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source: trunk/GSASIIIO.py @ 2068

Last change on this file since 2068 was 2068, checked in by toby, 8 years ago
cleanup image reader documetation
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2015-11-24 18:39:12 +0000 (Tue, 24 Nov 2015) $
4	# $Author: toby $
5	# $Revision: 2068 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 2068 2015-11-24 18:39:12Z 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: 2068 $")
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	wave = 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:
115	print Comment
116	if 'wavelength' in Comment:
117	wave = float(Comment.split('=')[1])
118	Peaks = []
119	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
120	for peak in peaks:
121	dsp = peak[0]
122	sth = wave/(2.0*dsp)
123	if sth < 1.0:
124	tth = 2.0*asind(sth)
125	else:
126	break
127	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
128	else: #2-thetas - assume Cuka (for now)
129	for peak in peaks:
130	tth = peak[0]
131	dsp = wave/(2.0*sind(tth/2.0))
132	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
133	limits = [1000.,0.]
134	for peak in Peaks:
135	limits[0] = min(limits[0],peak[0])
136	limits[1] = max(limits[1],peak[0])
137	limits[0] = max(1.,(int(limits[0]-1.)/5)*5.)
138	limits[1] = min(170.,(int(limits[1]+1.)/5)*5.)
139	return Comments,Peaks,limits,wave
140
141	def CheckImageFile(G2frame,imagefile):
142	'''Try to locate an image file if the project and image have been moved
143	together. If the image file cannot be found, request the location from
144	the user.
145
146	:param wx.Frame G2frame: main GSAS-II Frame and data object
147	:param str imagefile: name of image file
148	:returns: imagefile, if it exists, or the name of a file
149	that does exist or False if the user presses Cancel
150
151	'''
152	if not os.path.exists(imagefile):
153	print 'Image file '+imagefile+' not found'
154	fil = imagefile.replace('\\','/') # windows?!
155	# see if we can find a file with same name or in a similarly named sub-dir
156	pth,fil = os.path.split(fil)
157	prevpth = None
158	while pth and pth != prevpth:
159	prevpth = pth
160	if os.path.exists(os.path.join(G2frame.dirname,fil)):
161	print 'found image file '+os.path.join(G2frame.dirname,fil)
162	return os.path.join(G2frame.dirname,fil)
163	pth,enddir = os.path.split(pth)
164	fil = os.path.join(enddir,fil)
165	# not found as a subdirectory, drop common parts of path for last saved & image file names
166	# if image was .../A/B/C/imgs/ima.ge
167	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
168	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
169	Controls = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
170	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
171	imgPath = imagefile.replace('\\','/').split('/')
172	for p1,p2 in zip(gpxPath,imgPath):
173	if p1 == p2:
174	gpxPath.pop(0),imgPath.pop(0)
175	else:
176	break
177	fil = os.path.join(*imgPath) # file with non-common prefix elements
178	prevpth = None
179	pth = os.path.abspath(G2frame.dirname)
180	while pth and pth != prevpth:
181	prevpth = pth
182	if os.path.exists(os.path.join(pth,fil)):
183	print 'found image file '+os.path.join(pth,fil)
184	return os.path.join(pth,fil)
185	pth,enddir = os.path.split(pth)
186	#GSASIIpath.IPyBreak()
187
188	if not os.path.exists(imagefile):
189	dlg = wx.FileDialog(G2frame, 'Previous image file not found; open here', '.', '',\
190	'Any image file (.edf;.tif;.tiff;.mar;.ge;.avg;.sum;.img;.cor;.stl)\
191	\|.edf;.tif;.tiff;.mar;.ge;.avg;.sum;.img;.cor;.stl\|\
192	European detector file (.edf)\|.edf\|\
193	Any detector tif (.tif;.tiff)\|.tif;.tiff\|\
194	MAR file (.mar)\|.mar\|\
195	GE Image (.ge;.avg;.sum;.cor)\|.ge;.avg;.sum;.cor\|\
196	ADSC Image (.img)\|.img\|\
197	Rigaku-Axis4 (.stl)\|.stl\|\
198	All files (.)\|.',wx.OPEN\|wx.CHANGE_DIR)
199	try:
200	dlg.SetFilename(''+ospath.split(imagefile)[1])
201	if dlg.ShowModal() == wx.ID_OK:
202	imagefile = dlg.GetPath()
203	else:
204	imagefile = False
205	finally:
206	dlg.Destroy()
207	return imagefile
208
209	def EditImageParms(parent,Data,Comments,Image,filename):
210	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
211	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
212	def onClose(event):
213	dlg.EndModal(wx.ID_OK)
214	mainsizer = wx.BoxSizer(wx.VERTICAL)
215	h,w = Image.shape[:2]
216	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,
217	'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
218	0,wx.ALIGN_LEFT\|wx.ALL, 2)
219
220	vsizer = wx.BoxSizer(wx.HORIZONTAL)
221	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
222	0,wx.ALIGN_LEFT\|wx.ALL, 2)
223	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
224	vsizer.Add(wdgt)
225	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
226
227	vsizer = wx.BoxSizer(wx.HORIZONTAL)
228	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
229	0,wx.ALIGN_LEFT\|wx.ALL, 2)
230	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
231	size=(50,-1))
232	vsizer.Add(wdgt)
233	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),
234	wx.ALIGN_LEFT\|wx.ALL, 2)
235	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,
236	size=(50,-1))
237	vsizer.Add(wdgt)
238	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
239
240	vsizer = wx.BoxSizer(wx.HORIZONTAL)
241	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
242	0,wx.ALIGN_LEFT\|wx.ALL, 2)
243	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
244	vsizer.Add(wdgt)
245	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
246
247	vsizer = wx.BoxSizer(wx.HORIZONTAL)
248	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
249	0,wx.ALIGN_LEFT\|wx.ALL, 2)
250	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,
251	size=(75,-1))
252	vsizer.Add(wdgt)
253	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),
254	wx.ALIGN_LEFT\|wx.ALL, 2)
255	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,
256	size=(75,-1))
257	vsizer.Add(wdgt)
258	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
259
260	vsizer = wx.BoxSizer(wx.HORIZONTAL)
261	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
262	0,wx.ALIGN_LEFT\|wx.ALL, 2)
263	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
264	vsizer.Add(wdgt)
265	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
266
267	btnsizer = wx.StdDialogButtonSizer()
268	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
269	OKbtn.SetDefault()
270	OKbtn.Bind(wx.EVT_BUTTON,onClose)
271	btnsizer.AddButton(OKbtn) # not sure why this is needed
272	btnsizer.Realize()
273	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
274	dlg.SetSizer(mainsizer)
275	dlg.CenterOnParent()
276	dlg.ShowModal()
277
278	def ReadLoadImage(imagefile,G2frame):
279	'''Read a GSAS-II image file and load it into the data tree
280	Called only from GSASII.OnImageRead (depreciated).
281	'''
282	# if a zip file, open and extract
283	if os.path.splitext(imagefile)[1].lower() == '.zip':
284	extractedfile = ExtractFileFromZip(imagefile,parent=G2frame)
285	if extractedfile is not None and extractedfile != imagefile:
286	imagefile = extractedfile
287	Comments,Data,Npix,Image = GetImageData(G2frame,imagefile) # can only read 1st image
288	if Comments:
289	LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image)
290
291	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
292	'''Load an image into the tree. Saves the location of the image, as well as the
293	ImageTag (where there is more than one image in the file), if defined.
294	'''
295	ImgNames = []
296	if G2frame.PatternTree.GetCount(): # get a list of existing Image entries
297	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
298	while item:
299	name = G2frame.PatternTree.GetItemText(item)
300	if name.startswith('IMG'): ImgNames.append(name)
301	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
302	TreeLbl = 'IMG '+os.path.basename(imagefile)
303	ImageTag = Data.get('ImageTag')
304	if ImageTag:
305	TreeLbl += ' #'+str(ImageTag)
306	imageInfo = (imagefile,ImageTag)
307	else:
308	imageInfo = imagefile
309	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
310	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=TreeName)
311	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
312	Imax = np.amax(Image)
313	Imin = max(0.0,np.amin(Image)) #force positive
314	if G2frame.imageDefault:
315	Data = copy.copy(G2frame.imageDefault)
316	Data['showLines'] = True
317	Data['ring'] = []
318	Data['rings'] = []
319	Data['cutoff'] = 10
320	Data['pixLimit'] = 20
321	Data['edgemin'] = 100000000
322	Data['calibdmin'] = 0.5
323	Data['calibskip'] = 0
324	Data['ellipses'] = []
325	Data['calibrant'] = ''
326	Data['GonioAngles'] = [0.,0.,0.]
327	Data['DetDepthRef'] = False
328	else:
329	Data['type'] = 'PWDR'
330	Data['color'] = 'Paired'
331	Data['tilt'] = 0.0
332	Data['rotation'] = 0.0
333	Data['showLines'] = False
334	Data['ring'] = []
335	Data['rings'] = []
336	Data['cutoff'] = 10
337	Data['pixLimit'] = 20
338	Data['calibdmin'] = 0.5
339	Data['calibskip'] = 0
340	Data['edgemin'] = 100000000
341	Data['ellipses'] = []
342	Data['GonioAngles'] = [0.,0.,0.]
343	Data['DetDepth'] = 0.
344	Data['DetDepthRef'] = False
345	Data['calibrant'] = ''
346	Data['IOtth'] = [2.0,5.0]
347	Data['LRazimuth'] = [135,225]
348	Data['azmthOff'] = 0.0
349	Data['outChannels'] = 2500
350	Data['outAzimuths'] = 1
351	Data['centerAzm'] = False
352	Data['fullIntegrate'] = False
353	Data['setRings'] = False
354	Data['background image'] = ['',-1.0]
355	Data['dark image'] = ['',-1.0]
356	Data['Flat Bkg'] = 0.0
357	Data['setDefault'] = False
358	Data['range'] = [(Imin,Imax),[Imin,Imax]]
359	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Image Controls'),Data)
360	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(Imin,Imax),[Imin,Imax]]}
361	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Masks'),Masks)
362	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Stress/Strain'),
363	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
364	G2frame.PatternTree.SetItemPyData(Id,[Npix,imageInfo])
365	G2frame.PickId = Id
366	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
367	G2frame.Image = Id
368
369	def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None):
370	'''Read a single image with an image importer.
371
372	:param wx.Frame G2frame: main GSAS-II Frame and data object.
373	:param str imagefile: name of image file
374	:param bool imageOnly: If True return only the image,
375	otherwise (default) return more (see below)
376	:param int/str ImageTag: specifies a particular image to be read from a file.
377	First image is read if None (default).
378
379	:returns: an image as a numpy array or a list of four items:
380	Comments, Data, Npix and the Image, as selected by imageOnly
381
382	'''
383	# determine which formats are compatible with this file
384	primaryReaders = []
385	secondaryReaders = []
386	for rd in G2frame.ImportImageReaderlist:
387	flag = rd.ExtensionValidator(imagefile)
388	if flag is None:
389	secondaryReaders.append(rd)
390	elif flag:
391	primaryReaders.append(rd)
392	if len(secondaryReaders) + len(primaryReaders) == 0:
393	print('Error: No matching format for file '+filename)
394	raise Exception('No image read')
395	fp = None
396	errorReport = ''
397	fp = open(imagefile,'Ur')
398	for rd in primaryReaders+secondaryReaders:
399	rd.ReInitialize() # purge anything from a previous read
400	fp.seek(0) # rewind
401	rd.errors = "" # clear out any old errors
402	if not rd.ContentsValidator(fp): # rejected on cursory check
403	errorReport += "\n "+rd.formatName + ' validator error'
404	if rd.errors:
405	errorReport += ': '+rd.errors
406	continue
407	rdbuffer = {} # create temporary storage for file reader
408	if imageOnly:
409	ParentFrame = None # prevent GUI access on reread
410	else:
411	ParentFrame = G2frame
412	if GSASIIpath.GetConfigValue('debug'):
413	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=ImageTag)
414	else:
415	flag = False
416	try:
417	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=ImageTag)
418	except rd.ImportException as detail:
419	rd.errors += "\n Read exception: "+str(detail)
420	except Exception as detail:
421	import traceback
422	rd.errors += "\n Unhandled read exception: "+str(detail)
423	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
424	if flag: # this read succeeded
425	if rd.Image is None:
426	raise Exception('No image read. Strange!')
427	if GSASIIpath.GetConfigValue('Transpose'):
428	print 'Transposing Image!'
429	rd.Image = rd.Image.T
430	#rd.readfilename = imagefile
431	if imageOnly:
432	return rd.Image
433	else:
434	return rd.Comments,rd.Data,rd.Npix,rd.Image
435	else:
436	print('Error reading file '+filename)
437	print('Error messages(s)\n'+errorReport)
438	raise Exception('No image read')
439
440	def ReadImages(G2frame,imagefile):
441	'''Read one or more images from a file and put them into the Tree
442	using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
443
444	:param wx.Frame G2frame: main GSAS-II Frame and data object.
445	:param str imagefile: name of image file
446
447	:returns: a list of the id's of the IMG tree items created
448	'''
449	# determine which formats are compatible with this file
450	primaryReaders = []
451	secondaryReaders = []
452	for rd in G2frame.ImportImageReaderlist:
453	flag = rd.ExtensionValidator(imagefile)
454	if flag is None:
455	secondaryReaders.append(rd)
456	elif flag:
457	primaryReaders.append(rd)
458	if len(secondaryReaders) + len(primaryReaders) == 0:
459	print('Error: No matching format for file '+filename)
460	raise Exception('No image read')
461	errorReport = ''
462	fp = open(imagefile,'Ur')
463	rdbuffer = {} # create temporary storage for file reader
464	for rd in primaryReaders+secondaryReaders:
465	rd.ReInitialize() # purge anything from a previous read
466	fp.seek(0) # rewind
467	rd.errors = "" # clear out any old errors
468	if not rd.ContentsValidator(fp): # rejected on cursory check
469	errorReport += "\n "+rd.formatName + ' validator error'
470	if rd.errors:
471	errorReport += ': '+rd.errors
472	continue
473	ParentFrame = G2frame
474	block = 0
475	repeat = True
476	CreatedIMGitems = []
477	while repeat: # loop if the reader asks for another pass on the file
478	block += 1
479	repeat = False
480	if GSASIIpath.GetConfigValue('debug'):
481	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=block,Buffer=rdbuffer)
482	else:
483	flag = False
484	try:
485	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=block,Buffer=rdbuffer)
486	except rd.ImportException as detail:
487	rd.errors += "\n Read exception: "+str(detail)
488	except Exception as detail:
489	import traceback
490	rd.errors += "\n Unhandled read exception: "+str(detail)
491	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
492	if flag: # this read succeeded
493	if rd.Image is None:
494	raise Exception('No image read. Strange!')
495	if GSASIIpath.GetConfigValue('Transpose'):
496	print 'Transposing Image!'
497	rd.Image = rd.Image.T
498	rd.Data['ImageTag'] = rd.repeatcount
499	LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
500	repeat = rd.repeat
501	CreatedIMGitems.append(G2frame.Image)
502	if CreatedIMGitems: return CreatedIMGitems
503	else:
504	print('Error reading file '+filename)
505	print('Error messages(s)\n'+errorReport)
506	return []
507	#raise Exception('No image read')
508
509	def PutG2Image(filename,Comments,Data,Npix,image):
510	'Write an image as a python pickle - might be better as an .edf file?'
511	File = open(filename,'wb')
512	cPickle.dump([Comments,Data,Npix,image],File,1)
513	File.close()
514	return
515
516	# should get moved to importer when ready to test
517	def GetEdfData(filename,imageOnly=False):
518	'Read European detector data edf file'
519	import struct as st
520	import array as ar
521	if not imageOnly:
522	print 'Read European detector data edf file: ',filename
523	File = open(filename,'rb')
524	fileSize = os.stat(filename).st_size
525	head = File.read(3072)
526	lines = head.split('\n')
527	sizexy = [0,0]
528	pixSize = [154,154] #Pixium4700?
529	cent = [0,0]
530	wave = 1.54187 #default <CuKa>
531	dist = 1000.
532	head = ['European detector data',]
533	for line in lines:
534	line = line.replace(';',' ').strip()
535	fields = line.split()
536	if 'Dim_1' in line:
537	sizexy[0] = int(fields[2])
538	elif 'Dim_2' in line:
539	sizexy[1] = int(fields[2])
540	elif 'DataType' in line:
541	dType = fields[2]
542	elif 'wavelength' in line:
543	wave = float(fields[2])
544	elif 'Size' in line:
545	imSize = int(fields[2])
546	# elif 'DataType' in lines:
547	# dType = fields[2]
548	elif 'pixel_size_x' in line:
549	pixSize[0] = float(fields[2])
550	elif 'pixel_size_y' in line:
551	pixSize[1] = float(fields[2])
552	elif 'beam_center_x' in line:
553	cent[0] = float(fields[2])
554	elif 'beam_center_y' in line:
555	cent[1] = float(fields[2])
556	elif 'refined_distance' in line:
557	dist = float(fields[2])
558	if line:
559	head.append(line)
560	else: #blank line at end of header
561	break
562	File.seek(fileSize-imSize)
563	if dType == 'UnsignedShort':
564	image = np.array(ar.array('H',File.read(imSize)),dtype=np.int32)
565	elif dType == 'UnsignedInt':
566	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
567	elif dType == 'UnsignedLong':
568	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
569	elif dType == 'SignedInteger':
570	image = np.array(ar.array('l',File.read(imSize)),dtype=np.int32)
571	image = np.reshape(image,(sizexy[1],sizexy[0]))
572	data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'size':sizexy}
573	Npix = sizexy[0]*sizexy[1]
574	File.close()
575	if imageOnly:
576	return image
577	else:
578	return head,data,Npix,image
579
580	# should get moved to importer when ready to test
581	def GetRigaku(filename,imageOnly=False):
582	'Read Rigaku R-Axis IV image file'
583	import struct as st
584	import array as ar
585	if not imageOnly:
586	print 'Read Rigaku R-Axis IV file: ',filename
587	File = open(filename,'rb')
588	fileSize = os.stat(filename).st_size
589	Npix = (fileSize-6000)/2
590	Head = File.read(6000)
591	head = ['Rigaku R-Axis IV detector data',]
592	image = np.array(ar.array('H',File.read(fileSize-6000)),dtype=np.int32)
593	print fileSize,image.shape
594	print head
595	if Npix == 9000000:
596	sizexy = [3000,3000]
597	pixSize = [100.,100.]
598	elif Npix == 2250000:
599	sizexy = [1500,1500]
600	pixSize = [200.,200.]
601	else:
602	sizexy = [6000,6000]
603	pixSize = [50.,50.]
604	image = np.reshape(image,(sizexy[1],sizexy[0]))
605	data = {'pixelSize':pixSize,'wavelength':1.5428,'distance':250.0,'center':[150.,150.],'size':sizexy}
606	File.close()
607	if imageOnly:
608	return image
609	else:
610	return head,data,Npix,image
611
612	# should get moved to importer when ready to test
613	def GetImgData(filename,imageOnly=False):
614	'Read an ADSC image file'
615	import struct as st
616	import array as ar
617	if not imageOnly:
618	print 'Read ADSC img file: ',filename
619	File = open(filename,'rb')
620	head = File.read(511)
621	lines = head.split('\n')
622	head = []
623	center = [0,0]
624	for line in lines[1:-2]:
625	line = line.strip()[:-1]
626	if line:
627	if 'SIZE1' in line:
628	size = int(line.split('=')[1])
629	Npix = size*size
630	elif 'WAVELENGTH' in line:
631	wave = float(line.split('=')[1])
632	elif 'BIN' in line:
633	if line.split('=')[1] == '2x2':
634	pixel=(102,102)
635	else:
636	pixel = (51,51)
637	elif 'DISTANCE' in line:
638	distance = float(line.split('=')[1])
639	elif 'CENTER_X' in line:
640	center[0] = float(line.split('=')[1])
641	elif 'CENTER_Y' in line:
642	center[1] = float(line.split('=')[1])
643	head.append(line)
644	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center,'size':[size,size]}
645	image = []
646	row = 0
647	pos = 512
648	File.seek(pos)
649	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
650	image = np.reshape(image,(sizexy[1],sizexy[0]))
651	# image = np.zeros(shape=(size,size),dtype=np.int32)
652	# while row < size:
653	# File.seek(pos)
654	# line = ar.array('H',File.read(2*size))
655	# image[row] = np.asarray(line)
656	# row += 1
657	# pos += 2*size
658	File.close()
659	if imageOnly:
660	return image
661	else:
662	return lines[1:-2],data,Npix,image
663
664	# should get moved to importer when ready to test
665	def GetMAR345Data(filename,imageOnly=False):
666	'Read a MAR-345 image plate image'
667	import array as ar
668	import struct as st
669	try:
670	import pack_f as pf
671	except:
672	msg = wx.MessageDialog(None, message="Unable to load the GSAS MAR image decompression, pack_f",
673	caption="Import Error",
674	style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
675	msg.ShowModal()
676	return None,None,None,None
677
678	if not imageOnly:
679	print 'Read Mar345 file: ',filename
680	File = open(filename,'rb')
681	head = File.read(4095)
682	numbers = st.unpack('<iiiiiiiiii',head[:40])
683	lines = head[128:].split('\n')
684	head = []
685	for line in lines:
686	line = line.strip()
687	if 'PIXEL' in line:
688	values = line.split()
689	pixel = (int(values[2]),int(values[4])) #in microns
690	elif 'WAVELENGTH' in line:
691	wave = float(line.split()[1])
692	elif 'DISTANCE' in line:
693	distance = float(line.split()[1]) #in mm
694	elif 'CENTER' in line:
695	values = line.split()
696	center = [float(values[2])/10.,float(values[4])/10.] #make in mm from pixels
697	if line:
698	head.append(line)
699	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center}
700	for line in head:
701	if 'FORMAT' in line[0:6]:
702	items = line.split()
703	sizex = int(items[1])
704	Npix = int(items[3])
705	sizey = int(Npix/sizex)
706	pos = 4096
707	data['size'] = [sizex,sizey]
708	File.seek(pos)
709	line = File.read(8)
710	while 'CCP4' not in line: #get past overflow list for now
711	line = File.read(8)
712	pos += 8
713	pos += 37
714	File.seek(pos)
715	raw = File.read()
716	File.close()
717	image = np.zeros(shape=(sizex,sizey),dtype=np.int32)
718
719	image = np.flipud(pf.pack_f(len(raw),raw,sizex,sizey,image).T) #transpose to get it right way around & flip
720	if imageOnly:
721	return image
722	else:
723	return head,data,Npix,image
724
725	def ProjFileOpen(G2frame):
726	'Read a GSAS-II project file and load into the G2 data tree'
727	if not os.path.exists(G2frame.GSASprojectfile):
728	print ('\n*** Error attempt to open project file that does not exist:\n '+
729	str(G2frame.GSASprojectfile))
730	return
731	LastSavedUsing = None
732	file = open(G2frame.GSASprojectfile,'rb')
733	print 'load from file: ',G2frame.GSASprojectfile
734	G2frame.SetTitle("GSAS-II data tree: "+
735	os.path.split(G2frame.GSASprojectfile)[1])
736	wx.BeginBusyCursor()
737	try:
738	while True:
739	try:
740	data = cPickle.load(file)
741	except EOFError:
742	break
743	datum = data[0]
744
745	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=datum[0])
746	if 'PWDR' in datum[0]:
747	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
748	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
749	G2frame.PatternTree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
750	elif datum[0].startswith('HKLF'):
751	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
752	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
753	G2frame.PatternTree.SetItemPyData(Id,datum[1])
754	else:
755	G2frame.PatternTree.SetItemPyData(Id,datum[1])
756	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
757	LastSavedUsing = datum[1]['LastSavedUsing']
758	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug'):
759	print('Packages used to create .GPX file:')
760	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
761	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
762	print("{:>14s}: {:s}".format(p[0],p[1]))
763	else:
764	for p in datum[1]['PythonVersions']:
765	print("{:<12s} {:s}".format(p[0]+':',p[1]))
766	for datus in data[1:]:
767	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
768	#patch
769	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
770	if 'PWDR' in datum[0]:
771	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
772	else:
773	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
774	for item in datus[1][0]: #zip makes tuples - now make lists!
775	datus[1][0][item] = list(datus[1][0][item])
776	#end patch
777	G2frame.PatternTree.SetItemPyData(sub,datus[1])
778	if 'IMG' in datum[0]: #retrieve image default flag & data if set
779	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
780	if Data['setDefault']:
781	G2frame.imageDefault = Data
782	file.close()
783	if LastSavedUsing:
784	print('GPX load successful. Last saved with GSAS-II version '+LastSavedUsing)
785	else:
786	print('project load successful')
787	G2frame.NewPlot = True
788	except:
789	msg = wx.MessageDialog(G2frame,message="Error reading file "+
790	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
791	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
792	msg.ShowModal()
793	finally:
794	wx.EndBusyCursor()
795	G2frame.Status.SetStatusText('To reorder tree items, use mouse RB to drag/drop them')
796
797	def ProjFileSave(G2frame):
798	'Save a GSAS-II project file'
799	if not G2frame.PatternTree.IsEmpty():
800	file = open(G2frame.GSASprojectfile,'wb')
801	print 'save to file: ',G2frame.GSASprojectfile
802	# stick the file name into the tree and version info into tree so they are saved.
803	# (Controls should always be created at this point)
804	try:
805	Controls = G2frame.PatternTree.GetItemPyData(
806	G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
807	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
808	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
809	Controls['PythonVersions'] = G2frame.PackageVersions
810	except:
811	pass
812	wx.BeginBusyCursor()
813	try:
814	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
815	while item:
816	data = []
817	name = G2frame.PatternTree.GetItemText(item)
818	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
819	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
820	while item2:
821	name = G2frame.PatternTree.GetItemText(item2)
822	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
823	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
824	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
825	cPickle.dump(data,file,1)
826	file.close()
827	finally:
828	wx.EndBusyCursor()
829	print('project save successful')
830
831	def SaveIntegration(G2frame,PickId,data):
832	'Save image integration results as powder pattern(s)'
833	azms = G2frame.Integrate[1]
834	X = G2frame.Integrate[2][:-1]
835	N = len(X)
836	Id = G2frame.PatternTree.GetItemParent(PickId)
837	name = G2frame.PatternTree.GetItemText(Id)
838	name = name.replace('IMG ',data['type']+' ')
839	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
840	if 'PWDR' in name:
841	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
842	codes = [0 for i in range(11)]
843	elif 'SASD' in name:
844	names = ['Type','Lam','Zero','Azimuth']
845	codes = [0 for i in range(4)]
846	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
847	Xminmax = [X[0],X[-1]]
848	LRazm = data['LRazimuth']
849	Azms = []
850	dazm = 0.
851	if data['fullIntegrate'] and data['outAzimuths'] == 1:
852	Azms = [45.0,] #a poor man's average?
853	else:
854	for i,azm in enumerate(azms[:-1]):
855	if azm > 360. and azms[i+1] > 360.:
856	Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
857	else:
858	Azms.append(G2img.meanAzm(azm,azms[i+1]))
859	dazm = np.min(np.abs(np.diff(azms)))/2.
860	G2frame.IntgOutList = []
861	for i,azm in enumerate(azms[:-1]):
862	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
863	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
864	nOcc = 0
865	while item:
866	Name = G2frame.PatternTree.GetItemText(item)
867	if Aname in Name:
868	nOcc += 1
869	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
870	if nOcc:
871	Aname += '(%d)'%(nOcc)
872	Sample = G2pdG.SetDefaultSample()
873	Sample['Gonio. radius'] = data['distance']
874	Sample['Omega'] = data['GonioAngles'][0]
875	Sample['Chi'] = data['GonioAngles'][1]
876	Sample['Phi'] = data['GonioAngles'][2]
877	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
878	if 'PWDR' in Aname:
879	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!
880	elif 'SASD' in Aname:
881	Sample['Trans'] = data['SampleAbs'][0]
882	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
883	Y = G2frame.Integrate[0][i]
884	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
885	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=Aname)
886	G2frame.IntgOutList.append(Id)
887	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
888	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
889	if 'PWDR' in Aname:
890	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
891	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
892	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
893	for item in inst[0]:
894	inst[0][item] = list(inst[0][item])
895	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
896	if 'PWDR' in Aname:
897	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
898	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
899	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[[],[]])
900	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
901	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
902	elif 'SASD' in Aname:
903	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
904	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
905	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
906	valuesdict = {
907	'wtFactor':1.0,
908	'Dummy':False,
909	'ranId':ran.randint(0,sys.maxint),
910	'Offset':[0.0,0.0],'delOffset':0.02,'refOffset':-1.0,'refDelt':0.01,
911	'qPlot':False,'dPlot':False,'sqrtPlot':False
912	}
913	G2frame.PatternTree.SetItemPyData(
914	Id,[valuesdict,
915	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
916	return Id #last powder pattern generated
917
918	# def powderFxyeSave(G2frame,exports,powderfile):
919	# 'Save a powder histogram as a GSAS FXYE file'
920	# head,tail = ospath.split(powderfile)
921	# name,ext = tail.split('.')
922	# for i,export in enumerate(exports):
923	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
924	# prmname = filename.strip(ext)+'prm'
925	# prm = open(prmname,'w') #old style GSAS parm file
926	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
927	# Inst = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, \
928	# PickId, 'Instrument Parameters'))[0]
929	# prm.write( ' 123456789012345678901234567890123456789012345678901234567890 '+'\n')
930	# prm.write( 'INS BANK 1 '+'\n')
931	# prm.write(('INS HTYPE %sR '+'\n')%(Inst['Type'][0]))
932	# if 'Lam1' in Inst: #Ka1 & Ka2
933	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam1'][0],Inst['Lam2'][0]))
934	# elif 'Lam' in Inst: #single wavelength
935	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam'][1],0.0))
936	# prm.write( 'INS 1 IRAD 0 '+'\n')
937	# prm.write( 'INS 1I HEAD '+'\n')
938	# prm.write( 'INS 1I ITYP 0 0.0000 180.0000 1 '+'\n')
939	# prm.write(('INS 1DETAZM%10.3f '+'\n')%(Inst['Azimuth'][0]))
940	# prm.write( 'INS 1PRCF1 3 8 0.00100 '+'\n')
941	# prm.write(('INS 1PRCF11 %15.6g%15.6g%15.6g%15.6g '+'\n')%(Inst['U'][1],Inst['V'][1],Inst['W'][1],0.0))
942	# 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.))
943	# prm.close()
944	# file = open(filename,'w')
945	# print 'save powder pattern to file: ',filename
946	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
947	# file.write(powderfile+'\n')
948	# file.write('Instrument parameter file:'+ospath.split(prmname)[1]+'\n')
949	# file.write('BANK 1 %d %d CONS %.2f %.2f 0 0 FXYE\n'%(len(x),len(x),\
950	# 100.x[0],100.(x[1]-x[0])))
951	# s = list(np.sqrt(1./np.array(w)))
952	# XYW = zip(x,y,s)
953	# for X,Y,S in XYW:
954	# file.write("%15.6g %15.6g %15.6g\n" % (100.*X,Y,max(S,1.0)))
955	# file.close()
956	# print 'powder pattern file '+filename+' written'
957
958	# def powderXyeSave(G2frame,exports,powderfile):
959	# 'Save a powder histogram as a Topas XYE file'
960	# head,tail = ospath.split(powderfile)
961	# name,ext = tail.split('.')
962	# for i,export in enumerate(exports):
963	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
964	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
965	# file = open(filename,'w')
966	# file.write('#%s\n'%(export))
967	# print 'save powder pattern to file: ',filename
968	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
969	# s = list(np.sqrt(1./np.array(w)))
970	# XYW = zip(x,y,s)
971	# for X,Y,W in XYW:
972	# file.write("%15.6g %15.6g %15.6g\n" % (X,Y,W))
973	# file.close()
974	# print 'powder pattern file '+filename+' written'
975
976	def PDFSave(G2frame,exports):
977	'Save a PDF G(r) and S(Q) in column formats'
978	for export in exports:
979	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
980	SQname = 'S(Q)'+export[4:]
981	GRname = 'G(R)'+export[4:]
982	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
983	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
984	sqId = G2gd.GetPatternTreeItemId(G2frame, PickId, SQname)
985	grId = G2gd.GetPatternTreeItemId(G2frame, PickId, GRname)
986	sqdata = np.array(G2frame.PatternTree.GetItemPyData(sqId)[1][:2]).T
987	grdata = np.array(G2frame.PatternTree.GetItemPyData(grId)[1][:2]).T
988	sqfile = open(sqfilename,'w')
989	grfile = open(grfilename,'w')
990	sqfile.write('#T S(Q) %s\n'%(export))
991	grfile.write('#T G(R) %s\n'%(export))
992	sqfile.write('#L Q S(Q)\n')
993	grfile.write('#L R G(R)\n')
994	for q,sq in sqdata:
995	sqfile.write("%15.6g %15.6g\n" % (q,sq))
996	sqfile.close()
997	for r,gr in grdata:
998	grfile.write("%15.6g %15.6g\n" % (r,gr))
999	grfile.close()
1000
1001	def PeakListSave(G2frame,file,peaks):
1002	'Save powder peaks to a data file'
1003	print 'save peak list to file: ',G2frame.peaklistfile
1004	if not peaks:
1005	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1006	try:
1007	result = dlg.ShowModal()
1008	finally:
1009	dlg.Destroy()
1010	return
1011	for peak in peaks:
1012	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1013	(peak[0],peak[2],peak[4],peak[6]))
1014	print 'peak list saved'
1015
1016	def IndexPeakListSave(G2frame,peaks):
1017	'Save powder peaks from the indexing list'
1018	file = open(G2frame.peaklistfile,'wa')
1019	print 'save index peak list to file: ',G2frame.peaklistfile
1020	wx.BeginBusyCursor()
1021	try:
1022	if not peaks:
1023	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1024	try:
1025	result = dlg.ShowModal()
1026	finally:
1027	dlg.Destroy()
1028	return
1029	for peak in peaks:
1030	file.write("%12.6f\n" % (peak[7]))
1031	file.close()
1032	finally:
1033	wx.EndBusyCursor()
1034	print 'index peak list saved'
1035
1036	def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1037	'''Create a new phase dict with default values for various parameters
1038
1039	:param str Name: Name for new Phase
1040
1041	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1042	defaults to data for P 1
1043
1044	:param list cell: unit cell parameter list; defaults to
1045	[1.0,1.0,1.0,90.,90,90.,1.]
1046
1047	'''
1048	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1049	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1050	phaseData = {
1051	'ranId':ran.randint(0,sys.maxint),
1052	'General':{
1053	'Name':Name,
1054	'Type':'nuclear',
1055	'AtomPtrs':[3,1,7,9],
1056	'SGData':SGData,
1057	'Cell':[False,]+cell,
1058	'Pawley dmin':1.0,
1059	'Data plot type':'None',
1060	'SH Texture':{
1061	'Order':0,
1062	'Model':'cylindrical',
1063	'Sample omega':[False,0.0],
1064	'Sample chi':[False,0.0],
1065	'Sample phi':[False,0.0],
1066	'SH Coeff':[False,{}],
1067	'SHShow':False,
1068	'PFhkl':[0,0,1],
1069	'PFxyz':[0,0,1],
1070	'PlotType':'Pole figure',
1071	'Penalty':[['',],0.1,False,1.0]}},
1072	'Atoms':[],
1073	'Drawing':{},
1074	'Histograms':{},
1075	'Pawley ref':[],
1076	'RBModels':{},
1077	}
1078	if Super and Super.get('Use',False):
1079	phaseData['General'].update({'Type':'modulated','Super':True,'SuperSg':Super['ssSymb']})
1080	phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])
1081	phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1082
1083	return phaseData
1084
1085	class MultipleChoicesDialog(wx.Dialog):
1086	'''A dialog that offers a series of choices, each with a
1087	title and a wx.Choice widget. Intended to be used Modally.
1088	typical input:
1089
1090	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1091	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1092
1093	selections are placed in self.chosen when OK is pressed
1094	'''
1095	def __init__(self,choicelist,headinglist,
1096	head='Select options',
1097	title='Please select from options below',
1098	parent=None):
1099	self.chosen = []
1100	wx.Dialog.__init__(
1101	self,parent,wx.ID_ANY,head,
1102	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1103	panel = wx.Panel(self)
1104	mainSizer = wx.BoxSizer(wx.VERTICAL)
1105	mainSizer.Add((10,10),1)
1106	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1107	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1108	self.ChItems = []
1109	for choice,lbl in zip(choicelist,headinglist):
1110	mainSizer.Add((10,10),1)
1111	self.chosen.append(0)
1112	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1113	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1114	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1115	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1116
1117	OkBtn = wx.Button(panel,-1,"Ok")
1118	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1119	cancelBtn = wx.Button(panel,-1,"Cancel")
1120	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1121	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1122	btnSizer.Add((20,20),1)
1123	btnSizer.Add(OkBtn)
1124	btnSizer.Add((20,20),1)
1125	btnSizer.Add(cancelBtn)
1126	btnSizer.Add((20,20),1)
1127	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1128	panel.SetSizer(mainSizer)
1129	panel.Fit()
1130	self.Fit()
1131
1132	def OnOk(self,event):
1133	parent = self.GetParent()
1134	if parent is not None: parent.Raise()
1135	# save the results from the choice widgets
1136	self.chosen = []
1137	for w in self.ChItems:
1138	self.chosen.append(w.GetSelection())
1139	self.EndModal(wx.ID_OK)
1140
1141	def OnCancel(self,event):
1142	parent = self.GetParent()
1143	if parent is not None: parent.Raise()
1144	self.chosen = []
1145	self.EndModal(wx.ID_CANCEL)
1146
1147	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1148	confirmoverwrite=True, parent=None,
1149	multipleselect=False):
1150	'''If the filename is a zip file, extract a file from that
1151	archive.
1152
1153	:param list Selection: used to predefine the name of the file
1154	to be extracted. Filename case and zip directory name are
1155	ignored in selection; the first matching file is used.
1156
1157	:param bool confirmread: if True asks the user to confirm before expanding
1158	the only file in a zip
1159
1160	:param bool confirmoverwrite: if True asks the user to confirm
1161	before overwriting if the extracted file already exists
1162
1163	:param bool multipleselect: if True allows more than one zip
1164	file to be extracted, a list of file(s) is returned.
1165	If only one file is present, do not ask which one, otherwise
1166	offer a list of choices (unless selection is used).
1167
1168	:returns: the name of the file that has been created or a
1169	list of files (see multipleselect)
1170
1171	If the file is not a zipfile, return the name of the input file.
1172	If the zipfile is empty or no file has been selected, return None
1173	'''
1174	import zipfile # do this now, since we can save startup time by doing this only on need
1175	import shutil
1176	zloc = os.path.split(filename)[0]
1177	if not zipfile.is_zipfile(filename):
1178	#print("not zip")
1179	return filename
1180
1181	z = zipfile.ZipFile(filename,'r')
1182	zinfo = z.infolist()
1183
1184	if len(zinfo) == 0:
1185	#print('Zip has no files!')
1186	zlist = [-1]
1187	if selection:
1188	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1189	if selection.lower() in choices:
1190	zlist = [choices.index(selection.lower())]
1191	else:
1192	print('debug: file '+str(selection)+' was not found in '+str(filename))
1193	zlist = [-1]
1194	elif len(zinfo) == 1 and confirmread:
1195	result = wx.ID_NO
1196	dlg = wx.MessageDialog(
1197	parent,
1198	'Is file '+str(zinfo[0].filename)+
1199	' what you want to extract from '+
1200	str(os.path.split(filename)[1])+'?',
1201	'Confirm file',
1202	wx.YES_NO \| wx.ICON_QUESTION)
1203	try:
1204	result = dlg.ShowModal()
1205	finally:
1206	dlg.Destroy()
1207	if result == wx.ID_NO:
1208	zlist = [-1]
1209	else:
1210	zlist = [0]
1211	elif len(zinfo) == 1:
1212	zlist = [0]
1213	elif multipleselect:
1214	# select one or more from a from list
1215	choices = [i.filename for i in zinfo]
1216	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1217	'Choose file(s)',choices)
1218	if dlg.ShowModal() == wx.ID_OK:
1219	zlist = dlg.GetSelections()
1220	else:
1221	zlist = []
1222	dlg.Destroy()
1223	else:
1224	# select one from a from list
1225	choices = [i.filename for i in zinfo]
1226	dlg = wx.SingleChoiceDialog(parent,
1227	'Select file to extract from zip file'+str(filename),'Choose file',
1228	choices,)
1229	if dlg.ShowModal() == wx.ID_OK:
1230	zlist = [dlg.GetSelection()]
1231	else:
1232	zlist = [-1]
1233	dlg.Destroy()
1234
1235	outlist = []
1236	for zindex in zlist:
1237	if zindex >= 0:
1238	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1239	if os.path.exists(efil) and confirmoverwrite:
1240	result = wx.ID_NO
1241	dlg = wx.MessageDialog(parent,
1242	'File '+str(efil)+' already exists. OK to overwrite it?',
1243	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1244	try:
1245	result = dlg.ShowModal()
1246	finally:
1247	dlg.Destroy()
1248	if result == wx.ID_NO:
1249	zindex = -1
1250	if zindex >= 0:
1251	# extract the file to the current directory, regardless of it's original path
1252	#z.extract(zinfo[zindex],zloc)
1253	eloc,efil = os.path.split(zinfo[zindex].filename)
1254	outfile = os.path.join(zloc, efil)
1255	fpin = z.open(zinfo[zindex])
1256	fpout = file(outfile, "wb")
1257	shutil.copyfileobj(fpin, fpout)
1258	fpin.close()
1259	fpout.close()
1260	outlist.append(outfile)
1261	z.close()
1262	if multipleselect and len(outlist) >= 1:
1263	return outlist
1264	elif len(outlist) == 1:
1265	return outlist[0]
1266	else:
1267	return None
1268
1269	######################################################################
1270	# base classes for reading various types of data files
1271	# not used directly, only by subclassing
1272	######################################################################
1273	try:
1274	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1275	except: # errors on doc build
1276	SGData = None
1277	P1SGData = SGData
1278	class ImportBaseclass(object):
1279	'''Defines a base class for the reading of input files (diffraction
1280	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1281	for an explanation on how to use a subclass of this class.
1282	'''
1283	class ImportException(Exception):
1284	'''Defines an Exception that is used when an import routine hits an expected error,
1285	usually in .Reader.
1286
1287	Good practice is that the Reader should define a value in self.errors that
1288	tells the user some information about what is wrong with their file.
1289	'''
1290	pass
1291
1292	def __init__(self,
1293	formatName,
1294	longFormatName=None,
1295	extensionlist=[],
1296	strictExtension=False,
1297	):
1298	self.formatName = formatName # short string naming file type
1299	if longFormatName: # longer string naming file type
1300	self.longFormatName = longFormatName
1301	else:
1302	self.longFormatName = formatName
1303	# define extensions that are allowed for the file type
1304	# for windows, remove any extensions that are duplicate, as case is ignored
1305	if sys.platform == 'windows' and extensionlist:
1306	extensionlist = list(set([s.lower() for s in extensionlist]))
1307	self.extensionlist = extensionlist
1308	# If strictExtension is True, the file will not be read, unless
1309	# the extension matches one in the extensionlist
1310	self.strictExtension = strictExtension
1311	self.errors = ''
1312	self.warnings = ''
1313	# used for readers that will use multiple passes to read
1314	# more than one data block
1315	self.repeat = False
1316	self.selections = []
1317	self.repeatcount = 0
1318	self.readfilename = '?'
1319	#print 'created',self.__class__
1320
1321	def ReInitialize(self):
1322	'Reinitialize the Reader to initial settings'
1323	self.errors = ''
1324	self.warnings = ''
1325	self.repeat = False
1326	self.repeatcount = 0
1327	self.readfilename = '?'
1328
1329	def BlockSelector(self, ChoiceList, ParentFrame=None,
1330	title='Select a block',
1331	size=None, header='Block Selector',
1332	useCancel=True):
1333	''' Provide a wx dialog to select a block if the file contains more
1334	than one set of data and one must be selected
1335	'''
1336	if useCancel:
1337	dlg = wx.SingleChoiceDialog(
1338	ParentFrame,title, header,ChoiceList)
1339	else:
1340	dlg = wx.SingleChoiceDialog(
1341	ParentFrame,title, header,ChoiceList,
1342	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1343	if size: dlg.SetSize(size)
1344	dlg.CenterOnParent()
1345	if dlg.ShowModal() == wx.ID_OK:
1346	sel = dlg.GetSelection()
1347	return sel
1348	else:
1349	return None
1350	dlg.Destroy()
1351
1352	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1353	title='Select a block',size=None, header='Block Selector'):
1354	'''Provide a wx dialog to select a block of data if the
1355	file contains more than one set of data and one must be
1356	selected.
1357
1358	:returns: a list of the selected blocks
1359	'''
1360	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1361	wx.CHOICEDLG_STYLE)
1362	dlg.CenterOnParent()
1363	if size: dlg.SetSize(size)
1364	if dlg.ShowModal() == wx.ID_OK:
1365	sel = dlg.GetSelections()
1366	else:
1367	return []
1368	dlg.Destroy()
1369	selected = []
1370	if len(ChoiceList) in sel:
1371	return range(len(ChoiceList))
1372	else:
1373	return sel
1374	return selected
1375
1376	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1377	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1378	widget. Typical input:
1379
1380	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1381
1382	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1383
1384	optional keyword parameters are: head (window title) and title
1385	returns a list of selected indicies for each choice (or None)
1386	'''
1387	result = None
1388	dlg = MultipleChoicesDialog(choicelist,headinglist,
1389	parent=ParentFrame, **kwargs)
1390	dlg.CenterOnParent()
1391	if dlg.ShowModal() == wx.ID_OK:
1392	result = dlg.chosen
1393	dlg.Destroy()
1394	return result
1395
1396	def ShowBusy(self):
1397	wx.BeginBusyCursor()
1398	# wx.Yield() # make it happen now!
1399
1400	def DoneBusy(self):
1401	wx.EndBusyCursor()
1402	wx.Yield() # make it happen now!
1403
1404	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1405	# '''This method must be supplied in the child class to read the file.
1406	# if the read fails either return False or raise an Exception
1407	# preferably of type ImportException.
1408	# '''
1409	# #start reading
1410	# raise ImportException("Error occurred while...")
1411	# self.errors += "Hint for user on why the error occur
1412	# return False # if an error occurs
1413	# return True # if read OK
1414
1415	def ExtensionValidator(self, filename):
1416	'''This methods checks if the file has the correct extension
1417	Return False if this filename will not be supported by this reader
1418	Return True if the extension matches the list supplied by the reader
1419	Return None if the reader allows un-registered extensions
1420	'''
1421	if filename:
1422	ext = os.path.splitext(filename)[1]
1423	if sys.platform == 'windows': ext = ext.lower()
1424	if ext in self.extensionlist: return True
1425	if self.strictExtension: return False
1426	return None
1427
1428	def ContentsValidator(self, filepointer):
1429	'''This routine will attempt to determine if the file can be read
1430	with the current format.
1431	This will typically be overridden with a method that
1432	takes a quick scan of [some of]
1433	the file contents to do a "sanity" check if the file
1434	appears to match the selected format.
1435	Expected to be called via self.Validator()
1436	'''
1437	#filepointer.seek(0) # rewind the file pointer
1438	return True
1439
1440	def CIFValidator(self, filepointer):
1441	'''A :meth:`ContentsValidator` for use to validate CIF files.
1442	'''
1443	for i,l in enumerate(filepointer):
1444	if i >= 1000: return True
1445	'''Encountered only blank lines or comments in first 1000
1446	lines. This is unlikely, but assume it is CIF anyway, since we are
1447	even less likely to find a file with nothing but hashes and
1448	blank lines'''
1449	line = l.strip()
1450	if len(line) == 0: # ignore blank lines
1451	continue
1452	elif line.startswith('#'): # ignore comments
1453	continue
1454	elif line.startswith('data_'): # on the right track, accept this file
1455	return True
1456	else: # found something invalid
1457	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1458	self.errors += ' '+str(l)
1459	self.errors += ' Note: a CIF should only have blank lines or comments before'
1460	self.errors += ' a data_ statement begins a block.'
1461	return False
1462
1463	class ImportPhase(ImportBaseclass):
1464	'''Defines a base class for the reading of files with coordinates
1465
1466	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1467	in :meth:`GSASII.GSASII.OnImportPhase`.
1468	See :ref:`Writing a Import Routine<Import_Routines>`
1469	for an explanation on how to use this class.
1470
1471	'''
1472	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1473	strictExtension=False,):
1474	# call parent __init__
1475	ImportBaseclass.__init__(self,formatName,longFormatName,
1476	extensionlist,strictExtension)
1477	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1478	self.Constraints = None
1479
1480	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1481	title='Select a phase', size=None,header='Phase Selector'):
1482	''' Provide a wx dialog to select a phase if the file contains more
1483	than one phase
1484	'''
1485	return self.BlockSelector(ChoiceList,ParentFrame,title,
1486	size,header)
1487
1488	class ImportStructFactor(ImportBaseclass):
1489	'''Defines a base class for the reading of files with tables
1490	of structure factors.
1491
1492	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1493	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1494	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1495	:meth:`Reader`.
1496
1497	See :ref:`Writing a Import Routine<Import_Routines>`
1498	for an explanation on how to use import classes in general. The specifics
1499	for reading a structure factor histogram require that
1500	the ``Reader()`` routine in the import
1501	class need to do only a few things: It
1502	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1503	and set :attr:`Parameters` with the instrument parameters
1504	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1505	'''
1506	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1507	strictExtension=False,):
1508	ImportBaseclass.__init__(self,formatName,longFormatName,
1509	extensionlist,strictExtension)
1510
1511	# define contents of Structure Factor entry
1512	self.Parameters = []
1513	'self.Parameters is a list with two dicts for data parameter settings'
1514	self.InitParameters()
1515	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1516	self.Banks = [] #for multi bank data (usually TOF)
1517	'''self.RefDict is a dict containing the reflection information, as read from the file.
1518	Item 'RefList' contains the reflection information. See the
1519	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1520	for the contents of each row. Dict element 'FF'
1521	contains the form factor values for each element type; if this entry
1522	is left as initialized (an empty list) it will be initialized as needed later.
1523	'''
1524	def ReInitialize(self):
1525	'Reinitialize the Reader to initial settings'
1526	ImportBaseclass.ReInitialize(self)
1527	self.InitParameters()
1528	self.Banks = [] #for multi bank data (usually TOF)
1529	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1530
1531	def InitParameters(self):
1532	'initialize the instrument parameters structure'
1533	Lambda = 0.70926
1534	HistType = 'SXC'
1535	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1536	'Lam':[Lambda,Lambda]
1537	}, {}]
1538	'Parameters is a list with two dicts for data parameter settings'
1539
1540	def UpdateParameters(self,Type=None,Wave=None):
1541	'Revise the instrument parameters'
1542	if Type is not None:
1543	self.Parameters[0]['Type'] = [Type,Type]
1544	if Wave is not None:
1545	self.Parameters[0]['Lam'] = [Wave,Wave]
1546
1547	######################################################################
1548	class ImportPowderData(ImportBaseclass):
1549	'''Defines a base class for the reading of files with powder data.
1550
1551	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1552	in :meth:`GSASII.GSASII.OnImportPowder`.
1553	See :ref:`Writing a Import Routine<Import_Routines>`
1554	for an explanation on how to use this class.
1555	'''
1556	def __init__(self,
1557	formatName,
1558	longFormatName=None,
1559	extensionlist=[],
1560	strictExtension=False,
1561	):
1562	ImportBaseclass.__init__(self,formatName,
1563	longFormatName,
1564	extensionlist,
1565	strictExtension)
1566	self.clockWd = None # used in TOF
1567	self.ReInitialize()
1568
1569	def ReInitialize(self):
1570	'Reinitialize the Reader to initial settings'
1571	ImportBaseclass.ReInitialize(self)
1572	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1573	self.powderdata = [] # Powder dataset
1574	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1575	np.array(x), # x-axis values
1576	np.array(y), # powder pattern intensities
1577	np.array(w), # 1/sig(intensity)^2 values (weights)
1578	np.array(yc), # calc. intensities (zero)
1579	np.array(yb), # calc. background (zero)
1580	np.array(yd), # obs-calc profiles
1581	'''
1582	self.comments = []
1583	self.idstring = ''
1584	self.Sample = G2pdG.SetDefaultSample() # default sample parameters
1585	self.Controls = {} # items to be placed in top-level Controls
1586	self.GSAS = None # used in TOF
1587	self.repeat_instparm = True # Should a parm file be
1588	# used for multiple histograms?
1589	self.instparm = None # name hint from file of instparm to use
1590	self.instfile = '' # full path name to instrument parameter file
1591	self.instbank = '' # inst parm bank number
1592	self.instmsg = '' # a label that gets printed to show
1593	# where instrument parameters are from
1594	self.numbanks = 1
1595	self.instdict = {} # place items here that will be transferred to the instrument parameters
1596	self.pwdparms = {} # place parameters that are transferred directly to the tree
1597	# here (typically from an existing GPX file)
1598	######################################################################
1599	class ImportSmallAngleData(ImportBaseclass):
1600	'''Defines a base class for the reading of files with small angle data.
1601	See :ref:`Writing a Import Routine<Import_Routines>`
1602	for an explanation on how to use this class.
1603	'''
1604	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1605	strictExtension=False,):
1606
1607	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1608	strictExtension)
1609	self.ReInitialize()
1610
1611	def ReInitialize(self):
1612	'Reinitialize the Reader to initial settings'
1613	ImportBaseclass.ReInitialize(self)
1614	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1615	self.smallangledata = [] # SASD dataset
1616	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1617	np.array(x), # x-axis values
1618	np.array(y), # powder pattern intensities
1619	np.array(w), # 1/sig(intensity)^2 values (weights)
1620	np.array(yc), # calc. intensities (zero)
1621	np.array(yd), # obs-calc profiles
1622	np.array(yb), # preset bkg
1623	'''
1624	self.comments = []
1625	self.idstring = ''
1626	self.Sample = G2pdG.SetDefaultSample()
1627	self.GSAS = None # used in TOF
1628	self.clockWd = None # used in TOF
1629	self.numbanks = 1
1630	self.instdict = {} # place items here that will be transferred to the instrument parameters
1631
1632	######################################################################
1633	class ImportImage(ImportBaseclass):
1634	'''Defines a base class for the reading of images
1635
1636	Images are read in only these places:
1637
1638	* Initial reading is typically done from a menu item
1639	with a call to :meth:`GSASII.GSASII.OnImportImage`
1640	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`. That calls
1641	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1642	:meth:`Reader`. This returns a list of reader objects for each read image.
1643
1644	* Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
1645	directly into the data tree.
1646
1647	* Images are reloaded with :func:`GSASIIIO.GetImageData`.
1648
1649	.. _Image_import_routines:
1650
1651	When reading an image, the ``Reader()`` routine in the ImportImage class
1652	should set:
1653
1654	* :attr:`Comments`: a list of strings (str),
1655	* :attr:`Npix`: the number of pixels in the image (int),
1656	* :attr:`Image`: the actual image as a numpy array (np.array)
1657	* :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
1658	data items are needed:
1659
1660	* 'pixelSize': size of each pixel in microns (such as ``[200,200]``.
1661	* 'wavelength': wavelength in Angstoms.
1662	* 'distance': distance of detector from sample in cm.
1663	* 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
1664	* 'size': size of image (such as ``[2048,2048]``).
1665	* 'ImageTag': image number or other keyword used to retrieve image from
1666	a multi-image data file (defaults to ``1`` if not specified).
1667
1668	optional data items:
1669
1670	* :attr:`repeat`: set to True if there are additional images to
1671	read in the file, False otherwise
1672	* :attr:`repeatcount`: set to the number of the image.
1673
1674	Note that the above is initialized with :meth:`InitParameters`.
1675	(Also see :ref:`Writing a Import Routine<Import_Routines>`
1676	for an explanation on how to use import classes in general.)
1677	'''
1678	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1679	strictExtension=False,):
1680	ImportBaseclass.__init__(self,formatName,longFormatName,
1681	extensionlist,strictExtension)
1682	self.InitParameters()
1683
1684	def ReInitialize(self):
1685	'Reinitialize the Reader to initial settings -- not used at present'
1686	ImportBaseclass.ReInitialize(self)
1687	self.InitParameters()
1688
1689	def InitParameters(self):
1690	'initialize the instrument parameters structure'
1691	self.Comments = ['No comments']
1692	self.Data = {}
1693	self.Npix = 0
1694	self.Image = None
1695	self.repeat = False
1696	self.repeatcount = 1
1697
1698	def LoadImage(self,ParentFrame,imagefile,imagetag=None):
1699	'''Optionally, call this after reading in an image to load it into the tree.
1700	This saves time by preventing a reread of the same information.
1701	'''
1702	if ParentFrame:
1703	ParentFrame.ImageZ = self.Image # store the image for plotting
1704	ParentFrame.oldImagefile = imagefile # save the name of the last image file read
1705	ParentFrame.oldImageTag = imagetag # save the tag of the last image file read
1706
1707	######################################################################
1708	class ExportBaseclass(object):
1709	'''Defines a base class for the exporting of GSAS-II results.
1710
1711	This class is subclassed in the various exports/G2export_*.py files. Those files
1712	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
1713	appropriate menu items for each one and the .Exporter method is called
1714	directly from the menu item.
1715
1716	Routines may also define a .Writer method, which is used to write a single
1717	file without invoking any GUI objects.
1718	'''
1719	def __init__(self,
1720	G2frame,
1721	formatName,
1722	extension,
1723	longFormatName=None,
1724	):
1725	self.G2frame = G2frame
1726	self.formatName = formatName # short string naming file type
1727	self.extension = extension
1728	if longFormatName: # longer string naming file type
1729	self.longFormatName = longFormatName
1730	else:
1731	self.longFormatName = formatName
1732	self.OverallParms = {}
1733	self.Phases = {}
1734	self.Histograms = {}
1735	self.powderDict = {}
1736	self.xtalDict = {}
1737	self.parmDict = {}
1738	self.sigDict = {}
1739	# updated in InitExport:
1740	self.currentExportType = None # type of export that has been requested
1741	# updated in ExportSelect (when used):
1742	self.phasenam = None # a list of selected phases
1743	self.histnam = None # a list of selected histograms
1744	self.filename = None # name of file to be written (single export) or template (multiple files)
1745	self.dirname = '' # name of directory where file(s) will be written
1746	self.fullpath = '' # name of file being written -- full path
1747
1748	# items that should be defined in a subclass of this class
1749	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1750	# The following types are defined: 'project', "phase", "powder", "single"
1751	self.multiple = False # set as True if the class can export multiple phases or histograms
1752	# self.multiple is ignored for "project" exports
1753
1754	def InitExport(self,event):
1755	'''Determines the type of menu that called the Exporter and
1756	misc initialization.
1757	'''
1758	self.filename = None # name of file to be written (single export)
1759	self.dirname = '' # name of file to be written (multiple export)
1760	if event:
1761	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1762
1763	def MakePWDRfilename(self,hist):
1764	'''Make a filename root (no extension) from a PWDR histogram name
1765
1766	:param str hist: the histogram name in data tree (starts with "PWDR ")
1767	'''
1768	file0 = ''
1769	file1 = hist[5:]
1770	# replace repeated blanks
1771	while file1 != file0:
1772	file0 = file1
1773	file1 = file0.replace(' ',' ').strip()
1774	file0 = file1.replace('Azm= ','A')
1775	# if angle has unneeded decimal places on aziumuth, remove them
1776	if file0[-3:] == '.00': file0 = file0[:-3]
1777	file0 = file0.replace('.','_')
1778	file0 = file0.replace(' ','_')
1779	return file0
1780
1781	def ExportSelect(self,AskFile='ask'):
1782	'''Selects histograms or phases when needed. Sets a default file name when
1783	requested in self.filename; always sets a default directory in self.dirname.
1784
1785	:param bool AskFile: Determines how this routine processes getting a
1786	location to store the current export(s).
1787
1788	* if AskFile is 'ask' (default option), get the name of the file to be written;
1789	self.filename and self.dirname are always set. In the case where
1790	multiple files must be generated, the export routine should do this
1791	based on self.filename as a template.
1792	* if AskFile is 'dir', get the name of the directory to be used;
1793	self.filename is not used, but self.dirname is always set. The export routine
1794	will always generate the file name.
1795	* if AskFile is 'single', get only the name of the directory to be used when
1796	multiple items will be written (as multiple files) are used
1797	or a complete file name is requested when a single file
1798	name is selected. self.dirname is always set and self.filename used
1799	only when a single file is selected.
1800	* if AskFile is 'default', creates a name of the file to be used from
1801	the name of the project (.gpx) file. If the project has not been saved,
1802	then the name of file is requested.
1803	self.filename and self.dirname are always set. In the case where
1804	multiple file names must be generated, the export routine should do this
1805	based on self.filename.
1806	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1807	file. If the project has not been saved, then a directory is requested.
1808	self.filename is not used.
1809
1810	:returns: True in case of an error
1811	'''
1812
1813	numselected = 1
1814	if self.currentExportType == 'phase':
1815	if len(self.Phases) == 0:
1816	self.G2frame.ErrorDialog(
1817	'Empty project',
1818	'Project does not contain any phases.')
1819	return True
1820	elif len(self.Phases) == 1:
1821	self.phasenam = self.Phases.keys()
1822	elif self.multiple:
1823	choices = sorted(self.Phases.keys())
1824	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1825	if phasenum is None: return True
1826	self.phasenam = [choices[i] for i in phasenum]
1827	if not self.phasenam: return True
1828	numselected = len(self.phasenam)
1829	else:
1830	choices = sorted(self.Phases.keys())
1831	phasenum = G2G.ItemSelector(choices,self.G2frame)
1832	if phasenum is None: return True
1833	self.phasenam = [choices[phasenum]]
1834	numselected = len(self.phasenam)
1835	elif self.currentExportType == 'single':
1836	if len(self.xtalDict) == 0:
1837	self.G2frame.ErrorDialog(
1838	'Empty project',
1839	'Project does not contain any single crystal data.')
1840	return True
1841	elif len(self.xtalDict) == 1:
1842	self.histnam = self.xtalDict.values()
1843	elif self.multiple:
1844	choices = sorted(self.xtalDict.values())
1845	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1846	if not hnum: return True
1847	self.histnam = [choices[i] for i in hnum]
1848	numselected = len(self.histnam)
1849	else:
1850	choices = sorted(self.xtalDict.values())
1851	hnum = G2G.ItemSelector(choices,self.G2frame)
1852	if hnum is None: return True
1853	self.histnam = [choices[hnum]]
1854	numselected = len(self.histnam)
1855	elif self.currentExportType == 'powder':
1856	if len(self.powderDict) == 0:
1857	self.G2frame.ErrorDialog(
1858	'Empty project',
1859	'Project does not contain any powder data.')
1860	return True
1861	elif len(self.powderDict) == 1:
1862	self.histnam = self.powderDict.values()
1863	elif self.multiple:
1864	choices = sorted(self.powderDict.values())
1865	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1866	if not hnum: return True
1867	self.histnam = [choices[i] for i in hnum]
1868	numselected = len(self.histnam)
1869	else:
1870	choices = sorted(self.powderDict.values())
1871	hnum = G2G.ItemSelector(choices,self.G2frame)
1872	if hnum is None: return True
1873	self.histnam = [choices[hnum]]
1874	numselected = len(self.histnam)
1875	elif self.currentExportType == 'image':
1876	if len(self.Histograms) == 0:
1877	self.G2frame.ErrorDialog(
1878	'Empty project',
1879	'Project does not contain any images.')
1880	return True
1881	elif len(self.Histograms) == 1:
1882	self.histnam = self.Histograms.keys()
1883	else:
1884	choices = sorted(self.Histograms.keys())
1885	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1886	if self.multiple:
1887	if not hnum: return True
1888	self.histnam = [choices[i] for i in hnum]
1889	else:
1890	if hnum is None: return True
1891	self.histnam = [choices[hnum]]
1892	numselected = len(self.histnam)
1893	if self.currentExportType == 'map':
1894	# search for phases with maps
1895	mapPhases = []
1896	choices = []
1897	for phasenam in sorted(self.Phases):
1898	phasedict = self.Phases[phasenam] # pointer to current phase info
1899	if len(phasedict['General']['Map'].get('rho',[])):
1900	mapPhases.append(phasenam)
1901	if phasedict['General']['Map'].get('Flip'):
1902	choices.append('Charge flip map: '+str(phasenam))
1903	elif phasedict['General']['Map'].get('MapType'):
1904	choices.append(
1905	str(phasedict['General']['Map'].get('MapType'))
1906	+ ' map: ' + str(phasenam))
1907	else:
1908	choices.append('unknown map: '+str(phasenam))
1909	# select a map if needed
1910	if len(mapPhases) == 0:
1911	self.G2frame.ErrorDialog(
1912	'Empty project',
1913	'Project does not contain any maps.')
1914	return True
1915	elif len(mapPhases) == 1:
1916	self.phasenam = mapPhases
1917	else:
1918	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1919	if self.multiple:
1920	if not phasenum: return True
1921	self.phasenam = [mapPhases[i] for i in phasenum]
1922	else:
1923	if phasenum is None: return True
1924	self.phasenam = [mapPhases[phasenum]]
1925	numselected = len(self.phasenam)
1926
1927	# items selected, now set self.dirname and usually self.filename
1928	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1929	AskFile == 'default' and not self.G2frame.GSASprojectfile
1930	):
1931	filename = self.askSaveFile()
1932	if not filename: return True
1933	self.dirname,self.filename = os.path.split(filename)
1934	elif AskFile == 'dir' or AskFile == 'single' or (
1935	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1936	):
1937	self.dirname = self.askSaveDirectory()
1938	if not self.dirname: return True
1939	elif AskFile == 'default-dir' or AskFile == 'default':
1940	self.dirname,self.filename = os.path.split(
1941	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1942	)
1943	else:
1944	raise Exception('This should not happen!')
1945
1946	def loadParmDict(self):
1947	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1948	refined values to those from the last cycle and set the uncertainties for the
1949	refined parameters in another dict (self.sigDict).
1950
1951	Expands the parm & sig dicts to include values derived from constraints.
1952	'''
1953	self.parmDict = {}
1954	self.sigDict = {}
1955	rigidbodyDict = {}
1956	covDict = {}
1957	consDict = {}
1958	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1959	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
1960	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
1961	while item:
1962	name = self.G2frame.PatternTree.GetItemText(item)
1963	if name == 'Rigid bodies':
1964	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
1965	elif name == 'Covariance':
1966	covDict = self.G2frame.PatternTree.GetItemPyData(item)
1967	elif name == 'Constraints':
1968	consDict = self.G2frame.PatternTree.GetItemPyData(item)
1969	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
1970	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1971	self.parmDict.update(rbDict)
1972	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1973	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,maxSSwave = G2stIO.GetPhaseData(
1974	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1975	self.parmDict.update(phaseDict)
1976	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
1977	Phases,Histograms,Print=False,resetRefList=False)
1978	self.parmDict.update(hapDict)
1979	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1980	self.parmDict.update(histDict)
1981	self.parmDict.update(zip(
1982	covDict.get('varyList',[]),
1983	covDict.get('variables',[])))
1984	self.sigDict = dict(zip(
1985	covDict.get('varyList',[]),
1986	covDict.get('sig',[])))
1987	# expand to include constraints: first compile a list of constraints
1988	constList = []
1989	for item in consDict:
1990	if item.startswith('_'): continue
1991	constList += consDict[item]
1992	# now process the constraints
1993	G2mv.InitVars()
1994	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
1995	varyList = covDict.get('varyListStart')
1996	if varyList is None and len(constDict) == 0:
1997	# no constraints can use varyList
1998	varyList = covDict.get('varyList')
1999	elif varyList is None:
2000	# old GPX file from before pre-constraint varyList is saved
2001	print ' * Old refinement: Please use Calculate/Refine to redo *'
2002	raise Exception(' * Export aborted *')
2003	else:
2004	varyList = list(varyList)
2005	try:
2006	groups,parmlist = G2mv.GroupConstraints(constDict)
2007	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
2008	except:
2009	# this really should not happen
2010	print ' * ERROR - constraints are internally inconsistent *'
2011	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
2012	print 'Errors',errmsg
2013	if warnmsg: print 'Warnings',warnmsg
2014	raise Exception(' * CIF creation aborted *')
2015	# add the constrained values to the parameter dictionary
2016	G2mv.Dict2Map(self.parmDict,varyList)
2017	# and add their uncertainties into the esd dictionary (sigDict)
2018	if covDict.get('covMatrix') is not None:
2019	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
2020
2021	def loadTree(self):
2022	'''Load the contents of the data tree into a set of dicts
2023	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2024	& self.xtalDict)
2025
2026	* The childrenless data tree items are overall parameters/controls for the
2027	entire project and are placed in self.OverallParms
2028	* Phase items are placed in self.Phases
2029	* Data items are placed in self.Histogram. The key for these data items
2030	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2031	'''
2032	self.OverallParms = {}
2033	self.powderDict = {}
2034	self.xtalDict = {}
2035	self.Phases = {}
2036	self.Histograms = {}
2037	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2038	histType = None
2039	if self.currentExportType == 'phase':
2040	# if exporting phases load them here
2041	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2042	if not sub:
2043	print 'no phases found'
2044	return True
2045	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2046	while item:
2047	phaseName = self.G2frame.PatternTree.GetItemText(item)
2048	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2049	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2050	return
2051	elif self.currentExportType == 'single':
2052	histType = 'HKLF'
2053	elif self.currentExportType == 'powder':
2054	histType = 'PWDR'
2055	elif self.currentExportType == 'image':
2056	histType = 'IMG'
2057
2058	if histType: # Loading just one kind of tree entry
2059	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2060	while item:
2061	name = self.G2frame.PatternTree.GetItemText(item)
2062	if name.startswith(histType):
2063	if self.Histograms.get(name): # there is already an item with this name
2064	print('Histogram name '+str(name)+' is repeated. Renaming')
2065	if name[-1] == '9':
2066	name = name[:-1] + '10'
2067	elif name[-1] in '012345678':
2068	name = name[:-1] + str(int(name[-1])+1)
2069	else:
2070	name += '-1'
2071	self.Histograms[name] = {}
2072	# the main info goes into Data, but the 0th
2073	# element contains refinement results, carry
2074	# that over too now.
2075	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2076	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2077	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2078	while item2:
2079	child = self.G2frame.PatternTree.GetItemText(item2)
2080	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2081	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2082	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2083	# index powder and single crystal histograms by number
2084	for hist in self.Histograms:
2085	if hist.startswith("PWDR"):
2086	d = self.powderDict
2087	elif hist.startswith("HKLF"):
2088	d = self.xtalDict
2089	else:
2090	return
2091	i = self.Histograms[hist].get('hId')
2092	if i is None and not d.keys():
2093	i = 0
2094	elif i is None or i in d.keys():
2095	i = max(d.keys())+1
2096	d[i] = hist
2097	return
2098	# else standard load: using all interlinked phases and histograms
2099	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2100	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2101	while item:
2102	name = self.G2frame.PatternTree.GetItemText(item)
2103	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2104	if not item2:
2105	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2106	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2107	# index powder and single crystal histograms
2108	for hist in self.Histograms:
2109	i = self.Histograms[hist]['hId']
2110	if hist.startswith("PWDR"):
2111	self.powderDict[i] = hist
2112	elif hist.startswith("HKLF"):
2113	self.xtalDict[i] = hist
2114
2115	def dumpTree(self,mode='type'):
2116	'''Print out information on the data tree dicts loaded in loadTree
2117	'''
2118	print '\nOverall'
2119	if mode == 'type':
2120	def Show(arg): return type(arg)
2121	else:
2122	def Show(arg): return arg
2123	for key in self.OverallParms:
2124	print ' ',key,Show(self.OverallParms[key])
2125	print 'Phases'
2126	for key1 in self.Phases:
2127	print ' ',key1,Show(self.Phases[key1])
2128	print 'Histogram'
2129	for key1 in self.Histograms:
2130	print ' ',key1,Show(self.Histograms[key1])
2131	for key2 in self.Histograms[key1]:
2132	print ' ',key2,Show(self.Histograms[key1][key2])
2133
2134	def defaultSaveFile(self):
2135	return os.path.abspath(
2136	os.path.splitext(self.G2frame.GSASprojectfile
2137	)[0]+self.extension)
2138
2139	def askSaveFile(self):
2140	'''Ask the user to supply a file name
2141
2142	:returns: a file name (str) or None if Cancel is pressed
2143	'''
2144	defnam = os.path.splitext(
2145	os.path.split(self.G2frame.GSASprojectfile)[1]
2146	)[0]+self.extension
2147	dlg = wx.FileDialog(
2148	self.G2frame, 'Input name for file to write', '.', defnam,
2149	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2150	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2151	dlg.CenterOnParent()
2152	try:
2153	if dlg.ShowModal() == wx.ID_OK:
2154	filename = dlg.GetPath()
2155	# make sure extension is correct
2156	filename = os.path.splitext(filename)[0]+self.extension
2157	else:
2158	filename = None
2159	finally:
2160	dlg.Destroy()
2161	return filename
2162
2163	def askSaveDirectory(self):
2164	'''Ask the user to supply a directory name. Path name is used as the
2165	starting point for the next export path search.
2166
2167	:returns: a directory name (str) or None if Cancel is pressed
2168	'''
2169	if self.G2frame.exportDir:
2170	startdir = self.G2frame.exportDir
2171	elif self.G2frame.GSASprojectfile:
2172	startdir = os.path.split(self.G2frame.GSASprojectfile)[0]
2173	elif self.G2frame.dirname:
2174	startdir = self.G2frame.dirname
2175	else:
2176	startdir = ''
2177	dlg = wx.DirDialog(
2178	self.G2frame, 'Input directory where file(s) will be written', startdir,
2179	wx.DD_DEFAULT_STYLE)
2180	dlg.CenterOnParent()
2181	try:
2182	if dlg.ShowModal() == wx.ID_OK:
2183	filename = dlg.GetPath()
2184	self.G2frame.exportDir = filename
2185	else:
2186	filename = None
2187	finally:
2188	dlg.Destroy()
2189	return filename
2190
2191	# Tools for file writing.
2192	def OpenFile(self,fil=None,mode='w'):
2193	'''Open the output file
2194
2195	:param str fil: The name of the file to open. If None (default)
2196	the name defaults to self.dirname + self.filename.
2197	If an extension is supplied, it is not overridded,
2198	but if not, the default extension is used.
2199	:returns: the file object opened by the routine which is also
2200	saved as self.fp
2201	'''
2202	if not fil:
2203	if not os.path.splitext(self.filename)[1]:
2204	self.filename += self.extension
2205	fil = os.path.join(self.dirname,self.filename)
2206	self.fullpath = os.path.abspath(fil)
2207	self.fp = open(self.fullpath,mode)
2208	return self.fp
2209
2210	def Write(self,line):
2211	'''write a line of output, attaching a line-end character
2212
2213	:param str line: the text to be written.
2214	'''
2215	self.fp.write(line+'\n')
2216	def CloseFile(self,fp=None):
2217	'''Close a file opened in OpenFile
2218
2219	:param file fp: the file object to be closed. If None (default)
2220	file object self.fp is closed.
2221	'''
2222	if fp is None:
2223	fp = self.fp
2224	self.fp = None
2225	fp.close()
2226	# Tools to pull information out of the data arrays
2227	def GetCell(self,phasenam):
2228	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2229
2230	:param str phasenam: the name for the selected phase
2231	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2232	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2233	cell values and `cellSig` has their uncertainties.
2234	"""
2235	phasedict = self.Phases[phasenam] # pointer to current phase info
2236	try:
2237	pfx = str(phasedict['pId'])+'::'
2238	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2239	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
2240	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2241	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2242	return cellList,cellSig
2243	except KeyError:
2244	cell = phasedict['General']['Cell'][1:]
2245	return cell,7*[0]
2246
2247	def GetAtoms(self,phasenam):
2248	"""Gets the atoms associated with a phase. Can be used with standard
2249	or macromolecular phases
2250
2251	:param str phasenam: the name for the selected phase
2252	:returns: a list of items for eac atom where each item is a list containing:
2253	label, typ, mult, xyz, and td, where
2254
2255	* label and typ are the atom label and the scattering factor type (str)
2256	* mult is the site multiplicity (int)
2257	* xyz is contains a list with four pairs of numbers:
2258	x, y, z and fractional occupancy and
2259	their standard uncertainty (or a negative value)
2260	* td is contains a list with either one or six pairs of numbers:
2261	if one number it is U\ :sub:`iso` and with six numbers it is
2262	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2263	paired with their standard uncertainty (or a negative value)
2264	"""
2265	phasedict = self.Phases[phasenam] # pointer to current phase info
2266	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2267	cfrac = cx+3
2268	fpfx = str(phasedict['pId'])+'::Afrac:'
2269	atomslist = []
2270	for i,at in enumerate(phasedict['Atoms']):
2271	if phasedict['General']['Type'] == 'macromolecular':
2272	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2273	else:
2274	label = at[ct-1]
2275	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2276	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2277	mult = at[cs+1]
2278	typ = at[ct]
2279	xyz = []
2280	for j,v in enumerate(('x','y','z')):
2281	val = at[cx+j]
2282	pfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2283	sig = self.sigDict.get(pfx,-0.000009)
2284	xyz.append((val,sig))
2285	xyz.append((fval,fsig))
2286	td = []
2287	if at[cia] == 'I':
2288	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2289	val = self.parmDict.get(pfx,at[cia+1])
2290	sig = self.sigDict.get(pfx,-0.0009)
2291	td.append((val,sig))
2292	else:
2293	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2294	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2295	val = self.parmDict.get(pfx,at[cia+2+i])
2296	sig = self.sigDict.get(pfx,-0.0009)
2297	td.append((val,sig))
2298	atomslist.append((label,typ,mult,xyz,td))
2299	return atomslist
2300	######################################################################
2301	def ExportPowderList(G2frame):
2302	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
2303
2304	:param wx.Frame G2frame: the GSAS-II main data tree window
2305	'''
2306	extList = []
2307	for obj in G2frame.exporterlist:
2308	if 'powder' in obj.exporttype:
2309	try:
2310	obj.Writer
2311	extList.append(obj.extension)
2312	except AttributeError:
2313	pass
2314	return extList
2315
2316	def ExportPowder(G2frame,TreeName,fileroot,extension):
2317	'''Writes a single powder histogram using the Export routines
2318
2319	:param wx.Frame G2frame: the GSAS-II main data tree window
2320	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
2321	:param str fileroot: name for file to be written, extension ignored
2322	:param str extension: extension for file to be written (start with '.'). Must
2323	match a powder export routine that has a Writer object.
2324	'''
2325	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
2326	for obj in G2frame.exporterlist:
2327	if obj.extension == extension and 'powder' in obj.exporttype:
2328	obj.currentExportType = 'powder'
2329	obj.InitExport(None)
2330	obj.loadTree() # load all histograms in tree into dicts
2331	if TreeName not in obj.Histograms:
2332	raise Exception('Histogram not found: '+str(TreeName))
2333	try:
2334	obj.Writer
2335	except AttributeError:
2336	continue
2337	try:
2338	obj.Writer(TreeName,filename)
2339	return
2340	except Exception,err:
2341	print('Export Routine for '+extension+' failed.')
2342	print err
2343	else:
2344	print('No Export routine supports extension '+extension)
2345
2346	def ReadCIF(URLorFile):
2347	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2348	(from James Hester).
2349	The open routine gets confused with DOS names that begin with a letter and colon
2350	"C:\dir\" so this routine will try to open the passed name as a file and if that
2351	fails, try it as a URL
2352
2353	:param str URLorFile: string containing a URL or a file name. Code will try first
2354	to open it as a file and then as a URL.
2355
2356	:returns: a PyCifRW CIF object.
2357	'''
2358	import CifFile as cif # PyCifRW from James Hester
2359
2360	# alternate approach:
2361	#import urllib
2362	#ciffile = 'file:'+urllib.pathname2url(filename)
2363
2364	try:
2365	fp = open(URLorFile,'r')
2366	cf = cif.ReadCif(fp)
2367	fp.close()
2368	return cf
2369	except IOError:
2370	return cif.ReadCif(URLorFile)
2371
2372	if __name__ == '__main__':
2373	app = wx.PySimpleApp()
2374	frm = wx.Frame(None) # create a frame
2375	frm.Show(True)
2376	filename = '/tmp/notzip.zip'
2377	filename = '/tmp/all.zip'
2378	#filename = '/tmp/11bmb_7652.zip'
2379
2380	#selection=None, confirmoverwrite=True, parent=None
2381	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2382	print ExtractFileFromZip(filename,multipleselect=True)
2383	#confirmread=False, confirmoverwrite=False)
2384
2385	# choicelist=[ ('a','b','c'),
2386	# ('test1','test2'),('no choice',)]
2387	# titles = [ 'a, b or c', 'tests', 'No option here']
2388	# dlg = MultipleChoicesDialog(
2389	# choicelist,titles,
2390	# parent=frm)
2391	# if dlg.ShowModal() == wx.ID_OK:
2392	# print 'Got OK'

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