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source: trunk/GSASIIIO.py @ 2035

Last change on this file since 2035 was 2035, checked in by toby, 8 years ago
try RTFD build again with new approach
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2015-10-29 21:25:57 +0000 (Thu, 29 Oct 2015) $
4	# $Author: toby $
5	# $Revision: 2035 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 2035 2015-10-29 21:25:57Z toby $
8	########### SVN repository information ###################
9	'''
10	GSASIIIO: Misc I/O routines
11	=============================
12
13	Module with miscellaneous routines for input and output. Many
14	are GUI routines to interact with user.
15
16	Includes support for image reading.
17
18	Also includes base classes for data import routines.
19
20	'''
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 cPickle
28	import sys
29	import re
30	import random as ran
31	import GSASIIpath
32	GSASIIpath.SetVersionNumber("$Revision: 2035 $")
33	import GSASIIgrid as G2gd
34	import GSASIIspc as G2spc
35	import GSASIIobj as G2obj
36	import GSASIIlattice as G2lat
37	import GSASIIpwdGUI as G2pdG
38	import GSASIIimage as G2img
39	import GSASIIElem as G2el
40	import GSASIIstrIO as G2stIO
41	import GSASIImapvars as G2mv
42	import GSASIIctrls as G2G
43	import os
44	import os.path as ospath
45
46	DEBUG = False #=True for various prints
47	TRANSP = False #=true to transpose images for testing
48	if GSASIIpath.GetConfigValue('Transpose'): TRANSP = True
49	npsind = lambda x: np.sin(x*np.pi/180.)
50
51	def sfloat(S):
52	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
53	if S.strip():
54	try:
55	return float(S)
56	except ValueError:
57	pass
58	return 0.0
59
60	def sint(S):
61	'Convert a string to int. An empty field is treated as zero'
62	if S.strip():
63	return int(S)
64	else:
65	return 0
66
67	def trim(val):
68	'''Simplify a string containing leading and trailing spaces
69	as well as newlines, tabs, repeated spaces etc. into a shorter and
70	more simple string, by replacing all ranges of whitespace
71	characters with a single space.
72
73	:param str val: the string to be simplified
74
75	:returns: the (usually) shortened version of the string
76	'''
77	return re.sub('\s+', ' ', val).strip()
78
79	def makeInstDict(names,data,codes):
80	inst = dict(zip(names,zip(data,data,codes)))
81	for item in inst:
82	inst[item] = list(inst[item])
83	return inst
84
85	def FileDlgFixExt(dlg,file):
86	'this is needed to fix a problem in linux wx.FileDialog'
87	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
88	if ext not in file:
89	file += ext
90	return file
91
92	def GetPowderPeaks(fileName):
93	'Read powder peaks from a file'
94	sind = lambda x: math.sin(x*math.pi/180.)
95	asind = lambda x: 180.*math.asin(x)/math.pi
96	Cuka = 1.54052
97	File = open(fileName,'Ur')
98	Comments = []
99	peaks = []
100	S = File.readline()
101	while S:
102	if S[:1] == '#':
103	Comments.append(S[:-1])
104	else:
105	item = S.split()
106	if len(item) == 1:
107	peaks.append([float(item[0]),1.0])
108	elif len(item) > 1:
109	peaks.append([float(item[0]),float(item[0])])
110	S = File.readline()
111	File.close()
112	if Comments:
113	print 'Comments on file:'
114	for Comment in Comments: print Comment
115	Peaks = []
116	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
117	for peak in peaks:
118	dsp = peak[0]
119	sth = Cuka/(2.0*dsp)
120	if sth < 1.0:
121	tth = 2.0*asind(sth)
122	else:
123	break
124	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
125	else: #2-thetas - assume Cuka (for now)
126	for peak in peaks:
127	tth = peak[0]
128	dsp = Cuka/(2.0*sind(tth/2.0))
129	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
130	return Comments,Peaks
131
132	def CheckImageFile(G2frame,imagefile):
133	'''Try to locate an image file if the project and image have been moved
134	together. If the image file cannot be found, request the location from
135	the user.
136
137	:param wx.Frame G2frame: main GSAS-II Frame and data object
138	:param str imagefile: name of image file
139	:returns: imagefile, if it exists, or the name of a file
140	that does exist or False if the user presses Cancel
141
142	'''
143	if not os.path.exists(imagefile):
144	print 'Image file '+imagefile+' not found'
145	fil = imagefile.replace('\\','/') # windows?!
146	# see if we can find a file with same name or in a similarly named sub-dir
147	pth,fil = os.path.split(fil)
148	prevpth = None
149	while pth and pth != prevpth:
150	prevpth = pth
151	if os.path.exists(os.path.join(G2frame.dirname,fil)):
152	print 'found image file '+os.path.join(G2frame.dirname,fil)
153	return os.path.join(G2frame.dirname,fil)
154	pth,enddir = os.path.split(pth)
155	fil = os.path.join(enddir,fil)
156	# not found as a subdirectory, drop common parts of path for last saved & image file names
157	# if image was .../A/B/C/imgs/ima.ge
158	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
159	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
160	Controls = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
161	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
162	imgPath = imagefile.replace('\\','/').split('/')
163	for p1,p2 in zip(gpxPath,imgPath):
164	if p1 == p2:
165	gpxPath.pop(0),imgPath.pop(0)
166	else:
167	break
168	fil = os.path.join(*imgPath) # file with non-common prefix elements
169	prevpth = None
170	pth = os.path.abspath(G2frame.dirname)
171	while pth and pth != prevpth:
172	prevpth = pth
173	if os.path.exists(os.path.join(pth,fil)):
174	print 'found image file '+os.path.join(pth,fil)
175	return os.path.join(pth,fil)
176	pth,enddir = os.path.split(pth)
177	#GSASIIpath.IPyBreak()
178
179	if not os.path.exists(imagefile):
180	dlg = wx.FileDialog(G2frame, 'Previous image file not found; open here', '.', '',\
181	'Any image file (.edf;.tif;.tiff;.mar;.ge;.avg;.sum;.img;.cor;.stl)\
182	\|.edf;.tif;.tiff;.mar;.ge;.avg;.sum;.img;.cor;.stl\|\
183	European detector file (.edf)\|.edf\|\
184	Any detector tif (.tif;.tiff)\|.tif;.tiff\|\
185	MAR file (.mar)\|.mar\|\
186	GE Image (.ge;.avg;.sum;.cor)\|.ge;.avg;.sum;.cor\|\
187	ADSC Image (.img)\|.img\|\
188	Rigaku-Axis4 (.stl)\|.stl\|\
189	All files (.)\|.',wx.OPEN\|wx.CHANGE_DIR)
190	try:
191	dlg.SetFilename(''+ospath.split(imagefile)[1])
192	if dlg.ShowModal() == wx.ID_OK:
193	imagefile = dlg.GetPath()
194	else:
195	imagefile = False
196	finally:
197	dlg.Destroy()
198	return imagefile
199
200	def EditImageParms(parent,Data,Comments,Image,filename):
201	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
202	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
203	def onClose(event):
204	dlg.EndModal(wx.ID_OK)
205	mainsizer = wx.BoxSizer(wx.VERTICAL)
206	h,w = Image.shape[:2]
207	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,
208	'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
209	0,wx.ALIGN_LEFT\|wx.ALL, 2)
210
211	vsizer = wx.BoxSizer(wx.HORIZONTAL)
212	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
213	0,wx.ALIGN_LEFT\|wx.ALL, 2)
214	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
215	vsizer.Add(wdgt)
216	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
217
218	vsizer = wx.BoxSizer(wx.HORIZONTAL)
219	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
220	0,wx.ALIGN_LEFT\|wx.ALL, 2)
221	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
222	size=(50,-1))
223	vsizer.Add(wdgt)
224	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),
225	wx.ALIGN_LEFT\|wx.ALL, 2)
226	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,
227	size=(50,-1))
228	vsizer.Add(wdgt)
229	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
230
231	vsizer = wx.BoxSizer(wx.HORIZONTAL)
232	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
233	0,wx.ALIGN_LEFT\|wx.ALL, 2)
234	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
235	vsizer.Add(wdgt)
236	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
237
238	vsizer = wx.BoxSizer(wx.HORIZONTAL)
239	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
240	0,wx.ALIGN_LEFT\|wx.ALL, 2)
241	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,
242	size=(75,-1))
243	vsizer.Add(wdgt)
244	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),
245	wx.ALIGN_LEFT\|wx.ALL, 2)
246	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,
247	size=(75,-1))
248	vsizer.Add(wdgt)
249	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
250
251	vsizer = wx.BoxSizer(wx.HORIZONTAL)
252	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
253	0,wx.ALIGN_LEFT\|wx.ALL, 2)
254	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
255	vsizer.Add(wdgt)
256	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
257
258	btnsizer = wx.StdDialogButtonSizer()
259	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
260	OKbtn.SetDefault()
261	OKbtn.Bind(wx.EVT_BUTTON,onClose)
262	btnsizer.AddButton(OKbtn) # not sure why this is needed
263	btnsizer.Realize()
264	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
265	dlg.SetSizer(mainsizer)
266	dlg.CenterOnParent()
267	dlg.ShowModal()
268
269	def ReadLoadImage(imagefile,G2frame):
270	'''Read a GSAS-II image file and load it into the data tree
271	'''
272	# if a zip file, open and extract
273	if os.path.splitext(imagefile)[1].lower() == '.zip':
274	extractedfile = ExtractFileFromZip(imagefile,parent=G2frame)
275	if extractedfile is not None and extractedfile != imagefile:
276	imagefile = extractedfile
277	Comments,Data,Npix,Image = GetImageData(G2frame,imagefile)
278	if Comments:
279	LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image)
280
281	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
282	'''Load an image into the tree
283	'''
284
285	ImgNames = []
286	if G2frame.PatternTree.GetCount(): # get a list of existing Image entries
287	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
288	while item:
289	name = G2frame.PatternTree.GetItemText(item)
290	if name.startswith('IMG'): ImgNames.append(name)
291	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
292	TreeName = G2obj.MakeUniqueLabel('IMG '+os.path.basename(imagefile),ImgNames)
293	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=TreeName)
294	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
295	Imax = np.amax(Image)
296	Imin = max(0.0,np.amin(Image)) #force positive
297	if G2frame.imageDefault:
298	Data = copy.copy(G2frame.imageDefault)
299	Data['showLines'] = True
300	Data['ring'] = []
301	Data['rings'] = []
302	Data['cutoff'] = 10
303	Data['pixLimit'] = 20
304	Data['edgemin'] = 100000000
305	Data['calibdmin'] = 0.5
306	Data['calibskip'] = 0
307	Data['ellipses'] = []
308	Data['calibrant'] = ''
309	Data['GonioAngles'] = [0.,0.,0.]
310	Data['DetDepthRef'] = False
311	else:
312	Data['type'] = 'PWDR'
313	Data['color'] = 'Paired'
314	Data['tilt'] = 0.0
315	Data['rotation'] = 0.0
316	Data['showLines'] = False
317	Data['ring'] = []
318	Data['rings'] = []
319	Data['cutoff'] = 10
320	Data['pixLimit'] = 20
321	Data['calibdmin'] = 0.5
322	Data['calibskip'] = 0
323	Data['edgemin'] = 100000000
324	Data['ellipses'] = []
325	Data['GonioAngles'] = [0.,0.,0.]
326	Data['DetDepth'] = 0.
327	Data['DetDepthRef'] = False
328	Data['calibrant'] = ''
329	Data['IOtth'] = [2.0,5.0]
330	Data['LRazimuth'] = [135,225]
331	Data['azmthOff'] = 0.0
332	Data['outChannels'] = 2500
333	Data['outAzimuths'] = 1
334	Data['centerAzm'] = False
335	Data['fullIntegrate'] = False
336	Data['setRings'] = False
337	Data['background image'] = ['',-1.0]
338	Data['dark image'] = ['',-1.0]
339	Data['Flat Bkg'] = 0.0
340	Data['setDefault'] = False
341	Data['range'] = [(Imin,Imax),[Imin,Imax]]
342	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Image Controls'),Data)
343	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(Imin,Imax),[Imin,Imax]]}
344	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Masks'),Masks)
345	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Stress/Strain'),
346	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
347	G2frame.PatternTree.SetItemPyData(Id,[Npix,imagefile])
348	G2frame.PickId = Id
349	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
350	G2frame.Image = Id
351
352	def ReadImageData(G2frame,imagefile,imageOnly=False):
353	'''Read a single image with an image importer. Replacement for GetImageData
354
355	:param wx.Frame G2frame: main GSAS-II Frame and data object.
356	:param str imagefile: name of image file
357	:param bool imageOnly: If True return only the image,
358	otherwise (default) return more (see below)
359
360	:returns: an image as a numpy array or a list of four items:
361	Comments, Data, Npix and the Image, as selected by imageOnly
362
363	'''
364	# determine which formats are compatible with this file
365	print 'Debug: using ReadImageData'
366	primaryReaders = []
367	secondaryReaders = []
368	for rd in G2frame.ImportImageReaderlist:
369	flag = rd.ExtensionValidator(imagefile)
370	if flag is None:
371	secondaryReaders.append(rd)
372	elif flag:
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)
396	else:
397	flag = False
398	try:
399	flag = rd.Reader(imagefile,fp,ParentFrame)
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 GetImageData(G2frame,imagefile,imageOnly=False):
423	'''Read an image with the file reader keyed by the
424	file extension.
425
426	This routine will be replaced by ReadImageData, which will be renamed to this.
427
428	:param wx.Frame G2frame: main GSAS-II Frame and data object.
429
430	:param str imagefile: name of image file
431
432	:param bool imageOnly: If True return only the image,
433	otherwise (default) return more (see below)
434
435	:returns: an image as a numpy array or a list of four items:
436	Comments, Data, Npix and the Image, as selected by imageOnly
437
438	'''
439	if GSASIIpath.GetConfigValue('debug'): # test out using replacement routine
440	return ReadImageData(G2frame,imagefile,imageOnly)
441
442	ext = ospath.splitext(imagefile)[1]
443	Comments = []
444	Image = None
445	if ext == '.tif' or ext == '.tiff':
446	Comments,Data,Npix,Image = GetTifData(imagefile)
447	if Npix == 0:
448	print("GetTifData failed to read "+str(imagefile)+" Trying PIL")
449	import scipy.misc
450	Image = scipy.misc.imread(imagefile,flatten=True)
451	Npix = Image.size
452	Comments = ['no metadata']
453	Data = {'wavelength': 0.1, 'pixelSize': [200, 200], 'distance': 100.0}
454	Data['size'] = list(Image.shape)
455	Data['center'] = [int(i/2) for i in Image.shape]
456	if not imageOnly:
457	EditImageParms(G2frame,Data,Comments,Image,imagefile)
458	elif ext == '.edf':
459	Comments,Data,Npix,Image = GetEdfData(imagefile)
460	elif ext == '.img':
461	Comments,Data,Npix,Image = GetImgData(imagefile)
462	Image[0][0] = 0
463	elif ext in ['.mar3450','.mar2300','.mar2560']:
464	Comments,Data,Npix,Image = GetMAR345Data(imagefile)
465	elif ext in ['.sum','.avg','.cor'] or 'ge' in ext:
466	Comments,Data,Npix,Image = GetGEsumData(imagefile)
467	elif ext == '.G2img':
468	Comments,Data,Npix,Image = GetG2Image(imagefile)
469	elif ext == '.png':
470	Comments,Data,Npix,Image = GetPNGData(imagefile)
471	if not imageOnly:
472	EditImageParms(G2frame,Data,Comments,Image,imagefile)
473	elif ext == '.stl':
474	Comments,Data,Npix,Image = GetRigaku(imagefile)
475	# if not imageOnly:
476	# EditImageParms(G2frame,Data,Comments,Image,imagefile)
477	else:
478	print 'Extension for file '+imagefile+' not recognized'
479	if Image is None:
480	raise Exception('No image read')
481	if imageOnly:
482	if TRANSP:
483	print 'Transposing Image!'
484	return Image.T
485	else:
486	return Image
487	else:
488	if TRANSP:
489	print 'Transposing Image!'
490	return Comments,Data,Npix,Image.T
491	else:
492	return Comments,Data,Npix,Image
493
494	def PutG2Image(filename,Comments,Data,Npix,image):
495	'Write an image as a python pickle - might be better as an .edf file?'
496	File = open(filename,'wb')
497	cPickle.dump([Comments,Data,Npix,image],File,1)
498	File.close()
499	return
500
501	def GetG2Image(filename):
502	'Read an image as a python pickle'
503	File = open(filename,'rb')
504	Comments,Data,Npix,image = cPickle.load(File)
505	File.close()
506	return Comments,Data,Npix,image
507
508	def GetEdfData(filename,imageOnly=False):
509	'Read European detector data edf file'
510	import struct as st
511	import array as ar
512	if not imageOnly:
513	print 'Read European detector data edf file: ',filename
514	File = open(filename,'rb')
515	fileSize = os.stat(filename).st_size
516	head = File.read(3072)
517	lines = head.split('\n')
518	sizexy = [0,0]
519	pixSize = [154,154] #Pixium4700?
520	cent = [0,0]
521	wave = 1.54187 #default <CuKa>
522	dist = 1000.
523	head = ['European detector data',]
524	for line in lines:
525	line = line.replace(';',' ').strip()
526	fields = line.split()
527	if 'Dim_1' in line:
528	sizexy[0] = int(fields[2])
529	elif 'Dim_2' in line:
530	sizexy[1] = int(fields[2])
531	elif 'DataType' in line:
532	dType = fields[2]
533	elif 'wavelength' in line:
534	wave = float(fields[2])
535	elif 'Size' in line:
536	imSize = int(fields[2])
537	# elif 'DataType' in lines:
538	# dType = fields[2]
539	elif 'pixel_size_x' in line:
540	pixSize[0] = float(fields[2])
541	elif 'pixel_size_y' in line:
542	pixSize[1] = float(fields[2])
543	elif 'beam_center_x' in line:
544	cent[0] = float(fields[2])
545	elif 'beam_center_y' in line:
546	cent[1] = float(fields[2])
547	elif 'refined_distance' in line:
548	dist = float(fields[2])
549	if line:
550	head.append(line)
551	else: #blank line at end of header
552	break
553	File.seek(fileSize-imSize)
554	if dType == 'UnsignedShort':
555	image = np.array(ar.array('H',File.read(imSize)),dtype=np.int32)
556	elif dType == 'UnsignedInt':
557	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
558	elif dType == 'UnsignedLong':
559	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
560	elif dType == 'SignedInteger':
561	image = np.array(ar.array('l',File.read(imSize)),dtype=np.int32)
562	image = np.reshape(image,(sizexy[1],sizexy[0]))
563	data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'size':sizexy}
564	Npix = sizexy[0]*sizexy[1]
565	File.close()
566	if imageOnly:
567	return image
568	else:
569	return head,data,Npix,image
570
571	def GetRigaku(filename,imageOnly=False):
572	'Read Rigaku R-Axis IV image file'
573	import struct as st
574	import array as ar
575	if not imageOnly:
576	print 'Read Rigaku R-Axis IV file: ',filename
577	File = open(filename,'rb')
578	fileSize = os.stat(filename).st_size
579	Npix = (fileSize-6000)/2
580	Head = File.read(6000)
581	head = ['Rigaku R-Axis IV detector data',]
582	image = np.array(ar.array('H',File.read(fileSize-6000)),dtype=np.int32)
583	print fileSize,image.shape
584	print head
585	if Npix == 9000000:
586	sizexy = [3000,3000]
587	pixSize = [100.,100.]
588	elif Npix == 2250000:
589	sizexy = [1500,1500]
590	pixSize = [200.,200.]
591	else:
592	sizexy = [6000,6000]
593	pixSize = [50.,50.]
594	image = np.reshape(image,(sizexy[1],sizexy[0]))
595	data = {'pixelSize':pixSize,'wavelength':1.5428,'distance':250.0,'center':[150.,150.],'size':sizexy}
596	File.close()
597	if imageOnly:
598	return image
599	else:
600	return head,data,Npix,image
601
602	def GetGEsumData(filename,imageOnly=False):
603	'Read SUM file as produced at 1-ID from G.E. images'
604	import struct as st
605	import array as ar
606	if not imageOnly:
607	print 'Read GE sum file: ',filename
608	File = open(filename,'rb')
609	if '.sum' in filename or '.cor' in filename:
610	head = ['GE detector sum or cor data from APS 1-ID',]
611	sizexy = [2048,2048]
612	elif '.avg' in filename or '.ge' in filename:
613	head = ['GE detector avg or ge* data from APS 1-ID',]
614	sizexy = [2048,2048]
615	else:
616	head = ['GE detector raw data from APS 1-ID',]
617	File.seek(18)
618	size,nframes = st.unpack('<ih',File.read(6))
619	sizexy = [2048,2048]
620	pos = 8192
621	File.seek(pos)
622	Npix = sizexy[0]*sizexy[1]
623	if '.sum' in filename or '.cor' in filename:
624	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.int32)
625	elif '.avg' in filename or '.ge' in filename:
626	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
627	else:
628	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
629	while nframes > 1:
630	image += np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
631	nframes -= 1
632	image = np.reshape(image,(sizexy[1],sizexy[0]))
633	data = {'pixelSize':[200,200],'wavelength':0.15,'distance':250.0,'center':[204.8,204.8],'size':sizexy}
634	File.close()
635	if imageOnly:
636	return image
637	else:
638	return head,data,Npix,image
639
640	def GetImgData(filename,imageOnly=False):
641	'Read an ADSC image file'
642	import struct as st
643	import array as ar
644	if not imageOnly:
645	print 'Read ADSC img file: ',filename
646	File = open(filename,'rb')
647	head = File.read(511)
648	lines = head.split('\n')
649	head = []
650	center = [0,0]
651	for line in lines[1:-2]:
652	line = line.strip()[:-1]
653	if line:
654	if 'SIZE1' in line:
655	size = int(line.split('=')[1])
656	Npix = size*size
657	elif 'WAVELENGTH' in line:
658	wave = float(line.split('=')[1])
659	elif 'BIN' in line:
660	if line.split('=')[1] == '2x2':
661	pixel=(102,102)
662	else:
663	pixel = (51,51)
664	elif 'DISTANCE' in line:
665	distance = float(line.split('=')[1])
666	elif 'CENTER_X' in line:
667	center[0] = float(line.split('=')[1])
668	elif 'CENTER_Y' in line:
669	center[1] = float(line.split('=')[1])
670	head.append(line)
671	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center,'size':[size,size]}
672	image = []
673	row = 0
674	pos = 512
675	File.seek(pos)
676	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
677	image = np.reshape(image,(sizexy[1],sizexy[0]))
678	# image = np.zeros(shape=(size,size),dtype=np.int32)
679	# while row < size:
680	# File.seek(pos)
681	# line = ar.array('H',File.read(2*size))
682	# image[row] = np.asarray(line)
683	# row += 1
684	# pos += 2*size
685	File.close()
686	if imageOnly:
687	return image
688	else:
689	return lines[1:-2],data,Npix,image
690
691	def GetMAR345Data(filename,imageOnly=False):
692	'Read a MAR-345 image plate image'
693	import array as ar
694	import struct as st
695	try:
696	import pack_f as pf
697	except:
698	msg = wx.MessageDialog(None, message="Unable to load the GSAS MAR image decompression, pack_f",
699	caption="Import Error",
700	style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
701	msg.ShowModal()
702	return None,None,None,None
703
704	if not imageOnly:
705	print 'Read Mar345 file: ',filename
706	File = open(filename,'rb')
707	head = File.read(4095)
708	numbers = st.unpack('<iiiiiiiiii',head[:40])
709	lines = head[128:].split('\n')
710	head = []
711	for line in lines:
712	line = line.strip()
713	if 'PIXEL' in line:
714	values = line.split()
715	pixel = (int(values[2]),int(values[4])) #in microns
716	elif 'WAVELENGTH' in line:
717	wave = float(line.split()[1])
718	elif 'DISTANCE' in line:
719	distance = float(line.split()[1]) #in mm
720	elif 'CENTER' in line:
721	values = line.split()
722	center = [float(values[2])/10.,float(values[4])/10.] #make in mm from pixels
723	if line:
724	head.append(line)
725	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center}
726	for line in head:
727	if 'FORMAT' in line[0:6]:
728	items = line.split()
729	sizex = int(items[1])
730	Npix = int(items[3])
731	sizey = int(Npix/sizex)
732	pos = 4096
733	data['size'] = [sizex,sizey]
734	File.seek(pos)
735	line = File.read(8)
736	while 'CCP4' not in line: #get past overflow list for now
737	line = File.read(8)
738	pos += 8
739	pos += 37
740	File.seek(pos)
741	raw = File.read()
742	File.close()
743	image = np.zeros(shape=(sizex,sizey),dtype=np.int32)
744
745	image = np.flipud(pf.pack_f(len(raw),raw,sizex,sizey,image).T) #transpose to get it right way around & flip
746	if imageOnly:
747	return image
748	else:
749	return head,data,Npix,image
750
751	def GetPNGData(filename,imageOnly=False):
752	'''Read an image in a png format, assumes image is converted from CheMin tif file
753	so default parameters are that machine.
754	'''
755	import scipy.misc
756	Image = scipy.misc.imread(filename,flatten=True)
757	Npix = Image.size
758	Comments = ['no metadata']
759	pixy = list(Image.shape)
760	sizexy = [40,40]
761	Data = {'wavelength': 1.78892, 'pixelSize': sizexy, 'distance': 18.0,'size':pixy}
762	Data['center'] = [pixy[0]sizexy[0]/1000,pixy[1]sizexy[1]/2000]
763	if imageOnly:
764	return Image.T
765	else:
766	return Comments,Data,Npix,Image.T
767
768	def GetTifData(filename,imageOnly=False):
769	'''Read an image in a pseudo-tif format,
770	as produced by a wide variety of software, almost always
771	incorrectly in some way.
772	'''
773	import struct as st
774	try:
775	import Image as Im
776	except ImportError:
777	try:
778	from PIL import Image as Im
779	except ImportError:
780	print "PIL/pillow Image module not present. TIFs cannot be read without this"
781	raise Exception("PIL/pillow Image module not found")
782	import array as ar
783	import ReadMarCCDFrame as rmf
784	File = open(filename,'rb')
785	dataType = 5
786	center = [None,None]
787	wavelength = None
788	distance = None
789	try:
790	Meta = open(filename+'.metadata','Ur')
791	head = Meta.readlines()
792	for line in head:
793	line = line.strip()
794	if 'dataType=' in line:
795	dataType = int(line.split('=')[1])
796	Meta.close()
797	except IOError:
798	print 'no metadata file found - will try to read file anyway'
799	head = ['no metadata file found',]
800
801	tag = File.read(2)
802	byteOrd = '<'
803	if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
804	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
805	elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
806	byteOrd = '>'
807	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
808	else:
809	lines = ['not a detector tiff file',]
810	return lines,0,0,0
811	File.seek(IFD) #get number of directory entries
812	NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
813	IFD = {}
814	nSlice = 1
815	for ied in range(NED):
816	Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
817	nVal = st.unpack(byteOrd+'i',File.read(4))[0]
818	if DEBUG: print 'Try:',Tag,Type,nVal
819	if Type == 1:
820	Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
821	elif Type == 2:
822	Value = st.unpack(byteOrd+'i',File.read(4))
823	elif Type == 3:
824	Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
825	x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
826	elif Type == 4:
827	if Tag in [273,279]:
828	nSlice = nVal
829	nVal = 1
830	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
831	elif Type == 5:
832	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
833	elif Type == 11:
834	Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
835	IFD[Tag] = [Type,nVal,Value]
836	if DEBUG: print Tag,IFD[Tag]
837	sizexy = [IFD[256][2][0],IFD[257][2][0]]
838	[nx,ny] = sizexy
839	Npix = nx*ny
840	if 34710 in IFD:
841	if not imageOnly:
842	print 'Read MAR CCD tiff file: ',filename
843	marFrame = rmf.marFrame(File,byteOrd,IFD)
844	image = np.flipud(np.array(np.asarray(marFrame.image),dtype=np.int32))
845	tifType = marFrame.filetitle
846	pixy = [marFrame.pixelsizeX/1000.0,marFrame.pixelsizeY/1000.0]
847	head = marFrame.outputHead()
848	# extract resonable wavelength from header
849	wavelength = marFrame.sourceWavelength*1e-5
850	wavelength = (marFrame.opticsWavelength > 0) and marFrame.opticsWavelength*1e-5 or wavelength
851	wavelength = (wavelength <= 0) and None or wavelength
852	# extract resonable distance from header
853	distance = (marFrame.startXtalToDetector+marFrame.endXtalToDetector)*5e-4
854	distance = (distance <= 0) and marFrame.xtalToDetector*1e-3 or distance
855	distance = (distance <= 0) and None or distance
856	# extract resonable center from header
857	center = [marFrame.beamXmarFrame.pixelsizeX1e-9,marFrame.beamYmarFrame.pixelsizeY1e-9]
858	center = (center[0] != 0 and center[1] != 0) and center or [None,None]
859	#print head,tifType,pixy
860	elif nSlice > 1: #CheMin multislice tif file!
861	tifType = 'CheMin'
862	pixy = [40,40]
863	image = np.flipud(np.array(Im.open(filename)))*10.
864	distance = 18.0
865	center = [pixy[0]*sizexy[0]/2000,0] #the CheMin beam stop is here
866	wavelength = 1.78892
867	elif 272 in IFD:
868	ifd = IFD[272]
869	File.seek(ifd[2][0])
870	S = File.read(ifd[1])
871	if 'PILATUS' in S:
872	tifType = 'Pilatus'
873	dataType = 0
874	pixy = [172,172]
875	File.seek(4096)
876	if not imageOnly:
877	print 'Read Pilatus tiff file: ',filename
878	image = ar.array('L',File.read(4*Npix))
879	image = np.array(np.asarray(image),dtype=np.int32)
880	else:
881	if IFD[258][2][0] == 16:
882	tifType = 'GE'
883	pixy = [200,200]
884	File.seek(8)
885	if not imageOnly:
886	print 'Read GE-detector tiff file: ',filename
887	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
888	elif IFD[258][2][0] == 32:
889	tifType = 'CHESS'
890	pixy = [200,200]
891	File.seek(8)
892	if not imageOnly:
893	print 'Read CHESS-detector tiff file: ',filename
894	image = np.array(ar.array('L',File.read(4*Npix)),dtype=np.int32)
895
896	elif 262 in IFD and IFD[262][2][0] > 4:
897	tifType = 'DND'
898	pixy = [158,158]
899	File.seek(512)
900	if not imageOnly:
901	print 'Read DND SAX/WAX-detector tiff file: ',filename
902	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
903	elif sizexy == [1536,1536]:
904	tifType = 'APS Gold'
905	pixy = [150,150]
906	File.seek(64)
907	if not imageOnly:
908	print 'Read Gold tiff file:',filename
909	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
910	elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
911	if IFD[273][2][0] == 8:
912	if IFD[258][2][0] == 32:
913	tifType = 'PE'
914	pixy = [200,200]
915	File.seek(8)
916	if not imageOnly:
917	print 'Read APS PE-detector tiff file: ',filename
918	if dataType == 5:
919	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
920	else:
921	image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
922	elif IFD[258][2][0] == 16:
923	tifType = 'MedOptics D1'
924	pixy = [46.9,46.9]
925	File.seek(8)
926	if not imageOnly:
927	print 'Read MedOptics D1 tiff file: ',filename
928	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
929
930	elif IFD[273][2][0] == 4096:
931	if sizexy[0] == 3072:
932	pixy = [73,73]
933	tifType = 'MAR225'
934	else:
935	pixy = [158,158]
936	tifType = 'MAR325'
937	File.seek(4096)
938	if not imageOnly:
939	print 'Read MAR CCD tiff file: ',filename
940	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
941	elif IFD[273][2][0] == 512:
942	tiftype = '11-ID-C'
943	pixy = [200,200]
944	File.seek(512)
945	if not imageOnly:
946	print 'Read 11-ID-C tiff file: ',filename
947	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
948	elif sizexy == [4096,4096]:
949	if IFD[273][2][0] == 8:
950	if IFD[258][2][0] == 16:
951	tifType = 'scanCCD'
952	pixy = [9,9]
953	File.seek(8)
954	if not imageOnly:
955	print 'Read APS scanCCD tiff file: ',filename
956	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
957	elif IFD[273][2][0] == 4096:
958	tifType = 'Rayonix'
959	pixy = [73.242,73.242]
960	File.seek(4096)
961	if not imageOnly:
962	print 'Read Rayonix MX300HE tiff file: ',filename
963	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
964	# elif sizexy == [960,960]:
965	# tiftype = 'PE-BE'
966	# pixy = (200,200)
967	# File.seek(8)
968	# if not imageOnly:
969	# print 'Read Gold tiff file:',filename
970	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
971
972	else:
973	lines = ['not a known detector tiff file',]
974	return lines,0,0,0
975
976	if sizexy[1]*sizexy[0] != image.size: # test is resize is allowed
977	lines = ['not a known detector tiff file',]
978	return lines,0,0,0
979
980	image = np.reshape(image,(sizexy[1],sizexy[0]))
981	center = (not center[0]) and [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000] or center
982	wavelength = (not wavelength) and 0.10 or wavelength
983	distance = (not distance) and 100.0 or distance
984	data = {'pixelSize':pixy,'wavelength':wavelength,'distance':distance,'center':center,'size':sizexy}
985	File.close()
986	if imageOnly:
987	return image
988	else:
989	return head,data,Npix,image
990
991	#def GetTifData(filename,imageOnly=False):
992	# import struct as st
993	# import array as ar
994	# File = open(filename,'rb')
995	# dataType = 5
996	# try:
997	# Meta = open(filename+'.metadata','Ur')
998	# head = Meta.readlines()
999	# for line in head:
1000	# line = line.strip()
1001	# if 'dataType=' in line:
1002	# dataType = int(line.split('=')[1])
1003	# Meta.close()
1004	# except IOError:
1005	# print 'no metadata file found - will try to read file anyway'
1006	# head = ['no metadata file found',]
1007	#
1008	# tag = File.read(2)
1009	# byteOrd = '<'
1010	# if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
1011	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
1012	# elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
1013	# byteOrd = '>'
1014	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
1015	# else:
1016	# lines = ['not a detector tiff file',]
1017	# return lines,0,0,0
1018	# File.seek(IFD) #get number of directory entries
1019	# NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
1020	# IFD = {}
1021	# for ied in range(NED):
1022	# Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
1023	# nVal = st.unpack(byteOrd+'i',File.read(4))[0]
1024	# if Type == 1:
1025	# Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
1026	# elif Type == 2:
1027	# Value = st.unpack(byteOrd+'i',File.read(4))
1028	# elif Type == 3:
1029	# Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
1030	# x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
1031	# elif Type == 4:
1032	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
1033	# elif Type == 5:
1034	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
1035	# elif Type == 11:
1036	# Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
1037	# IFD[Tag] = [Type,nVal,Value]
1038	## print Tag,IFD[Tag]
1039	# sizexy = [IFD[256][2][0],IFD[257][2][0]]
1040	# [nx,ny] = sizexy
1041	# Npix = nx*ny
1042	# if 272 in IFD:
1043	# ifd = IFD[272]
1044	# File.seek(ifd[2][0])
1045	# S = File.read(ifd[1])
1046	# if 'PILATUS' in S:
1047	# tifType = 'Pilatus'
1048	# dataType = 0
1049	# pixy = (172,172)
1050	# File.seek(4096)
1051	# if not imageOnly:
1052	# print 'Read Pilatus tiff file: ',filename
1053	# image = ar.array('L',File.read(4*Npix))
1054	# image = np.array(np.asarray(image),dtype=np.int32)
1055	# elif 262 in IFD and IFD[262][2][0] > 4:
1056	# tifType = 'DND'
1057	# pixy = (158,158)
1058	# File.seek(512)
1059	# if not imageOnly:
1060	# print 'Read DND SAX/WAX-detector tiff file: ',filename
1061	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
1062	# elif sizexy == [1536,1536]:
1063	# tifType = 'APS Gold'
1064	# pixy = (150,150)
1065	# File.seek(64)
1066	# if not imageOnly:
1067	# print 'Read Gold tiff file:',filename
1068	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
1069	# elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
1070	# if IFD[273][2][0] == 8:
1071	# if IFD[258][2][0] == 32:
1072	# tifType = 'PE'
1073	# pixy = (200,200)
1074	# File.seek(8)
1075	# if not imageOnly:
1076	# print 'Read APS PE-detector tiff file: ',filename
1077	# if dataType == 5:
1078	# image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
1079	# else:
1080	# image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
1081	# elif IFD[273][2][0] == 4096:
1082	# if sizexy[0] == 3072:
1083	# pixy = (73,73)
1084	# tifType = 'MAR225'
1085	# else:
1086	# pixy = (158,158)
1087	# tifType = 'MAR325'
1088	# File.seek(4096)
1089	# if not imageOnly:
1090	# print 'Read MAR CCD tiff file: ',filename
1091	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
1092	# elif IFD[273][2][0] == 512:
1093	# tiftype = '11-ID-C'
1094	# pixy = [200,200]
1095	# File.seek(512)
1096	# if not imageOnly:
1097	# print 'Read 11-ID-C tiff file: ',filename
1098	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
1099	# elif sizexy == [4096,4096]:
1100	# if IFD[273][2][0] == 8:
1101	# if IFD[258][2][0] == 16:
1102	# tifType = 'scanCCD'
1103	# pixy = (9,9)
1104	# File.seek(8)
1105	# if not imageOnly:
1106	# print 'Read APS scanCCD tiff file: ',filename
1107	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
1108	# elif IFD[273][2][0] == 4096:
1109	# tifType = 'Rayonix'
1110	# pixy = (73.242,73.242)
1111	# File.seek(4096)
1112	# if not imageOnly:
1113	# print 'Read Rayonix MX300HE tiff file: ',filename
1114	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
1115	## elif sizexy == [960,960]:
1116	## tiftype = 'PE-BE'
1117	## pixy = (200,200)
1118	## File.seek(8)
1119	## if not imageOnly:
1120	## print 'Read Gold tiff file:',filename
1121	## image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
1122	#
1123	# else:
1124	# lines = ['not a known detector tiff file',]
1125	# return lines,0,0,0
1126	#
1127	# image = np.reshape(image,(sizexy[1],sizexy[0]))
1128	# center = [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000]
1129	# data = {'pixelSize':pixy,'wavelength':0.10,'distance':100.0,'center':center,'size':sizexy}
1130	# File.close()
1131	# if imageOnly:
1132	# return image
1133	# else:
1134	# return head,data,Npix,image
1135	#
1136	def ProjFileOpen(G2frame):
1137	'Read a GSAS-II project file and load into the G2 data tree'
1138	if not os.path.exists(G2frame.GSASprojectfile):
1139	print ('\n*** Error attempt to open project file that does not exist:\n '+
1140	str(G2frame.GSASprojectfile))
1141	return
1142	LastSavedUsing = None
1143	file = open(G2frame.GSASprojectfile,'rb')
1144	print 'load from file: ',G2frame.GSASprojectfile
1145	G2frame.SetTitle("GSAS-II data tree: "+
1146	os.path.split(G2frame.GSASprojectfile)[1])
1147	wx.BeginBusyCursor()
1148	try:
1149	while True:
1150	try:
1151	data = cPickle.load(file)
1152	except EOFError:
1153	break
1154	datum = data[0]
1155
1156	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=datum[0])
1157	if 'PWDR' in datum[0]:
1158	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
1159	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
1160	G2frame.PatternTree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
1161	elif datum[0].startswith('HKLF'):
1162	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
1163	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
1164	G2frame.PatternTree.SetItemPyData(Id,datum[1])
1165	else:
1166	G2frame.PatternTree.SetItemPyData(Id,datum[1])
1167	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
1168	LastSavedUsing = datum[1]['LastSavedUsing']
1169	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug'):
1170	print('Packages used to create .GPX file:')
1171	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
1172	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
1173	print("{:>14s}: {:s}".format(p[0],p[1]))
1174	else:
1175	for p in datum[1]['PythonVersions']:
1176	print("{:<12s} {:s}".format(p[0]+':',p[1]))
1177	for datus in data[1:]:
1178	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
1179	#patch
1180	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
1181	if 'PWDR' in datum[0]:
1182	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
1183	else:
1184	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
1185	for item in datus[1][0]: #zip makes tuples - now make lists!
1186	datus[1][0][item] = list(datus[1][0][item])
1187	#end patch
1188	G2frame.PatternTree.SetItemPyData(sub,datus[1])
1189	if 'IMG' in datum[0]: #retrieve image default flag & data if set
1190	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
1191	if Data['setDefault']:
1192	G2frame.imageDefault = Data
1193	file.close()
1194	if LastSavedUsing:
1195	print('GPX load successful. Last saved with GSAS-II version '+LastSavedUsing)
1196	else:
1197	print('project load successful')
1198	G2frame.NewPlot = True
1199	except:
1200	msg = wx.MessageDialog(G2frame,message="Error reading file "+
1201	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
1202	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
1203	msg.ShowModal()
1204	finally:
1205	wx.EndBusyCursor()
1206	G2frame.Status.SetStatusText('To reorder tree items, use mouse RB to drag/drop them')
1207
1208	def ProjFileSave(G2frame):
1209	'Save a GSAS-II project file'
1210	if not G2frame.PatternTree.IsEmpty():
1211	file = open(G2frame.GSASprojectfile,'wb')
1212	print 'save to file: ',G2frame.GSASprojectfile
1213	# stick the file name into the tree and version info into tree so they are saved.
1214	# (Controls should always be created at this point)
1215	try:
1216	Controls = G2frame.PatternTree.GetItemPyData(
1217	G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
1218	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
1219	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
1220	Controls['PythonVersions'] = G2frame.PackageVersions
1221	except:
1222	pass
1223	wx.BeginBusyCursor()
1224	try:
1225	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
1226	while item:
1227	data = []
1228	name = G2frame.PatternTree.GetItemText(item)
1229	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
1230	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
1231	while item2:
1232	name = G2frame.PatternTree.GetItemText(item2)
1233	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
1234	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
1235	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1236	cPickle.dump(data,file,1)
1237	file.close()
1238	finally:
1239	wx.EndBusyCursor()
1240	print('project save successful')
1241
1242	def SaveIntegration(G2frame,PickId,data):
1243	'Save image integration results as powder pattern(s)'
1244	azms = G2frame.Integrate[1]
1245	X = G2frame.Integrate[2][:-1]
1246	N = len(X)
1247	Id = G2frame.PatternTree.GetItemParent(PickId)
1248	name = G2frame.PatternTree.GetItemText(Id)
1249	name = name.replace('IMG ',data['type']+' ')
1250	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
1251	if 'PWDR' in name:
1252	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
1253	codes = [0 for i in range(11)]
1254	elif 'SASD' in name:
1255	names = ['Type','Lam','Zero','Azimuth']
1256	codes = [0 for i in range(4)]
1257	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
1258	Xminmax = [X[0],X[-1]]
1259	LRazm = data['LRazimuth']
1260	Azms = []
1261	dazm = 0.
1262	if data['fullIntegrate'] and data['outAzimuths'] == 1:
1263	Azms = [45.0,] #a poor man's average?
1264	else:
1265	for i,azm in enumerate(azms[:-1]):
1266	if azm > 360. and azms[i+1] > 360.:
1267	Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
1268	else:
1269	Azms.append(G2img.meanAzm(azm,azms[i+1]))
1270	dazm = np.min(np.abs(np.diff(azms)))/2.
1271	G2frame.IntgOutList = []
1272	for i,azm in enumerate(azms[:-1]):
1273	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
1274	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
1275	nOcc = 0
1276	while item:
1277	Name = G2frame.PatternTree.GetItemText(item)
1278	if Aname in Name:
1279	nOcc += 1
1280	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1281	if nOcc:
1282	Aname += '(%d)'%(nOcc)
1283	Sample = G2pdG.SetDefaultSample()
1284	Sample['Gonio. radius'] = data['distance']
1285	Sample['Omega'] = data['GonioAngles'][0]
1286	Sample['Chi'] = data['GonioAngles'][1]
1287	Sample['Phi'] = data['GonioAngles'][2]
1288	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
1289	if 'PWDR' in Aname:
1290	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!
1291	elif 'SASD' in Aname:
1292	Sample['Trans'] = data['SampleAbs'][0]
1293	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
1294	Y = G2frame.Integrate[0][i]
1295	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
1296	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=Aname)
1297	G2frame.IntgOutList.append(Id)
1298	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
1299	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
1300	if 'PWDR' in Aname:
1301	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
1302	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
1303	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
1304	for item in inst[0]:
1305	inst[0][item] = list(inst[0][item])
1306	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
1307	if 'PWDR' in Aname:
1308	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1309	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
1310	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[[],[]])
1311	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
1312	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
1313	elif 'SASD' in Aname:
1314	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
1315	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1316	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
1317	valuesdict = {
1318	'wtFactor':1.0,
1319	'Dummy':False,
1320	'ranId':ran.randint(0,sys.maxint),
1321	'Offset':[0.0,0.0],'delOffset':0.02,'refOffset':-1.0,'refDelt':0.01,
1322	'qPlot':False,'dPlot':False,'sqrtPlot':False
1323	}
1324	G2frame.PatternTree.SetItemPyData(
1325	Id,[valuesdict,
1326	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
1327	return Id #last powder pattern generated
1328
1329	# def powderFxyeSave(G2frame,exports,powderfile):
1330	# 'Save a powder histogram as a GSAS FXYE file'
1331	# head,tail = ospath.split(powderfile)
1332	# name,ext = tail.split('.')
1333	# for i,export in enumerate(exports):
1334	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1335	# prmname = filename.strip(ext)+'prm'
1336	# prm = open(prmname,'w') #old style GSAS parm file
1337	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1338	# Inst = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, \
1339	# PickId, 'Instrument Parameters'))[0]
1340	# prm.write( ' 123456789012345678901234567890123456789012345678901234567890 '+'\n')
1341	# prm.write( 'INS BANK 1 '+'\n')
1342	# prm.write(('INS HTYPE %sR '+'\n')%(Inst['Type'][0]))
1343	# if 'Lam1' in Inst: #Ka1 & Ka2
1344	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam1'][0],Inst['Lam2'][0]))
1345	# elif 'Lam' in Inst: #single wavelength
1346	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam'][1],0.0))
1347	# prm.write( 'INS 1 IRAD 0 '+'\n')
1348	# prm.write( 'INS 1I HEAD '+'\n')
1349	# prm.write( 'INS 1I ITYP 0 0.0000 180.0000 1 '+'\n')
1350	# prm.write(('INS 1DETAZM%10.3f '+'\n')%(Inst['Azimuth'][0]))
1351	# prm.write( 'INS 1PRCF1 3 8 0.00100 '+'\n')
1352	# prm.write(('INS 1PRCF11 %15.6g%15.6g%15.6g%15.6g '+'\n')%(Inst['U'][1],Inst['V'][1],Inst['W'][1],0.0))
1353	# prm.write(('INS 1PRCF12 %15.6g%15.6g%15.6g%15.6g '+'\n')%(Inst['X'][1],Inst['Y'][1],Inst['SH/L'][1]/2.,Inst['SH/L'][1]/2.))
1354	# prm.close()
1355	# file = open(filename,'w')
1356	# print 'save powder pattern to file: ',filename
1357	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1358	# file.write(powderfile+'\n')
1359	# file.write('Instrument parameter file:'+ospath.split(prmname)[1]+'\n')
1360	# file.write('BANK 1 %d %d CONS %.2f %.2f 0 0 FXYE\n'%(len(x),len(x),\
1361	# 100.x[0],100.(x[1]-x[0])))
1362	# s = list(np.sqrt(1./np.array(w)))
1363	# XYW = zip(x,y,s)
1364	# for X,Y,S in XYW:
1365	# file.write("%15.6g %15.6g %15.6g\n" % (100.*X,Y,max(S,1.0)))
1366	# file.close()
1367	# print 'powder pattern file '+filename+' written'
1368
1369	# def powderXyeSave(G2frame,exports,powderfile):
1370	# 'Save a powder histogram as a Topas XYE file'
1371	# head,tail = ospath.split(powderfile)
1372	# name,ext = tail.split('.')
1373	# for i,export in enumerate(exports):
1374	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1375	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1376	# file = open(filename,'w')
1377	# file.write('#%s\n'%(export))
1378	# print 'save powder pattern to file: ',filename
1379	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1380	# s = list(np.sqrt(1./np.array(w)))
1381	# XYW = zip(x,y,s)
1382	# for X,Y,W in XYW:
1383	# file.write("%15.6g %15.6g %15.6g\n" % (X,Y,W))
1384	# file.close()
1385	# print 'powder pattern file '+filename+' written'
1386
1387	def PDFSave(G2frame,exports):
1388	'Save a PDF G(r) and S(Q) in column formats'
1389	for export in exports:
1390	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1391	SQname = 'S(Q)'+export[4:]
1392	GRname = 'G(R)'+export[4:]
1393	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
1394	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
1395	sqId = G2gd.GetPatternTreeItemId(G2frame, PickId, SQname)
1396	grId = G2gd.GetPatternTreeItemId(G2frame, PickId, GRname)
1397	sqdata = np.array(G2frame.PatternTree.GetItemPyData(sqId)[1][:2]).T
1398	grdata = np.array(G2frame.PatternTree.GetItemPyData(grId)[1][:2]).T
1399	sqfile = open(sqfilename,'w')
1400	grfile = open(grfilename,'w')
1401	sqfile.write('#T S(Q) %s\n'%(export))
1402	grfile.write('#T G(R) %s\n'%(export))
1403	sqfile.write('#L Q S(Q)\n')
1404	grfile.write('#L R G(R)\n')
1405	for q,sq in sqdata:
1406	sqfile.write("%15.6g %15.6g\n" % (q,sq))
1407	sqfile.close()
1408	for r,gr in grdata:
1409	grfile.write("%15.6g %15.6g\n" % (r,gr))
1410	grfile.close()
1411
1412	def PeakListSave(G2frame,file,peaks):
1413	'Save powder peaks to a data file'
1414	print 'save peak list to file: ',G2frame.peaklistfile
1415	if not peaks:
1416	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1417	try:
1418	result = dlg.ShowModal()
1419	finally:
1420	dlg.Destroy()
1421	return
1422	for peak in peaks:
1423	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1424	(peak[0],peak[2],peak[4],peak[6]))
1425	print 'peak list saved'
1426
1427	def IndexPeakListSave(G2frame,peaks):
1428	'Save powder peaks from the indexing list'
1429	file = open(G2frame.peaklistfile,'wa')
1430	print 'save index peak list to file: ',G2frame.peaklistfile
1431	wx.BeginBusyCursor()
1432	try:
1433	if not peaks:
1434	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1435	try:
1436	result = dlg.ShowModal()
1437	finally:
1438	dlg.Destroy()
1439	return
1440	for peak in peaks:
1441	file.write("%12.6f\n" % (peak[7]))
1442	file.close()
1443	finally:
1444	wx.EndBusyCursor()
1445	print 'index peak list saved'
1446
1447	def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1448	'''Create a new phase dict with default values for various parameters
1449
1450	:param str Name: Name for new Phase
1451
1452	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1453	defaults to data for P 1
1454
1455	:param list cell: unit cell parameter list; defaults to
1456	[1.0,1.0,1.0,90.,90,90.,1.]
1457
1458	'''
1459	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1460	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1461	phaseData = {
1462	'ranId':ran.randint(0,sys.maxint),
1463	'General':{
1464	'Name':Name,
1465	'Type':'nuclear',
1466	'AtomPtrs':[3,1,7,9],
1467	'SGData':SGData,
1468	'Cell':[False,]+cell,
1469	'Pawley dmin':1.0,
1470	'Data plot type':'None',
1471	'SH Texture':{
1472	'Order':0,
1473	'Model':'cylindrical',
1474	'Sample omega':[False,0.0],
1475	'Sample chi':[False,0.0],
1476	'Sample phi':[False,0.0],
1477	'SH Coeff':[False,{}],
1478	'SHShow':False,
1479	'PFhkl':[0,0,1],
1480	'PFxyz':[0,0,1],
1481	'PlotType':'Pole figure',
1482	'Penalty':[['',],0.1,False,1.0]}},
1483	'Atoms':[],
1484	'Drawing':{},
1485	'Histograms':{},
1486	'Pawley ref':[],
1487	'RBModels':{},
1488	}
1489	if Super and Super.get('Use',False):
1490	phaseData['General'].update({'Type':'modulated','Super':True,'SuperSg':Super['ssSymb']})
1491	phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])
1492	phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1493
1494	return phaseData
1495
1496	class MultipleChoicesDialog(wx.Dialog):
1497	'''A dialog that offers a series of choices, each with a
1498	title and a wx.Choice widget. Intended to be used Modally.
1499	typical input:
1500
1501	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1502	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1503
1504	selections are placed in self.chosen when OK is pressed
1505	'''
1506	def __init__(self,choicelist,headinglist,
1507	head='Select options',
1508	title='Please select from options below',
1509	parent=None):
1510	self.chosen = []
1511	wx.Dialog.__init__(
1512	self,parent,wx.ID_ANY,head,
1513	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1514	panel = wx.Panel(self)
1515	mainSizer = wx.BoxSizer(wx.VERTICAL)
1516	mainSizer.Add((10,10),1)
1517	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1518	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1519	self.ChItems = []
1520	for choice,lbl in zip(choicelist,headinglist):
1521	mainSizer.Add((10,10),1)
1522	self.chosen.append(0)
1523	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1524	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1525	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1526	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1527
1528	OkBtn = wx.Button(panel,-1,"Ok")
1529	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1530	cancelBtn = wx.Button(panel,-1,"Cancel")
1531	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1532	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1533	btnSizer.Add((20,20),1)
1534	btnSizer.Add(OkBtn)
1535	btnSizer.Add((20,20),1)
1536	btnSizer.Add(cancelBtn)
1537	btnSizer.Add((20,20),1)
1538	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1539	panel.SetSizer(mainSizer)
1540	panel.Fit()
1541	self.Fit()
1542
1543	def OnOk(self,event):
1544	parent = self.GetParent()
1545	if parent is not None: parent.Raise()
1546	# save the results from the choice widgets
1547	self.chosen = []
1548	for w in self.ChItems:
1549	self.chosen.append(w.GetSelection())
1550	self.EndModal(wx.ID_OK)
1551
1552	def OnCancel(self,event):
1553	parent = self.GetParent()
1554	if parent is not None: parent.Raise()
1555	self.chosen = []
1556	self.EndModal(wx.ID_CANCEL)
1557
1558	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1559	confirmoverwrite=True, parent=None,
1560	multipleselect=False):
1561	'''If the filename is a zip file, extract a file from that
1562	archive.
1563
1564	:param list Selection: used to predefine the name of the file
1565	to be extracted. Filename case and zip directory name are
1566	ignored in selection; the first matching file is used.
1567
1568	:param bool confirmread: if True asks the user to confirm before expanding
1569	the only file in a zip
1570
1571	:param bool confirmoverwrite: if True asks the user to confirm
1572	before overwriting if the extracted file already exists
1573
1574	:param bool multipleselect: if True allows more than one zip
1575	file to be extracted, a list of file(s) is returned.
1576	If only one file is present, do not ask which one, otherwise
1577	offer a list of choices (unless selection is used).
1578
1579	:returns: the name of the file that has been created or a
1580	list of files (see multipleselect)
1581
1582	If the file is not a zipfile, return the name of the input file.
1583	If the zipfile is empty or no file has been selected, return None
1584	'''
1585	import zipfile # do this now, since we can save startup time by doing this only on need
1586	import shutil
1587	zloc = os.path.split(filename)[0]
1588	if not zipfile.is_zipfile(filename):
1589	#print("not zip")
1590	return filename
1591
1592	z = zipfile.ZipFile(filename,'r')
1593	zinfo = z.infolist()
1594
1595	if len(zinfo) == 0:
1596	#print('Zip has no files!')
1597	zlist = [-1]
1598	if selection:
1599	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1600	if selection.lower() in choices:
1601	zlist = [choices.index(selection.lower())]
1602	else:
1603	print('debug: file '+str(selection)+' was not found in '+str(filename))
1604	zlist = [-1]
1605	elif len(zinfo) == 1 and confirmread:
1606	result = wx.ID_NO
1607	dlg = wx.MessageDialog(
1608	parent,
1609	'Is file '+str(zinfo[0].filename)+
1610	' what you want to extract from '+
1611	str(os.path.split(filename)[1])+'?',
1612	'Confirm file',
1613	wx.YES_NO \| wx.ICON_QUESTION)
1614	try:
1615	result = dlg.ShowModal()
1616	finally:
1617	dlg.Destroy()
1618	if result == wx.ID_NO:
1619	zlist = [-1]
1620	else:
1621	zlist = [0]
1622	elif len(zinfo) == 1:
1623	zlist = [0]
1624	elif multipleselect:
1625	# select one or more from a from list
1626	choices = [i.filename for i in zinfo]
1627	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1628	'Choose file(s)',choices)
1629	if dlg.ShowModal() == wx.ID_OK:
1630	zlist = dlg.GetSelections()
1631	else:
1632	zlist = []
1633	dlg.Destroy()
1634	else:
1635	# select one from a from list
1636	choices = [i.filename for i in zinfo]
1637	dlg = wx.SingleChoiceDialog(parent,
1638	'Select file to extract from zip file'+str(filename),'Choose file',
1639	choices,)
1640	if dlg.ShowModal() == wx.ID_OK:
1641	zlist = [dlg.GetSelection()]
1642	else:
1643	zlist = [-1]
1644	dlg.Destroy()
1645
1646	outlist = []
1647	for zindex in zlist:
1648	if zindex >= 0:
1649	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1650	if os.path.exists(efil) and confirmoverwrite:
1651	result = wx.ID_NO
1652	dlg = wx.MessageDialog(parent,
1653	'File '+str(efil)+' already exists. OK to overwrite it?',
1654	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1655	try:
1656	result = dlg.ShowModal()
1657	finally:
1658	dlg.Destroy()
1659	if result == wx.ID_NO:
1660	zindex = -1
1661	if zindex >= 0:
1662	# extract the file to the current directory, regardless of it's original path
1663	#z.extract(zinfo[zindex],zloc)
1664	eloc,efil = os.path.split(zinfo[zindex].filename)
1665	outfile = os.path.join(zloc, efil)
1666	fpin = z.open(zinfo[zindex])
1667	fpout = file(outfile, "wb")
1668	shutil.copyfileobj(fpin, fpout)
1669	fpin.close()
1670	fpout.close()
1671	outlist.append(outfile)
1672	z.close()
1673	if multipleselect and len(outlist) >= 1:
1674	return outlist
1675	elif len(outlist) == 1:
1676	return outlist[0]
1677	else:
1678	return None
1679
1680	######################################################################
1681	# base classes for reading various types of data files
1682	# not used directly, only by subclassing
1683	######################################################################
1684	try:
1685	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1686	except: # errors on doc build
1687	SGData = None
1688	P1SGData = SGData
1689	class ImportBaseclass(object):
1690	'''Defines a base class for the reading of input files (diffraction
1691	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1692	for an explanation on how to use a subclass of this class.
1693	'''
1694	class ImportException(Exception):
1695	'''Defines an Exception that is used when an import routine hits an expected error,
1696	usually in .Reader.
1697
1698	Good practice is that the Reader should define a value in self.errors that
1699	tells the user some information about what is wrong with their file.
1700	'''
1701	pass
1702
1703	def __init__(self,
1704	formatName,
1705	longFormatName=None,
1706	extensionlist=[],
1707	strictExtension=False,
1708	):
1709	self.formatName = formatName # short string naming file type
1710	if longFormatName: # longer string naming file type
1711	self.longFormatName = longFormatName
1712	else:
1713	self.longFormatName = formatName
1714	# define extensions that are allowed for the file type
1715	# for windows, remove any extensions that are duplicate, as case is ignored
1716	if sys.platform == 'windows' and extensionlist:
1717	extensionlist = list(set([s.lower() for s in extensionlist]))
1718	self.extensionlist = extensionlist
1719	# If strictExtension is True, the file will not be read, unless
1720	# the extension matches one in the extensionlist
1721	self.strictExtension = strictExtension
1722	self.errors = ''
1723	self.warnings = ''
1724	# used for readers that will use multiple passes to read
1725	# more than one data block
1726	self.repeat = False
1727	self.selections = []
1728	self.repeatcount = 0
1729	self.readfilename = '?'
1730	#print 'created',self.__class__
1731
1732	def ReInitialize(self):
1733	'Reinitialize the Reader to initial settings'
1734	self.errors = ''
1735	self.warnings = ''
1736	self.repeat = False
1737	self.repeatcount = 0
1738	self.readfilename = '?'
1739
1740	def BlockSelector(self, ChoiceList, ParentFrame=None,
1741	title='Select a block',
1742	size=None, header='Block Selector',
1743	useCancel=True):
1744	''' Provide a wx dialog to select a block if the file contains more
1745	than one set of data and one must be selected
1746	'''
1747	if useCancel:
1748	dlg = wx.SingleChoiceDialog(
1749	ParentFrame,title, header,ChoiceList)
1750	else:
1751	dlg = wx.SingleChoiceDialog(
1752	ParentFrame,title, header,ChoiceList,
1753	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1754	if size: dlg.SetSize(size)
1755	dlg.CenterOnParent()
1756	if dlg.ShowModal() == wx.ID_OK:
1757	sel = dlg.GetSelection()
1758	return sel
1759	else:
1760	return None
1761	dlg.Destroy()
1762
1763	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1764	title='Select a block',size=None, header='Block Selector'):
1765	'''Provide a wx dialog to select a block of data if the
1766	file contains more than one set of data and one must be
1767	selected.
1768
1769	:returns: a list of the selected blocks
1770	'''
1771	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1772	wx.CHOICEDLG_STYLE)
1773	dlg.CenterOnParent()
1774	if size: dlg.SetSize(size)
1775	if dlg.ShowModal() == wx.ID_OK:
1776	sel = dlg.GetSelections()
1777	else:
1778	return []
1779	dlg.Destroy()
1780	selected = []
1781	if len(ChoiceList) in sel:
1782	return range(len(ChoiceList))
1783	else:
1784	return sel
1785	return selected
1786
1787	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1788	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1789	widget. Typical input:
1790
1791	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1792
1793	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1794
1795	optional keyword parameters are: head (window title) and title
1796	returns a list of selected indicies for each choice (or None)
1797	'''
1798	result = None
1799	dlg = MultipleChoicesDialog(choicelist,headinglist,
1800	parent=ParentFrame, **kwargs)
1801	dlg.CenterOnParent()
1802	if dlg.ShowModal() == wx.ID_OK:
1803	result = dlg.chosen
1804	dlg.Destroy()
1805	return result
1806
1807	def ShowBusy(self):
1808	wx.BeginBusyCursor()
1809	# wx.Yield() # make it happen now!
1810
1811	def DoneBusy(self):
1812	wx.EndBusyCursor()
1813	wx.Yield() # make it happen now!
1814
1815	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1816	# '''This method must be supplied in the child class to read the file.
1817	# if the read fails either return False or raise an Exception
1818	# preferably of type ImportException.
1819	# '''
1820	# #start reading
1821	# raise ImportException("Error occurred while...")
1822	# self.errors += "Hint for user on why the error occur
1823	# return False # if an error occurs
1824	# return True # if read OK
1825
1826	def ExtensionValidator(self, filename):
1827	'''This methods checks if the file has the correct extension
1828	Return False if this filename will not be supported by this reader
1829	Return True if the extension matches the list supplied by the reader
1830	Return None if the reader allows un-registered extensions
1831	'''
1832	if filename:
1833	ext = os.path.splitext(filename)[1]
1834	if sys.platform == 'windows': ext = ext.lower()
1835	if ext in self.extensionlist: return True
1836	if self.strictExtension: return False
1837	return None
1838
1839	def ContentsValidator(self, filepointer):
1840	'''This routine will attempt to determine if the file can be read
1841	with the current format.
1842	This will typically be overridden with a method that
1843	takes a quick scan of [some of]
1844	the file contents to do a "sanity" check if the file
1845	appears to match the selected format.
1846	Expected to be called via self.Validator()
1847	'''
1848	#filepointer.seek(0) # rewind the file pointer
1849	return True
1850
1851	def CIFValidator(self, filepointer):
1852	'''A :meth:`ContentsValidator` for use to validate CIF files.
1853	'''
1854	for i,l in enumerate(filepointer):
1855	if i >= 1000: return True
1856	'''Encountered only blank lines or comments in first 1000
1857	lines. This is unlikely, but assume it is CIF anyway, since we are
1858	even less likely to find a file with nothing but hashes and
1859	blank lines'''
1860	line = l.strip()
1861	if len(line) == 0: # ignore blank lines
1862	continue
1863	elif line.startswith('#'): # ignore comments
1864	continue
1865	elif line.startswith('data_'): # on the right track, accept this file
1866	return True
1867	else: # found something invalid
1868	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1869	self.errors += ' '+str(l)
1870	self.errors += ' Note: a CIF should only have blank lines or comments before'
1871	self.errors += ' a data_ statement begins a block.'
1872	return False
1873
1874	class ImportPhase(ImportBaseclass):
1875	'''Defines a base class for the reading of files with coordinates
1876
1877	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1878	in :meth:`GSASII.GSASII.OnImportPhase`.
1879	See :ref:`Writing a Import Routine<Import_Routines>`
1880	for an explanation on how to use this class.
1881
1882	'''
1883	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1884	strictExtension=False,):
1885	# call parent __init__
1886	ImportBaseclass.__init__(self,formatName,longFormatName,
1887	extensionlist,strictExtension)
1888	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1889	self.Constraints = None
1890
1891	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1892	title='Select a phase', size=None,header='Phase Selector'):
1893	''' Provide a wx dialog to select a phase if the file contains more
1894	than one phase
1895	'''
1896	return self.BlockSelector(ChoiceList,ParentFrame,title,
1897	size,header)
1898
1899	class ImportStructFactor(ImportBaseclass):
1900	'''Defines a base class for the reading of files with tables
1901	of structure factors.
1902
1903	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1904	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1905	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1906	:meth:`Reader`.
1907
1908	See :ref:`Writing a Import Routine<Import_Routines>`
1909	for an explanation on how to use import classes in general. The specifics
1910	for reading a structure factor histogram require that
1911	the ``Reader()`` routine in the import
1912	class need to do only a few things: It
1913	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1914	and set :attr:`Parameters` with the instrument parameters
1915	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1916	'''
1917	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1918	strictExtension=False,):
1919	ImportBaseclass.__init__(self,formatName,longFormatName,
1920	extensionlist,strictExtension)
1921
1922	# define contents of Structure Factor entry
1923	self.Parameters = []
1924	'self.Parameters is a list with two dicts for data parameter settings'
1925	self.InitParameters()
1926	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1927	self.Banks = [] #for multi bank data (usually TOF)
1928	'''self.RefDict is a dict containing the reflection information, as read from the file.
1929	Item 'RefList' contains the reflection information. See the
1930	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1931	for the contents of each row. Dict element 'FF'
1932	contains the form factor values for each element type; if this entry
1933	is left as initialized (an empty list) it will be initialized as needed later.
1934	'''
1935	def ReInitialize(self):
1936	'Reinitialize the Reader to initial settings'
1937	ImportBaseclass.ReInitialize(self)
1938	self.InitParameters()
1939	self.Banks = [] #for multi bank data (usually TOF)
1940	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1941
1942	def InitParameters(self):
1943	'initialize the instrument parameters structure'
1944	Lambda = 0.70926
1945	HistType = 'SXC'
1946	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1947	'Lam':[Lambda,Lambda]
1948	}, {}]
1949	'Parameters is a list with two dicts for data parameter settings'
1950
1951	def UpdateParameters(self,Type=None,Wave=None):
1952	'Revise the instrument parameters'
1953	if Type is not None:
1954	self.Parameters[0]['Type'] = [Type,Type]
1955	if Wave is not None:
1956	self.Parameters[0]['Lam'] = [Wave,Wave]
1957
1958	######################################################################
1959	class ImportPowderData(ImportBaseclass):
1960	'''Defines a base class for the reading of files with powder data.
1961
1962	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1963	in :meth:`GSASII.GSASII.OnImportPowder`.
1964	See :ref:`Writing a Import Routine<Import_Routines>`
1965	for an explanation on how to use this class.
1966	'''
1967	def __init__(self,
1968	formatName,
1969	longFormatName=None,
1970	extensionlist=[],
1971	strictExtension=False,
1972	):
1973	ImportBaseclass.__init__(self,formatName,
1974	longFormatName,
1975	extensionlist,
1976	strictExtension)
1977	self.clockWd = None # used in TOF
1978	self.ReInitialize()
1979
1980	def ReInitialize(self):
1981	'Reinitialize the Reader to initial settings'
1982	ImportBaseclass.ReInitialize(self)
1983	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1984	self.powderdata = [] # Powder dataset
1985	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1986	np.array(x), # x-axis values
1987	np.array(y), # powder pattern intensities
1988	np.array(w), # 1/sig(intensity)^2 values (weights)
1989	np.array(yc), # calc. intensities (zero)
1990	np.array(yb), # calc. background (zero)
1991	np.array(yd), # obs-calc profiles
1992	'''
1993	self.comments = []
1994	self.idstring = ''
1995	self.Sample = G2pdG.SetDefaultSample() # default sample parameters
1996	self.Controls = {} # items to be placed in top-level Controls
1997	self.GSAS = None # used in TOF
1998	self.repeat_instparm = True # Should a parm file be
1999	# used for multiple histograms?
2000	self.instparm = None # name hint from file of instparm to use
2001	self.instfile = '' # full path name to instrument parameter file
2002	self.instbank = '' # inst parm bank number
2003	self.instmsg = '' # a label that gets printed to show
2004	# where instrument parameters are from
2005	self.numbanks = 1
2006	self.instdict = {} # place items here that will be transferred to the instrument parameters
2007	self.pwdparms = {} # place parameters that are transferred directly to the tree
2008	# here (typically from an existing GPX file)
2009	######################################################################
2010	class ImportSmallAngleData(ImportBaseclass):
2011	'''Defines a base class for the reading of files with small angle data.
2012	See :ref:`Writing a Import Routine<Import_Routines>`
2013	for an explanation on how to use this class.
2014	'''
2015	def __init__(self,formatName,longFormatName=None,extensionlist=[],
2016	strictExtension=False,):
2017
2018	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
2019	strictExtension)
2020	self.ReInitialize()
2021
2022	def ReInitialize(self):
2023	'Reinitialize the Reader to initial settings'
2024	ImportBaseclass.ReInitialize(self)
2025	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
2026	self.smallangledata = [] # SASD dataset
2027	'''A small angle data set is a list with items [x,y,w,yc,yd]:
2028	np.array(x), # x-axis values
2029	np.array(y), # powder pattern intensities
2030	np.array(w), # 1/sig(intensity)^2 values (weights)
2031	np.array(yc), # calc. intensities (zero)
2032	np.array(yd), # obs-calc profiles
2033	np.array(yb), # preset bkg
2034	'''
2035	self.comments = []
2036	self.idstring = ''
2037	self.Sample = G2pdG.SetDefaultSample()
2038	self.GSAS = None # used in TOF
2039	self.clockWd = None # used in TOF
2040	self.numbanks = 1
2041	self.instdict = {} # place items here that will be transferred to the instrument parameters
2042
2043	######################################################################
2044	class ImportImage(ImportBaseclass):
2045	'''Defines a base class for the reading of images
2046
2047	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportImage`
2048	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
2049	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
2050	:meth:`Reader`.
2051
2052	See :ref:`Writing a Import Routine<Import_Routines>`
2053	for an explanation on how to use import classes in general. The specifics
2054	for reading an image requires that the ``Reader()`` routine in the import
2055	class need to do only a few things:...
2056
2057	(should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
2058	(and set :attr:`Parameters` with the instrument parameters
2059	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
2060	'''
2061	def __init__(self,formatName,longFormatName=None,extensionlist=[],
2062	strictExtension=False,):
2063	ImportBaseclass.__init__(self,formatName,longFormatName,
2064	extensionlist,strictExtension)
2065	self.InitParameters()
2066
2067	def ReInitialize(self):
2068	'Reinitialize the Reader to initial settings -- not used at present'
2069	ImportBaseclass.ReInitialize(self)
2070	self.InitParameters()
2071
2072	def InitParameters(self):
2073	'initialize the instrument parameters structure'
2074	self.Comments = ['No comments']
2075	self.Data = {}
2076	self.Npix = 0
2077	self.Image = None
2078
2079	def LoadImage(self,ParentFrame,imagefile):
2080	'''Optionally, call this after reading in an image to load it into the tree.
2081	This does saves time by preventing a reread of the same information.
2082	'''
2083	if ParentFrame:
2084	ParentFrame.ImageZ = self.Image # store the image for plotting
2085	ParentFrame.oldImagefile = imagefile # save the name of the last image file read
2086
2087
2088	######################################################################
2089	class ExportBaseclass(object):
2090	'''Defines a base class for the exporting of GSAS-II results.
2091
2092	This class is subclassed in the various exports/G2export_*.py files. Those files
2093	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
2094	appropriate menu items for each one and the .Exporter method is called
2095	directly from the menu item.
2096
2097	Routines may also define a .Writer method, which is used to write a single
2098	file without invoking any GUI objects.
2099	'''
2100	def __init__(self,
2101	G2frame,
2102	formatName,
2103	extension,
2104	longFormatName=None,
2105	):
2106	self.G2frame = G2frame
2107	self.formatName = formatName # short string naming file type
2108	self.extension = extension
2109	if longFormatName: # longer string naming file type
2110	self.longFormatName = longFormatName
2111	else:
2112	self.longFormatName = formatName
2113	self.OverallParms = {}
2114	self.Phases = {}
2115	self.Histograms = {}
2116	self.powderDict = {}
2117	self.xtalDict = {}
2118	self.parmDict = {}
2119	self.sigDict = {}
2120	# updated in InitExport:
2121	self.currentExportType = None # type of export that has been requested
2122	# updated in ExportSelect (when used):
2123	self.phasenam = None # a list of selected phases
2124	self.histnam = None # a list of selected histograms
2125	self.filename = None # name of file to be written (single export) or template (multiple files)
2126	self.dirname = '' # name of directory where file(s) will be written
2127	self.fullpath = '' # name of file being written -- full path
2128
2129	# items that should be defined in a subclass of this class
2130	self.exporttype = [] # defines the type(s) of exports that the class can handle.
2131	# The following types are defined: 'project', "phase", "powder", "single"
2132	self.multiple = False # set as True if the class can export multiple phases or histograms
2133	# self.multiple is ignored for "project" exports
2134
2135	def InitExport(self,event):
2136	'''Determines the type of menu that called the Exporter and
2137	misc initialization.
2138	'''
2139	self.filename = None # name of file to be written (single export)
2140	self.dirname = '' # name of file to be written (multiple export)
2141	if event:
2142	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
2143
2144	def MakePWDRfilename(self,hist):
2145	'''Make a filename root (no extension) from a PWDR histogram name
2146
2147	:param str hist: the histogram name in data tree (starts with "PWDR ")
2148	'''
2149	file0 = ''
2150	file1 = hist[5:]
2151	# replace repeated blanks
2152	while file1 != file0:
2153	file0 = file1
2154	file1 = file0.replace(' ',' ').strip()
2155	file0 = file1.replace('Azm= ','A')
2156	# if angle has unneeded decimal places on aziumuth, remove them
2157	if file0[-3:] == '.00': file0 = file0[:-3]
2158	file0 = file0.replace('.','_')
2159	file0 = file0.replace(' ','_')
2160	return file0
2161
2162	def ExportSelect(self,AskFile='ask'):
2163	'''Selects histograms or phases when needed. Sets a default file name when
2164	requested in self.filename; always sets a default directory in self.dirname.
2165
2166	:param bool AskFile: Determines how this routine processes getting a
2167	location to store the current export(s).
2168
2169	* if AskFile is 'ask' (default option), get the name of the file to be written;
2170	self.filename and self.dirname are always set. In the case where
2171	multiple files must be generated, the export routine should do this
2172	based on self.filename as a template.
2173	* if AskFile is 'dir', get the name of the directory to be used;
2174	self.filename is not used, but self.dirname is always set. The export routine
2175	will always generate the file name.
2176	* if AskFile is 'single', get only the name of the directory to be used when
2177	multiple items will be written (as multiple files) are used
2178	or a complete file name is requested when a single file
2179	name is selected. self.dirname is always set and self.filename used
2180	only when a single file is selected.
2181	* if AskFile is 'default', creates a name of the file to be used from
2182	the name of the project (.gpx) file. If the project has not been saved,
2183	then the name of file is requested.
2184	self.filename and self.dirname are always set. In the case where
2185	multiple file names must be generated, the export routine should do this
2186	based on self.filename.
2187	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
2188	file. If the project has not been saved, then a directory is requested.
2189	self.filename is not used.
2190
2191	:returns: True in case of an error
2192	'''
2193
2194	numselected = 1
2195	if self.currentExportType == 'phase':
2196	if len(self.Phases) == 0:
2197	self.G2frame.ErrorDialog(
2198	'Empty project',
2199	'Project does not contain any phases.')
2200	return True
2201	elif len(self.Phases) == 1:
2202	self.phasenam = self.Phases.keys()
2203	elif self.multiple:
2204	choices = sorted(self.Phases.keys())
2205	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
2206	if phasenum is None: return True
2207	self.phasenam = [choices[i] for i in phasenum]
2208	if not self.phasenam: return True
2209	numselected = len(self.phasenam)
2210	else:
2211	choices = sorted(self.Phases.keys())
2212	phasenum = G2G.ItemSelector(choices,self.G2frame)
2213	if phasenum is None: return True
2214	self.phasenam = [choices[phasenum]]
2215	numselected = len(self.phasenam)
2216	elif self.currentExportType == 'single':
2217	if len(self.xtalDict) == 0:
2218	self.G2frame.ErrorDialog(
2219	'Empty project',
2220	'Project does not contain any single crystal data.')
2221	return True
2222	elif len(self.xtalDict) == 1:
2223	self.histnam = self.xtalDict.values()
2224	elif self.multiple:
2225	choices = sorted(self.xtalDict.values())
2226	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
2227	if not hnum: return True
2228	self.histnam = [choices[i] for i in hnum]
2229	numselected = len(self.histnam)
2230	else:
2231	choices = sorted(self.xtalDict.values())
2232	hnum = G2G.ItemSelector(choices,self.G2frame)
2233	if hnum is None: return True
2234	self.histnam = [choices[hnum]]
2235	numselected = len(self.histnam)
2236	elif self.currentExportType == 'powder':
2237	if len(self.powderDict) == 0:
2238	self.G2frame.ErrorDialog(
2239	'Empty project',
2240	'Project does not contain any powder data.')
2241	return True
2242	elif len(self.powderDict) == 1:
2243	self.histnam = self.powderDict.values()
2244	elif self.multiple:
2245	choices = sorted(self.powderDict.values())
2246	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
2247	if not hnum: return True
2248	self.histnam = [choices[i] for i in hnum]
2249	numselected = len(self.histnam)
2250	else:
2251	choices = sorted(self.powderDict.values())
2252	hnum = G2G.ItemSelector(choices,self.G2frame)
2253	if hnum is None: return True
2254	self.histnam = [choices[hnum]]
2255	numselected = len(self.histnam)
2256	elif self.currentExportType == 'image':
2257	if len(self.Histograms) == 0:
2258	self.G2frame.ErrorDialog(
2259	'Empty project',
2260	'Project does not contain any images.')
2261	return True
2262	elif len(self.Histograms) == 1:
2263	self.histnam = self.Histograms.keys()
2264	else:
2265	choices = sorted(self.Histograms.keys())
2266	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
2267	if self.multiple:
2268	if not hnum: return True
2269	self.histnam = [choices[i] for i in hnum]
2270	else:
2271	if hnum is None: return True
2272	self.histnam = [choices[hnum]]
2273	numselected = len(self.histnam)
2274	if self.currentExportType == 'map':
2275	# search for phases with maps
2276	mapPhases = []
2277	choices = []
2278	for phasenam in sorted(self.Phases):
2279	phasedict = self.Phases[phasenam] # pointer to current phase info
2280	if len(phasedict['General']['Map'].get('rho',[])):
2281	mapPhases.append(phasenam)
2282	if phasedict['General']['Map'].get('Flip'):
2283	choices.append('Charge flip map: '+str(phasenam))
2284	elif phasedict['General']['Map'].get('MapType'):
2285	choices.append(
2286	str(phasedict['General']['Map'].get('MapType'))
2287	+ ' map: ' + str(phasenam))
2288	else:
2289	choices.append('unknown map: '+str(phasenam))
2290	# select a map if needed
2291	if len(mapPhases) == 0:
2292	self.G2frame.ErrorDialog(
2293	'Empty project',
2294	'Project does not contain any maps.')
2295	return True
2296	elif len(mapPhases) == 1:
2297	self.phasenam = mapPhases
2298	else:
2299	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
2300	if self.multiple:
2301	if not phasenum: return True
2302	self.phasenam = [mapPhases[i] for i in phasenum]
2303	else:
2304	if phasenum is None: return True
2305	self.phasenam = [mapPhases[phasenum]]
2306	numselected = len(self.phasenam)
2307
2308	# items selected, now set self.dirname and usually self.filename
2309	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
2310	AskFile == 'default' and not self.G2frame.GSASprojectfile
2311	):
2312	filename = self.askSaveFile()
2313	if not filename: return True
2314	self.dirname,self.filename = os.path.split(filename)
2315	elif AskFile == 'dir' or AskFile == 'single' or (
2316	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
2317	):
2318	self.dirname = self.askSaveDirectory()
2319	if not self.dirname: return True
2320	elif AskFile == 'default-dir' or AskFile == 'default':
2321	self.dirname,self.filename = os.path.split(
2322	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
2323	)
2324	else:
2325	raise Exception('This should not happen!')
2326
2327	def loadParmDict(self):
2328	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
2329	refined values to those from the last cycle and set the uncertainties for the
2330	refined parameters in another dict (self.sigDict).
2331
2332	Expands the parm & sig dicts to include values derived from constraints.
2333	'''
2334	self.parmDict = {}
2335	self.sigDict = {}
2336	rigidbodyDict = {}
2337	covDict = {}
2338	consDict = {}
2339	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2340	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2341	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2342	while item:
2343	name = self.G2frame.PatternTree.GetItemText(item)
2344	if name == 'Rigid bodies':
2345	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
2346	elif name == 'Covariance':
2347	covDict = self.G2frame.PatternTree.GetItemPyData(item)
2348	elif name == 'Constraints':
2349	consDict = self.G2frame.PatternTree.GetItemPyData(item)
2350	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2351	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
2352	self.parmDict.update(rbDict)
2353	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
2354	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,maxSSwave = G2stIO.GetPhaseData(
2355	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
2356	self.parmDict.update(phaseDict)
2357	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
2358	Phases,Histograms,Print=False,resetRefList=False)
2359	self.parmDict.update(hapDict)
2360	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
2361	self.parmDict.update(histDict)
2362	self.parmDict.update(zip(
2363	covDict.get('varyList',[]),
2364	covDict.get('variables',[])))
2365	self.sigDict = dict(zip(
2366	covDict.get('varyList',[]),
2367	covDict.get('sig',[])))
2368	# expand to include constraints: first compile a list of constraints
2369	constList = []
2370	for item in consDict:
2371	if item.startswith('_'): continue
2372	constList += consDict[item]
2373	# now process the constraints
2374	G2mv.InitVars()
2375	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
2376	varyList = covDict.get('varyListStart')
2377	if varyList is None and len(constDict) == 0:
2378	# no constraints can use varyList
2379	varyList = covDict.get('varyList')
2380	elif varyList is None:
2381	# old GPX file from before pre-constraint varyList is saved
2382	print ' * Old refinement: Please use Calculate/Refine to redo *'
2383	raise Exception(' * Export aborted *')
2384	else:
2385	varyList = list(varyList)
2386	try:
2387	groups,parmlist = G2mv.GroupConstraints(constDict)
2388	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
2389	except:
2390	# this really should not happen
2391	print ' * ERROR - constraints are internally inconsistent *'
2392	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
2393	print 'Errors',errmsg
2394	if warnmsg: print 'Warnings',warnmsg
2395	raise Exception(' * CIF creation aborted *')
2396	# add the constrained values to the parameter dictionary
2397	G2mv.Dict2Map(self.parmDict,varyList)
2398	# and add their uncertainties into the esd dictionary (sigDict)
2399	if covDict.get('covMatrix') is not None:
2400	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
2401
2402	def loadTree(self):
2403	'''Load the contents of the data tree into a set of dicts
2404	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2405	& self.xtalDict)
2406
2407	* The childrenless data tree items are overall parameters/controls for the
2408	entire project and are placed in self.OverallParms
2409	* Phase items are placed in self.Phases
2410	* Data items are placed in self.Histogram. The key for these data items
2411	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2412	'''
2413	self.OverallParms = {}
2414	self.powderDict = {}
2415	self.xtalDict = {}
2416	self.Phases = {}
2417	self.Histograms = {}
2418	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2419	histType = None
2420	if self.currentExportType == 'phase':
2421	# if exporting phases load them here
2422	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2423	if not sub:
2424	print 'no phases found'
2425	return True
2426	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2427	while item:
2428	phaseName = self.G2frame.PatternTree.GetItemText(item)
2429	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2430	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2431	return
2432	elif self.currentExportType == 'single':
2433	histType = 'HKLF'
2434	elif self.currentExportType == 'powder':
2435	histType = 'PWDR'
2436	elif self.currentExportType == 'image':
2437	histType = 'IMG'
2438
2439	if histType: # Loading just one kind of tree entry
2440	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2441	while item:
2442	name = self.G2frame.PatternTree.GetItemText(item)
2443	if name.startswith(histType):
2444	if self.Histograms.get(name): # there is already an item with this name
2445	print('Histogram name '+str(name)+' is repeated. Renaming')
2446	if name[-1] == '9':
2447	name = name[:-1] + '10'
2448	elif name[-1] in '012345678':
2449	name = name[:-1] + str(int(name[-1])+1)
2450	else:
2451	name += '-1'
2452	self.Histograms[name] = {}
2453	# the main info goes into Data, but the 0th
2454	# element contains refinement results, carry
2455	# that over too now.
2456	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2457	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2458	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2459	while item2:
2460	child = self.G2frame.PatternTree.GetItemText(item2)
2461	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2462	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2463	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2464	# index powder and single crystal histograms by number
2465	for hist in self.Histograms:
2466	if hist.startswith("PWDR"):
2467	d = self.powderDict
2468	elif hist.startswith("HKLF"):
2469	d = self.xtalDict
2470	else:
2471	return
2472	i = self.Histograms[hist].get('hId')
2473	if i is None and not d.keys():
2474	i = 0
2475	elif i is None or i in d.keys():
2476	i = max(d.keys())+1
2477	d[i] = hist
2478	return
2479	# else standard load: using all interlinked phases and histograms
2480	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2481	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2482	while item:
2483	name = self.G2frame.PatternTree.GetItemText(item)
2484	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2485	if not item2:
2486	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2487	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2488	# index powder and single crystal histograms
2489	for hist in self.Histograms:
2490	i = self.Histograms[hist]['hId']
2491	if hist.startswith("PWDR"):
2492	self.powderDict[i] = hist
2493	elif hist.startswith("HKLF"):
2494	self.xtalDict[i] = hist
2495
2496	def dumpTree(self,mode='type'):
2497	'''Print out information on the data tree dicts loaded in loadTree
2498	'''
2499	print '\nOverall'
2500	if mode == 'type':
2501	def Show(arg): return type(arg)
2502	else:
2503	def Show(arg): return arg
2504	for key in self.OverallParms:
2505	print ' ',key,Show(self.OverallParms[key])
2506	print 'Phases'
2507	for key1 in self.Phases:
2508	print ' ',key1,Show(self.Phases[key1])
2509	print 'Histogram'
2510	for key1 in self.Histograms:
2511	print ' ',key1,Show(self.Histograms[key1])
2512	for key2 in self.Histograms[key1]:
2513	print ' ',key2,Show(self.Histograms[key1][key2])
2514
2515	def defaultSaveFile(self):
2516	return os.path.abspath(
2517	os.path.splitext(self.G2frame.GSASprojectfile
2518	)[0]+self.extension)
2519
2520	def askSaveFile(self):
2521	'''Ask the user to supply a file name
2522
2523	:returns: a file name (str) or None if Cancel is pressed
2524	'''
2525	defnam = os.path.splitext(
2526	os.path.split(self.G2frame.GSASprojectfile)[1]
2527	)[0]+self.extension
2528	dlg = wx.FileDialog(
2529	self.G2frame, 'Input name for file to write', '.', defnam,
2530	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2531	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2532	dlg.CenterOnParent()
2533	try:
2534	if dlg.ShowModal() == wx.ID_OK:
2535	filename = dlg.GetPath()
2536	# make sure extension is correct
2537	filename = os.path.splitext(filename)[0]+self.extension
2538	else:
2539	filename = None
2540	finally:
2541	dlg.Destroy()
2542	return filename
2543
2544	def askSaveDirectory(self):
2545	'''Ask the user to supply a directory name. Path name is used as the
2546	starting point for the next export path search.
2547
2548	:returns: a directory name (str) or None if Cancel is pressed
2549	'''
2550	if self.G2frame.exportDir:
2551	startdir = self.G2frame.exportDir
2552	elif self.G2frame.GSASprojectfile:
2553	startdir = os.path.split(self.G2frame.GSASprojectfile)[0]
2554	elif self.G2frame.dirname:
2555	startdir = self.G2frame.dirname
2556	else:
2557	startdir = ''
2558	dlg = wx.DirDialog(
2559	self.G2frame, 'Input directory where file(s) will be written', startdir,
2560	wx.DD_DEFAULT_STYLE)
2561	dlg.CenterOnParent()
2562	try:
2563	if dlg.ShowModal() == wx.ID_OK:
2564	filename = dlg.GetPath()
2565	self.G2frame.exportDir = filename
2566	else:
2567	filename = None
2568	finally:
2569	dlg.Destroy()
2570	return filename
2571
2572	# Tools for file writing.
2573	def OpenFile(self,fil=None,mode='w'):
2574	'''Open the output file
2575
2576	:param str fil: The name of the file to open. If None (default)
2577	the name defaults to self.dirname + self.filename.
2578	If an extension is supplied, it is not overridded,
2579	but if not, the default extension is used.
2580	:returns: the file object opened by the routine which is also
2581	saved as self.fp
2582	'''
2583	if not fil:
2584	if not os.path.splitext(self.filename)[1]:
2585	self.filename += self.extension
2586	fil = os.path.join(self.dirname,self.filename)
2587	self.fullpath = os.path.abspath(fil)
2588	self.fp = open(self.fullpath,mode)
2589	return self.fp
2590
2591	def Write(self,line):
2592	'''write a line of output, attaching a line-end character
2593
2594	:param str line: the text to be written.
2595	'''
2596	self.fp.write(line+'\n')
2597	def CloseFile(self,fp=None):
2598	'''Close a file opened in OpenFile
2599
2600	:param file fp: the file object to be closed. If None (default)
2601	file object self.fp is closed.
2602	'''
2603	if fp is None:
2604	fp = self.fp
2605	self.fp = None
2606	fp.close()
2607	# Tools to pull information out of the data arrays
2608	def GetCell(self,phasenam):
2609	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2610
2611	:param str phasenam: the name for the selected phase
2612	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2613	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2614	cell values and `cellSig` has their uncertainties.
2615	"""
2616	phasedict = self.Phases[phasenam] # pointer to current phase info
2617	try:
2618	pfx = str(phasedict['pId'])+'::'
2619	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2620	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
2621	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2622	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2623	return cellList,cellSig
2624	except KeyError:
2625	cell = phasedict['General']['Cell'][1:]
2626	return cell,7*[0]
2627
2628	def GetAtoms(self,phasenam):
2629	"""Gets the atoms associated with a phase. Can be used with standard
2630	or macromolecular phases
2631
2632	:param str phasenam: the name for the selected phase
2633	:returns: a list of items for eac atom where each item is a list containing:
2634	label, typ, mult, xyz, and td, where
2635
2636	* label and typ are the atom label and the scattering factor type (str)
2637	* mult is the site multiplicity (int)
2638	* xyz is contains a list with four pairs of numbers:
2639	x, y, z and fractional occupancy and
2640	their standard uncertainty (or a negative value)
2641	* td is contains a list with either one or six pairs of numbers:
2642	if one number it is U\ :sub:`iso` and with six numbers it is
2643	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2644	paired with their standard uncertainty (or a negative value)
2645	"""
2646	phasedict = self.Phases[phasenam] # pointer to current phase info
2647	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2648	cfrac = cx+3
2649	fpfx = str(phasedict['pId'])+'::Afrac:'
2650	atomslist = []
2651	for i,at in enumerate(phasedict['Atoms']):
2652	if phasedict['General']['Type'] == 'macromolecular':
2653	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2654	else:
2655	label = at[ct-1]
2656	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2657	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2658	mult = at[cs+1]
2659	typ = at[ct]
2660	xyz = []
2661	for j,v in enumerate(('x','y','z')):
2662	val = at[cx+j]
2663	pfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2664	sig = self.sigDict.get(pfx,-0.000009)
2665	xyz.append((val,sig))
2666	xyz.append((fval,fsig))
2667	td = []
2668	if at[cia] == 'I':
2669	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2670	val = self.parmDict.get(pfx,at[cia+1])
2671	sig = self.sigDict.get(pfx,-0.0009)
2672	td.append((val,sig))
2673	else:
2674	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2675	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2676	val = self.parmDict.get(pfx,at[cia+2+i])
2677	sig = self.sigDict.get(pfx,-0.0009)
2678	td.append((val,sig))
2679	atomslist.append((label,typ,mult,xyz,td))
2680	return atomslist
2681	######################################################################
2682	def ExportPowderList(G2frame):
2683	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
2684
2685	:param wx.Frame G2frame: the GSAS-II main data tree window
2686	'''
2687	extList = []
2688	for obj in G2frame.exporterlist:
2689	if 'powder' in obj.exporttype:
2690	try:
2691	obj.Writer
2692	extList.append(obj.extension)
2693	except AttributeError:
2694	pass
2695	return extList
2696
2697	def ExportPowder(G2frame,TreeName,fileroot,extension):
2698	'''Writes a single powder histogram using the Export routines
2699
2700	:param wx.Frame G2frame: the GSAS-II main data tree window
2701	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
2702	:param str fileroot: name for file to be written, extension ignored
2703	:param str extension: extension for file to be written (start with '.'). Must
2704	match a powder export routine that has a Writer object.
2705	'''
2706	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
2707	for obj in G2frame.exporterlist:
2708	if obj.extension == extension and 'powder' in obj.exporttype:
2709	obj.currentExportType = 'powder'
2710	obj.InitExport(None)
2711	obj.loadTree() # load all histograms in tree into dicts
2712	if TreeName not in obj.Histograms:
2713	raise Exception('Histogram not found: '+str(TreeName))
2714	try:
2715	obj.Writer
2716	except AttributeError:
2717	continue
2718	try:
2719	obj.Writer(TreeName,filename)
2720	return
2721	except Exception,err:
2722	print('Export Routine for '+extension+' failed.')
2723	print err
2724	else:
2725	print('No Export routine supports extension '+extension)
2726
2727	def ReadCIF(URLorFile):
2728	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2729	(from James Hester).
2730	The open routine gets confused with DOS names that begin with a letter and colon
2731	"C:\dir\" so this routine will try to open the passed name as a file and if that
2732	fails, try it as a URL
2733
2734	:param str URLorFile: string containing a URL or a file name. Code will try first
2735	to open it as a file and then as a URL.
2736
2737	:returns: a PyCifRW CIF object.
2738	'''
2739	import CifFile as cif # PyCifRW from James Hester
2740
2741	# alternate approach:
2742	#import urllib
2743	#ciffile = 'file:'+urllib.pathname2url(filename)
2744
2745	try:
2746	fp = open(URLorFile,'r')
2747	cf = cif.ReadCif(fp)
2748	fp.close()
2749	return cf
2750	except IOError:
2751	return cif.ReadCif(URLorFile)
2752
2753	if __name__ == '__main__':
2754	app = wx.PySimpleApp()
2755	frm = wx.Frame(None) # create a frame
2756	frm.Show(True)
2757	filename = '/tmp/notzip.zip'
2758	filename = '/tmp/all.zip'
2759	#filename = '/tmp/11bmb_7652.zip'
2760
2761	#selection=None, confirmoverwrite=True, parent=None
2762	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2763	print ExtractFileFromZip(filename,multipleselect=True)
2764	#confirmread=False, confirmoverwrite=False)
2765
2766	# choicelist=[ ('a','b','c'),
2767	# ('test1','test2'),('no choice',)]
2768	# titles = [ 'a, b or c', 'tests', 'No option here']
2769	# dlg = MultipleChoicesDialog(
2770	# choicelist,titles,
2771	# parent=frm)
2772	# if dlg.ShowModal() == wx.ID_OK:
2773	# print 'Got OK'

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