.0
327	Data['outChannels'] = 2500
328	Data['outAzimuths'] = 1
329	Data['centerAzm'] = False
330	Data['fullIntegrate'] = False
331	Data['setRings'] = False
332	Data['background image'] = ['',-1.0]
333	Data['dark image'] = ['',-1.0]
334	Data['Flat Bkg'] = 0.0
335	Data['setDefault'] = False
336	Data['range'] = [(0,Imax),[0,Imax]]
337	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Image Controls'),Data)
338	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(0,Imax),[0,Imax]]}
339	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Masks'),Masks)
340	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Stress/Strain'),
341	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
342	G2frame.PatternTree.SetItemPyData(Id,[Npix,imageInfo])
343	G2frame.PickId = Id
344	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
345	G2frame.Image = Id
346
347	def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None,FormatName=''):
348	'''Read a single image with an image importer.
349
350	:param wx.Frame G2frame: main GSAS-II Frame and data object.
351	:param str imagefile: name of image file
352	:param bool imageOnly: If True return only the image,
353	otherwise (default) return more (see below)
354	:param int/str ImageTag: specifies a particular image to be read from a file.
355	First image is read if None (default).
356	:param str formatName: the image reader formatName
357
358	:returns: an image as a numpy array or a list of four items:
359	Comments, Data, Npix and the Image, as selected by imageOnly
360
361	'''
362	# determine which formats are compatible with this file
363	primaryReaders = []
364	secondaryReaders = []
365	for rd in G2frame.ImportImageReaderlist:
366	flag = rd.ExtensionValidator(imagefile)
367	if flag is None:
368	secondaryReaders.append(rd)
369	elif flag:
370	if not FormatName:
371	primaryReaders.append(rd)
372	elif FormatName == rd.formatName:
373	primaryReaders.append(rd)
374	if len(secondaryReaders) + len(primaryReaders) == 0:
375	print('Error: No matching format for file '+filename)
376	raise Exception('No image read')
377	fp = None
378	errorReport = ''
379	fp = open(imagefile,'Ur')
380	for rd in primaryReaders+secondaryReaders:
381	rd.ReInitialize() # purge anything from a previous read
382	fp.seek(0) # rewind
383	rd.errors = "" # clear out any old errors
384	if not rd.ContentsValidator(fp): # rejected on cursory check
385	errorReport += "\n "+rd.formatName + ' validator error'
386	if rd.errors:
387	errorReport += ': '+rd.errors
388	continue
389	rdbuffer = {} # create temporary storage for file reader
390	if imageOnly:
391	ParentFrame = None # prevent GUI access on reread
392	else:
393	ParentFrame = G2frame
394	if GSASIIpath.GetConfigValue('debug'):
395	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=ImageTag)
396	else:
397	flag = False
398	try:
399	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=ImageTag)
400	except rd.ImportException as detail:
401	rd.errors += "\n Read exception: "+str(detail)
402	except Exception as detail:
403	import traceback
404	rd.errors += "\n Unhandled read exception: "+str(detail)
405	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
406	if flag: # this read succeeded
407	if rd.Image is None:
408	raise Exception('No image read. Strange!')
409	if GSASIIpath.GetConfigValue('Transpose'):
410	print 'Transposing Image!'
411	rd.Image = rd.Image.T
412	#rd.readfilename = imagefile
413	if imageOnly:
414	return rd.Image
415	else:
416	return rd.Comments,rd.Data,rd.Npix,rd.Image
417	else:
418	print('Error reading file '+filename)
419	print('Error messages(s)\n'+errorReport)
420	raise Exception('No image read')
421
422	def ReadImages(G2frame,imagefile):
423	'''Read one or more images from a file and put them into the Tree
424	using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
425
426	:param wx.Frame G2frame: main GSAS-II Frame and data object.
427	:param str imagefile: name of image file
428
429	:returns: a list of the id's of the IMG tree items created
430	'''
431	# determine which formats are compatible with this file
432	primaryReaders = []
433	secondaryReaders = []
434	for rd in G2frame.ImportImageReaderlist:
435	flag = rd.ExtensionValidator(imagefile)
436	if flag is None:
437	secondaryReaders.append(rd)
438	elif flag:
439	primaryReaders.append(rd)
440	if len(secondaryReaders) + len(primaryReaders) == 0:
441	print('Error: No matching format for file '+filename)
442	raise Exception('No image read')
443	errorReport = ''
444	fp = open(imagefile,'Ur')
445	rdbuffer = {} # create temporary storage for file reader
446	for rd in primaryReaders+secondaryReaders:
447	rd.ReInitialize() # purge anything from a previous read
448	fp.seek(0) # rewind
449	rd.errors = "" # clear out any old errors
450	if not rd.ContentsValidator(fp): # rejected on cursory check
451	errorReport += "\n "+rd.formatName + ' validator error'
452	if rd.errors:
453	errorReport += ': '+rd.errors
454	continue
455	ParentFrame = G2frame
456	block = 0
457	repeat = True
458	CreatedIMGitems = []
459	while repeat: # loop if the reader asks for another pass on the file
460	block += 1
461	repeat = False
462	if GSASIIpath.GetConfigValue('debug'):
463	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=block,Buffer=rdbuffer)
464	else:
465	flag = False
466	try:
467	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=block,Buffer=rdbuffer)
468	except rd.ImportException as detail:
469	rd.errors += "\n Read exception: "+str(detail)
470	except Exception as detail:
471	import traceback
472	rd.errors += "\n Unhandled read exception: "+str(detail)
473	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
474	if flag: # this read succeeded
475	if rd.Image is None:
476	raise Exception('No image read. Strange!')
477	if GSASIIpath.GetConfigValue('Transpose'):
478	print 'Transposing Image!'
479	rd.Image = rd.Image.T
480	rd.Data['ImageTag'] = rd.repeatcount
481	LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
482	repeat = rd.repeat
483	CreatedIMGitems.append(G2frame.Image)
484	if CreatedIMGitems: return CreatedIMGitems
485	else:
486	print('Error reading file '+filename)
487	print('Error messages(s)\n'+errorReport)
488	return []
489	#raise Exception('No image read')
490
491	def SaveMultipleImg(G2frame):
492	if not G2frame.PatternTree.GetCount():
493	print 'no images!'
494	return
495	choices = G2gd.GetPatternTreeDataNames(G2frame,['IMG ',])
496	if len(choices) == 1:
497	names = choices
498	else:
499	dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices)
500	dlg.SetSelections([])
501	names = []
502	if dlg.ShowModal() == wx.ID_OK:
503	names = [choices[sel] for sel in dlg.GetSelections()]
504	dlg.Destroy()
505	if not names: return
506	for name in names:
507	Id = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, name)
508	Npix,imagefile,imagetag = G2frame.PatternTree.GetImageLoc(Id)
509	imroot = os.path.splitext(imagefile)[0]
510	if imagetag:
511	imroot += '_' + str(imagetag)
512	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Image Controls'))
513	print('Writing '+imroot+'.imctrl')
514	File = open(imroot+'.imctrl','w')
515	keys = ['type','wavelength','calibrant','distance','center',
516	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth',
517	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
518	'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg',
519	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image']
520	for key in keys:
521	if key not in Data: continue #uncalibrated!
522	File.write(key+':'+str(Data[key])+'\n')
523	File.close()
524	mask = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Masks'))
525	G2imG.CleanupMasks(mask)
526	print('Writing '+imroot+'.immask')
527	File = open(imroot+'.immask','w')
528	for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
529	File.write(key+':'+str(mask[key])+'\n')
530	File.close()
531
532	def PutG2Image(filename,Comments,Data,Npix,image):
533	'Write an image as a python pickle - might be better as an .edf file?'
534	File = open(filename,'wb')
535	cPickle.dump([Comments,Data,Npix,image],File,1)
536	File.close()
537	return
538
539	# should get moved to importer when ready to test
540	def GetEdfData(filename,imageOnly=False):
541	'Read European detector data edf file'
542	import struct as st
543	import array as ar
544	if not imageOnly:
545	print 'Read European detector data edf file: ',filename
546	File = open(filename,'rb')
547	fileSize = os.stat(filename).st_size
548	head = File.read(3072)
549	lines = head.split('\n')
550	sizexy = [0,0]
551	pixSize = [154,154] #Pixium4700?
552	cent = [0,0]
553	wave = 1.54187 #default <CuKa>
554	dist = 1000.
555	head = ['European detector data',]
556	for line in lines:
557	line = line.replace(';',' ').strip()
558	fields = line.split()
559	if 'Dim_1' in line:
560	sizexy[0] = int(fields[2])
561	elif 'Dim_2' in line:
562	sizexy[1] = int(fields[2])
563	elif 'DataType' in line:
564	dType = fields[2]
565	elif 'wavelength' in line:
566	wave = float(fields[2])
567	elif 'Size' in line:
568	imSize = int(fields[2])
569	# elif 'DataType' in lines:
570	# dType = fields[2]
571	elif 'pixel_size_x' in line:
572	pixSize[0] = float(fields[2])
573	elif 'pixel_size_y' in line:
574	pixSize[1] = float(fields[2])
575	elif 'beam_center_x' in line:
576	cent[0] = float(fields[2])
577	elif 'beam_center_y' in line:
578	cent[1] = float(fields[2])
579	elif 'refined_distance' in line:
580	dist = float(fields[2])
581	if line:
582	head.append(line)
583	else: #blank line at end of header
584	break
585	File.seek(fileSize-imSize)
586	if dType == 'UnsignedShort':
587	image = np.array(ar.array('H',File.read(imSize)),dtype=np.int32)
588	elif dType == 'UnsignedInt':
589	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
590	elif dType == 'UnsignedLong':
591	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
592	elif dType == 'SignedInteger':
593	image = np.array(ar.array('l',File.read(imSize)),dtype=np.int32)
594	image = np.reshape(image,(sizexy[1],sizexy[0]))
595	data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'size':sizexy}
596	Npix = sizexy[0]*sizexy[1]
597	File.close()
598	if imageOnly:
599	return image
600	else:
601	return head,data,Npix,image
602
603	# should get moved to importer when ready to test
604	def GetRigaku(filename,imageOnly=False):
605	'Read Rigaku R-Axis IV image file'
606	import struct as st
607	import array as ar
608	if not imageOnly:
609	print 'Read Rigaku R-Axis IV file: ',filename
610	File = open(filename,'rb')
611	fileSize = os.stat(filename).st_size
612	Npix = (fileSize-6000)/2
613	Head = File.read(6000)
614	head = ['Rigaku R-Axis IV detector data',]
615	image = np.array(ar.array('H',File.read(fileSize-6000)),dtype=np.int32)
616	print fileSize,image.shape
617	print head
618	if Npix == 9000000:
619	sizexy = [3000,3000]
620	pixSize = [100.,100.]
621	elif Npix == 2250000:
622	sizexy = [1500,1500]
623	pixSize = [200.,200.]
624	else:
625	sizexy = [6000,6000]
626	pixSize = [50.,50.]
627	image = np.reshape(image,(sizexy[1],sizexy[0]))
628	data = {'pixelSize':pixSize,'wavelength':1.5428,'distance':250.0,'center':[150.,150.],'size':sizexy}
629	File.close()
630	if imageOnly:
631	return image
632	else:
633	return head,data,Npix,image
634
635	# should get moved to importer when ready to test
636	def GetImgData(filename,imageOnly=False):
637	'Read an ADSC image file'
638	import struct as st
639	import array as ar
640	if not imageOnly:
641	print 'Read ADSC img file: ',filename
642	File = open(filename,'rb')
643	head = File.read(511)
644	lines = head.split('\n')
645	head = []
646	center = [0,0]
647	for line in lines[1:-2]:
648	line = line.strip()[:-1]
649	if line:
650	if 'SIZE1' in line:
651	size = int(line.split('=')[1])
652	Npix = size*size
653	elif 'WAVELENGTH' in line:
654	wave = float(line.split('=')[1])
655	elif 'BIN' in line:
656	if line.split('=')[1] == '2x2':
657	pixel=(102,102)
658	else:
659	pixel = (51,51)
660	elif 'DISTANCE' in line:
661	distance = float(line.split('=')[1])
662	elif 'CENTER_X' in line:
663	center[0] = float(line.split('=')[1])
664	elif 'CENTER_Y' in line:
665	center[1] = float(line.split('=')[1])
666	head.append(line)
667	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center,'size':[size,size]}
668	image = []
669	row = 0
670	pos = 512
671	File.seek(pos)
672	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
673	image = np.reshape(image,(sizexy[1],sizexy[0]))
674	# image = np.zeros(shape=(size,size),dtype=np.int32)
675	# while row < size:
676	# File.seek(pos)
677	# line = ar.array('H',File.read(2*size))
678	# image[row] = np.asarray(line)
679	# row += 1
680	# pos += 2*size
681	File.close()
682	if imageOnly:
683	return image
684	else:
685	return lines[1:-2],data,Npix,image
686
687	# should get moved to importer when ready to test
688	def GetMAR345Data(filename,imageOnly=False):
689	'Read a MAR-345 image plate image'
690	import array as ar
691	import struct as st
692	try:
693	import pack_f as pf
694	except:
695	msg = wx.MessageDialog(None, message="Unable to load the GSAS MAR image decompression, pack_f",
696	caption="Import Error",
697	style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
698	msg.ShowModal()
699	return None,None,None,None
700
701	if not imageOnly:
702	print 'Read Mar345 file: ',filename
703	File = open(filename,'rb')
704	head = File.read(4095)
705	numbers = st.unpack('<iiiiiiiiii',head[:40])
706	lines = head[128:].split('\n')
707	head = []
708	for line in lines:
709	line = line.strip()
710	if 'PIXEL' in line:
711	values = line.split()
712	pixel = (int(values[2]),int(values[4])) #in microns
713	elif 'WAVELENGTH' in line:
714	wave = float(line.split()[1])
715	elif 'DISTANCE' in line:
716	distance = float(line.split()[1]) #in mm
717	if not distance:
718	distance = 500.
719	elif 'CENTER' in line:
720	values = line.split()
721	center = [float(values[2])/10.,float(values[4])/10.] #make in mm from pixels
722	if line:
723	head.append(line)
724	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center}
725	for line in head:
726	if 'FORMAT' in line[0:6]:
727	items = line.split()
728	sizex = int(items[1])
729	Npix = int(items[3])
730	sizey = int(Npix/sizex)
731	pos = 4096
732	data['size'] = [sizex,sizey]
733	File.seek(pos)
734	line = File.read(8)
735	while 'CCP4' not in line: #get past overflow list for now
736	line = File.read(8)
737	pos += 8
738	pos += 37
739	File.seek(pos)
740	raw = File.read()
741	File.close()
742	image = np.zeros(shape=(sizex,sizey),dtype=np.int32)
743
744	image = np.flipud(pf.pack_f(len(raw),raw,sizex,sizey,image).T) #transpose to get it right way around & flip
745	if imageOnly:
746	return image
747	else:
748	return head,data,Npix,image
749
750	def ProjFileOpen(G2frame,showProvenance=True):
751	'Read a GSAS-II project file and load into the G2 data tree'
752	if not os.path.exists(G2frame.GSASprojectfile):
753	print ('\n*** Error attempt to open project file that does not exist:\n '+
754	str(G2frame.GSASprojectfile))
755	return
756	LastSavedUsing = None
757	file = open(G2frame.GSASprojectfile,'rb')
758	if showProvenance: print 'loading from file: ',G2frame.GSASprojectfile
759	G2frame.SetTitle("GSAS-II data tree: "+
760	os.path.split(G2frame.GSASprojectfile)[1])
761	wx.BeginBusyCursor()
762	try:
763	while True:
764	try:
765	data = cPickle.load(file)
766	except EOFError:
767	break
768	datum = data[0]
769
770	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=datum[0])
771	if 'PWDR' in datum[0]:
772	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
773	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
774	G2frame.PatternTree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
775	elif datum[0].startswith('HKLF'):
776	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
777	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
778	G2frame.PatternTree.SetItemPyData(Id,datum[1])
779	else:
780	G2frame.PatternTree.SetItemPyData(Id,datum[1])
781	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
782	LastSavedUsing = datum[1]['LastSavedUsing']
783	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance:
784	print('Packages used to create .GPX file:')
785	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
786	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
787	print("{:>14s}: {:s}".format(p[0],p[1]))
788	else:
789	for p in datum[1]['PythonVersions']:
790	print("{:<12s} {:s}".format(p[0]+':',p[1]))
791	for datus in data[1:]:
792	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
793	#patch
794	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
795	if 'PWDR' in datum[0]:
796	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
797	else:
798	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
799	for item in datus[1][0]: #zip makes tuples - now make lists!
800	datus[1][0][item] = list(datus[1][0][item])
801	#end patch
802	G2frame.PatternTree.SetItemPyData(sub,datus[1])
803	if 'IMG' in datum[0]: #retrieve image default flag & data if set
804	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
805	if Data['setDefault']:
806	G2frame.imageDefault = Data
807	file.close()
808	if LastSavedUsing:
809	print('GPX load successful. Last saved with GSAS-II version '+LastSavedUsing)
810	else:
811	print('project load successful')
812	G2frame.NewPlot = True
813	except:
814	msg = wx.MessageDialog(G2frame,message="Error reading file "+
815	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
816	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
817	msg.ShowModal()
818	finally:
819	wx.EndBusyCursor()
820	G2frame.Status.SetStatusText('To reorder tree items, use mouse RB to drag/drop them')
821
822	def ProjFileSave(G2frame):
823	'Save a GSAS-II project file'
824	if not G2frame.PatternTree.IsEmpty():
825	file = open(G2frame.GSASprojectfile,'wb')
826	print 'save to file: ',G2frame.GSASprojectfile
827	# stick the file name into the tree and version info into tree so they are saved.
828	# (Controls should always be created at this point)
829	try:
830	Controls = G2frame.PatternTree.GetItemPyData(
831	G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
832	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
833	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
834	Controls['PythonVersions'] = G2frame.PackageVersions
835	except:
836	pass
837	wx.BeginBusyCursor()
838	try:
839	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
840	while item:
841	data = []
842	name = G2frame.PatternTree.GetItemText(item)
843	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
844	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
845	while item2:
846	name = G2frame.PatternTree.GetItemText(item2)
847	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
848	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
849	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
850	cPickle.dump(data,file,1)
851	file.close()
852	pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
853	if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
854	G2frame.LastGPXdir = pth
855	finally:
856	wx.EndBusyCursor()
857	print('project save successful')
858
859	def SaveIntegration(G2frame,PickId,data,Overwrite=False):
860	'Save image integration results as powder pattern(s)'
861	azms = G2frame.Integrate[1]
862	X = G2frame.Integrate[2][:-1]
863	N = len(X)
864	Id = G2frame.PatternTree.GetItemParent(PickId)
865	name = G2frame.PatternTree.GetItemText(Id)
866	name = name.replace('IMG ',data['type']+' ')
867	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
868	if 'PWDR' in name:
869	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
870	codes = [0 for i in range(11)]
871	elif 'SASD' in name:
872	names = ['Type','Lam','Zero','Azimuth']
873	codes = [0 for i in range(4)]
874	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
875	Xminmax = [X[0],X[-1]]
876	LRazm = data['LRazimuth']
877	Azms = []
878	dazm = 0.
879	if data['fullIntegrate'] and data['outAzimuths'] == 1:
880	Azms = [45.0,] #a poor man's average?
881	else:
882	for i,azm in enumerate(azms[:-1]):
883	if azm > 360. and azms[i+1] > 360.:
884	Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
885	else:
886	Azms.append(G2img.meanAzm(azm,azms[i+1]))
887	dazm = np.min(np.abs(np.diff(azms)))/2.
888	G2frame.IntgOutList = []
889	for i,azm in enumerate(azms[:-1]):
890	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
891	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
892	# if Overwrite delete any duplicate
893	if Overwrite and G2gd.GetPatternTreeItemId(G2frame,G2frame.root,Aname):
894	print('Replacing '+Aname)
895	item = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,Aname)
896	G2frame.PatternTree.Delete(item)
897	else:
898	nOcc = 0
899	while item:
900	Name = G2frame.PatternTree.GetItemText(item)
901	if Aname in Name:
902	nOcc += 1
903	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
904	if nOcc:
905	Aname += '(%d)'%(nOcc)
906	Sample = G2pdG.SetDefaultSample()
907	Sample['Gonio. radius'] = data['distance']
908	Sample['Omega'] = data['GonioAngles'][0]
909	Sample['Chi'] = data['GonioAngles'][1]
910	Sample['Phi'] = data['GonioAngles'][2]
911	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
912	if 'PWDR' in Aname:
913	parms = ['PXC',data['wavelength'],0.0,0.99,1.0,-0.10,0.4,0.30,1.0,0.0001,Azms[i]] #set polarization for synchrotron radiation!
914	elif 'SASD' in Aname:
915	Sample['Trans'] = data['SampleAbs'][0]
916	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
917	Y = G2frame.Integrate[0][i]
918	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
919	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=Aname)
920	G2frame.IntgOutList.append(Id)
921	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
922	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
923	if 'PWDR' in Aname:
924	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
925	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
926	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
927	for item in inst[0]:
928	inst[0][item] = list(inst[0][item])
929	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
930	if 'PWDR' in Aname:
931	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
932	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
933	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[[],[]])
934	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
935	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
936	elif 'SASD' in Aname:
937	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
938	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
939	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
940	valuesdict = {
941	'wtFactor':1.0,
942	'Dummy':False,
943	'ranId':ran.randint(0,sys.maxint),
944	'Offset':[0.0,0.0],'delOffset':0.02,'refOffset':-1.0,'refDelt':0.01,
945	'qPlot':False,'dPlot':False,'sqrtPlot':False
946	}
947	G2frame.PatternTree.SetItemPyData(
948	Id,[valuesdict,
949	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
950	return Id #last powder pattern generated
951
952	def XYsave(G2frame,XY,labelX='X',labelY='Y',names=None):
953	'Save XY table data'
954	pth = G2G.GetExportPath(G2frame)
955	dlg = wx.FileDialog(
956	G2frame, 'Enter csv filename for XY table', pth, '',
957	'XY table file (.csv)\|.csv',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
958	try:
959	if dlg.ShowModal() == wx.ID_OK:
960	filename = dlg.GetPath()
961	filename = os.path.splitext(filename)[0]+'.csv'
962	File = open(filename,'w')
963	else:
964	filename = None
965	finally:
966	dlg.Destroy()
967	if not filename:
968	return
969	for i in range(len(XY)):
970	if names != None:
971	header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
972	else:
973	header = '%s,%s(%d)\n'%(labelX,labelY,i)
974	File.write(header)
975	for x,y in XY[i].T:
976	File.write('%.3f,%.3f\n'%(x,y))
977	File.close()
978	print ' XY data saved to: ',filename
979
980	def PDFSave(G2frame,exports):
981	'Save a PDF G(r) and F(Q), S(Q) in column formats'
982	for export in exports:
983	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
984	SQname = 'S(Q)'+export[4:]
985	FQname = 'F(Q)'+export[4:]
986	GRname = 'G(R)'+export[4:]
987	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
988	fqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.fq')
989	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
990	sqId = G2gd.GetPatternTreeItemId(G2frame, PickId, SQname)
991	fqId = G2gd.GetPatternTreeItemId(G2frame, PickId, FQname)
992	grId = G2gd.GetPatternTreeItemId(G2frame, PickId, GRname)
993	sqdata = np.array(G2frame.PatternTree.GetItemPyData(sqId)[1][:2]).T
994	fqdata = np.array(G2frame.PatternTree.GetItemPyData(fqId)[1][:2]).T
995	grdata = np.array(G2frame.PatternTree.GetItemPyData(grId)[1][:2]).T
996	sqfile = open(sqfilename,'w')
997	fqfile = open(sqfilename,'w')
998	grfile = open(grfilename,'w')
999	sqfile.write('#T S(Q) %s\n'%(export))
1000	fqfile.write('#T F(Q) %s\n'%(export))
1001	grfile.write('#T G(R) %s\n'%(export))
1002	sqfile.write('#L Q S(Q)\n')
1003	sqfile.write('#L Q F(Q)\n')
1004	grfile.write('#L R G(R)\n')
1005	for q,sq in sqdata:
1006	sqfile.write("%15.6g %15.6g\n" % (q,sq))
1007	sqfile.close()
1008	print ' S(Q) saved to: ',sqfilename
1009	for q,fq in fqdata:
1010	fqfile.write("%15.6g %15.6g\n" % (q,fq))
1011	fqfile.close()
1012	print ' F(Q) saved to: ',fqfilename
1013	for r,gr in grdata:
1014	grfile.write("%15.6g %15.6g\n" % (r,gr))
1015	grfile.close()
1016	print ' G)R) saved to: ',grfilename
1017
1018	def PeakListSave(G2frame,file,peaks):
1019	'Save powder peaks to a data file'
1020	print 'save peak list to file: ',G2frame.peaklistfile
1021	if not peaks:
1022	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1023	try:
1024	result = dlg.ShowModal()
1025	finally:
1026	dlg.Destroy()
1027	return
1028	for peak in peaks:
1029	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1030	(peak[0],peak[2],peak[4],peak[6]))
1031	print 'peak list saved'
1032
1033	def IndexPeakListSave(G2frame,peaks):
1034	'Save powder peaks from the indexing list'
1035	file = open(G2frame.peaklistfile,'wa')
1036	print 'save index peak list to file: ',G2frame.peaklistfile
1037	wx.BeginBusyCursor()
1038	try:
1039	if not peaks:
1040	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1041	try:
1042	result = dlg.ShowModal()
1043	finally:
1044	dlg.Destroy()
1045	return
1046	for peak in peaks:
1047	file.write("%12.6f\n" % (peak[7]))
1048	file.close()
1049	finally:
1050	wx.EndBusyCursor()
1051	print 'index peak list saved'
1052
1053	def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1054	'''Create a new phase dict with default values for various parameters
1055
1056	:param str Name: Name for new Phase
1057
1058	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1059	defaults to data for P 1
1060
1061	:param list cell: unit cell parameter list; defaults to
1062	[1.0,1.0,1.0,90.,90,90.,1.]
1063
1064	'''
1065	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1066	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1067	phaseData = {
1068	'ranId':ran.randint(0,sys.maxint),
1069	'General':{
1070	'Name':Name,
1071	'Type':'nuclear',
1072	'Modulated':False,
1073	'AtomPtrs':[3,1,7,9],
1074	'SGData':SGData,
1075	'Cell':[False,]+cell,
1076	'Pawley dmin':1.0,
1077	'Data plot type':'None',
1078	'SH Texture':{
1079	'Order':0,
1080	'Model':'cylindrical',
1081	'Sample omega':[False,0.0],
1082	'Sample chi':[False,0.0],
1083	'Sample phi':[False,0.0],
1084	'SH Coeff':[False,{}],
1085	'SHShow':False,
1086	'PFhkl':[0,0,1],
1087	'PFxyz':[0,0,1],
1088	'PlotType':'Pole figure',
1089	'Penalty':[['',],0.1,False,1.0]}},
1090	'Atoms':[],
1091	'Drawing':{},
1092	'Histograms':{},
1093	'Pawley ref':[],
1094	'RBModels':{},
1095	}
1096	if Super and Super.get('Use',False):
1097	phaseData['General'].update({'Modulated':True,'Super':True,'SuperSg':Super['ssSymb']})
1098	phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])
1099	phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1100
1101	return phaseData
1102
1103	class MultipleChoicesDialog(wx.Dialog):
1104	'''A dialog that offers a series of choices, each with a
1105	title and a wx.Choice widget. Intended to be used Modally.
1106	typical input:
1107
1108	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1109	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1110
1111	selections are placed in self.chosen when OK is pressed
1112
1113	Also see GSASIIctrls
1114	'''
1115	def __init__(self,choicelist,headinglist,
1116	head='Select options',
1117	title='Please select from options below',
1118	parent=None):
1119	self.chosen = []
1120	wx.Dialog.__init__(
1121	self,parent,wx.ID_ANY,head,
1122	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1123	panel = wx.Panel(self)
1124	mainSizer = wx.BoxSizer(wx.VERTICAL)
1125	mainSizer.Add((10,10),1)
1126	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1127	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1128	self.ChItems = []
1129	for choice,lbl in zip(choicelist,headinglist):
1130	mainSizer.Add((10,10),1)
1131	self.chosen.append(0)
1132	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1133	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1134	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1135	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1136
1137	OkBtn = wx.Button(panel,-1,"Ok")
1138	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1139	cancelBtn = wx.Button(panel,-1,"Cancel")
1140	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1141	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1142	btnSizer.Add((20,20),1)
1143	btnSizer.Add(OkBtn)
1144	btnSizer.Add((20,20),1)
1145	btnSizer.Add(cancelBtn)
1146	btnSizer.Add((20,20),1)
1147	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1148	panel.SetSizer(mainSizer)
1149	panel.Fit()
1150	self.Fit()
1151
1152	def OnOk(self,event):
1153	parent = self.GetParent()
1154	if parent is not None: parent.Raise()
1155	# save the results from the choice widgets
1156	self.chosen = []
1157	for w in self.ChItems:
1158	self.chosen.append(w.GetSelection())
1159	self.EndModal(wx.ID_OK)
1160
1161	def OnCancel(self,event):
1162	parent = self.GetParent()
1163	if parent is not None: parent.Raise()
1164	self.chosen = []
1165	self.EndModal(wx.ID_CANCEL)
1166
1167	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1168	confirmoverwrite=True, parent=None,
1169	multipleselect=False):
1170	'''If the filename is a zip file, extract a file from that
1171	archive.
1172
1173	:param list Selection: used to predefine the name of the file
1174	to be extracted. Filename case and zip directory name are
1175	ignored in selection; the first matching file is used.
1176
1177	:param bool confirmread: if True asks the user to confirm before expanding
1178	the only file in a zip
1179
1180	:param bool confirmoverwrite: if True asks the user to confirm
1181	before overwriting if the extracted file already exists
1182
1183	:param bool multipleselect: if True allows more than one zip
1184	file to be extracted, a list of file(s) is returned.
1185	If only one file is present, do not ask which one, otherwise
1186	offer a list of choices (unless selection is used).
1187
1188	:returns: the name of the file that has been created or a
1189	list of files (see multipleselect)
1190
1191	If the file is not a zipfile, return the name of the input file.
1192	If the zipfile is empty or no file has been selected, return None
1193	'''
1194	import zipfile # do this now, since we can save startup time by doing this only on need
1195	import shutil
1196	zloc = os.path.split(filename)[0]
1197	if not zipfile.is_zipfile(filename):
1198	#print("not zip")
1199	return filename
1200
1201	z = zipfile.ZipFile(filename,'r')
1202	zinfo = z.infolist()
1203
1204	if len(zinfo) == 0:
1205	#print('Zip has no files!')
1206	zlist = [-1]
1207	if selection:
1208	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1209	if selection.lower() in choices:
1210	zlist = [choices.index(selection.lower())]
1211	else:
1212	print('debug: file '+str(selection)+' was not found in '+str(filename))
1213	zlist = [-1]
1214	elif len(zinfo) == 1 and confirmread:
1215	result = wx.ID_NO
1216	dlg = wx.MessageDialog(
1217	parent,
1218	'Is file '+str(zinfo[0].filename)+
1219	' what you want to extract from '+
1220	str(os.path.split(filename)[1])+'?',
1221	'Confirm file',
1222	wx.YES_NO \| wx.ICON_QUESTION)
1223	try:
1224	result = dlg.ShowModal()
1225	finally:
1226	dlg.Destroy()
1227	if result == wx.ID_NO:
1228	zlist = [-1]
1229	else:
1230	zlist = [0]
1231	elif len(zinfo) == 1:
1232	zlist = [0]
1233	elif multipleselect:
1234	# select one or more from a from list
1235	choices = [i.filename for i in zinfo]
1236	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1237	'Choose file(s)',choices)
1238	if dlg.ShowModal() == wx.ID_OK:
1239	zlist = dlg.GetSelections()
1240	else:
1241	zlist = []
1242	dlg.Destroy()
1243	else:
1244	# select one from a from list
1245	choices = [i.filename for i in zinfo]
1246	dlg = wx.SingleChoiceDialog(parent,
1247	'Select file to extract from zip file'+str(filename),'Choose file',
1248	choices,)
1249	if dlg.ShowModal() == wx.ID_OK:
1250	zlist = [dlg.GetSelection()]
1251	else:
1252	zlist = [-1]
1253	dlg.Destroy()
1254
1255	outlist = []
1256	for zindex in zlist:
1257	if zindex >= 0:
1258	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1259	if os.path.exists(efil) and confirmoverwrite:
1260	result = wx.ID_NO
1261	dlg = wx.MessageDialog(parent,
1262	'File '+str(efil)+' already exists. OK to overwrite it?',
1263	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1264	try:
1265	result = dlg.ShowModal()
1266	finally:
1267	dlg.Destroy()
1268	if result == wx.ID_NO:
1269	zindex = -1
1270	if zindex >= 0:
1271	# extract the file to the current directory, regardless of it's original path
1272	#z.extract(zinfo[zindex],zloc)
1273	eloc,efil = os.path.split(zinfo[zindex].filename)
1274	outfile = os.path.join(zloc, efil)
1275	fpin = z.open(zinfo[zindex])
1276	fpout = file(outfile, "wb")
1277	shutil.copyfileobj(fpin, fpout)
1278	fpin.close()
1279	fpout.close()
1280	outlist.append(outfile)
1281	z.close()
1282	if multipleselect and len(outlist) >= 1:
1283	return outlist
1284	elif len(outlist) == 1:
1285	return outlist[0]
1286	else:
1287	return None
1288
1289	######################################################################
1290	# base classes for reading various types of data files
1291	# not used directly, only by subclassing
1292	######################################################################
1293	try:
1294	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1295	except: # errors on doc build
1296	SGData = None
1297	P1SGData = SGData
1298	######################################################################
1299	class ImportBaseclass(object):
1300	'''Defines a base class for the reading of input files (diffraction
1301	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1302	for an explanation on how to use a subclass of this class.
1303	'''
1304	class ImportException(Exception):
1305	'''Defines an Exception that is used when an import routine hits an expected error,
1306	usually in .Reader.
1307
1308	Good practice is that the Reader should define a value in self.errors that
1309	tells the user some information about what is wrong with their file.
1310	'''
1311	pass
1312
1313	UseReader = True # in __init__ set value of self.UseReader to False to skip use of current importer
1314	def __init__(self,formatName,longFormatName=None,
1315	extensionlist=[],strictExtension=False,):
1316	self.formatName = formatName # short string naming file type
1317	if longFormatName: # longer string naming file type
1318	self.longFormatName = longFormatName
1319	else:
1320	self.longFormatName = formatName
1321	# define extensions that are allowed for the file type
1322	# for windows, remove any extensions that are duplicate, as case is ignored
1323	if sys.platform == 'windows' and extensionlist:
1324	extensionlist = list(set([s.lower() for s in extensionlist]))
1325	self.extensionlist = extensionlist
1326	# If strictExtension is True, the file will not be read, unless
1327	# the extension matches one in the extensionlist
1328	self.strictExtension = strictExtension
1329	self.errors = ''
1330	self.warnings = ''
1331	# used for readers that will use multiple passes to read
1332	# more than one data block
1333	self.repeat = False
1334	self.selections = []
1335	self.repeatcount = 0
1336	self.readfilename = '?'
1337	#print 'created',self.__class__
1338
1339	def ReInitialize(self):
1340	'Reinitialize the Reader to initial settings'
1341	self.errors = ''
1342	self.warnings = ''
1343	self.repeat = False
1344	self.repeatcount = 0
1345	self.readfilename = '?'
1346
1347	def BlockSelector(self, ChoiceList, ParentFrame=None,title='Select a block',
1348	size=None, header='Block Selector',useCancel=True):
1349	''' Provide a wx dialog to select a block if the file contains more
1350	than one set of data and one must be selected
1351	'''
1352	if useCancel:
1353	dlg = wx.SingleChoiceDialog(
1354	ParentFrame,title, header,ChoiceList)
1355	else:
1356	dlg = wx.SingleChoiceDialog(
1357	ParentFrame,title, header,ChoiceList,
1358	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1359	if size: dlg.SetSize(size)
1360	dlg.CenterOnParent()
1361	if dlg.ShowModal() == wx.ID_OK:
1362	sel = dlg.GetSelection()
1363	return sel
1364	else:
1365	return None
1366	dlg.Destroy()
1367
1368	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1369	title='Select a block',size=None, header='Block Selector'):
1370	'''Provide a wx dialog to select a block of data if the
1371	file contains more than one set of data and one must be
1372	selected.
1373
1374	:returns: a list of the selected blocks
1375	'''
1376	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1377	wx.CHOICEDLG_STYLE)
1378	dlg.CenterOnScreen()
1379	if size: dlg.SetSize(size)
1380	if dlg.ShowModal() == wx.ID_OK:
1381	sel = dlg.GetSelections()
1382	else:
1383	return []
1384	dlg.Destroy()
1385	selected = []
1386	if len(ChoiceList) in sel:
1387	return range(len(ChoiceList))
1388	else:
1389	return sel
1390	return selected
1391
1392	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1393	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1394	widget. Typical input:
1395
1396	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1397
1398	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1399
1400	optional keyword parameters are: head (window title) and title
1401	returns a list of selected indicies for each choice (or None)
1402	'''
1403	result = None
1404	dlg = MultipleChoicesDialog(choicelist,headinglist,
1405	parent=ParentFrame, **kwargs)
1406	dlg.CenterOnParent()
1407	if dlg.ShowModal() == wx.ID_OK:
1408	result = dlg.chosen
1409	dlg.Destroy()
1410	return result
1411
1412	def ShowBusy(self):
1413	wx.BeginBusyCursor()
1414	# wx.Yield() # make it happen now!
1415
1416	def DoneBusy(self):
1417	wx.EndBusyCursor()
1418	wx.Yield() # make it happen now!
1419
1420	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1421	# '''This method must be supplied in the child class to read the file.
1422	# if the read fails either return False or raise an Exception
1423	# preferably of type ImportException.
1424	# '''
1425	# #start reading
1426	# raise ImportException("Error occurred while...")
1427	# self.errors += "Hint for user on why the error occur
1428	# return False # if an error occurs
1429	# return True # if read OK
1430
1431	def ExtensionValidator(self, filename):
1432	'''This methods checks if the file has the correct extension
1433	Return False if this filename will not be supported by this reader
1434	Return True if the extension matches the list supplied by the reader
1435	Return None if the reader allows un-registered extensions
1436	'''
1437	if filename:
1438	ext = os.path.splitext(filename)[1]
1439	if sys.platform == 'windows': ext = ext.lower()
1440	if ext in self.extensionlist: return True
1441	if self.strictExtension: return False
1442	return None
1443
1444	def ContentsValidator(self, filepointer):
1445	'''This routine will attempt to determine if the file can be read
1446	with the current format.
1447	This will typically be overridden with a method that
1448	takes a quick scan of [some of]
1449	the file contents to do a "sanity" check if the file
1450	appears to match the selected format.
1451	Expected to be called via self.Validator()
1452	'''
1453	#filepointer.seek(0) # rewind the file pointer
1454	return True
1455
1456	def CIFValidator(self, filepointer):
1457	'''A :meth:`ContentsValidator` for use to validate CIF files.
1458	'''
1459	for i,l in enumerate(filepointer):
1460	if i >= 1000: return True
1461	'''Encountered only blank lines or comments in first 1000
1462	lines. This is unlikely, but assume it is CIF anyway, since we are
1463	even less likely to find a file with nothing but hashes and
1464	blank lines'''
1465	line = l.strip()
1466	if len(line) == 0: # ignore blank lines
1467	continue
1468	elif line.startswith('#'): # ignore comments
1469	continue
1470	elif line.startswith('data_'): # on the right track, accept this file
1471	return True
1472	else: # found something invalid
1473	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1474	if all([ord(c) < 128 and ord(c) != 0 for c in str(l)]): # show only if ASCII
1475	self.errors += ' '+str(l)
1476	else:
1477	self.errors += ' (binary)'
1478	self.errors += '\n Note: a CIF should only have blank lines or comments before'
1479	self.errors += '\n a data_ statement begins a block.'
1480	return False
1481
1482	######################################################################
1483	class ImportPhase(ImportBaseclass):
1484	'''Defines a base class for the reading of files with coordinates
1485
1486	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1487	in :meth:`GSASII.GSASII.OnImportPhase`.
1488	See :ref:`Writing a Import Routine<Import_Routines>`
1489	for an explanation on how to use this class.
1490
1491	'''
1492	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1493	strictExtension=False,):
1494	# call parent __init__
1495	ImportBaseclass.__init__(self,formatName,longFormatName,
1496	extensionlist,strictExtension)
1497	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1498	self.Constraints = None
1499
1500	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1501	title='Select a phase', size=None,header='Phase Selector'):
1502	''' Provide a wx dialog to select a phase if the file contains more
1503	than one phase
1504	'''
1505	return self.BlockSelector(ChoiceList,ParentFrame,title,
1506	size,header)
1507
1508	######################################################################
1509	class ImportStructFactor(ImportBaseclass):
1510	'''Defines a base class for the reading of files with tables
1511	of structure factors.
1512
1513	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1514	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1515	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1516	:meth:`Reader`.
1517
1518	See :ref:`Writing a Import Routine<Import_Routines>`
1519	for an explanation on how to use import classes in general. The specifics
1520	for reading a structure factor histogram require that
1521	the ``Reader()`` routine in the import
1522	class need to do only a few things: It
1523	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1524	and set :attr:`Parameters` with the instrument parameters
1525	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1526	'''
1527	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1528	strictExtension=False,):
1529	ImportBaseclass.__init__(self,formatName,longFormatName,
1530	extensionlist,strictExtension)
1531
1532	# define contents of Structure Factor entry
1533	self.Parameters = []
1534	'self.Parameters is a list with two dicts for data parameter settings'
1535	self.InitParameters()
1536	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1537	self.Banks = [] #for multi bank data (usually TOF)
1538	'''self.RefDict is a dict containing the reflection information, as read from the file.
1539	Item 'RefList' contains the reflection information. See the
1540	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1541	for the contents of each row. Dict element 'FF'
1542	contains the form factor values for each element type; if this entry
1543	is left as initialized (an empty list) it will be initialized as needed later.
1544	'''
1545	def ReInitialize(self):
1546	'Reinitialize the Reader to initial settings'
1547	ImportBaseclass.ReInitialize(self)
1548	self.InitParameters()
1549	self.Banks = [] #for multi bank data (usually TOF)
1550	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1551
1552	def InitParameters(self):
1553	'initialize the instrument parameters structure'
1554	Lambda = 0.70926
1555	HistType = 'SXC'
1556	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1557	'Lam':[Lambda,Lambda]
1558	}, {}]
1559	'Parameters is a list with two dicts for data parameter settings'
1560
1561	def UpdateParameters(self,Type=None,Wave=None):
1562	'Revise the instrument parameters'
1563	if Type is not None:
1564	self.Parameters[0]['Type'] = [Type,Type]
1565	if Wave is not None:
1566	self.Parameters[0]['Lam'] = [Wave,Wave]
1567
1568	######################################################################
1569	class ImportPowderData(ImportBaseclass):
1570	'''Defines a base class for the reading of files with powder data.
1571
1572	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1573	in :meth:`GSASII.GSASII.OnImportPowder`.
1574	See :ref:`Writing a Import Routine<Import_Routines>`
1575	for an explanation on how to use this class.
1576	'''
1577	def __init__(self,formatName,longFormatName=None,
1578	extensionlist=[],strictExtension=False,):
1579	ImportBaseclass.__init__(self,formatName,longFormatName,
1580	extensionlist,strictExtension)
1581	self.clockWd = None # used in TOF
1582	self.ReInitialize()
1583
1584	def ReInitialize(self):
1585	'Reinitialize the Reader to initial settings'
1586	ImportBaseclass.ReInitialize(self)
1587	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1588	self.powderdata = [] # Powder dataset
1589	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1590	np.array(x), # x-axis values
1591	np.array(y), # powder pattern intensities
1592	np.array(w), # 1/sig(intensity)^2 values (weights)
1593	np.array(yc), # calc. intensities (zero)
1594	np.array(yb), # calc. background (zero)
1595	np.array(yd), # obs-calc profiles
1596	'''
1597	self.comments = []
1598	self.idstring = ''
1599	self.Sample = G2pdG.SetDefaultSample() # default sample parameters
1600	self.Controls = {} # items to be placed in top-level Controls
1601	self.GSAS = None # used in TOF
1602	self.repeat_instparm = True # Should a parm file be
1603	# used for multiple histograms?
1604	self.instparm = None # name hint from file of instparm to use
1605	self.instfile = '' # full path name to instrument parameter file
1606	self.instbank = '' # inst parm bank number
1607	self.instmsg = '' # a label that gets printed to show
1608	# where instrument parameters are from
1609	self.numbanks = 1
1610	self.instdict = {} # place items here that will be transferred to the instrument parameters
1611	self.pwdparms = {} # place parameters that are transferred directly to the tree
1612	# here (typically from an existing GPX file)
1613	######################################################################
1614	class ImportSmallAngleData(ImportBaseclass):
1615	'''Defines a base class for the reading of files with small angle data.
1616	See :ref:`Writing a Import Routine<Import_Routines>`
1617	for an explanation on how to use this class.
1618	'''
1619	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1620	strictExtension=False,):
1621
1622	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1623	strictExtension)
1624	self.ReInitialize()
1625
1626	def ReInitialize(self):
1627	'Reinitialize the Reader to initial settings'
1628	ImportBaseclass.ReInitialize(self)
1629	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1630	self.smallangledata = [] # SASD dataset
1631	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1632	np.array(x), # x-axis values
1633	np.array(y), # powder pattern intensities
1634	np.array(w), # 1/sig(intensity)^2 values (weights)
1635	np.array(yc), # calc. intensities (zero)
1636	np.array(yd), # obs-calc profiles
1637	np.array(yb), # preset bkg
1638	'''
1639	self.comments = []
1640	self.idstring = ''
1641	self.Sample = G2pdG.SetDefaultSample()
1642	self.GSAS = None # used in TOF
1643	self.clockWd = None # used in TOF
1644	self.numbanks = 1
1645	self.instdict = {} # place items here that will be transferred to the instrument parameters
1646
1647	######################################################################
1648	class ImportImage(ImportBaseclass):
1649	'''Defines a base class for the reading of images
1650
1651	Images are read in only these places:
1652
1653	* Initial reading is typically done from a menu item
1654	with a call to :meth:`GSASII.GSASII.OnImportImage`
1655	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`. That calls
1656	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1657	:meth:`Reader`. This returns a list of reader objects for each read image.
1658
1659	* Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
1660	directly into the data tree.
1661
1662	* Images are reloaded with :func:`GSASIIIO.GetImageData`.
1663
1664	.. _Image_import_routines:
1665
1666	When reading an image, the ``Reader()`` routine in the ImportImage class
1667	should set:
1668
1669	* :attr:`Comments`: a list of strings (str),
1670	* :attr:`Npix`: the number of pixels in the image (int),
1671	* :attr:`Image`: the actual image as a numpy array (np.array)
1672	* :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
1673	data items are needed:
1674
1675	* 'pixelSize': size of each pixel in microns (such as ``[200,200]``.
1676	* 'wavelength': wavelength in Angstoms.
1677	* 'distance': distance of detector from sample in cm.
1678	* 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
1679	* 'size': size of image (such as ``[2048,2048]``).
1680	* 'ImageTag': image number or other keyword used to retrieve image from
1681	a multi-image data file (defaults to ``1`` if not specified).
1682	* 'sumfile': holds sum image file name if a sum was produced from a multi image file
1683
1684	optional data items:
1685
1686	* :attr:`repeat`: set to True if there are additional images to
1687	read in the file, False otherwise
1688	* :attr:`repeatcount`: set to the number of the image.
1689
1690	Note that the above is initialized with :meth:`InitParameters`.
1691	(Also see :ref:`Writing a Import Routine<Import_Routines>`
1692	for an explanation on how to use import classes in general.)
1693	'''
1694	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1695	strictExtension=False,):
1696	ImportBaseclass.__init__(self,formatName,longFormatName,
1697	extensionlist,strictExtension)
1698	self.InitParameters()
1699
1700	def ReInitialize(self):
1701	'Reinitialize the Reader to initial settings -- not used at present'
1702	ImportBaseclass.ReInitialize(self)
1703	self.InitParameters()
1704
1705	def InitParameters(self):
1706	'initialize the instrument parameters structure'
1707	self.Comments = ['No comments']
1708	self.Data = {}
1709	self.Npix = 0
1710	self.Image = None
1711	self.repeat = False
1712	self.repeatcount = 1
1713	self.sumfile = ''
1714
1715	def LoadImage(self,ParentFrame,imagefile,imagetag=None):
1716	'''Optionally, call this after reading in an image to load it into the tree.
1717	This saves time by preventing a reread of the same information.
1718	'''
1719	if ParentFrame:
1720	ParentFrame.ImageZ = self.Image # store the image for plotting
1721	ParentFrame.oldImagefile = imagefile # save the name of the last image file read
1722	ParentFrame.oldImageTag = imagetag # save the tag of the last image file read
1723
1724	######################################################################
1725	def striphist(var,insChar=''):
1726	'strip a histogram number from a var name'
1727	sv = var.split(':')
1728	if len(sv) <= 1: return var
1729	if sv[1]:
1730	sv[1] = insChar
1731	return ':'.join(sv)
1732	class ExportBaseclass(object):
1733	'''Defines a base class for the exporting of GSAS-II results.
1734
1735	This class is subclassed in the various exports/G2export_*.py files. Those files
1736	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
1737	appropriate menu items for each one and the .Exporter method is called
1738	directly from the menu item.
1739
1740	Routines may also define a .Writer method, which is used to write a single
1741	file without invoking any GUI objects.
1742	'''
1743	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1744	self.G2frame = G2frame
1745	self.formatName = formatName # short string naming file type
1746	self.extension = extension
1747	if longFormatName: # longer string naming file type
1748	self.longFormatName = longFormatName
1749	else:
1750	self.longFormatName = formatName
1751	self.OverallParms = {}
1752	self.Phases = {}
1753	self.Histograms = {}
1754	self.powderDict = {}
1755	self.xtalDict = {}
1756	self.parmDict = {}
1757	self.sigDict = {}
1758	# updated in InitExport:
1759	self.currentExportType = None # type of export that has been requested
1760	# updated in ExportSelect (when used):
1761	self.phasenam = None # a list of selected phases
1762	self.histnam = None # a list of selected histograms
1763	self.filename = None # name of file to be written (single export) or template (multiple files)
1764	self.dirname = '' # name of directory where file(s) will be written
1765	self.fullpath = '' # name of file being written -- full path
1766
1767	# items that should be defined in a subclass of this class
1768	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1769	# The following types are defined: 'project', "phase", "powder", "single"
1770	self.multiple = False # set as True if the class can export multiple phases or histograms
1771	# self.multiple is ignored for "project" exports
1772
1773	def InitExport(self,event):
1774	'''Determines the type of menu that called the Exporter and
1775	misc initialization.
1776	'''
1777	self.filename = None # name of file to be written (single export)
1778	self.dirname = '' # name of file to be written (multiple export)
1779	if event:
1780	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1781
1782	def MakePWDRfilename(self,hist):
1783	'''Make a filename root (no extension) from a PWDR histogram name
1784
1785	:param str hist: the histogram name in data tree (starts with "PWDR ")
1786	'''
1787	file0 = ''
1788	file1 = hist[5:]
1789	# replace repeated blanks
1790	while file1 != file0:
1791	file0 = file1
1792	file1 = file0.replace(' ',' ').strip()
1793	file0 = file1.replace('Azm= ','A')
1794	# if angle has unneeded decimal places on aziumuth, remove them
1795	if file0[-3:] == '.00': file0 = file0[:-3]
1796	file0 = file0.replace('.','_')
1797	file0 = file0.replace(' ','_')
1798	return file0
1799
1800	def ExportSelect(self,AskFile='ask'):
1801	'''Selects histograms or phases when needed. Sets a default file name when
1802	requested in self.filename; always sets a default directory in self.dirname.
1803
1804	:param bool AskFile: Determines how this routine processes getting a
1805	location to store the current export(s).
1806
1807	* if AskFile is 'ask' (default option), get the name of the file to be written;
1808	self.filename and self.dirname are always set. In the case where
1809	multiple files must be generated, the export routine should do this
1810	based on self.filename as a template.
1811	* if AskFile is 'dir', get the name of the directory to be used;
1812	self.filename is not used, but self.dirname is always set. The export routine
1813	will always generate the file name.
1814	* if AskFile is 'single', get only the name of the directory to be used when
1815	multiple items will be written (as multiple files) are used
1816	or a complete file name is requested when a single file
1817	name is selected. self.dirname is always set and self.filename used
1818	only when a single file is selected.
1819	* if AskFile is 'default', creates a name of the file to be used from
1820	the name of the project (.gpx) file. If the project has not been saved,
1821	then the name of file is requested.
1822	self.filename and self.dirname are always set. In the case where
1823	multiple file names must be generated, the export routine should do this
1824	based on self.filename.
1825	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1826	file. If the project has not been saved, then a directory is requested.
1827	self.filename is not used.
1828
1829	:returns: True in case of an error
1830	'''
1831
1832	numselected = 1
1833	if self.currentExportType == 'phase':
1834	if len(self.Phases) == 0:
1835	self.G2frame.ErrorDialog(
1836	'Empty project',
1837	'Project does not contain any phases.')
1838	return True
1839	elif len(self.Phases) == 1:
1840	self.phasenam = self.Phases.keys()
1841	elif self.multiple:
1842	choices = sorted(self.Phases.keys())
1843	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1844	if phasenum is None: return True
1845	self.phasenam = [choices[i] for i in phasenum]
1846	if not self.phasenam: return True
1847	numselected = len(self.phasenam)
1848	else:
1849	choices = sorted(self.Phases.keys())
1850	phasenum = G2G.ItemSelector(choices,self.G2frame)
1851	if phasenum is None: return True
1852	self.phasenam = [choices[phasenum]]
1853	numselected = len(self.phasenam)
1854	elif self.currentExportType == 'single':
1855	if len(self.xtalDict) == 0:
1856	self.G2frame.ErrorDialog(
1857	'Empty project',
1858	'Project does not contain any single crystal data.')
1859	return True
1860	elif len(self.xtalDict) == 1:
1861	self.histnam = self.xtalDict.values()
1862	elif self.multiple:
1863	choices = sorted(self.xtalDict.values())
1864	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1865	if not hnum: return True
1866	self.histnam = [choices[i] for i in hnum]
1867	numselected = len(self.histnam)
1868	else:
1869	choices = sorted(self.xtalDict.values())
1870	hnum = G2G.ItemSelector(choices,self.G2frame)
1871	if hnum is None: return True
1872	self.histnam = [choices[hnum]]
1873	numselected = len(self.histnam)
1874	elif self.currentExportType == 'powder':
1875	if len(self.powderDict) == 0:
1876	self.G2frame.ErrorDialog(
1877	'Empty project',
1878	'Project does not contain any powder data.')
1879	return True
1880	elif len(self.powderDict) == 1:
1881	self.histnam = self.powderDict.values()
1882	elif self.multiple:
1883	choices = sorted(self.powderDict.values())
1884	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1885	if not hnum: return True
1886	self.histnam = [choices[i] for i in hnum]
1887	numselected = len(self.histnam)
1888	else:
1889	choices = sorted(self.powderDict.values())
1890	hnum = G2G.ItemSelector(choices,self.G2frame)
1891	if hnum is None: return True
1892	self.histnam = [choices[hnum]]
1893	numselected = len(self.histnam)
1894	elif self.currentExportType == 'image':
1895	if len(self.Histograms) == 0:
1896	self.G2frame.ErrorDialog(
1897	'Empty project',
1898	'Project does not contain any images.')
1899	return True
1900	elif len(self.Histograms) == 1:
1901	self.histnam = self.Histograms.keys()
1902	else:
1903	choices = sorted(self.Histograms.keys())
1904	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1905	if self.multiple:
1906	if not hnum: return True
1907	self.histnam = [choices[i] for i in hnum]
1908	else:
1909	if hnum is None: return True
1910	self.histnam = [choices[hnum]]
1911	numselected = len(self.histnam)
1912	if self.currentExportType == 'map':
1913	# search for phases with maps
1914	mapPhases = []
1915	choices = []
1916	for phasenam in sorted(self.Phases):
1917	phasedict = self.Phases[phasenam] # pointer to current phase info
1918	if len(phasedict['General']['Map'].get('rho',[])):
1919	mapPhases.append(phasenam)
1920	if phasedict['General']['Map'].get('Flip'):
1921	choices.append('Charge flip map: '+str(phasenam))
1922	elif phasedict['General']['Map'].get('MapType'):
1923	choices.append(
1924	str(phasedict['General']['Map'].get('MapType'))
1925	+ ' map: ' + str(phasenam))
1926	else:
1927	choices.append('unknown map: '+str(phasenam))
1928	# select a map if needed
1929	if len(mapPhases) == 0:
1930	self.G2frame.ErrorDialog(
1931	'Empty project',
1932	'Project does not contain any maps.')
1933	return True
1934	elif len(mapPhases) == 1:
1935	self.phasenam = mapPhases
1936	else:
1937	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1938	if self.multiple:
1939	if not phasenum: return True
1940	self.phasenam = [mapPhases[i] for i in phasenum]
1941	else:
1942	if phasenum is None: return True
1943	self.phasenam = [mapPhases[phasenum]]
1944	numselected = len(self.phasenam)
1945
1946	# items selected, now set self.dirname and usually self.filename
1947	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1948	AskFile == 'default' and not self.G2frame.GSASprojectfile
1949	):
1950	filename = self.askSaveFile()
1951	if not filename: return True
1952	self.dirname,self.filename = os.path.split(filename)
1953	elif AskFile == 'dir' or AskFile == 'single' or (
1954	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1955	):
1956	self.dirname = self.askSaveDirectory()
1957	if not self.dirname: return True
1958	elif AskFile == 'default-dir' or AskFile == 'default':
1959	self.dirname,self.filename = os.path.split(
1960	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1961	)
1962	else:
1963	raise Exception('This should not happen!')
1964
1965	def loadParmDict(self):
1966	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1967	refined values to those from the last cycle and set the uncertainties for the
1968	refined parameters in another dict (self.sigDict).
1969
1970	Expands the parm & sig dicts to include values derived from constraints.
1971	'''
1972	self.parmDict = {}
1973	self.sigDict = {}
1974	rigidbodyDict = {}
1975	covDict = {}
1976	consDict = {}
1977	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1978	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
1979	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
1980	while item:
1981	name = self.G2frame.PatternTree.GetItemText(item)
1982	if name == 'Rigid bodies':
1983	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
1984	elif name == 'Covariance':
1985	covDict = self.G2frame.PatternTree.GetItemPyData(item)
1986	elif name == 'Constraints':
1987	consDict = self.G2frame.PatternTree.GetItemPyData(item)
1988	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
1989	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1990	self.parmDict.update(rbDict)
1991	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1992	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,maxSSwave = G2stIO.GetPhaseData(
1993	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1994	self.parmDict.update(phaseDict)
1995	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
1996	Phases,Histograms,Print=False,resetRefList=False)
1997	self.parmDict.update(hapDict)
1998	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1999	self.parmDict.update(histDict)
2000	self.parmDict.update(zip(
2001	covDict.get('varyList',[]),
2002	covDict.get('variables',[])))
2003	self.sigDict = dict(zip(
2004	covDict.get('varyList',[]),
2005	covDict.get('sig',[])))
2006	# expand to include constraints: first compile a list of constraints
2007	constList = []
2008	for item in consDict:
2009	if item.startswith('_'): continue
2010	constList += consDict[item]
2011	# now process the constraints
2012	G2mv.InitVars()
2013	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
2014	varyList = covDict.get('varyListStart')
2015	if varyList is None and len(constDict) == 0:
2016	# no constraints can use varyList
2017	varyList = covDict.get('varyList')
2018	elif varyList is None:
2019	# old GPX file from before pre-constraint varyList is saved
2020	print ' * Old refinement: Please use Calculate/Refine to redo *'
2021	raise Exception(' * Export aborted *')
2022	else:
2023	varyList = list(varyList)
2024	try:
2025	groups,parmlist = G2mv.GroupConstraints(constDict)
2026	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
2027	except:
2028	# this really should not happen
2029	print ' * ERROR - constraints are internally inconsistent *'
2030	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
2031	print 'Errors',errmsg
2032	if warnmsg: print 'Warnings',warnmsg
2033	raise Exception(' * CIF creation aborted *')
2034	# add the constrained values to the parameter dictionary
2035	G2mv.Dict2Map(self.parmDict,varyList)
2036	# and add their uncertainties into the esd dictionary (sigDict)
2037	if covDict.get('covMatrix') is not None:
2038	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
2039
2040	def loadTree(self):
2041	'''Load the contents of the data tree into a set of dicts
2042	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2043	& self.xtalDict)
2044
2045	* The childrenless data tree items are overall parameters/controls for the
2046	entire project and are placed in self.OverallParms
2047	* Phase items are placed in self.Phases
2048	* Data items are placed in self.Histogram. The key for these data items
2049	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2050	'''
2051	self.OverallParms = {}
2052	self.powderDict = {}
2053	self.xtalDict = {}
2054	self.Phases = {}
2055	self.Histograms = {}
2056	self.SeqRefdata = None
2057	self.SeqRefhist = None
2058	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2059	histType = None
2060	if self.currentExportType == 'phase':
2061	# if exporting phases load them here
2062	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2063	if not sub:
2064	print 'no phases found'
2065	return True
2066	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2067	while item:
2068	phaseName = self.G2frame.PatternTree.GetItemText(item)
2069	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2070	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2071	return
2072	elif self.currentExportType == 'single':
2073	histType = 'HKLF'
2074	elif self.currentExportType == 'powder':
2075	histType = 'PWDR'
2076	elif self.currentExportType == 'image':
2077	histType = 'IMG'
2078
2079	if histType: # Loading just one kind of tree entry
2080	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2081	while item:
2082	name = self.G2frame.PatternTree.GetItemText(item)
2083	if name.startswith(histType):
2084	if self.Histograms.get(name): # there is already an item with this name
2085	print('Histogram name '+str(name)+' is repeated. Renaming')
2086	if name[-1] == '9':
2087	name = name[:-1] + '10'
2088	elif name[-1] in '012345678':
2089	name = name[:-1] + str(int(name[-1])+1)
2090	else:
2091	name += '-1'
2092	self.Histograms[name] = {}
2093	# the main info goes into Data, but the 0th
2094	# element contains refinement results, carry
2095	# that over too now.
2096	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2097	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2098	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2099	while item2:
2100	child = self.G2frame.PatternTree.GetItemText(item2)
2101	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2102	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2103	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2104	# index powder and single crystal histograms by number
2105	for hist in self.Histograms:
2106	if hist.startswith("PWDR"):
2107	d = self.powderDict
2108	elif hist.startswith("HKLF"):
2109	d = self.xtalDict
2110	else:
2111	return
2112	i = self.Histograms[hist].get('hId')
2113	if i is None and not d.keys():
2114	i = 0
2115	elif i is None or i in d.keys():
2116	i = max(d.keys())+1
2117	d[i] = hist
2118	return
2119	# else standard load: using all interlinked phases and histograms
2120	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2121	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2122	while item:
2123	name = self.G2frame.PatternTree.GetItemText(item)
2124	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2125	if not item2:
2126	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2127	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2128	# index powder and single crystal histograms
2129	for hist in self.Histograms:
2130	i = self.Histograms[hist]['hId']
2131	if hist.startswith("PWDR"):
2132	self.powderDict[i] = hist
2133	elif hist.startswith("HKLF"):
2134	self.xtalDict[i] = hist
2135
2136	def dumpTree(self,mode='type'):
2137	'''Print out information on the data tree dicts loaded in loadTree.
2138	Used for testing only.
2139	'''
2140	if self.SeqRefdata and self.SeqRefhist:
2141	print('Note that dumpTree does not show sequential results')
2142	print '\nOverall'
2143	if mode == 'type':
2144	def Show(arg): return type(arg)
2145	else:
2146	def Show(arg): return arg
2147	for key in self.OverallParms:
2148	print ' ',key,Show(self.OverallParms[key])
2149	print 'Phases'
2150	for key1 in self.Phases:
2151	print ' ',key1,Show(self.Phases[key1])
2152	print 'Histogram'
2153	for key1 in self.Histograms:
2154	print ' ',key1,Show(self.Histograms[key1])
2155	for key2 in self.Histograms[key1]:
2156	print ' ',key2,Show(self.Histograms[key1][key2])
2157
2158	def defaultSaveFile(self):
2159	return os.path.abspath(
2160	os.path.splitext(self.G2frame.GSASprojectfile
2161	)[0]+self.extension)
2162
2163	def askSaveFile(self):
2164	'''Ask the user to supply a file name
2165
2166	:returns: a file name (str) or None if Cancel is pressed
2167	'''
2168
2169	pth = G2G.GetExportPath(self.G2frame)
2170	defnam = os.path.splitext(
2171	os.path.split(self.G2frame.GSASprojectfile)[1]
2172	)[0]+self.extension
2173	dlg = wx.FileDialog(
2174	self.G2frame, 'Input name for file to write', pth, defnam,
2175	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2176	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
2177	dlg.CenterOnParent()
2178	try:
2179	if dlg.ShowModal() == wx.ID_OK:
2180	filename = dlg.GetPath()
2181	self.G2frame.LastExportDir = os.path.split(filename)[0]
2182	filename = os.path.splitext(filename)[0]+self.extension # make sure extension is correct
2183	else:
2184	filename = None
2185	finally:
2186	dlg.Destroy()
2187	return filename
2188
2189	def askSaveDirectory(self):
2190	'''Ask the user to supply a directory name. Path name is used as the
2191	starting point for the next export path search.
2192
2193	:returns: a directory name (str) or None if Cancel is pressed
2194	'''
2195	pth = G2G.GetExportPath(self.G2frame)
2196	dlg = wx.DirDialog(
2197	self.G2frame, 'Input directory where file(s) will be written', pth,
2198	wx.DD_DEFAULT_STYLE)
2199	dlg.CenterOnParent()
2200	try:
2201	if dlg.ShowModal() == wx.ID_OK:
2202	filename = dlg.GetPath()
2203	self.G2frame.LastExportDir = filename
2204	else:
2205	filename = None
2206	finally:
2207	dlg.Destroy()
2208	return filename
2209
2210	# Tools for file writing.
2211	def OpenFile(self,fil=None,mode='w'):
2212	'''Open the output file
2213
2214	:param str fil: The name of the file to open. If None (default)
2215	the name defaults to self.dirname + self.filename.
2216	If an extension is supplied, it is not overridded,
2217	but if not, the default extension is used.
2218	:returns: the file object opened by the routine which is also
2219	saved as self.fp
2220	'''
2221	if mode == 'd': # debug mode
2222	self.fullpath = '(stdout)'
2223	self.fp = sys.stdout
2224	return
2225	if not fil:
2226	if not os.path.splitext(self.filename)[1]:
2227	self.filename += self.extension
2228	fil = os.path.join(self.dirname,self.filename)
2229	self.fullpath = os.path.abspath(fil)
2230	self.fp = open(self.fullpath,mode)
2231	return self.fp
2232
2233	def Write(self,line):
2234	'''write a line of output, attaching a line-end character
2235
2236	:param str line: the text to be written.
2237	'''
2238	self.fp.write(line+'\n')
2239
2240	def CloseFile(self,fp=None):
2241	'''Close a file opened in OpenFile
2242
2243	:param file fp: the file object to be closed. If None (default)
2244	file object self.fp is closed.
2245	'''
2246	if self.fp == sys.stdout: return # debug mode
2247	if fp is None:
2248	fp = self.fp
2249	self.fp = None
2250	fp.close()
2251
2252	def SetSeqRef(self,data,hist):
2253	'''Set the exporter to retrieve results from a sequential refinement
2254	rather than the main tree
2255	'''
2256	self.SeqRefdata = data
2257	self.SeqRefhist = hist
2258	data_name = data[hist]
2259	for i,val in zip(data_name['varyList'],data_name['sig']):
2260	self.sigDict[i] = val
2261	self.sigDict[striphist(i)] = val
2262	for i in data_name['parmDict']:
2263	self.parmDict[striphist(i)] = data_name['parmDict'][i]
2264	self.parmDict[i] = data_name['parmDict'][i]
2265	# zero out the dA[xyz] terms, they would only bring confusion
2266	key = i.split(':')
2267	if len(key) < 3: continue
2268	if key[2].startswith('dA'):
2269	self.parmDict[i] = 0.0
2270	for i,(val,sig) in data_name.get('depParmDict',{}).iteritems():
2271	self.parmDict[i] = val
2272	self.sigDict[i] = sig
2273	#GSASIIpath.IPyBreak()
2274
2275	# Tools to pull information out of the data arrays
2276	def GetCell(self,phasenam):
2277	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2278
2279	:param str phasenam: the name for the selected phase
2280	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2281	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2282	cell values and `cellSig` has their uncertainties.
2283	"""
2284	if self.SeqRefdata and self.SeqRefhist:
2285	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
2286	phasedict = self.Phases[phasenam] # pointer to current phase info
2287	try:
2288	pfx = str(phasedict['pId'])+'::'
2289	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2290	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
2291	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2292	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2293	return cellList,cellSig
2294	except KeyError:
2295	cell = phasedict['General']['Cell'][1:]
2296	return cell,7*[0]
2297
2298	def GetSeqCell(self,phasenam,data_name):
2299	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2300	and histogram in a sequential fit
2301
2302	:param str phasenam: the name for the selected phase
2303	:param dict data_name: the sequential refinement parameters for the selected histogram
2304	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2305	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2306	cell values and `cellSig` has their uncertainties.
2307	"""
2308	phasedict = self.Phases[phasenam]
2309	SGdata = phasedict['General']['SGData']
2310	pId = phasedict['pId']
2311	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
2312	ESDlookup = {}
2313	Dlookup = {}
2314	varied = [striphist(i) for i in data_name['varyList']]
2315	for item,val in data_name['newCellDict'].iteritems():
2316	if item in varied:
2317	ESDlookup[val[0]] = item
2318	Dlookup[item] = val[0]
2319	A = RecpCellTerms[:]
2320	for i in range(6):
2321	var = str(pId)+'::A'+str(i)
2322	if var in ESDlookup:
2323	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
2324	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
2325	zeroDict = {i:0.0 for i in cellDict}
2326	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
2327	covData = {
2328	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
2329	'covMatrix': data_name['covMatrix']
2330	}
2331	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
2332
2333	def GetAtoms(self,phasenam):
2334	"""Gets the atoms associated with a phase. Can be used with standard
2335	or macromolecular phases
2336
2337	:param str phasenam: the name for the selected phase
2338	:returns: a list of items for eac atom where each item is a list containing:
2339	label, typ, mult, xyz, and td, where
2340
2341	* label and typ are the atom label and the scattering factor type (str)
2342	* mult is the site multiplicity (int)
2343	* xyz is contains a list with four pairs of numbers:
2344	x, y, z and fractional occupancy and
2345	their standard uncertainty (or a negative value)
2346	* td is contains a list with either one or six pairs of numbers:
2347	if one number it is U\ :sub:`iso` and with six numbers it is
2348	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2349	paired with their standard uncertainty (or a negative value)
2350	"""
2351	phasedict = self.Phases[phasenam] # pointer to current phase info
2352	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2353	cfrac = cx+3
2354	fpfx = str(phasedict['pId'])+'::Afrac:'
2355	atomslist = []
2356	for i,at in enumerate(phasedict['Atoms']):
2357	if phasedict['General']['Type'] == 'macromolecular':
2358	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2359	else:
2360	label = at[ct-1]
2361	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2362	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2363	mult = at[cs+1]
2364	typ = at[ct]
2365	xyz = []
2366	for j,v in enumerate(('x','y','z')):
2367	val = at[cx+j]
2368	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
2369	val = self.parmDict.get(pfx, val)
2370	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2371	sig = self.sigDict.get(dpfx,-0.000009)
2372	xyz.append((val,sig))
2373	xyz.append((fval,fsig))
2374	td = []
2375	if at[cia] == 'I':
2376	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2377	val = self.parmDict.get(pfx,at[cia+1])
2378	sig = self.sigDict.get(pfx,-0.0009)
2379	td.append((val,sig))
2380	else:
2381	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2382	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2383	val = self.parmDict.get(pfx,at[cia+2+i])
2384	sig = self.sigDict.get(pfx,-0.0009)
2385	td.append((val,sig))
2386	atomslist.append((label,typ,mult,xyz,td))
2387	return atomslist
2388	######################################################################
2389	def ExportPowderList(G2frame):
2390	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
2391	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
2392
2393	:param wx.Frame G2frame: the GSAS-II main data tree window
2394	'''
2395	extList = []
2396	for obj in G2frame.exporterlist:
2397	if 'powder' in obj.exporttype:
2398	try:
2399	obj.Writer
2400	extList.append(obj.extension)
2401	except AttributeError:
2402	pass
2403	return extList
2404
2405	def ExportPowder(G2frame,TreeName,fileroot,extension):
2406	'''Writes a single powder histogram using the Export routines.
2407	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
2408
2409	:param wx.Frame G2frame: the GSAS-II main data tree window
2410	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
2411	:param str fileroot: name for file to be written, extension ignored
2412	:param str extension: extension for file to be written (start with '.'). Must
2413	match a powder export routine that has a Writer object.
2414	'''
2415	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
2416	for obj in G2frame.exporterlist:
2417	if obj.extension == extension and 'powder' in obj.exporttype:
2418	obj.currentExportType = 'powder'
2419	obj.InitExport(None)
2420	obj.loadTree() # load all histograms in tree into dicts
2421	if TreeName not in obj.Histograms:
2422	raise Exception('Histogram not found: '+str(TreeName))
2423	try:
2424	obj.Writer
2425	except AttributeError:
2426	continue
2427	try:
2428	obj.Writer(TreeName,filename)
2429	return
2430	except Exception,err:
2431	print('Export Routine for '+extension+' failed.')
2432	print err
2433	else:
2434	print('No Export routine supports extension '+extension)
2435
2436	def ExportSequential(G2frame,data,obj,exporttype):
2437	'''
2438	Used to export from every phase/dataset in a sequential refinement using
2439	a .Writer method for either projects or phases. Prompts to select histograms
2440	and for phase exports, which phase(s).
2441
2442	:param wx.Frame G2frame: the GSAS-II main data tree window
2443	:param dict data: the sequential refinement data object
2444	:param str exporttype: indicates the type of export ('project' or 'phase')
2445	'''
2446	if len(data['histNames']) == 0:
2447	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
2448	obj.InitExport(None)
2449	obj.loadTree()
2450	obj.loadParmDict()
2451	if len(data['histNames']) == 1:
2452	histlist = data['histNames']
2453	else:
2454	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
2455	'Select histograms',data['histNames'])
2456	if dlg.ShowModal() == wx.ID_OK:
2457	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
2458	dlg.Destroy()
2459	else:
2460	dlg.Destroy()
2461	return
2462	if exporttype == 'Phase':
2463	phaselist = obj.Phases.keys()
2464	if len(obj.Phases) == 0:
2465	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
2466	return
2467	elif len(obj.Phases) > 1:
2468	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
2469	'Select phases', phaselist)
2470	if dlg.ShowModal() == wx.ID_OK:
2471	phaselist = [phaselist[l] for l in dlg.GetSelections()]
2472	dlg.Destroy()
2473	else:
2474	dlg.Destroy()
2475	return
2476	filename = obj.askSaveFile()
2477	if not filename: return True
2478	obj.dirname,obj.filename = os.path.split(filename)
2479	print('Writing output to file '+str(obj.filename)+"...")
2480	mode = 'w'
2481	for p in phaselist:
2482	for h in histlist:
2483	obj.SetSeqRef(data,h)
2484	#GSASIIpath.IPyBreak()
2485	obj.Writer(h,phasenam=p,mode=mode)
2486	mode = 'a'
2487	print('...done')
2488	elif exporttype == 'Project':
2489	filename = obj.askSaveFile()
2490	if not filename: return True
2491	obj.dirname,obj.filename = os.path.split(filename)
2492	print('Writing output to file '+str(obj.filename)+"...")
2493	mode = 'w'
2494	for h in histlist:
2495	obj.SetSeqRef(data,h)
2496	obj.Writer(h,mode=mode)
2497	print('\t'+str(h)+' written')
2498	mode = 'a'
2499	print('...done')
2500
2501	def ReadDIFFaX(DIFFaXfile):
2502	print 'read ',DIFFaXfile
2503	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
2504	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
2505	df = open(DIFFaXfile,'r')
2506	lines = df.readlines()
2507	df.close()
2508	struct = False
2509	Struct = []
2510	stack = False
2511	Stack = []
2512	trans = False
2513	Trans = []
2514	instr = False
2515	for diff in lines:
2516	diff = diff[:-1].lower()
2517	if '!' in diff:
2518	continue
2519	while '}' in diff: #strip comments
2520	iB = diff.index('{')
2521	iF = diff.index('}')+1
2522	if iB:
2523	diff = diff[:iB]
2524	else:
2525	diff = diff[iF:]
2526	if not diff:
2527	continue
2528	if diff.strip() == 'instrumental':
2529	instr = True
2530	continue
2531	if diff.strip() == 'structural':
2532	instr = False
2533	struct = True
2534	continue
2535	elif diff.strip() == 'stacking':
2536	struct = False
2537	stack = True
2538	continue
2539	elif diff.strip() == 'transitions':
2540	stack = False
2541	trans = True
2542	continue
2543	diff = diff.strip()
2544	if struct:
2545	if diff:
2546	Struct.append(diff)
2547	elif stack:
2548	if diff:
2549	Stack.append(diff)
2550	elif trans:
2551	if diff:
2552	Trans.append(diff)
2553
2554	#STRUCTURE records
2555	laueRec = Struct[1].split()
2556	Layer['Laue'] = laueRec[0]
2557	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2558	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2559	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2560	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2561	cell = Struct[0].split()
2562	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2563	nLayers = int(Struct[2])
2564	N = 3
2565	if 'layer' not in Struct[3]:
2566	N = 4
2567	if Struct[3] != 'infinite':
2568	width = Struct[3].split()
2569	Layer['Width'][0] = [float(width[0]),float(width[1])]
2570	for nL in range(nLayers):
2571	if '=' in Struct[N]:
2572	name = Struct[N].split('=')
2573	sameas = int(name[1])-1
2574	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2575	N += 1
2576	continue
2577	Symm = 'None'
2578	if 'centro' in Struct[N+1]: Symm = '-1'
2579	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2580	N += 2
2581	iatm = 0
2582	while 'layer' not in Struct[N]:
2583	atom = Struct[N][4:].split()
2584	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2585	if atomType not in Layer['AtInfo']:
2586	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2587	atomName = '%s(%s)'%(atomType,atom[0])
2588	newVals = []
2589	for val in atom[1:6]:
2590	if '/' in val:
2591	newVals.append(eval(val+'.'))
2592	else:
2593	newVals.append(float(val))
2594	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2595	Layer['Layers'][-1]['Atoms'].append(atomRec)
2596	N += 1
2597	if N > len(Struct)-1:
2598	break
2599	#TRANSITIONS records
2600	transArray = []
2601	N = 0
2602	for i in range(nLayers):
2603	transArray.append([])
2604	for j in range(nLayers):
2605	vals = Trans[N].split()
2606	newVals = []
2607	for val in vals[:4]:
2608	if '/' in val:
2609	newVals.append(eval(val+'.'))
2610	else:
2611	newVals.append(float(val))
2612	transArray[-1].append(newVals+['',False])
2613	N += 1
2614	Layer['Transitions'] = transArray
2615	#STACKING records
2616	Layer['Stacking'] = [Stack[0],'']
2617	if Stack[0] == 'recursive':
2618	Layer['Stacking'][1] = Stack[1]
2619	elif Stack[0] == 'explicit':
2620	if Stack[1] == 'random':
2621	Layer['Stacking'][1] = Stack[1]
2622	else:
2623	Layer['Stacking'][1] = 'list'
2624	Layer['Stacking'].append('')
2625	for stack in Stack[2:]:
2626	Layer['Stacking'][2] += ' '+stack
2627	return Layer
2628
2629	def ReadCIF(URLorFile):
2630	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2631	(from James Hester).
2632	The open routine gets confused with DOS names that begin with a letter and colon
2633	"C:\dir\" so this routine will try to open the passed name as a file and if that
2634	fails, try it as a URL
2635
2636	:param str URLorFile: string containing a URL or a file name. Code will try first
2637	to open it as a file and then as a URL.
2638
2639	:returns: a PyCifRW CIF object.
2640	'''
2641	import CifFile as cif # PyCifRW from James Hester
2642
2643	# alternate approach:
2644	#import urllib
2645	#ciffile = 'file:'+urllib.pathname2url(filename)
2646
2647	try:
2648	fp = open(URLorFile,'r')
2649	cf = cif.ReadCif(fp)
2650	fp.close()
2651	return cf
2652	except IOError:
2653	return cif.ReadCif(URLorFile)
2654
2655	if __name__ == '__main__':
2656	import GSASII
2657	application = GSASII.GSASIImain(0)
2658	G2frame = application.main
2659	#app = wx.PySimpleApp()
2660	#G2frame = wx.Frame(None) # create a frame
2661	#frm.Show(True)
2662	#filename = '/tmp/notzip.zip'
2663	#filename = '/tmp/all.zip'
2664	#filename = '/tmp/11bmb_7652.zip'
2665
2666	#selection=None, confirmoverwrite=True, parent=None
2667	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2668	#print ExtractFileFromZip(filename,multipleselect=True)
2669	# #confirmread=False, confirmoverwrite=False)
2670
2671	# choicelist=[ ('a','b','c'),
2672	# ('test1','test2'),('no choice',)]
2673	# titles = [ 'a, b or c', 'tests', 'No option here']
2674	# dlg = MultipleChoicesDialog(
2675	# choicelist,titles,
2676	# parent=frm)
2677	# if dlg.ShowModal() == wx.ID_OK:
2678	# print 'Got OK'
2679	imagefile = '/tmp/NDC5_00237_3.ge3'
2680	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2681
2682	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2683
2684	GSASIIpath.IPyBreak_base()

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