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source: trunk/GSASIIIO.py @ 2820

Last change on this file since 2820 was 2818, checked in by vondreele, 8 years ago
add GetPhaseNames?(fl) to G2obj - uses opened gpx file fix PhaseSelector? & remove ShowBusy? & DoneBusy? from G2IO - not used ever
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
File size: 90.0 KB

Rev	Line
[762]	1	# -- coding: utf-8 --
	2	########### SVN repository information ###################
	3	# $Date: 2017-05-02 18:39:22 +0000 (Tue, 02 May 2017) $
	4	# $Author: vondreele $
	5	# $Revision: 2818 $
	6	# $URL: trunk/GSASIIIO.py $
	7	# $Id: GSASIIIO.py 2818 2017-05-02 18:39:22Z vondreele $
	8	########### SVN repository information ###################
[923]	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	"""
[762]	24	import wx
	25	import math
	26	import numpy as np
[2214]	27	import copy
[762]	28	import cPickle
	29	import sys
[1057]	30	import re
[762]	31	import random as ran
	32	import GSASIIpath
	33	GSASIIpath.SetVersionNumber("$Revision: 2818 $")
	34	import GSASIIgrid as G2gd
[1997]	35	import GSASIIobj as G2obj
[762]	36	import GSASIIlattice as G2lat
[2712]	37	import GSASIImath as G2mth
[762]	38	import GSASIIpwdGUI as G2pdG
[2083]	39	import GSASIIimgGUI as G2imG
[1694]	40	import GSASIIimage as G2img
[762]	41	import GSASIIElem as G2el
[956]	42	import GSASIIstrIO as G2stIO
	43	import GSASIImapvars as G2mv
[1619]	44	import GSASIIctrls as G2G
[762]	45	import os
	46	import os.path as ospath
	47
[1157]	48	DEBUG = False #=True for various prints
[1165]	49	TRANSP = False #=true to transpose images for testing
[2003]	50	if GSASIIpath.GetConfigValue('Transpose'): TRANSP = True
[1204]	51	npsind = lambda x: np.sin(x*np.pi/180.)
[1157]	52
[762]	53	def sfloat(S):
[1892]	54	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
[762]	55	if S.strip():
[1892]	56	try:
	57	return float(S)
	58	except ValueError:
	59	pass
	60	return 0.0
[762]	61
	62	def sint(S):
[923]	63	'Convert a string to int. An empty field is treated as zero'
[762]	64	if S.strip():
	65	return int(S)
	66	else:
	67	return 0
	68
[1057]	69	def trim(val):
	70	'''Simplify a string containing leading and trailing spaces
	71	as well as newlines, tabs, repeated spaces etc. into a shorter and
	72	more simple string, by replacing all ranges of whitespace
	73	characters with a single space.
	74
	75	:param str val: the string to be simplified
	76
	77	:returns: the (usually) shortened version of the string
	78	'''
	79	return re.sub('\s+', ' ', val).strip()
	80
[795]	81	def makeInstDict(names,data,codes):
	82	inst = dict(zip(names,zip(data,data,codes)))
	83	for item in inst:
	84	inst[item] = list(inst[item])
	85	return inst
	86
[762]	87	def FileDlgFixExt(dlg,file):
[923]	88	'this is needed to fix a problem in linux wx.FileDialog'
[762]	89	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
	90	if ext not in file:
	91	file += ext
	92	return file
	93
	94	def GetPowderPeaks(fileName):
[923]	95	'Read powder peaks from a file'
[762]	96	sind = lambda x: math.sin(x*math.pi/180.)
	97	asind = lambda x: 180.*math.asin(x)/math.pi
[2056]	98	wave = 1.54052
[762]	99	File = open(fileName,'Ur')
	100	Comments = []
	101	peaks = []
	102	S = File.readline()
	103	while S:
	104	if S[:1] == '#':
	105	Comments.append(S[:-1])
	106	else:
	107	item = S.split()
	108	if len(item) == 1:
	109	peaks.append([float(item[0]),1.0])
	110	elif len(item) > 1:
	111	peaks.append([float(item[0]),float(item[0])])
	112	S = File.readline()
	113	File.close()
	114	if Comments:
	115	print 'Comments on file:'
[2056]	116	for Comment in Comments:
	117	print Comment
	118	if 'wavelength' in Comment:
	119	wave = float(Comment.split('=')[1])
[762]	120	Peaks = []
	121	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
	122	for peak in peaks:
	123	dsp = peak[0]
[2056]	124	sth = wave/(2.0*dsp)
[762]	125	if sth < 1.0:
	126	tth = 2.0*asind(sth)
	127	else:
	128	break
	129	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
	130	else: #2-thetas - assume Cuka (for now)
	131	for peak in peaks:
	132	tth = peak[0]
[2056]	133	dsp = wave/(2.0*sind(tth/2.0))
[762]	134	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
[2056]	135	limits = [1000.,0.]
	136	for peak in Peaks:
	137	limits[0] = min(limits[0],peak[0])
	138	limits[1] = max(limits[1],peak[0])
	139	limits[0] = max(1.,(int(limits[0]-1.)/5)*5.)
	140	limits[1] = min(170.,(int(limits[1]+1.)/5)*5.)
	141	return Comments,Peaks,limits,wave
[762]	142
[2610]	143	def GetCheckImageFile(G2frame,treeId):
[2001]	144	'''Try to locate an image file if the project and image have been moved
	145	together. If the image file cannot be found, request the location from
	146	the user.
[923]	147
	148	:param wx.Frame G2frame: main GSAS-II Frame and data object
[2610]	149	:param wx.Id treeId: Id for the main tree item for the image
	150	:returns: Npix,imagefile,imagetag with (Npix) number of pixels,
	151	imagefile, if it exists, or the name of a file that does exist or False if the user presses Cancel
	152	and (imagetag) an optional image number
[923]	153
	154	'''
[2721]	155	Npix,Imagefile,imagetag = G2frame.PatternTree.GetImageLoc(treeId)
	156	if isinstance(Imagefile,list):
	157	imagefile,imagetag = Imagefile
	158	else:
	159	imagefile = Imagefile
[1576]	160	if not os.path.exists(imagefile):
	161	print 'Image file '+imagefile+' not found'
	162	fil = imagefile.replace('\\','/') # windows?!
	163	# see if we can find a file with same name or in a similarly named sub-dir
	164	pth,fil = os.path.split(fil)
	165	prevpth = None
	166	while pth and pth != prevpth:
	167	prevpth = pth
	168	if os.path.exists(os.path.join(G2frame.dirname,fil)):
	169	print 'found image file '+os.path.join(G2frame.dirname,fil)
[2610]	170	imagefile = os.path.join(G2frame.dirname,fil)
[2625]	171	G2frame.PatternTree.UpdateImageLoc(treeId,imagefile)
[2610]	172	return Npix,imagefile,imagetag
[1576]	173	pth,enddir = os.path.split(pth)
	174	fil = os.path.join(enddir,fil)
	175	# not found as a subdirectory, drop common parts of path for last saved & image file names
	176	# if image was .../A/B/C/imgs/ima.ge
	177	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
	178	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
	179	Controls = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
	180	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
	181	imgPath = imagefile.replace('\\','/').split('/')
	182	for p1,p2 in zip(gpxPath,imgPath):
	183	if p1 == p2:
	184	gpxPath.pop(0),imgPath.pop(0)
	185	else:
	186	break
	187	fil = os.path.join(*imgPath) # file with non-common prefix elements
	188	prevpth = None
	189	pth = os.path.abspath(G2frame.dirname)
	190	while pth and pth != prevpth:
	191	prevpth = pth
	192	if os.path.exists(os.path.join(pth,fil)):
	193	print 'found image file '+os.path.join(pth,fil)
[2610]	194	imagefile = os.path.join(pth,fil)
[2625]	195	G2frame.PatternTree.UpdateImageLoc(treeId,imagefile)
[2610]	196	return Npix,imagefile,imagetag
[1576]	197	pth,enddir = os.path.split(pth)
[1814]	198	#GSASIIpath.IPyBreak()
[1576]	199
	200	if not os.path.exists(imagefile):
[2109]	201	prevnam = os.path.split(imagefile)[1]
	202	prevext = os.path.splitext(imagefile)[1]
	203	wildcard = 'Image format ('+prevext+')\|'+prevext
	204	dlg = wx.FileDialog(G2frame, 'Previous image file ('+prevnam+') not found; open here', '.', prevnam,
	205	wildcard,wx.OPEN)
[762]	206	try:
	207	dlg.SetFilename(''+ospath.split(imagefile)[1])
	208	if dlg.ShowModal() == wx.ID_OK:
	209	imagefile = dlg.GetPath()
[2625]	210	G2frame.PatternTree.UpdateImageLoc(treeId,imagefile)
[762]	211	else:
	212	imagefile = False
	213	finally:
	214	dlg.Destroy()
[2610]	215	return Npix,imagefile,imagetag
[1215]	216
	217	def EditImageParms(parent,Data,Comments,Image,filename):
	218	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
	219	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
	220	def onClose(event):
	221	dlg.EndModal(wx.ID_OK)
	222	mainsizer = wx.BoxSizer(wx.VERTICAL)
	223	h,w = Image.shape[:2]
[2817]	224	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
	225	0,wx.ALIGN_LEFT\|wx.ALL, 2)
[1215]	226
	227	vsizer = wx.BoxSizer(wx.HORIZONTAL)
	228	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
[2817]	229	0,wx.ALIGN_LEFT\|wx.ALL, 2)
[1619]	230	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
[1215]	231	vsizer.Add(wdgt)
	232	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
	233
	234	vsizer = wx.BoxSizer(wx.HORIZONTAL)
	235	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
[2817]	236	0,wx.ALIGN_LEFT\|wx.ALL, 2)
[1619]	237	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
[1215]	238	size=(50,-1))
	239	vsizer.Add(wdgt)
[2817]	240	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),wx.ALIGN_LEFT\|wx.ALL, 2)
	241	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,size=(50,-1))
[1215]	242	vsizer.Add(wdgt)
	243	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
	244
	245	vsizer = wx.BoxSizer(wx.HORIZONTAL)
	246	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
[2817]	247	0,wx.ALIGN_LEFT\|wx.ALL, 2)
[1619]	248	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
[1215]	249	vsizer.Add(wdgt)
	250	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
	251
	252	vsizer = wx.BoxSizer(wx.HORIZONTAL)
	253	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
[2817]	254	0,wx.ALIGN_LEFT\|wx.ALL, 2)
	255	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,size=(75,-1))
[1215]	256	vsizer.Add(wdgt)
[2817]	257	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),wx.ALIGN_LEFT\|wx.ALL, 2)
	258	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,size=(75,-1))
[1215]	259	vsizer.Add(wdgt)
	260	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
	261
	262	vsizer = wx.BoxSizer(wx.HORIZONTAL)
	263	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
[2817]	264	0,wx.ALIGN_LEFT\|wx.ALL, 2)
[1619]	265	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
[1215]	266	vsizer.Add(wdgt)
	267	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
	268
	269	btnsizer = wx.StdDialogButtonSizer()
	270	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
	271	OKbtn.SetDefault()
	272	OKbtn.Bind(wx.EVT_BUTTON,onClose)
	273	btnsizer.AddButton(OKbtn) # not sure why this is needed
	274	btnsizer.Realize()
	275	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
	276	dlg.SetSizer(mainsizer)
	277	dlg.CenterOnParent()
	278	dlg.ShowModal()
[1997]	279
[2026]	280	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
[2065]	281	'''Load an image into the tree. Saves the location of the image, as well as the
	282	ImageTag (where there is more than one image in the file), if defined.
[2001]	283	'''
[2227]	284	ImgNames = G2gd.GetPatternTreeDataNames(G2frame,['IMG ',])
[2065]	285	TreeLbl = 'IMG '+os.path.basename(imagefile)
	286	ImageTag = Data.get('ImageTag')
	287	if ImageTag:
[2296]	288	TreeLbl += ' #'+'%04d'%(ImageTag)
[2065]	289	imageInfo = (imagefile,ImageTag)
	290	else:
	291	imageInfo = imagefile
	292	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
[2001]	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	if G2frame.imageDefault:
	297	Data = copy.copy(G2frame.imageDefault)
	298	Data['showLines'] = True
	299	Data['ring'] = []
	300	Data['rings'] = []
	301	Data['cutoff'] = 10
	302	Data['pixLimit'] = 20
	303	Data['edgemin'] = 100000000
	304	Data['calibdmin'] = 0.5
	305	Data['calibskip'] = 0
	306	Data['ellipses'] = []
	307	Data['calibrant'] = ''
	308	Data['GonioAngles'] = [0.,0.,0.]
	309	Data['DetDepthRef'] = False
	310	else:
	311	Data['type'] = 'PWDR'
	312	Data['color'] = 'Paired'
	313	Data['tilt'] = 0.0
	314	Data['rotation'] = 0.0
	315	Data['showLines'] = False
	316	Data['ring'] = []
	317	Data['rings'] = []
	318	Data['cutoff'] = 10
	319	Data['pixLimit'] = 20
	320	Data['calibdmin'] = 0.5
	321	Data['calibskip'] = 0
	322	Data['edgemin'] = 100000000
	323	Data['ellipses'] = []
	324	Data['GonioAngles'] = [0.,0.,0.]
	325	Data['DetDepth'] = 0.
	326	Data['DetDepthRef'] = False
	327	Data['calibrant'] = ''
	328	Data['IOtth'] = [2.0,5.0]
[2436]	329	Data['LRazimuth'] = [0.,180.]
[2001]	330	Data['azmthOff'] = 0.0
	331	Data['outChannels'] = 2500
	332	Data['outAzimuths'] = 1
	333	Data['centerAzm'] = False
	334	Data['fullIntegrate'] = False
	335	Data['setRings'] = False
	336	Data['background image'] = ['',-1.0]
	337	Data['dark image'] = ['',-1.0]
	338	Data['Flat Bkg'] = 0.0
	339	Data['setDefault'] = False
[2223]	340	Data['range'] = [(0,Imax),[0,Imax]]
[2001]	341	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Image Controls'),Data)
[2223]	342	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(0,Imax),[0,Imax]]}
[2001]	343	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Masks'),Masks)
	344	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Stress/Strain'),
	345	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
[2065]	346	G2frame.PatternTree.SetItemPyData(Id,[Npix,imageInfo])
[2001]	347	G2frame.PickId = Id
	348	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
	349	G2frame.Image = Id
[2003]	350
[2290]	351	def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None,FormatName=''):
[2065]	352	'''Read a single image with an image importer.
	353
[2003]	354	:param wx.Frame G2frame: main GSAS-II Frame and data object.
	355	:param str imagefile: name of image file
	356	:param bool imageOnly: If True return only the image,
	357	otherwise (default) return more (see below)
[2065]	358	:param int/str ImageTag: specifies a particular image to be read from a file.
	359	First image is read if None (default).
[2290]	360	:param str formatName: the image reader formatName
[2003]	361
	362	:returns: an image as a numpy array or a list of four items:
	363	Comments, Data, Npix and the Image, as selected by imageOnly
	364
	365	'''
	366	# determine which formats are compatible with this file
	367	primaryReaders = []
	368	secondaryReaders = []
	369	for rd in G2frame.ImportImageReaderlist:
	370	flag = rd.ExtensionValidator(imagefile)
	371	if flag is None:
	372	secondaryReaders.append(rd)
	373	elif flag:
[2290]	374	if not FormatName:
	375	primaryReaders.append(rd)
	376	elif FormatName == rd.formatName:
	377	primaryReaders.append(rd)
[2003]	378	if len(secondaryReaders) + len(primaryReaders) == 0:
[2522]	379	print('Error: No matching format for file '+imagefile)
[2003]	380	raise Exception('No image read')
	381	fp = None
	382	errorReport = ''
[2555]	383	if not imagefile:
	384	return
[2003]	385	fp = open(imagefile,'Ur')
	386	for rd in primaryReaders+secondaryReaders:
	387	rd.ReInitialize() # purge anything from a previous read
	388	fp.seek(0) # rewind
	389	rd.errors = "" # clear out any old errors
	390	if not rd.ContentsValidator(fp): # rejected on cursory check
	391	errorReport += "\n "+rd.formatName + ' validator error'
	392	if rd.errors:
	393	errorReport += ': '+rd.errors
[2065]	394	continue
[2015]	395	if imageOnly:
	396	ParentFrame = None # prevent GUI access on reread
	397	else:
	398	ParentFrame = G2frame
[2003]	399	if GSASIIpath.GetConfigValue('debug'):
[2065]	400	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=ImageTag)
[2003]	401	else:
	402	flag = False
	403	try:
[2065]	404	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=ImageTag)
[2003]	405	except rd.ImportException as detail:
	406	rd.errors += "\n Read exception: "+str(detail)
	407	except Exception as detail:
	408	import traceback
	409	rd.errors += "\n Unhandled read exception: "+str(detail)
	410	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
	411	if flag: # this read succeeded
	412	if rd.Image is None:
	413	raise Exception('No image read. Strange!')
	414	if GSASIIpath.GetConfigValue('Transpose'):
[2012]	415	print 'Transposing Image!'
[2003]	416	rd.Image = rd.Image.T
	417	#rd.readfilename = imagefile
	418	if imageOnly:
[2011]	419	return rd.Image
[2003]	420	else:
	421	return rd.Comments,rd.Data,rd.Npix,rd.Image
	422	else:
[2522]	423	print('Error reading file '+imagefile)
[2003]	424	print('Error messages(s)\n'+errorReport)
[2042]	425	raise Exception('No image read')
[2065]	426
	427	def ReadImages(G2frame,imagefile):
	428	'''Read one or more images from a file and put them into the Tree
	429	using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
	430
	431	:param wx.Frame G2frame: main GSAS-II Frame and data object.
	432	:param str imagefile: name of image file
	433
	434	:returns: a list of the id's of the IMG tree items created
	435	'''
	436	# determine which formats are compatible with this file
	437	primaryReaders = []
	438	secondaryReaders = []
	439	for rd in G2frame.ImportImageReaderlist:
	440	flag = rd.ExtensionValidator(imagefile)
	441	if flag is None:
	442	secondaryReaders.append(rd)
	443	elif flag:
	444	primaryReaders.append(rd)
	445	if len(secondaryReaders) + len(primaryReaders) == 0:
[2522]	446	print('Error: No matching format for file '+imagefile)
[2065]	447	raise Exception('No image read')
	448	errorReport = ''
	449	fp = open(imagefile,'Ur')
	450	rdbuffer = {} # create temporary storage for file reader
	451	for rd in primaryReaders+secondaryReaders:
	452	rd.ReInitialize() # purge anything from a previous read
	453	fp.seek(0) # rewind
	454	rd.errors = "" # clear out any old errors
	455	if not rd.ContentsValidator(fp): # rejected on cursory check
	456	errorReport += "\n "+rd.formatName + ' validator error'
	457	if rd.errors:
	458	errorReport += ': '+rd.errors
	459	continue
	460	ParentFrame = G2frame
	461	block = 0
	462	repeat = True
	463	CreatedIMGitems = []
	464	while repeat: # loop if the reader asks for another pass on the file
	465	block += 1
	466	repeat = False
	467	if GSASIIpath.GetConfigValue('debug'):
	468	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=block,Buffer=rdbuffer)
	469	else:
	470	flag = False
	471	try:
	472	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=block,Buffer=rdbuffer)
	473	except rd.ImportException as detail:
	474	rd.errors += "\n Read exception: "+str(detail)
	475	except Exception as detail:
	476	import traceback
	477	rd.errors += "\n Unhandled read exception: "+str(detail)
	478	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
	479	if flag: # this read succeeded
	480	if rd.Image is None:
	481	raise Exception('No image read. Strange!')
	482	if GSASIIpath.GetConfigValue('Transpose'):
	483	print 'Transposing Image!'
	484	rd.Image = rd.Image.T
[2068]	485	rd.Data['ImageTag'] = rd.repeatcount
[2065]	486	LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
	487	repeat = rd.repeat
	488	CreatedIMGitems.append(G2frame.Image)
	489	if CreatedIMGitems: return CreatedIMGitems
	490	else:
[2522]	491	print('Error reading file '+imagefile)
[2065]	492	print('Error messages(s)\n'+errorReport)
	493	return []
	494	#raise Exception('No image read')
[2083]	495
	496	def SaveMultipleImg(G2frame):
	497	if not G2frame.PatternTree.GetCount():
	498	print 'no images!'
	499	return
	500	choices = G2gd.GetPatternTreeDataNames(G2frame,['IMG ',])
	501	if len(choices) == 1:
	502	names = choices
	503	else:
	504	dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices)
	505	dlg.SetSelections([])
	506	names = []
	507	if dlg.ShowModal() == wx.ID_OK:
	508	names = [choices[sel] for sel in dlg.GetSelections()]
	509	dlg.Destroy()
	510	if not names: return
	511	for name in names:
	512	Id = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, name)
	513	Npix,imagefile,imagetag = G2frame.PatternTree.GetImageLoc(Id)
	514	imroot = os.path.splitext(imagefile)[0]
	515	if imagetag:
	516	imroot += '_' + str(imagetag)
	517	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Image Controls'))
	518	print('Writing '+imroot+'.imctrl')
	519	File = open(imroot+'.imctrl','w')
	520	keys = ['type','wavelength','calibrant','distance','center',
	521	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth',
	522	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
	523	'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg',
	524	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image']
	525	for key in keys:
	526	if key not in Data: continue #uncalibrated!
	527	File.write(key+':'+str(Data[key])+'\n')
	528	File.close()
	529	mask = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Masks'))
	530	G2imG.CleanupMasks(mask)
	531	print('Writing '+imroot+'.immask')
	532	File = open(imroot+'.immask','w')
	533	for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
	534	File.write(key+':'+str(mask[key])+'\n')
	535	File.close()
[762]	536
	537	def PutG2Image(filename,Comments,Data,Npix,image):
[1386]	538	'Write an image as a python pickle - might be better as an .edf file?'
[762]	539	File = open(filename,'wb')
	540	cPickle.dump([Comments,Data,Npix,image],File,1)
	541	File.close()
	542	return
	543
[2196]	544	def ProjFileOpen(G2frame,showProvenance=True):
[1138]	545	'Read a GSAS-II project file and load into the G2 data tree'
[1355]	546	if not os.path.exists(G2frame.GSASprojectfile):
	547	print ('\n*** Error attempt to open project file that does not exist:\n '+
	548	str(G2frame.GSASprojectfile))
	549	return
[1960]	550	LastSavedUsing = None
[762]	551	file = open(G2frame.GSASprojectfile,'rb')
[2196]	552	if showProvenance: print 'loading from file: ',G2frame.GSASprojectfile
[762]	553	G2frame.SetTitle("GSAS-II data tree: "+
	554	os.path.split(G2frame.GSASprojectfile)[1])
	555	wx.BeginBusyCursor()
	556	try:
	557	while True:
	558	try:
	559	data = cPickle.load(file)
	560	except EOFError:
	561	break
	562	datum = data[0]
	563
	564	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=datum[0])
[2555]	565	if datum[0].startswith('PWDR'):
[1138]	566	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
	567	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
	568	G2frame.PatternTree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
	569	elif datum[0].startswith('HKLF'):
	570	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
	571	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
	572	G2frame.PatternTree.SetItemPyData(Id,datum[1])
[762]	573	else:
[1960]	574	G2frame.PatternTree.SetItemPyData(Id,datum[1])
	575	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
	576	LastSavedUsing = datum[1]['LastSavedUsing']
[2196]	577	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance:
[1961]	578	print('Packages used to create .GPX file:')
[1962]	579	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
	580	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
[2532]	581	print(" {:<14s}: {:s}".format(p[0],p[1]))
[1962]	582	else:
	583	for p in datum[1]['PythonVersions']:
[2532]	584	print(" {:<12s} {:s}".format(p[0]+':',p[1]))
[2659]	585	oldPDF = False
[762]	586	for datus in data[1:]:
[2659]	587	#patch - 1/23/17 PDF cleanup
	588	if datus[0][:4] in ['I(Q)','S(Q)','F(Q)','G(R)']:
	589	oldPDF = True
	590	data[1][1][datus[0][:4]] = copy.deepcopy(datus[1][:2])
	591	continue
	592	#end PDF cleanup
[762]	593	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
[792]	594	#patch
[796]	595	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
[2555]	596	if datum[0].startswith('PWDR'):
[796]	597	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
[795]	598	else:
[796]	599	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
	600	for item in datus[1][0]: #zip makes tuples - now make lists!
	601	datus[1][0][item] = list(datus[1][0][item])
[792]	602	#end patch
[762]	603	G2frame.PatternTree.SetItemPyData(sub,datus[1])
[2659]	604	if 'PDF ' in datum[0][:4] and oldPDF:
	605	sub = G2frame.PatternTree.AppendItem(Id,'PDF Peaks')
	606	G2frame.PatternTree.SetItemPyData(sub,{'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
[2555]	607	if datum[0].startswith('IMG'): #retrieve image default flag & data if set
[762]	608	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
	609	if Data['setDefault']:
	610	G2frame.imageDefault = Data
	611	file.close()
[1960]	612	if LastSavedUsing:
[2532]	613	print('GPX load successful. Last saved with GSAS-II revision '+LastSavedUsing)
[1960]	614	else:
	615	print('project load successful')
[762]	616	G2frame.NewPlot = True
	617	except:
	618	msg = wx.MessageDialog(G2frame,message="Error reading file "+
	619	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
	620	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
	621	msg.ShowModal()
	622	finally:
	623	wx.EndBusyCursor()
[2530]	624	G2frame.Status.SetStatusText('Mouse RB click item to refresh/raise; RB drag/drop to reorder')
[762]	625
	626	def ProjFileSave(G2frame):
[923]	627	'Save a GSAS-II project file'
[762]	628	if not G2frame.PatternTree.IsEmpty():
	629	file = open(G2frame.GSASprojectfile,'wb')
	630	print 'save to file: ',G2frame.GSASprojectfile
[1961]	631	# stick the file name into the tree and version info into tree so they are saved.
	632	# (Controls should always be created at this point)
[1588]	633	try:
	634	Controls = G2frame.PatternTree.GetItemPyData(
	635	G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
	636	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
[1960]	637	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
[1961]	638	Controls['PythonVersions'] = G2frame.PackageVersions
[1588]	639	except:
	640	pass
[762]	641	wx.BeginBusyCursor()
	642	try:
	643	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
	644	while item:
	645	data = []
	646	name = G2frame.PatternTree.GetItemText(item)
	647	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
	648	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
	649	while item2:
	650	name = G2frame.PatternTree.GetItemText(item2)
	651	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
	652	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
	653	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
	654	cPickle.dump(data,file,1)
	655	file.close()
[2109]	656	pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
	657	if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
	658	G2frame.LastGPXdir = pth
[762]	659	finally:
	660	wx.EndBusyCursor()
[1138]	661	print('project save successful')
[762]	662
[2093]	663	def SaveIntegration(G2frame,PickId,data,Overwrite=False):
[923]	664	'Save image integration results as powder pattern(s)'
[762]	665	azms = G2frame.Integrate[1]
	666	X = G2frame.Integrate[2][:-1]
	667	N = len(X)
	668	Id = G2frame.PatternTree.GetItemParent(PickId)
	669	name = G2frame.PatternTree.GetItemText(Id)
[1199]	670	name = name.replace('IMG ',data['type']+' ')
[762]	671	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
[1199]	672	if 'PWDR' in name:
	673	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
	674	codes = [0 for i in range(11)]
	675	elif 'SASD' in name:
	676	names = ['Type','Lam','Zero','Azimuth']
	677	codes = [0 for i in range(4)]
[1204]	678	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
	679	Xminmax = [X[0],X[-1]]
[762]	680	Azms = []
[1834]	681	dazm = 0.
[762]	682	if data['fullIntegrate'] and data['outAzimuths'] == 1:
	683	Azms = [45.0,] #a poor man's average?
	684	else:
	685	for i,azm in enumerate(azms[:-1]):
[1778]	686	if azm > 360. and azms[i+1] > 360.:
	687	Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
	688	else:
	689	Azms.append(G2img.meanAzm(azm,azms[i+1]))
[1834]	690	dazm = np.min(np.abs(np.diff(azms)))/2.
[2026]	691	G2frame.IntgOutList = []
[762]	692	for i,azm in enumerate(azms[:-1]):
[1834]	693	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
[762]	694	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
[2093]	695	# if Overwrite delete any duplicate
	696	if Overwrite and G2gd.GetPatternTreeItemId(G2frame,G2frame.root,Aname):
	697	print('Replacing '+Aname)
	698	item = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,Aname)
	699	G2frame.PatternTree.Delete(item)
	700	else:
	701	nOcc = 0
	702	while item:
	703	Name = G2frame.PatternTree.GetItemText(item)
	704	if Aname in Name:
	705	nOcc += 1
	706	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
[2298]	707	if nOcc:
	708	Aname += '(%d)'%(nOcc)
[2817]	709	Sample = G2obj.SetDefaultSample() #set as Debye-Scherrer
[1203]	710	Sample['Gonio. radius'] = data['distance']
	711	Sample['Omega'] = data['GonioAngles'][0]
	712	Sample['Chi'] = data['GonioAngles'][1]
	713	Sample['Phi'] = data['GonioAngles'][2]
[1834]	714	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
[2563]	715	polariz = 0.99 #set default polarization for synchrotron radiation!
	716	for item in Comments:
	717	if 'polariz' in item:
	718	try:
	719	polariz = float(item.split('=')[1])
	720	except:
	721	polariz = 0.99
[1376]	722	if 'PWDR' in Aname:
[2563]	723	parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0001,Azms[i]]
[1376]	724	elif 'SASD' in Aname:
[1219]	725	Sample['Trans'] = data['SampleAbs'][0]
[1203]	726	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
[762]	727	Y = G2frame.Integrate[0][i]
[2701]	728	Ymin = np.min(Y)
[2486]	729	Ymax = np.max(Y)
[1321]	730	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
[1376]	731	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=Aname)
[2026]	732	G2frame.IntgOutList.append(Id)
[1275]	733	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
	734	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
[1376]	735	if 'PWDR' in Aname:
[1275]	736	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
	737	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
	738	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
	739	for item in inst[0]:
	740	inst[0][item] = list(inst[0][item])
	741	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
[1376]	742	if 'PWDR' in Aname:
[1275]	743	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
[1528]	744	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
[1603]	745	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[[],[]])
[1275]	746	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
	747	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
[1376]	748	elif 'SASD' in Aname:
[1275]	749	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
	750	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
	751	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
	752	valuesdict = {
	753	'wtFactor':1.0,
	754	'Dummy':False,
	755	'ranId':ran.randint(0,sys.maxint),
[2486]	756	'Offset':[0.0,0.0],'delOffset':0.02Ymax,'refOffset':-0.1Ymax,'refDelt':0.1*Ymax,
[2701]	757	'qPlot':False,'dPlot':False,'sqrtPlot':False,'Yminmax':[Ymin,Ymax]
[1275]	758	}
[1138]	759	G2frame.PatternTree.SetItemPyData(
	760	Id,[valuesdict,
	761	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
[1331]	762	return Id #last powder pattern generated
[2422]	763
	764	def XYsave(G2frame,XY,labelX='X',labelY='Y',names=None):
	765	'Save XY table data'
	766	pth = G2G.GetExportPath(G2frame)
	767	dlg = wx.FileDialog(
	768	G2frame, 'Enter csv filename for XY table', pth, '',
	769	'XY table file (.csv)\|.csv',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
	770	try:
	771	if dlg.ShowModal() == wx.ID_OK:
	772	filename = dlg.GetPath()
	773	filename = os.path.splitext(filename)[0]+'.csv'
	774	File = open(filename,'w')
	775	else:
	776	filename = None
	777	finally:
	778	dlg.Destroy()
	779	if not filename:
	780	return
	781	for i in range(len(XY)):
	782	if names != None:
	783	header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
	784	else:
	785	header = '%s,%s(%d)\n'%(labelX,labelY,i)
	786	File.write(header)
	787	for x,y in XY[i].T:
	788	File.write('%.3f,%.3f\n'%(x,y))
	789	File.close()
	790	print ' XY data saved to: ',filename
[762]	791
[2710]	792	def PDFSave(G2frame,exports,PDFsaves):
	793	'Save a PDF I(Q), S(Q), F(Q) and G(r) in column formats'
[2561]	794	import scipy.interpolate as scintp
[762]	795	for export in exports:
	796	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
[2659]	797	PDFControls = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, PickId,'PDF Controls'))
[2710]	798	if PDFsaves[0]: #I(Q)
	799	iqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.iq')
	800	iqdata = PDFControls['I(Q)'][0]
	801	iqfxn = scintp.interp1d(iqdata[0],iqdata[1],kind='linear')
	802	iqfile = open(iqfilename,'w')
	803	iqfile.write('#T I(Q) %s\n'%(export))
	804	iqfile.write('#L Q I(Q)\n')
	805	qnew = np.arange(iqdata[0][0],iqdata[0][-1],0.005)
	806	iqnew = zip(qnew,iqfxn(qnew))
	807	for q,iq in iqnew:
	808	iqfile.write("%15.6g %15.6g\n" % (q,iq))
	809	iqfile.close()
	810	print ' I(Q) saved to: ',iqfilename
	811
	812	if PDFsaves[1]: #S(Q)
	813	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
	814	sqdata = PDFControls['S(Q)'][1]
	815	sqfxn = scintp.interp1d(sqdata[0],sqdata[1],kind='linear')
	816	sqfile = open(sqfilename,'w')
	817	sqfile.write('#T S(Q) %s\n'%(export))
	818	sqfile.write('#L Q S(Q)\n')
	819	qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
	820	sqnew = zip(qnew,sqfxn(qnew))
	821	for q,sq in sqnew:
	822	sqfile.write("%15.6g %15.6g\n" % (q,sq))
	823	sqfile.close()
	824	print ' S(Q) saved to: ',sqfilename
	825
	826	if PDFsaves[2]: #F(Q)
	827	fqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.fq')
	828	fqdata = PDFControls['F(Q)'][1]
	829	fqfxn = scintp.interp1d(fqdata[0],fqdata[1],kind='linear')
	830	fqfile = open(sqfilename,'w')
	831	fqfile.write('#T F(Q) %s\n'%(export))
	832	fqfile.write('#L Q F(Q)\n')
	833	qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
	834	fqnew = zip(qnew,fqfxn(qnew))
	835	for q,fq in fqnew:
	836	fqfile.write("%15.6g %15.6g\n" % (q,fq))
	837	fqfile.close()
	838	print ' F(Q) saved to: ',fqfilename
	839
	840	if PDFsaves[3]: #G(R)
	841	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
	842	grdata = PDFControls['G(R)'][1]
	843	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
	844	grfile = open(grfilename,'w')
	845	grfile.write('#T G(R) %s\n'%(export))
	846	grfile.write('#L R G(R)\n')
	847	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
	848	grnew = zip(rnew,grfxn(rnew))
	849	for r,gr in grnew:
	850	grfile.write("%15.6g %15.6g\n" % (r,gr))
	851	grfile.close()
[2712]	852	print ' G(R) saved to: ',grfilename
	853
	854	if PDFsaves[4]: #pdfGUI file for G(R)
	855	pId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, 'PWDR'+export[4:])
	856	Inst = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, pId,'Instrument Parameters'))[0]
	857	Limits = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, pId,'Limits'))
	858	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
	859	grdata = PDFControls['G(R)'][1]
	860	qdata = PDFControls['I(Q)'][1][0]
	861	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
	862	grfile = open(grfilename,'w')
	863	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
	864	grnew = zip(rnew,grfxn(rnew))
	865
	866	grfile.write('[DEFAULT]\n')
	867	grfile.write('\n')
	868	grfile.write('version = GSAS-II-v'+str(GSASIIpath.GetVersionNumber())+'\n')
	869	grfile.write('\n')
	870	grfile.write('# input and output specifications\n')
	871	grfile.write('dataformat = Qnm\n')
	872	grfile.write('inputfile = %s\n'%(PDFControls['Sample']['Name']))
	873	grfile.write('backgroundfile = %s\n'%(PDFControls['Sample Bkg.']['Name']))
	874	grfile.write('outputtype = gr\n')
	875	grfile.write('\n')
	876	grfile.write('# PDF calculation setup\n')
	877	if 'x' in Inst['Type']:
	878	grfile.write('mode = %s\n'%('xray'))
	879	elif 'N' in Inst['Type']:
	880	grfile.write('mode = %s\n'%('neutron'))
	881	wave = G2mth.getMeanWave(Inst)
	882	grfile.write('wavelength = %.5f\n'%(wave))
	883	formula = ''
	884	for el in PDFControls['ElList']:
	885	formula += el
	886	num = PDFControls['ElList'][el]['FormulaNo']
	887	if num == round(num):
	888	formula += '%d'%(int(num))
	889	else:
	890	formula += '%.2f'%(num)
	891	grfile.write('composition = %s\n'%(formula))
	892	grfile.write('bgscale = %.3f\n'%(-PDFControls['Sample Bkg.']['Mult']))
	893	highQ = 2.*np.pi/G2lat.Pos2dsp(Inst,Limits[1][1])
	894	grfile.write('qmaxinst = %.2f\n'%(highQ))
	895	grfile.write('qmin = %.5f\n'%(qdata[0]))
	896	grfile.write('qmax = %.4f\n'%(qdata[-1]))
	897	grfile.write('rmin = %.2f\n'%(PDFControls['Rmin']))
	898	grfile.write('rmax = %.2f\n'%(PDFControls['Rmax']))
	899	grfile.write('rstep = 0.01\n')
	900
	901
	902	grfile.write('\n')
	903	grfile.write('# End of config '+63*'-')
	904	grfile.write('\n')
	905	grfile.write('#### start data\n')
	906	grfile.write('#S 1\n')
	907	grfile.write('#L r($\AA$) G($\AA^{-2}$)\n')
	908	for r,gr in grnew:
	909	grfile.write("%15.2F %15.6F\n" % (r,gr))
	910	grfile.close()
	911	print ' G(R) saved to: ',grfilename
[762]	912
	913	def PeakListSave(G2frame,file,peaks):
[923]	914	'Save powder peaks to a data file'
[762]	915	print 'save peak list to file: ',G2frame.peaklistfile
	916	if not peaks:
	917	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
	918	try:
[2544]	919	dlg.ShowModal()
[762]	920	finally:
	921	dlg.Destroy()
	922	return
	923	for peak in peaks:
	924	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
	925	(peak[0],peak[2],peak[4],peak[6]))
	926	print 'peak list saved'
	927
	928	def IndexPeakListSave(G2frame,peaks):
[923]	929	'Save powder peaks from the indexing list'
[762]	930	file = open(G2frame.peaklistfile,'wa')
	931	print 'save index peak list to file: ',G2frame.peaklistfile
	932	wx.BeginBusyCursor()
	933	try:
	934	if not peaks:
	935	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
	936	try:
[2544]	937	dlg.ShowModal()
[762]	938	finally:
	939	dlg.Destroy()
	940	return
	941	for peak in peaks:
	942	file.write("%12.6f\n" % (peak[7]))
	943	file.close()
	944	finally:
	945	wx.EndBusyCursor()
	946	print 'index peak list saved'
	947
	948	class MultipleChoicesDialog(wx.Dialog):
[923]	949	'''A dialog that offers a series of choices, each with a
	950	title and a wx.Choice widget. Intended to be used Modally.
[762]	951	typical input:
[923]	952
	953	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
	954	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
	955
[762]	956	selections are placed in self.chosen when OK is pressed
[2433]	957
	958	Also see GSASIIctrls
[762]	959	'''
	960	def __init__(self,choicelist,headinglist,
	961	head='Select options',
	962	title='Please select from options below',
	963	parent=None):
	964	self.chosen = []
	965	wx.Dialog.__init__(
	966	self,parent,wx.ID_ANY,head,
	967	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
	968	panel = wx.Panel(self)
	969	mainSizer = wx.BoxSizer(wx.VERTICAL)
	970	mainSizer.Add((10,10),1)
	971	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
	972	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
	973	self.ChItems = []
	974	for choice,lbl in zip(choicelist,headinglist):
	975	mainSizer.Add((10,10),1)
	976	self.chosen.append(0)
	977	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
	978	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
	979	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
	980	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
	981
	982	OkBtn = wx.Button(panel,-1,"Ok")
	983	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
	984	cancelBtn = wx.Button(panel,-1,"Cancel")
	985	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
	986	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
	987	btnSizer.Add((20,20),1)
	988	btnSizer.Add(OkBtn)
	989	btnSizer.Add((20,20),1)
	990	btnSizer.Add(cancelBtn)
	991	btnSizer.Add((20,20),1)
	992	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
	993	panel.SetSizer(mainSizer)
	994	panel.Fit()
	995	self.Fit()
	996
	997	def OnOk(self,event):
	998	parent = self.GetParent()
	999	if parent is not None: parent.Raise()
	1000	# save the results from the choice widgets
	1001	self.chosen = []
	1002	for w in self.ChItems:
	1003	self.chosen.append(w.GetSelection())
	1004	self.EndModal(wx.ID_OK)
	1005
	1006	def OnCancel(self,event):
	1007	parent = self.GetParent()
	1008	if parent is not None: parent.Raise()
	1009	self.chosen = []
	1010	self.EndModal(wx.ID_CANCEL)
	1011
	1012	def ExtractFileFromZip(filename, selection=None, confirmread=True,
	1013	confirmoverwrite=True, parent=None,
	1014	multipleselect=False):
[923]	1015	'''If the filename is a zip file, extract a file from that
	1016	archive.
	1017
	1018	:param list Selection: used to predefine the name of the file
	1019	to be extracted. Filename case and zip directory name are
	1020	ignored in selection; the first matching file is used.
	1021
	1022	:param bool confirmread: if True asks the user to confirm before expanding
	1023	the only file in a zip
	1024
	1025	:param bool confirmoverwrite: if True asks the user to confirm
	1026	before overwriting if the extracted file already exists
	1027
	1028	:param bool multipleselect: if True allows more than one zip
	1029	file to be extracted, a list of file(s) is returned.
	1030	If only one file is present, do not ask which one, otherwise
	1031	offer a list of choices (unless selection is used).
	1032
	1033	:returns: the name of the file that has been created or a
	1034	list of files (see multipleselect)
	1035
	1036	If the file is not a zipfile, return the name of the input file.
	1037	If the zipfile is empty or no file has been selected, return None
[762]	1038	'''
	1039	import zipfile # do this now, since we can save startup time by doing this only on need
	1040	import shutil
	1041	zloc = os.path.split(filename)[0]
	1042	if not zipfile.is_zipfile(filename):
	1043	#print("not zip")
	1044	return filename
	1045
	1046	z = zipfile.ZipFile(filename,'r')
	1047	zinfo = z.infolist()
	1048
	1049	if len(zinfo) == 0:
	1050	#print('Zip has no files!')
	1051	zlist = [-1]
	1052	if selection:
	1053	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
	1054	if selection.lower() in choices:
	1055	zlist = [choices.index(selection.lower())]
	1056	else:
	1057	print('debug: file '+str(selection)+' was not found in '+str(filename))
	1058	zlist = [-1]
	1059	elif len(zinfo) == 1 and confirmread:
	1060	result = wx.ID_NO
	1061	dlg = wx.MessageDialog(
	1062	parent,
	1063	'Is file '+str(zinfo[0].filename)+
	1064	' what you want to extract from '+
	1065	str(os.path.split(filename)[1])+'?',
	1066	'Confirm file',
	1067	wx.YES_NO \| wx.ICON_QUESTION)
	1068	try:
	1069	result = dlg.ShowModal()
	1070	finally:
	1071	dlg.Destroy()
	1072	if result == wx.ID_NO:
	1073	zlist = [-1]
	1074	else:
	1075	zlist = [0]
	1076	elif len(zinfo) == 1:
	1077	zlist = [0]
	1078	elif multipleselect:
	1079	# select one or more from a from list
	1080	choices = [i.filename for i in zinfo]
[1770]	1081	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
[1276]	1082	'Choose file(s)',choices)
[762]	1083	if dlg.ShowModal() == wx.ID_OK:
	1084	zlist = dlg.GetSelections()
	1085	else:
	1086	zlist = []
	1087	dlg.Destroy()
	1088	else:
	1089	# select one from a from list
	1090	choices = [i.filename for i in zinfo]
	1091	dlg = wx.SingleChoiceDialog(parent,
	1092	'Select file to extract from zip file'+str(filename),'Choose file',
	1093	choices,)
	1094	if dlg.ShowModal() == wx.ID_OK:
	1095	zlist = [dlg.GetSelection()]
	1096	else:
	1097	zlist = [-1]
	1098	dlg.Destroy()
	1099
	1100	outlist = []
	1101	for zindex in zlist:
	1102	if zindex >= 0:
	1103	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
	1104	if os.path.exists(efil) and confirmoverwrite:
	1105	result = wx.ID_NO
	1106	dlg = wx.MessageDialog(parent,
	1107	'File '+str(efil)+' already exists. OK to overwrite it?',
	1108	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
	1109	try:
	1110	result = dlg.ShowModal()
	1111	finally:
	1112	dlg.Destroy()
	1113	if result == wx.ID_NO:
	1114	zindex = -1
	1115	if zindex >= 0:
	1116	# extract the file to the current directory, regardless of it's original path
	1117	#z.extract(zinfo[zindex],zloc)
	1118	eloc,efil = os.path.split(zinfo[zindex].filename)
	1119	outfile = os.path.join(zloc, efil)
	1120	fpin = z.open(zinfo[zindex])
	1121	fpout = file(outfile, "wb")
	1122	shutil.copyfileobj(fpin, fpout)
	1123	fpin.close()
	1124	fpout.close()
	1125	outlist.append(outfile)
	1126	z.close()
	1127	if multipleselect and len(outlist) >= 1:
	1128	return outlist
	1129	elif len(outlist) == 1:
	1130	return outlist[0]
	1131	else:
	1132	return None
	1133
	1134	######################################################################
	1135	# base classes for reading various types of data files
	1136	# not used directly, only by subclassing
	1137	######################################################################
[2817]	1138	def BlockSelector(ChoiceList, ParentFrame=None,title='Select a block',
	1139	size=None, header='Block Selector',useCancel=True):
	1140	''' Provide a wx dialog to select a block if the file contains more
	1141	than one set of data and one must be selected
[762]	1142	'''
[2817]	1143	if useCancel:
	1144	dlg = wx.SingleChoiceDialog(
	1145	ParentFrame,title, header,ChoiceList)
	1146	else:
	1147	dlg = wx.SingleChoiceDialog(
	1148	ParentFrame,title, header,ChoiceList,
	1149	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
	1150	if size: dlg.SetSize(size)
	1151	dlg.CenterOnParent()
	1152	if dlg.ShowModal() == wx.ID_OK:
	1153	sel = dlg.GetSelection()
	1154	return sel
	1155	else:
[762]	1156	return None
[2817]	1157	dlg.Destroy()
[762]	1158
[2817]	1159	def MultipleBlockSelector(ChoiceList, ParentFrame=None,
	1160	title='Select a block',size=None, header='Block Selector'):
	1161	'''Provide a wx dialog to select a block of data if the
	1162	file contains more than one set of data and one must be
	1163	selected.
[762]	1164
[2817]	1165	:returns: a list of the selected blocks
[762]	1166	'''
[2817]	1167	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
	1168	wx.CHOICEDLG_STYLE)
	1169	dlg.CenterOnScreen()
	1170	if size: dlg.SetSize(size)
	1171	if dlg.ShowModal() == wx.ID_OK:
	1172	sel = dlg.GetSelections()
	1173	else:
	1174	return []
	1175	dlg.Destroy()
	1176	selected = []
	1177	if len(ChoiceList) in sel:
	1178	return range(len(ChoiceList))
	1179	else:
	1180	return sel
	1181	return selected
[762]	1182
[2817]	1183	def MultipleChoicesSelector(choicelist, headinglist, ParentFrame=None, **kwargs):
	1184	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
	1185	widget. Typical input:
	1186
	1187	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
	1188
	1189	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
	1190
	1191	optional keyword parameters are: head (window title) and title
	1192	returns a list of selected indicies for each choice (or None)
[1084]	1193	'''
[2817]	1194	result = None
	1195	dlg = MultipleChoicesDialog(choicelist,headinglist,
	1196	parent=ParentFrame, **kwargs)
	1197	dlg.CenterOnParent()
	1198	if dlg.ShowModal() == wx.ID_OK:
	1199	result = dlg.chosen
	1200	dlg.Destroy()
	1201	return result
[1084]	1202
[2818]	1203	def PhaseSelector(ChoiceList, ParentFrame=None,
[2817]	1204	title='Select a phase', size=None,header='Phase Selector'):
	1205	''' Provide a wx dialog to select a phase if the file contains more
	1206	than one phase
[1084]	1207	'''
[2817]	1208	return BlockSelector(ChoiceList,ParentFrame,title,
	1209	size,header)
[2001]	1210
[2754]	1211	######################################################################
[2433]	1212	def striphist(var,insChar=''):
	1213	'strip a histogram number from a var name'
	1214	sv = var.split(':')
	1215	if len(sv) <= 1: return var
	1216	if sv[1]:
	1217	sv[1] = insChar
	1218	return ':'.join(sv)
[938]	1219	class ExportBaseclass(object):
[1261]	1220	'''Defines a base class for the exporting of GSAS-II results.
	1221
	1222	This class is subclassed in the various exports/G2export_*.py files. Those files
	1223	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
	1224	appropriate menu items for each one and the .Exporter method is called
	1225	directly from the menu item.
[1997]	1226
	1227	Routines may also define a .Writer method, which is used to write a single
	1228	file without invoking any GUI objects.
[938]	1229	'''
[2152]	1230	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
[938]	1231	self.G2frame = G2frame
	1232	self.formatName = formatName # short string naming file type
[1020]	1233	self.extension = extension
[938]	1234	if longFormatName: # longer string naming file type
	1235	self.longFormatName = longFormatName
	1236	else:
	1237	self.longFormatName = formatName
	1238	self.OverallParms = {}
[956]	1239	self.Phases = {}
	1240	self.Histograms = {}
[1080]	1241	self.powderDict = {}
	1242	self.xtalDict = {}
[1117]	1243	self.parmDict = {}
	1244	self.sigDict = {}
[1115]	1245	# updated in InitExport:
[1080]	1246	self.currentExportType = None # type of export that has been requested
[1115]	1247	# updated in ExportSelect (when used):
[1102]	1248	self.phasenam = None # a list of selected phases
	1249	self.histnam = None # a list of selected histograms
[1261]	1250	self.filename = None # name of file to be written (single export) or template (multiple files)
	1251	self.dirname = '' # name of directory where file(s) will be written
	1252	self.fullpath = '' # name of file being written -- full path
[1080]	1253
	1254	# items that should be defined in a subclass of this class
	1255	self.exporttype = [] # defines the type(s) of exports that the class can handle.
	1256	# The following types are defined: 'project', "phase", "powder", "single"
[1102]	1257	self.multiple = False # set as True if the class can export multiple phases or histograms
[1115]	1258	# self.multiple is ignored for "project" exports
[938]	1259
[1115]	1260	def InitExport(self,event):
[1261]	1261	'''Determines the type of menu that called the Exporter and
	1262	misc initialization.
[1115]	1263	'''
[1261]	1264	self.filename = None # name of file to be written (single export)
	1265	self.dirname = '' # name of file to be written (multiple export)
[1115]	1266	if event:
	1267	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
[1080]	1268
[1236]	1269	def MakePWDRfilename(self,hist):
	1270	'''Make a filename root (no extension) from a PWDR histogram name
	1271
	1272	:param str hist: the histogram name in data tree (starts with "PWDR ")
	1273	'''
	1274	file0 = ''
	1275	file1 = hist[5:]
	1276	# replace repeated blanks
	1277	while file1 != file0:
	1278	file0 = file1
	1279	file1 = file0.replace(' ',' ').strip()
	1280	file0 = file1.replace('Azm= ','A')
	1281	# if angle has unneeded decimal places on aziumuth, remove them
	1282	if file0[-3:] == '.00': file0 = file0[:-3]
	1283	file0 = file0.replace('.','_')
	1284	file0 = file0.replace(' ','_')
	1285	return file0
	1286
[1261]	1287	def ExportSelect(self,AskFile='ask'):
	1288	'''Selects histograms or phases when needed. Sets a default file name when
[2449]	1289	requested into self.filename; always sets a default directory in self.dirname.
[1115]	1290
[1261]	1291	:param bool AskFile: Determines how this routine processes getting a
	1292	location to store the current export(s).
[1298]	1293
[1261]	1294	* if AskFile is 'ask' (default option), get the name of the file to be written;
	1295	self.filename and self.dirname are always set. In the case where
	1296	multiple files must be generated, the export routine should do this
	1297	based on self.filename as a template.
	1298	* if AskFile is 'dir', get the name of the directory to be used;
	1299	self.filename is not used, but self.dirname is always set. The export routine
	1300	will always generate the file name.
	1301	* if AskFile is 'single', get only the name of the directory to be used when
	1302	multiple items will be written (as multiple files) are used
	1303	or a complete file name is requested when a single file
	1304	name is selected. self.dirname is always set and self.filename used
	1305	only when a single file is selected.
	1306	* if AskFile is 'default', creates a name of the file to be used from
	1307	the name of the project (.gpx) file. If the project has not been saved,
	1308	then the name of file is requested.
	1309	self.filename and self.dirname are always set. In the case where
	1310	multiple file names must be generated, the export routine should do this
	1311	based on self.filename.
	1312	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
	1313	file. If the project has not been saved, then a directory is requested.
	1314	self.filename is not used.
	1315
[1102]	1316	:returns: True in case of an error
[1080]	1317	'''
	1318
[1261]	1319	numselected = 1
[1080]	1320	if self.currentExportType == 'phase':
	1321	if len(self.Phases) == 0:
	1322	self.G2frame.ErrorDialog(
	1323	'Empty project',
[1115]	1324	'Project does not contain any phases.')
[1080]	1325	return True
[1117]	1326	elif len(self.Phases) == 1:
	1327	self.phasenam = self.Phases.keys()
[1080]	1328	elif self.multiple:
[1117]	1329	choices = sorted(self.Phases.keys())
[1831]	1330	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
[1117]	1331	if phasenum is None: return True
	1332	self.phasenam = [choices[i] for i in phasenum]
	1333	if not self.phasenam: return True
[1261]	1334	numselected = len(self.phasenam)
[1080]	1335	else:
[1117]	1336	choices = sorted(self.Phases.keys())
[1831]	1337	phasenum = G2G.ItemSelector(choices,self.G2frame)
[1117]	1338	if phasenum is None: return True
	1339	self.phasenam = [choices[phasenum]]
[1261]	1340	numselected = len(self.phasenam)
[1080]	1341	elif self.currentExportType == 'single':
	1342	if len(self.xtalDict) == 0:
	1343	self.G2frame.ErrorDialog(
	1344	'Empty project',
[1115]	1345	'Project does not contain any single crystal data.')
[1080]	1346	return True
[1117]	1347	elif len(self.xtalDict) == 1:
	1348	self.histnam = self.xtalDict.values()
[1080]	1349	elif self.multiple:
[1117]	1350	choices = sorted(self.xtalDict.values())
[1831]	1351	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
[1117]	1352	if not hnum: return True
	1353	self.histnam = [choices[i] for i in hnum]
[1261]	1354	numselected = len(self.histnam)
[1080]	1355	else:
[1117]	1356	choices = sorted(self.xtalDict.values())
[1831]	1357	hnum = G2G.ItemSelector(choices,self.G2frame)
[1117]	1358	if hnum is None: return True
	1359	self.histnam = [choices[hnum]]
[1261]	1360	numselected = len(self.histnam)
[1080]	1361	elif self.currentExportType == 'powder':
	1362	if len(self.powderDict) == 0:
	1363	self.G2frame.ErrorDialog(
	1364	'Empty project',
[1115]	1365	'Project does not contain any powder data.')
[1080]	1366	return True
[1117]	1367	elif len(self.powderDict) == 1:
	1368	self.histnam = self.powderDict.values()
[1080]	1369	elif self.multiple:
[1117]	1370	choices = sorted(self.powderDict.values())
[1831]	1371	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
[1117]	1372	if not hnum: return True
	1373	self.histnam = [choices[i] for i in hnum]
[1261]	1374	numselected = len(self.histnam)
[1080]	1375	else:
[1117]	1376	choices = sorted(self.powderDict.values())
[1831]	1377	hnum = G2G.ItemSelector(choices,self.G2frame)
[1117]	1378	if hnum is None: return True
	1379	self.histnam = [choices[hnum]]
[1261]	1380	numselected = len(self.histnam)
[1115]	1381	elif self.currentExportType == 'image':
	1382	if len(self.Histograms) == 0:
	1383	self.G2frame.ErrorDialog(
	1384	'Empty project',
	1385	'Project does not contain any images.')
	1386	return True
	1387	elif len(self.Histograms) == 1:
	1388	self.histnam = self.Histograms.keys()
	1389	else:
	1390	choices = sorted(self.Histograms.keys())
[1831]	1391	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
[1115]	1392	if self.multiple:
[1117]	1393	if not hnum: return True
[1115]	1394	self.histnam = [choices[i] for i in hnum]
	1395	else:
[1117]	1396	if hnum is None: return True
[1115]	1397	self.histnam = [choices[hnum]]
[1261]	1398	numselected = len(self.histnam)
[1117]	1399	if self.currentExportType == 'map':
	1400	# search for phases with maps
	1401	mapPhases = []
	1402	choices = []
	1403	for phasenam in sorted(self.Phases):
	1404	phasedict = self.Phases[phasenam] # pointer to current phase info
	1405	if len(phasedict['General']['Map'].get('rho',[])):
	1406	mapPhases.append(phasenam)
	1407	if phasedict['General']['Map'].get('Flip'):
	1408	choices.append('Charge flip map: '+str(phasenam))
	1409	elif phasedict['General']['Map'].get('MapType'):
	1410	choices.append(
	1411	str(phasedict['General']['Map'].get('MapType'))
	1412	+ ' map: ' + str(phasenam))
	1413	else:
	1414	choices.append('unknown map: '+str(phasenam))
	1415	# select a map if needed
	1416	if len(mapPhases) == 0:
	1417	self.G2frame.ErrorDialog(
	1418	'Empty project',
	1419	'Project does not contain any maps.')
	1420	return True
	1421	elif len(mapPhases) == 1:
	1422	self.phasenam = mapPhases
	1423	else:
[1831]	1424	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
[1117]	1425	if self.multiple:
	1426	if not phasenum: return True
	1427	self.phasenam = [mapPhases[i] for i in phasenum]
	1428	else:
	1429	if phasenum is None: return True
	1430	self.phasenam = [mapPhases[phasenum]]
[1261]	1431	numselected = len(self.phasenam)
[1117]	1432
[1261]	1433	# items selected, now set self.dirname and usually self.filename
	1434	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
	1435	AskFile == 'default' and not self.G2frame.GSASprojectfile
	1436	):
	1437	filename = self.askSaveFile()
	1438	if not filename: return True
	1439	self.dirname,self.filename = os.path.split(filename)
	1440	elif AskFile == 'dir' or AskFile == 'single' or (
	1441	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
	1442	):
	1443	self.dirname = self.askSaveDirectory()
	1444	if not self.dirname: return True
	1445	elif AskFile == 'default-dir' or AskFile == 'default':
	1446	self.dirname,self.filename = os.path.split(
	1447	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
	1448	)
[1115]	1449	else:
[1261]	1450	raise Exception('This should not happen!')
[2433]	1451
[956]	1452	def loadParmDict(self):
	1453	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
	1454	refined values to those from the last cycle and set the uncertainties for the
	1455	refined parameters in another dict (self.sigDict).
[938]	1456
[956]	1457	Expands the parm & sig dicts to include values derived from constraints.
	1458	'''
	1459	self.parmDict = {}
	1460	self.sigDict = {}
	1461	rigidbodyDict = {}
	1462	covDict = {}
	1463	consDict = {}
	1464	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
	1465	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
	1466	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
	1467	while item:
	1468	name = self.G2frame.PatternTree.GetItemText(item)
	1469	if name == 'Rigid bodies':
	1470	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
	1471	elif name == 'Covariance':
	1472	covDict = self.G2frame.PatternTree.GetItemPyData(item)
	1473	elif name == 'Constraints':
	1474	consDict = self.G2frame.PatternTree.GetItemPyData(item)
	1475	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
	1476	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
	1477	self.parmDict.update(rbDict)
	1478	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
[2491]	1479	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
[956]	1480	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
	1481	self.parmDict.update(phaseDict)
[981]	1482	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
	1483	Phases,Histograms,Print=False,resetRefList=False)
[956]	1484	self.parmDict.update(hapDict)
	1485	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
	1486	self.parmDict.update(histDict)
	1487	self.parmDict.update(zip(
	1488	covDict.get('varyList',[]),
	1489	covDict.get('variables',[])))
	1490	self.sigDict = dict(zip(
	1491	covDict.get('varyList',[]),
	1492	covDict.get('sig',[])))
	1493	# expand to include constraints: first compile a list of constraints
	1494	constList = []
	1495	for item in consDict:
[1160]	1496	if item.startswith('_'): continue
[956]	1497	constList += consDict[item]
	1498	# now process the constraints
	1499	G2mv.InitVars()
[960]	1500	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
	1501	varyList = covDict.get('varyListStart')
	1502	if varyList is None and len(constDict) == 0:
	1503	# no constraints can use varyList
	1504	varyList = covDict.get('varyList')
	1505	elif varyList is None:
	1506	# old GPX file from before pre-constraint varyList is saved
	1507	print ' * Old refinement: Please use Calculate/Refine to redo *'
[1138]	1508	raise Exception(' * Export aborted *')
[960]	1509	else:
	1510	varyList = list(varyList)
[956]	1511	try:
	1512	groups,parmlist = G2mv.GroupConstraints(constDict)
[1243]	1513	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
[956]	1514	except:
	1515	# this really should not happen
	1516	print ' * ERROR - constraints are internally inconsistent *'
	1517	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
	1518	print 'Errors',errmsg
	1519	if warnmsg: print 'Warnings',warnmsg
	1520	raise Exception(' * CIF creation aborted *')
	1521	# add the constrained values to the parameter dictionary
	1522	G2mv.Dict2Map(self.parmDict,varyList)
	1523	# and add their uncertainties into the esd dictionary (sigDict)
	1524	if covDict.get('covMatrix') is not None:
[960]	1525	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
[956]	1526
	1527	def loadTree(self):
	1528	'''Load the contents of the data tree into a set of dicts
[1080]	1529	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
	1530	& self.xtalDict)
[938]	1531
[956]	1532	* The childrenless data tree items are overall parameters/controls for the
	1533	entire project and are placed in self.OverallParms
	1534	* Phase items are placed in self.Phases
	1535	* Data items are placed in self.Histogram. The key for these data items
	1536	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
[938]	1537	'''
	1538	self.OverallParms = {}
[1115]	1539	self.powderDict = {}
	1540	self.xtalDict = {}
[1198]	1541	self.Phases = {}
	1542	self.Histograms = {}
[2433]	1543	self.SeqRefdata = None
	1544	self.SeqRefhist = None
[1115]	1545	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
	1546	histType = None
	1547	if self.currentExportType == 'phase':
	1548	# if exporting phases load them here
	1549	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
	1550	if not sub:
	1551	print 'no phases found'
	1552	return True
	1553	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
	1554	while item:
	1555	phaseName = self.G2frame.PatternTree.GetItemText(item)
	1556	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
	1557	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
	1558	return
	1559	elif self.currentExportType == 'single':
	1560	histType = 'HKLF'
	1561	elif self.currentExportType == 'powder':
	1562	histType = 'PWDR'
	1563	elif self.currentExportType == 'image':
	1564	histType = 'IMG'
	1565
	1566	if histType: # Loading just one kind of tree entry
	1567	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
	1568	while item:
	1569	name = self.G2frame.PatternTree.GetItemText(item)
	1570	if name.startswith(histType):
	1571	if self.Histograms.get(name): # there is already an item with this name
[1198]	1572	print('Histogram name '+str(name)+' is repeated. Renaming')
[1115]	1573	if name[-1] == '9':
	1574	name = name[:-1] + '10'
	1575	elif name[-1] in '012345678':
[1198]	1576	name = name[:-1] + str(int(name[-1])+1)
[1115]	1577	else:
	1578	name += '-1'
	1579	self.Histograms[name] = {}
[1127]	1580	# the main info goes into Data, but the 0th
	1581	# element contains refinement results, carry
	1582	# that over too now.
[1115]	1583	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
[1127]	1584	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
[1115]	1585	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
	1586	while item2:
	1587	child = self.G2frame.PatternTree.GetItemText(item2)
	1588	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
	1589	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
	1590	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
	1591	# index powder and single crystal histograms by number
	1592	for hist in self.Histograms:
	1593	if hist.startswith("PWDR"):
	1594	d = self.powderDict
	1595	elif hist.startswith("HKLF"):
	1596	d = self.xtalDict
	1597	else:
	1598	return
	1599	i = self.Histograms[hist].get('hId')
	1600	if i is None and not d.keys():
	1601	i = 0
	1602	elif i is None or i in d.keys():
	1603	i = max(d.keys())+1
	1604	d[i] = hist
	1605	return
	1606	# else standard load: using all interlinked phases and histograms
[956]	1607	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
	1608	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
[938]	1609	while item:
[956]	1610	name = self.G2frame.PatternTree.GetItemText(item)
	1611	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
	1612	if not item2:
	1613	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
	1614	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
[1080]	1615	# index powder and single crystal histograms
	1616	for hist in self.Histograms:
	1617	i = self.Histograms[hist]['hId']
	1618	if hist.startswith("PWDR"):
	1619	self.powderDict[i] = hist
	1620	elif hist.startswith("HKLF"):
	1621	self.xtalDict[i] = hist
[938]	1622
	1623	def dumpTree(self,mode='type'):
[2433]	1624	'''Print out information on the data tree dicts loaded in loadTree.
	1625	Used for testing only.
[938]	1626	'''
[2433]	1627	if self.SeqRefdata and self.SeqRefhist:
	1628	print('Note that dumpTree does not show sequential results')
[938]	1629	print '\nOverall'
	1630	if mode == 'type':
	1631	def Show(arg): return type(arg)
	1632	else:
	1633	def Show(arg): return arg
	1634	for key in self.OverallParms:
	1635	print ' ',key,Show(self.OverallParms[key])
[956]	1636	print 'Phases'
	1637	for key1 in self.Phases:
	1638	print ' ',key1,Show(self.Phases[key1])
	1639	print 'Histogram'
	1640	for key1 in self.Histograms:
	1641	print ' ',key1,Show(self.Histograms[key1])
	1642	for key2 in self.Histograms[key1]:
	1643	print ' ',key2,Show(self.Histograms[key1][key2])
[1020]	1644
[1080]	1645	def defaultSaveFile(self):
[1020]	1646	return os.path.abspath(
	1647	os.path.splitext(self.G2frame.GSASprojectfile
	1648	)[0]+self.extension)
	1649
	1650	def askSaveFile(self):
	1651	'''Ask the user to supply a file name
	1652
[1261]	1653	:returns: a file name (str) or None if Cancel is pressed
[1020]	1654	'''
[2109]	1655
	1656	pth = G2G.GetExportPath(self.G2frame)
[1020]	1657	defnam = os.path.splitext(
	1658	os.path.split(self.G2frame.GSASprojectfile)[1]
	1659	)[0]+self.extension
	1660	dlg = wx.FileDialog(
[2109]	1661	self.G2frame, 'Input name for file to write', pth, defnam,
[1020]	1662	self.longFormatName+' ('+self.extension+')\|'+self.extension,
[2109]	1663	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
[1102]	1664	dlg.CenterOnParent()
[1020]	1665	try:
	1666	if dlg.ShowModal() == wx.ID_OK:
	1667	filename = dlg.GetPath()
[2109]	1668	self.G2frame.LastExportDir = os.path.split(filename)[0]
	1669	filename = os.path.splitext(filename)[0]+self.extension # make sure extension is correct
[1020]	1670	else:
	1671	filename = None
	1672	finally:
	1673	dlg.Destroy()
	1674	return filename
[1006]	1675
[1261]	1676	def askSaveDirectory(self):
	1677	'''Ask the user to supply a directory name. Path name is used as the
	1678	starting point for the next export path search.
	1679
	1680	:returns: a directory name (str) or None if Cancel is pressed
	1681	'''
[2109]	1682	pth = G2G.GetExportPath(self.G2frame)
[1261]	1683	dlg = wx.DirDialog(
[2109]	1684	self.G2frame, 'Input directory where file(s) will be written', pth,
[1261]	1685	wx.DD_DEFAULT_STYLE)
	1686	dlg.CenterOnParent()
	1687	try:
	1688	if dlg.ShowModal() == wx.ID_OK:
	1689	filename = dlg.GetPath()
[2109]	1690	self.G2frame.LastExportDir = filename
[1261]	1691	else:
	1692	filename = None
	1693	finally:
	1694	dlg.Destroy()
	1695	return filename
	1696
[1102]	1697	# Tools for file writing.
[1261]	1698	def OpenFile(self,fil=None,mode='w'):
[1084]	1699	'''Open the output file
[1102]	1700
	1701	:param str fil: The name of the file to open. If None (default)
[1261]	1702	the name defaults to self.dirname + self.filename.
	1703	If an extension is supplied, it is not overridded,
	1704	but if not, the default extension is used.
[1102]	1705	:returns: the file object opened by the routine which is also
	1706	saved as self.fp
[762]	1707	'''
[2433]	1708	if mode == 'd': # debug mode
	1709	self.fullpath = '(stdout)'
	1710	self.fp = sys.stdout
	1711	return
[1084]	1712	if not fil:
[1261]	1713	if not os.path.splitext(self.filename)[1]:
	1714	self.filename += self.extension
	1715	fil = os.path.join(self.dirname,self.filename)
[1997]	1716	self.fullpath = os.path.abspath(fil)
[2026]	1717	self.fp = open(self.fullpath,mode)
[1084]	1718	return self.fp
[1261]	1719
[1084]	1720	def Write(self,line):
[1102]	1721	'''write a line of output, attaching a line-end character
	1722
	1723	:param str line: the text to be written.
	1724	'''
[1084]	1725	self.fp.write(line+'\n')
[2433]	1726
[1084]	1727	def CloseFile(self,fp=None):
[1102]	1728	'''Close a file opened in OpenFile
	1729
	1730	:param file fp: the file object to be closed. If None (default)
	1731	file object self.fp is closed.
	1732	'''
[2433]	1733	if self.fp == sys.stdout: return # debug mode
[1084]	1734	if fp is None:
	1735	fp = self.fp
	1736	self.fp = None
	1737	fp.close()
[2433]	1738
	1739	def SetSeqRef(self,data,hist):
	1740	'''Set the exporter to retrieve results from a sequential refinement
	1741	rather than the main tree
	1742	'''
	1743	self.SeqRefdata = data
	1744	self.SeqRefhist = hist
	1745	data_name = data[hist]
	1746	for i,val in zip(data_name['varyList'],data_name['sig']):
	1747	self.sigDict[i] = val
	1748	self.sigDict[striphist(i)] = val
	1749	for i in data_name['parmDict']:
	1750	self.parmDict[striphist(i)] = data_name['parmDict'][i]
	1751	self.parmDict[i] = data_name['parmDict'][i]
	1752	# zero out the dA[xyz] terms, they would only bring confusion
	1753	key = i.split(':')
	1754	if len(key) < 3: continue
	1755	if key[2].startswith('dA'):
	1756	self.parmDict[i] = 0.0
	1757	for i,(val,sig) in data_name.get('depParmDict',{}).iteritems():
	1758	self.parmDict[i] = val
	1759	self.sigDict[i] = sig
	1760	#GSASIIpath.IPyBreak()
	1761
[1102]	1762	# Tools to pull information out of the data arrays
	1763	def GetCell(self,phasenam):
	1764	"""Gets the unit cell parameters and their s.u.'s for a selected phase
	1765
	1766	:param str phasenam: the name for the selected phase
	1767	:returns: `cellList,cellSig` where each is a 7 element list corresponding
	1768	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
	1769	cell values and `cellSig` has their uncertainties.
	1770	"""
[2433]	1771	if self.SeqRefdata and self.SeqRefhist:
	1772	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
[1115]	1773	phasedict = self.Phases[phasenam] # pointer to current phase info
	1774	try:
	1775	pfx = str(phasedict['pId'])+'::'
	1776	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
[1663]	1777	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
	1778	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
[1115]	1779	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
	1780	return cellList,cellSig
	1781	except KeyError:
	1782	cell = phasedict['General']['Cell'][1:]
	1783	return cell,7*[0]
[2433]	1784
	1785	def GetSeqCell(self,phasenam,data_name):
	1786	"""Gets the unit cell parameters and their s.u.'s for a selected phase
	1787	and histogram in a sequential fit
	1788
	1789	:param str phasenam: the name for the selected phase
	1790	:param dict data_name: the sequential refinement parameters for the selected histogram
	1791	:returns: `cellList,cellSig` where each is a 7 element list corresponding
	1792	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
	1793	cell values and `cellSig` has their uncertainties.
	1794	"""
	1795	phasedict = self.Phases[phasenam]
	1796	SGdata = phasedict['General']['SGData']
	1797	pId = phasedict['pId']
	1798	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
	1799	ESDlookup = {}
	1800	Dlookup = {}
	1801	varied = [striphist(i) for i in data_name['varyList']]
	1802	for item,val in data_name['newCellDict'].iteritems():
	1803	if item in varied:
	1804	ESDlookup[val[0]] = item
	1805	Dlookup[item] = val[0]
	1806	A = RecpCellTerms[:]
	1807	for i in range(6):
	1808	var = str(pId)+'::A'+str(i)
	1809	if var in ESDlookup:
	1810	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
	1811	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
	1812	zeroDict = {i:0.0 for i in cellDict}
	1813	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
	1814	covData = {
	1815	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
	1816	'covMatrix': data_name['covMatrix']
	1817	}
	1818	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
	1819
[1102]	1820	def GetAtoms(self,phasenam):
	1821	"""Gets the atoms associated with a phase. Can be used with standard
	1822	or macromolecular phases
	1823
	1824	:param str phasenam: the name for the selected phase
	1825	:returns: a list of items for eac atom where each item is a list containing:
	1826	label, typ, mult, xyz, and td, where
	1827
	1828	* label and typ are the atom label and the scattering factor type (str)
	1829	* mult is the site multiplicity (int)
	1830	* xyz is contains a list with four pairs of numbers:
	1831	x, y, z and fractional occupancy and
	1832	their standard uncertainty (or a negative value)
	1833	* td is contains a list with either one or six pairs of numbers:
[1115]	1834	if one number it is U\ :sub:`iso` and with six numbers it is
[1102]	1835	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
	1836	paired with their standard uncertainty (or a negative value)
	1837	"""
	1838	phasedict = self.Phases[phasenam] # pointer to current phase info
	1839	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
	1840	cfrac = cx+3
	1841	fpfx = str(phasedict['pId'])+'::Afrac:'
	1842	atomslist = []
	1843	for i,at in enumerate(phasedict['Atoms']):
	1844	if phasedict['General']['Type'] == 'macromolecular':
	1845	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
	1846	else:
	1847	label = at[ct-1]
	1848	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
	1849	fsig = self.sigDict.get(fpfx+str(i),-0.009)
	1850	mult = at[cs+1]
	1851	typ = at[ct]
	1852	xyz = []
	1853	for j,v in enumerate(('x','y','z')):
	1854	val = at[cx+j]
[2433]	1855	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
	1856	val = self.parmDict.get(pfx, val)
	1857	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
	1858	sig = self.sigDict.get(dpfx,-0.000009)
[1102]	1859	xyz.append((val,sig))
	1860	xyz.append((fval,fsig))
	1861	td = []
	1862	if at[cia] == 'I':
	1863	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
	1864	val = self.parmDict.get(pfx,at[cia+1])
	1865	sig = self.sigDict.get(pfx,-0.0009)
	1866	td.append((val,sig))
	1867	else:
	1868	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
	1869	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
	1870	val = self.parmDict.get(pfx,at[cia+2+i])
	1871	sig = self.sigDict.get(pfx,-0.0009)
	1872	td.append((val,sig))
	1873	atomslist.append((label,typ,mult,xyz,td))
	1874	return atomslist
[1084]	1875	######################################################################
[1997]	1876	def ExportPowderList(G2frame):
	1877	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
[2433]	1878	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
[1997]	1879
	1880	:param wx.Frame G2frame: the GSAS-II main data tree window
	1881	'''
	1882	extList = []
	1883	for obj in G2frame.exporterlist:
	1884	if 'powder' in obj.exporttype:
	1885	try:
	1886	obj.Writer
	1887	extList.append(obj.extension)
	1888	except AttributeError:
	1889	pass
	1890	return extList
[762]	1891
[1997]	1892	def ExportPowder(G2frame,TreeName,fileroot,extension):
[2433]	1893	'''Writes a single powder histogram using the Export routines.
	1894	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
[1997]	1895
	1896	:param wx.Frame G2frame: the GSAS-II main data tree window
	1897	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
	1898	:param str fileroot: name for file to be written, extension ignored
	1899	:param str extension: extension for file to be written (start with '.'). Must
	1900	match a powder export routine that has a Writer object.
	1901	'''
[2026]	1902	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
[1997]	1903	for obj in G2frame.exporterlist:
	1904	if obj.extension == extension and 'powder' in obj.exporttype:
	1905	obj.currentExportType = 'powder'
	1906	obj.InitExport(None)
	1907	obj.loadTree() # load all histograms in tree into dicts
	1908	if TreeName not in obj.Histograms:
[2026]	1909	raise Exception('Histogram not found: '+str(TreeName))
[1997]	1910	try:
[2026]	1911	obj.Writer
	1912	except AttributeError:
	1913	continue
	1914	try:
[1997]	1915	obj.Writer(TreeName,filename)
	1916	return
[2026]	1917	except Exception,err:
	1918	print('Export Routine for '+extension+' failed.')
	1919	print err
[1997]	1920	else:
	1921	print('No Export routine supports extension '+extension)
[2433]	1922
	1923	def ExportSequential(G2frame,data,obj,exporttype):
	1924	'''
	1925	Used to export from every phase/dataset in a sequential refinement using
	1926	a .Writer method for either projects or phases. Prompts to select histograms
	1927	and for phase exports, which phase(s).
	1928
	1929	:param wx.Frame G2frame: the GSAS-II main data tree window
	1930	:param dict data: the sequential refinement data object
	1931	:param str exporttype: indicates the type of export ('project' or 'phase')
	1932	'''
	1933	if len(data['histNames']) == 0:
	1934	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
	1935	obj.InitExport(None)
	1936	obj.loadTree()
	1937	obj.loadParmDict()
	1938	if len(data['histNames']) == 1:
	1939	histlist = data['histNames']
	1940	else:
	1941	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
	1942	'Select histograms',data['histNames'])
	1943	if dlg.ShowModal() == wx.ID_OK:
	1944	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
	1945	dlg.Destroy()
	1946	else:
	1947	dlg.Destroy()
	1948	return
	1949	if exporttype == 'Phase':
	1950	phaselist = obj.Phases.keys()
	1951	if len(obj.Phases) == 0:
	1952	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
	1953	return
	1954	elif len(obj.Phases) > 1:
	1955	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
	1956	'Select phases', phaselist)
	1957	if dlg.ShowModal() == wx.ID_OK:
	1958	phaselist = [phaselist[l] for l in dlg.GetSelections()]
	1959	dlg.Destroy()
	1960	else:
	1961	dlg.Destroy()
	1962	return
	1963	filename = obj.askSaveFile()
	1964	if not filename: return True
	1965	obj.dirname,obj.filename = os.path.split(filename)
	1966	print('Writing output to file '+str(obj.filename)+"...")
	1967	mode = 'w'
	1968	for p in phaselist:
	1969	for h in histlist:
	1970	obj.SetSeqRef(data,h)
	1971	#GSASIIpath.IPyBreak()
	1972	obj.Writer(h,phasenam=p,mode=mode)
	1973	mode = 'a'
	1974	print('...done')
	1975	elif exporttype == 'Project':
	1976	filename = obj.askSaveFile()
	1977	if not filename: return True
	1978	obj.dirname,obj.filename = os.path.split(filename)
	1979	print('Writing output to file '+str(obj.filename)+"...")
	1980	mode = 'w'
	1981	for h in histlist:
	1982	obj.SetSeqRef(data,h)
	1983	obj.Writer(h,mode=mode)
	1984	print('\t'+str(h)+' written')
	1985	mode = 'a'
	1986	print('...done')
	1987
[2161]	1988	def ReadDIFFaX(DIFFaXfile):
	1989	print 'read ',DIFFaXfile
	1990	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
[2163]	1991	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
[2161]	1992	df = open(DIFFaXfile,'r')
	1993	lines = df.readlines()
	1994	df.close()
	1995	struct = False
	1996	Struct = []
	1997	stack = False
	1998	Stack = []
	1999	trans = False
	2000	Trans = []
	2001	for diff in lines:
	2002	diff = diff[:-1].lower()
	2003	if '!' in diff:
	2004	continue
	2005	while '}' in diff: #strip comments
	2006	iB = diff.index('{')
	2007	iF = diff.index('}')+1
	2008	if iB:
	2009	diff = diff[:iB]
	2010	else:
	2011	diff = diff[iF:]
	2012	if not diff:
	2013	continue
	2014	if diff.strip() == 'instrumental':
	2015	continue
	2016	if diff.strip() == 'structural':
	2017	struct = True
	2018	continue
	2019	elif diff.strip() == 'stacking':
	2020	struct = False
	2021	stack = True
	2022	continue
	2023	elif diff.strip() == 'transitions':
	2024	stack = False
	2025	trans = True
	2026	continue
	2027	diff = diff.strip()
	2028	if struct:
	2029	if diff:
	2030	Struct.append(diff)
	2031	elif stack:
	2032	if diff:
	2033	Stack.append(diff)
	2034	elif trans:
	2035	if diff:
	2036	Trans.append(diff)
	2037
	2038	#STRUCTURE records
	2039	laueRec = Struct[1].split()
	2040	Layer['Laue'] = laueRec[0]
	2041	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
	2042	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
	2043	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
	2044	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
	2045	cell = Struct[0].split()
	2046	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
	2047	nLayers = int(Struct[2])
	2048	N = 3
	2049	if 'layer' not in Struct[3]:
	2050	N = 4
	2051	if Struct[3] != 'infinite':
	2052	width = Struct[3].split()
	2053	Layer['Width'][0] = [float(width[0]),float(width[1])]
	2054	for nL in range(nLayers):
	2055	if '=' in Struct[N]:
	2056	name = Struct[N].split('=')
	2057	sameas = int(name[1])-1
	2058	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
	2059	N += 1
	2060	continue
	2061	Symm = 'None'
	2062	if 'centro' in Struct[N+1]: Symm = '-1'
	2063	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
	2064	N += 2
	2065	while 'layer' not in Struct[N]:
	2066	atom = Struct[N][4:].split()
[2163]	2067	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
	2068	if atomType not in Layer['AtInfo']:
	2069	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
[2161]	2070	atomName = '%s(%s)'%(atomType,atom[0])
	2071	newVals = []
	2072	for val in atom[1:6]:
	2073	if '/' in val:
	2074	newVals.append(eval(val+'.'))
	2075	else:
	2076	newVals.append(float(val))
[2167]	2077	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
[2161]	2078	Layer['Layers'][-1]['Atoms'].append(atomRec)
	2079	N += 1
	2080	if N > len(Struct)-1:
	2081	break
	2082	#TRANSITIONS records
	2083	transArray = []
	2084	N = 0
	2085	for i in range(nLayers):
	2086	transArray.append([])
	2087	for j in range(nLayers):
	2088	vals = Trans[N].split()
	2089	newVals = []
	2090	for val in vals[:4]:
	2091	if '/' in val:
	2092	newVals.append(eval(val+'.'))
	2093	else:
	2094	newVals.append(float(val))
	2095	transArray[-1].append(newVals+['',False])
	2096	N += 1
	2097	Layer['Transitions'] = transArray
	2098	#STACKING records
	2099	Layer['Stacking'] = [Stack[0],'']
	2100	if Stack[0] == 'recursive':
	2101	Layer['Stacking'][1] = Stack[1]
	2102	elif Stack[0] == 'explicit':
	2103	if Stack[1] == 'random':
	2104	Layer['Stacking'][1] = Stack[1]
	2105	else:
	2106	Layer['Stacking'][1] = 'list'
	2107	Layer['Stacking'].append('')
	2108	for stack in Stack[2:]:
	2109	Layer['Stacking'][2] += ' '+stack
	2110	return Layer
[1997]	2111
[762]	2112	if __name__ == '__main__':
[2071]	2113	import GSASII
	2114	application = GSASII.GSASIImain(0)
	2115	G2frame = application.main
	2116	#app = wx.PySimpleApp()
	2117	#G2frame = wx.Frame(None) # create a frame
	2118	#frm.Show(True)
	2119	#filename = '/tmp/notzip.zip'
	2120	#filename = '/tmp/all.zip'
[762]	2121	#filename = '/tmp/11bmb_7652.zip'
	2122
	2123	#selection=None, confirmoverwrite=True, parent=None
	2124	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
[2071]	2125	#print ExtractFileFromZip(filename,multipleselect=True)
	2126	# #confirmread=False, confirmoverwrite=False)
[762]	2127
	2128	# choicelist=[ ('a','b','c'),
	2129	# ('test1','test2'),('no choice',)]
	2130	# titles = [ 'a, b or c', 'tests', 'No option here']
	2131	# dlg = MultipleChoicesDialog(
	2132	# choicelist,titles,
	2133	# parent=frm)
	2134	# if dlg.ShowModal() == wx.ID_OK:
	2135	# print 'Got OK'
[2071]	2136	imagefile = '/tmp/NDC5_00237_3.ge3'
	2137	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
	2138
	2139	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
	2140
	2141	GSASIIpath.IPyBreak_base()

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