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source: trunk/GSASIIIO.py @ 1215

Last change on this file since 1215 was 1215, checked in by toby, 8 years ago
add .png reading
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2014-02-09 02:06:33 +0000 (Sun, 09 Feb 2014) $
4	# $Author: toby $
5	# $Revision: 1215 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 1215 2014-02-09 02:06:33Z 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: 1215 $")
33	import GSASIIgrid as G2gd
34	import GSASIIspc as G2spc
35	import GSASIIlattice as G2lat
36	import GSASIIpwdGUI as G2pdG
37	import GSASIIElem as G2el
38	import GSASIIstrIO as G2stIO
39	import GSASIImapvars as G2mv
40	import os
41	import os.path as ospath
42
43	DEBUG = False #=True for various prints
44	TRANSP = False #=true to transpose images for testing
45	npsind = lambda x: np.sin(x*np.pi/180.)
46
47	def sfloat(S):
48	'Convert a string to float. An empty field is treated as zero'
49	if S.strip():
50	return float(S)
51	else:
52	return 0.0
53
54	def sint(S):
55	'Convert a string to int. An empty field is treated as zero'
56	if S.strip():
57	return int(S)
58	else:
59	return 0
60
61	def trim(val):
62	'''Simplify a string containing leading and trailing spaces
63	as well as newlines, tabs, repeated spaces etc. into a shorter and
64	more simple string, by replacing all ranges of whitespace
65	characters with a single space.
66
67	:param str val: the string to be simplified
68
69	:returns: the (usually) shortened version of the string
70	'''
71	return re.sub('\s+', ' ', val).strip()
72
73	def makeInstDict(names,data,codes):
74	inst = dict(zip(names,zip(data,data,codes)))
75	for item in inst:
76	inst[item] = list(inst[item])
77	return inst
78
79	def FileDlgFixExt(dlg,file):
80	'this is needed to fix a problem in linux wx.FileDialog'
81	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
82	if ext not in file:
83	file += ext
84	return file
85
86	def GetPowderPeaks(fileName):
87	'Read powder peaks from a file'
88	sind = lambda x: math.sin(x*math.pi/180.)
89	asind = lambda x: 180.*math.asin(x)/math.pi
90	Cuka = 1.54052
91	File = open(fileName,'Ur')
92	Comments = []
93	peaks = []
94	S = File.readline()
95	while S:
96	if S[:1] == '#':
97	Comments.append(S[:-1])
98	else:
99	item = S.split()
100	if len(item) == 1:
101	peaks.append([float(item[0]),1.0])
102	elif len(item) > 1:
103	peaks.append([float(item[0]),float(item[0])])
104	S = File.readline()
105	File.close()
106	if Comments:
107	print 'Comments on file:'
108	for Comment in Comments: print Comment
109	Peaks = []
110	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
111	for peak in peaks:
112	dsp = peak[0]
113	sth = Cuka/(2.0*dsp)
114	if sth < 1.0:
115	tth = 2.0*asind(sth)
116	else:
117	break
118	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
119	else: #2-thetas - assume Cuka (for now)
120	for peak in peaks:
121	tth = peak[0]
122	dsp = Cuka/(2.0*sind(tth/2.0))
123	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
124	return Comments,Peaks
125
126	def CheckImageFile(G2frame,imagefile):
127	'''Get an new image file name if the specified one does not
128	exist
129
130	:param wx.Frame G2frame: main GSAS-II Frame and data object
131
132	:param str imagefile: name of image file
133
134	:returns: imagefile, if it exists, or the name of a file
135	that does exist or False if the user presses Cancel
136
137	'''
138	if not ospath.exists(imagefile):
139	dlg = wx.FileDialog(G2frame, 'Bad image file name; choose name', '.', '',\
140	'Any image file (.edf;.tif;.tiff;.mar;.avg;.sum;.img)\
141	\|.edf;.tif;.tiff;.mar;.avg;.sum;.img\|\
142	European detector file (.edf)\|.edf\|\
143	Any detector tif (.tif;.tiff)\|.tif;.tiff\|\
144	MAR file (.mar)\|.mar\|\
145	GE Image (.avg;.sum)\|.avg;.sum\|\
146	ADSC Image (.img)\|.img\|\
147	All files (.)\|.',wx.OPEN\|wx.CHANGE_DIR)
148	try:
149	dlg.SetFilename(''+ospath.split(imagefile)[1])
150	if dlg.ShowModal() == wx.ID_OK:
151	imagefile = dlg.GetPath()
152	else:
153	imagefile = False
154	finally:
155	dlg.Destroy()
156	return imagefile
157
158	def EditImageParms(parent,Data,Comments,Image,filename):
159	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
160	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
161	def onClose(event):
162	dlg.EndModal(wx.ID_OK)
163	mainsizer = wx.BoxSizer(wx.VERTICAL)
164	h,w = Image.shape[:2]
165	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,
166	'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
167	0,wx.ALIGN_LEFT\|wx.ALL, 2)
168
169	vsizer = wx.BoxSizer(wx.HORIZONTAL)
170	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
171	0,wx.ALIGN_LEFT\|wx.ALL, 2)
172	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data,'wavelength')
173	vsizer.Add(wdgt)
174	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
175
176	vsizer = wx.BoxSizer(wx.HORIZONTAL)
177	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
178	0,wx.ALIGN_LEFT\|wx.ALL, 2)
179	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
180	size=(50,-1))
181	vsizer.Add(wdgt)
182	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),
183	wx.ALIGN_LEFT\|wx.ALL, 2)
184	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,
185	size=(50,-1))
186	vsizer.Add(wdgt)
187	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
188
189	vsizer = wx.BoxSizer(wx.HORIZONTAL)
190	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
191	0,wx.ALIGN_LEFT\|wx.ALL, 2)
192	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data,'distance')
193	vsizer.Add(wdgt)
194	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
195
196	vsizer = wx.BoxSizer(wx.HORIZONTAL)
197	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
198	0,wx.ALIGN_LEFT\|wx.ALL, 2)
199	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data['center'],0,
200	size=(75,-1))
201	vsizer.Add(wdgt)
202	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),
203	wx.ALIGN_LEFT\|wx.ALL, 2)
204	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data['center'],1,
205	size=(75,-1))
206	vsizer.Add(wdgt)
207	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
208
209	vsizer = wx.BoxSizer(wx.HORIZONTAL)
210	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
211	0,wx.ALIGN_LEFT\|wx.ALL, 2)
212	wdgt = G2gd.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
213	vsizer.Add(wdgt)
214	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
215
216	btnsizer = wx.StdDialogButtonSizer()
217	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
218	OKbtn.SetDefault()
219	OKbtn.Bind(wx.EVT_BUTTON,onClose)
220	btnsizer.AddButton(OKbtn) # not sure why this is needed
221	btnsizer.Realize()
222	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
223	dlg.SetSizer(mainsizer)
224	dlg.CenterOnParent()
225	dlg.ShowModal()
226
227	def GetImageData(G2frame,imagefile,imageOnly=False):
228	'''Read an image with the file reader keyed by the
229	file extension
230
231	:param wx.Frame G2frame: main GSAS-II Frame and data object.
232
233	:param str imagefile: name of image file
234
235	:param bool imageOnly: If True return only the image,
236	otherwise (default) return more (see below)
237
238	:returns: an image as a numpy array or a list of four items:
239	Comments, Data, Npix and the Image, as selected by imageOnly
240
241	'''
242	ext = ospath.splitext(imagefile)[1]
243	Comments = []
244	if ext == '.tif' or ext == '.tiff':
245	Comments,Data,Npix,Image = GetTifData(imagefile)
246	elif ext == '.edf':
247	Comments,Data,Npix,Image = GetEdfData(imagefile)
248	elif ext == '.img':
249	Comments,Data,Npix,Image = GetImgData(imagefile)
250	Image[0][0] = 0
251	elif ext == '.mar3450' or ext == '.mar2300':
252	Comments,Data,Npix,Image = GetMAR345Data(imagefile)
253	elif ext in ['.sum','.avg','']:
254	Comments,Data,Npix,Image = GetGEsumData(imagefile)
255	elif ext == '.G2img':
256	Comments,Data,Npix,Image = GetG2Image(imagefile)
257	elif ext == '.png':
258	import scipy.misc
259	Image = scipy.misc.imread(imagefile,flatten=True)
260	Npix = Image.size
261	Comments = ['no metadata']
262	Data = {'wavelength': 0.1, 'pixelSize': [200, 200], 'distance': 100.0}
263	Data['size'] = list(Image.shape)
264	Data['center'] = [int(i/2) for i in Image.shape]
265	if not imageOnly:
266	EditImageParms(G2frame,Data,Comments,Image,imagefile)
267	if imageOnly:
268	if TRANSP:
269	return Image.T
270	else:
271	return Image
272	else:
273	if TRANSP:
274	return Comments,Data,Npix,Image.T
275	else:
276	return Comments,Data,Npix,Image
277
278	def PutG2Image(filename,Comments,Data,Npix,image):
279	'Write an image as a python pickle'
280	File = open(filename,'wb')
281	cPickle.dump([Comments,Data,Npix,image],File,1)
282	File.close()
283	return
284
285	def GetG2Image(filename):
286	'Read an image as a python pickle'
287	File = open(filename,'rb')
288	Comments,Data,Npix,image = cPickle.load(File)
289	File.close()
290	return Comments,Data,Npix,image
291
292	def GetEdfData(filename,imageOnly=False):
293	'Read European detector data edf file'
294	import struct as st
295	import array as ar
296	if not imageOnly:
297	print 'Read European detector data edf file: ',filename
298	File = open(filename,'rb')
299	fileSize = os.stat(filename).st_size
300	head = File.read(3072)
301	lines = head.split('\n')
302	sizexy = [0,0]
303	pixSize = [0,0]
304	cent = [0,0]
305	head = ['European detector data',]
306	for line in lines:
307	fields = line.split()
308	if 'Dim_1' in line:
309	sizexy[0] = int(fields[2])
310	elif 'Dim_2' in line:
311	sizexy[1] = int(fields[2])
312	elif 'DataType' in line:
313	dType = fields[2]
314	elif 'refined_wavelength' in line:
315	wave = float(fields[2])
316	elif 'Size' in line:
317	imSize = int(fields[2])
318	elif 'DataType' in lines:
319	dType = fields[2]
320	elif 'pixel_size_x' in line:
321	pixSize[0] = float(fields[2])
322	elif 'pixel_size_y' in line:
323	pixSize[1] = float(fields[2])
324	elif 'beam_center_x' in line:
325	cent[0] = float(fields[2])
326	elif 'beam_center_y' in line:
327	cent[1] = float(fields[2])
328	elif 'refined_distance' in line:
329	dist = float(fields[2])
330	if line:
331	head.append(line)
332	File.seek(fileSize-imSize)
333	if dType == 'UnsignedShort':
334	image = np.array(ar.array('H',File.read(imSize)),dtype=np.int32)
335	elif dType == 'UnsignedInt':
336	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
337	image = np.reshape(image,(sizexy[1],sizexy[0]))
338	data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'size':sizexy}
339	Npix = sizexy[0]*sizexy[1]
340	File.close()
341	if imageOnly:
342	return image
343	else:
344	return head,data,Npix,image
345
346	def GetGEsumData(filename,imageOnly=False):
347	'Read SUM file as produced at 1-ID from G.E. images'
348	import struct as st
349	import array as ar
350	if not imageOnly:
351	print 'Read GE sum file: ',filename
352	File = open(filename,'rb')
353	if '.sum' in filename:
354	head = ['GE detector sum data from APS 1-ID',]
355	sizexy = [2048,2048]
356	elif '.avg' in filename:
357	head = ['GE detector avg data from APS 1-ID',]
358	sizexy = [2048,2048]
359	else:
360	head = ['GE detector raw data from APS 1-ID',]
361	File.seek(18)
362	size,nframes = st.unpack('<ih',File.read(6))
363	sizexy = [2048,2048]
364	pos = 8192
365	File.seek(pos)
366	Npix = sizexy[0]*sizexy[1]
367	if '.sum' in filename:
368	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.int32)
369	elif '.avg' in filename:
370	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
371	else:
372	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
373	while nframes > 1:
374	image += np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
375	nframes -= 1
376	image = np.reshape(image,(sizexy[1],sizexy[0]))
377	data = {'pixelSize':(200,200),'wavelength':0.15,'distance':250.0,'center':[204.8,204.8],'size':sizexy}
378	File.close()
379	if imageOnly:
380	return image
381	else:
382	return head,data,Npix,image
383
384	def GetImgData(filename,imageOnly=False):
385	'Read an ADSC image file'
386	import struct as st
387	import array as ar
388	if not imageOnly:
389	print 'Read ADSC img file: ',filename
390	File = open(filename,'rb')
391	head = File.read(511)
392	lines = head.split('\n')
393	head = []
394	center = [0,0]
395	for line in lines[1:-2]:
396	line = line.strip()[:-1]
397	if line:
398	if 'SIZE1' in line:
399	size = int(line.split('=')[1])
400	Npix = size*size
401	elif 'WAVELENGTH' in line:
402	wave = float(line.split('=')[1])
403	elif 'BIN' in line:
404	if line.split('=')[1] == '2x2':
405	pixel=(102,102)
406	else:
407	pixel = (51,51)
408	elif 'DISTANCE' in line:
409	distance = float(line.split('=')[1])
410	elif 'CENTER_X' in line:
411	center[0] = float(line.split('=')[1])
412	elif 'CENTER_Y' in line:
413	center[1] = float(line.split('=')[1])
414	head.append(line)
415	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center,'size':[size,size]}
416	image = []
417	row = 0
418	pos = 512
419	File.seek(pos)
420	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
421	image = np.reshape(image,(sizexy[1],sizexy[0]))
422	# image = np.zeros(shape=(size,size),dtype=np.int32)
423	# while row < size:
424	# File.seek(pos)
425	# line = ar.array('H',File.read(2*size))
426	# image[row] = np.asarray(line)
427	# row += 1
428	# pos += 2*size
429	File.close()
430	if imageOnly:
431	return image
432	else:
433	return lines[1:-2],data,Npix,image
434
435	def GetMAR345Data(filename,imageOnly=False):
436	'Read a MAR-345 image plate image'
437	import array as ar
438	import struct as st
439	try:
440	import pack_f as pf
441	except:
442	msg = wx.MessageDialog(None, message="Unable to load the GSAS MAR image decompression, pack_f",
443	caption="Import Error",
444	style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
445	msg.ShowModal()
446	return None,None,None,None
447
448	if not imageOnly:
449	print 'Read Mar345 file: ',filename
450	File = open(filename,'rb')
451	head = File.read(4095)
452	numbers = st.unpack('<iiiiiiiiii',head[:40])
453	lines = head[128:].split('\n')
454	head = []
455	for line in lines:
456	line = line.strip()
457	if 'PIXEL' in line:
458	values = line.split()
459	pixel = (int(values[2]),int(values[4])) #in microns
460	elif 'WAVELENGTH' in line:
461	wave = float(line.split()[1])
462	elif 'DISTANCE' in line:
463	distance = float(line.split()[1]) #in mm
464	elif 'CENTER' in line:
465	values = line.split()
466	center = [float(values[2])/10.,float(values[4])/10.] #make in mm from pixels
467	if line:
468	head.append(line)
469	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center}
470	for line in head:
471	if 'FORMAT' in line[0:6]:
472	items = line.split()
473	size = int(items[1])
474	Npix = size*size
475	pos = 4096
476	data['size'] = [size,size]
477	File.seek(pos)
478	line = File.read(8)
479	while 'CCP4' not in line: #get past overflow list for now
480	line = File.read(8)
481	pos += 8
482	pos += 37
483	File.seek(pos)
484	raw = File.read()
485	File.close()
486	image = np.zeros(shape=(size,size),dtype=np.int32)
487	image = np.flipud(pf.pack_f(len(raw),raw,size,image).T) #transpose to get it right way around & flip
488	if imageOnly:
489	return image
490	else:
491	return head,data,Npix,image
492
493	def GetTifData(filename,imageOnly=False):
494	'''Read an image in a pseudo-tif format,
495	as produced by a wide variety of software, almost always
496	incorrectly in some way.
497	'''
498	import struct as st
499	import array as ar
500	import ReadMarCCDFrame as rmf
501	File = open(filename,'rb')
502	dataType = 5
503	center = [None,None]
504	wavelength = None
505	distance = None
506	try:
507	Meta = open(filename+'.metadata','Ur')
508	head = Meta.readlines()
509	for line in head:
510	line = line.strip()
511	if 'dataType=' in line:
512	dataType = int(line.split('=')[1])
513	Meta.close()
514	except IOError:
515	print 'no metadata file found - will try to read file anyway'
516	head = ['no metadata file found',]
517
518	tag = File.read(2)
519	byteOrd = '<'
520	if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
521	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
522	elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
523	byteOrd = '>'
524	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
525	else:
526	lines = ['not a detector tiff file',]
527	return lines,0,0,0
528	File.seek(IFD) #get number of directory entries
529	NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
530	IFD = {}
531	for ied in range(NED):
532	Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
533	nVal = st.unpack(byteOrd+'i',File.read(4))[0]
534	if Type == 1:
535	Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
536	elif Type == 2:
537	Value = st.unpack(byteOrd+'i',File.read(4))
538	elif Type == 3:
539	Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
540	x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
541	elif Type == 4:
542	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
543	elif Type == 5:
544	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
545	elif Type == 11:
546	Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
547	IFD[Tag] = [Type,nVal,Value]
548	if DEBUG: print Tag,IFD[Tag]
549	sizexy = [IFD[256][2][0],IFD[257][2][0]]
550	[nx,ny] = sizexy
551	Npix = nx*ny
552	if 34710 in IFD:
553	if not imageOnly:
554	print 'Read MAR CCD tiff file: ',filename
555	marFrame = rmf.marFrame(File,byteOrd,IFD)
556	image = np.flipud(np.array(np.asarray(marFrame.image),dtype=np.int32))
557	tifType = marFrame.filetitle
558	pixy = (marFrame.pixelsizeX/1000.0,marFrame.pixelsizeY/1000.0)
559	head = marFrame.outputHead()
560	# extract resonable wavelength from header
561	wavelength = marFrame.sourceWavelength*1e-5
562	wavelength = (marFrame.opticsWavelength > 0) and marFrame.opticsWavelength*1e-5 or wavelength
563	wavelength = (wavelength <= 0) and None or wavelength
564	# extract resonable distance from header
565	distance = (marFrame.startXtalToDetector+marFrame.endXtalToDetector)*5e-4
566	distance = (distance <= 0) and marFrame.xtalToDetector*1e-3 or distance
567	distance = (distance <= 0) and None or distance
568	# extract resonable center from header
569	center = [marFrame.beamXmarFrame.pixelsizeX1e-9,marFrame.beamYmarFrame.pixelsizeY1e-9]
570	center = (center[0] != 0 and center[1] != 0) and center or [None,None]
571	#print head,tifType,pixy
572	elif 272 in IFD:
573	ifd = IFD[272]
574	File.seek(ifd[2][0])
575	S = File.read(ifd[1])
576	if 'PILATUS' in S:
577	tifType = 'Pilatus'
578	dataType = 0
579	pixy = (172,172)
580	File.seek(4096)
581	if not imageOnly:
582	print 'Read Pilatus tiff file: ',filename
583	image = ar.array('L',File.read(4*Npix))
584	image = np.array(np.asarray(image),dtype=np.int32)
585	else:
586	if IFD[258][2][0] == 16:
587	print sizexy
588	tifType = 'GE'
589	pixy = (200,200)
590	File.seek(8)
591	if not imageOnly:
592	print 'Read GE-detector tiff file: ',filename
593	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
594	elif IFD[258][2][0] == 32:
595	print sizexy
596	tifType = 'CHESS'
597	pixy = (200,200)
598	File.seek(8)
599	if not imageOnly:
600	print 'Read CHESS-detector tiff file: ',filename
601	image = np.array(ar.array('L',File.read(4*Npix)),dtype=np.int32)
602
603	elif 262 in IFD and IFD[262][2][0] > 4:
604	tifType = 'DND'
605	pixy = (158,158)
606	File.seek(512)
607	if not imageOnly:
608	print 'Read DND SAX/WAX-detector tiff file: ',filename
609	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
610	elif sizexy == [1536,1536]:
611	tifType = 'APS Gold'
612	pixy = (150,150)
613	File.seek(64)
614	if not imageOnly:
615	print 'Read Gold tiff file:',filename
616	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
617	elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
618	if IFD[273][2][0] == 8:
619	if IFD[258][2][0] == 32:
620	tifType = 'PE'
621	pixy = (200,200)
622	File.seek(8)
623	if not imageOnly:
624	print 'Read APS PE-detector tiff file: ',filename
625	if dataType == 5:
626	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
627	else:
628	image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
629
630	elif IFD[273][2][0] == 4096:
631	if sizexy[0] == 3072:
632	pixy = (73,73)
633	tifType = 'MAR225'
634	else:
635	pixy = (158,158)
636	tifType = 'MAR325'
637	File.seek(4096)
638	if not imageOnly:
639	print 'Read MAR CCD tiff file: ',filename
640	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
641	elif IFD[273][2][0] == 512:
642	tiftype = '11-ID-C'
643	pixy = [200,200]
644	File.seek(512)
645	if not imageOnly:
646	print 'Read 11-ID-C tiff file: ',filename
647	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
648	elif sizexy == [4096,4096]:
649	if IFD[273][2][0] == 8:
650	if IFD[258][2][0] == 16:
651	tifType = 'scanCCD'
652	pixy = (9,9)
653	File.seek(8)
654	if not imageOnly:
655	print 'Read APS scanCCD tiff file: ',filename
656	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
657	elif IFD[273][2][0] == 4096:
658	tifType = 'Rayonix'
659	pixy = (73.242,73.242)
660	File.seek(4096)
661	if not imageOnly:
662	print 'Read Rayonix MX300HE tiff file: ',filename
663	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
664	# elif sizexy == [960,960]:
665	# tiftype = 'PE-BE'
666	# pixy = (200,200)
667	# File.seek(8)
668	# if not imageOnly:
669	# print 'Read Gold tiff file:',filename
670	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
671
672	else:
673	lines = ['not a known detector tiff file',]
674	return lines,0,0,0
675
676	image = np.reshape(image,(sizexy[1],sizexy[0]))
677	center = (not center[0]) and [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000] or center
678	wavelength = (not wavelength) and 0.10 or wavelength
679	distance = (not distance) and 100.0 or distance
680	data = {'pixelSize':pixy,'wavelength':wavelength,'distance':distance,'center':center,'size':sizexy}
681	File.close()
682	if imageOnly:
683	return image
684	else:
685	return head,data,Npix,image
686
687	#def GetTifData(filename,imageOnly=False):
688	# import struct as st
689	# import array as ar
690	# File = open(filename,'rb')
691	# dataType = 5
692	# try:
693	# Meta = open(filename+'.metadata','Ur')
694	# head = Meta.readlines()
695	# for line in head:
696	# line = line.strip()
697	# if 'dataType=' in line:
698	# dataType = int(line.split('=')[1])
699	# Meta.close()
700	# except IOError:
701	# print 'no metadata file found - will try to read file anyway'
702	# head = ['no metadata file found',]
703	#
704	# tag = File.read(2)
705	# byteOrd = '<'
706	# if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
707	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
708	# elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
709	# byteOrd = '>'
710	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
711	# else:
712	# lines = ['not a detector tiff file',]
713	# return lines,0,0,0
714	# File.seek(IFD) #get number of directory entries
715	# NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
716	# IFD = {}
717	# for ied in range(NED):
718	# Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
719	# nVal = st.unpack(byteOrd+'i',File.read(4))[0]
720	# if Type == 1:
721	# Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
722	# elif Type == 2:
723	# Value = st.unpack(byteOrd+'i',File.read(4))
724	# elif Type == 3:
725	# Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
726	# x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
727	# elif Type == 4:
728	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
729	# elif Type == 5:
730	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
731	# elif Type == 11:
732	# Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
733	# IFD[Tag] = [Type,nVal,Value]
734	## print Tag,IFD[Tag]
735	# sizexy = [IFD[256][2][0],IFD[257][2][0]]
736	# [nx,ny] = sizexy
737	# Npix = nx*ny
738	# if 272 in IFD:
739	# ifd = IFD[272]
740	# File.seek(ifd[2][0])
741	# S = File.read(ifd[1])
742	# if 'PILATUS' in S:
743	# tifType = 'Pilatus'
744	# dataType = 0
745	# pixy = (172,172)
746	# File.seek(4096)
747	# if not imageOnly:
748	# print 'Read Pilatus tiff file: ',filename
749	# image = ar.array('L',File.read(4*Npix))
750	# image = np.array(np.asarray(image),dtype=np.int32)
751	# elif 262 in IFD and IFD[262][2][0] > 4:
752	# tifType = 'DND'
753	# pixy = (158,158)
754	# File.seek(512)
755	# if not imageOnly:
756	# print 'Read DND SAX/WAX-detector tiff file: ',filename
757	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
758	# elif sizexy == [1536,1536]:
759	# tifType = 'APS Gold'
760	# pixy = (150,150)
761	# File.seek(64)
762	# if not imageOnly:
763	# print 'Read Gold tiff file:',filename
764	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
765	# elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
766	# if IFD[273][2][0] == 8:
767	# if IFD[258][2][0] == 32:
768	# tifType = 'PE'
769	# pixy = (200,200)
770	# File.seek(8)
771	# if not imageOnly:
772	# print 'Read APS PE-detector tiff file: ',filename
773	# if dataType == 5:
774	# image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
775	# else:
776	# image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
777	# elif IFD[273][2][0] == 4096:
778	# if sizexy[0] == 3072:
779	# pixy = (73,73)
780	# tifType = 'MAR225'
781	# else:
782	# pixy = (158,158)
783	# tifType = 'MAR325'
784	# File.seek(4096)
785	# if not imageOnly:
786	# print 'Read MAR CCD tiff file: ',filename
787	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
788	# elif IFD[273][2][0] == 512:
789	# tiftype = '11-ID-C'
790	# pixy = [200,200]
791	# File.seek(512)
792	# if not imageOnly:
793	# print 'Read 11-ID-C tiff file: ',filename
794	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
795	# elif sizexy == [4096,4096]:
796	# if IFD[273][2][0] == 8:
797	# if IFD[258][2][0] == 16:
798	# tifType = 'scanCCD'
799	# pixy = (9,9)
800	# File.seek(8)
801	# if not imageOnly:
802	# print 'Read APS scanCCD tiff file: ',filename
803	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
804	# elif IFD[273][2][0] == 4096:
805	# tifType = 'Rayonix'
806	# pixy = (73.242,73.242)
807	# File.seek(4096)
808	# if not imageOnly:
809	# print 'Read Rayonix MX300HE tiff file: ',filename
810	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
811	## elif sizexy == [960,960]:
812	## tiftype = 'PE-BE'
813	## pixy = (200,200)
814	## File.seek(8)
815	## if not imageOnly:
816	## print 'Read Gold tiff file:',filename
817	## image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
818	#
819	# else:
820	# lines = ['not a known detector tiff file',]
821	# return lines,0,0,0
822	#
823	# image = np.reshape(image,(sizexy[1],sizexy[0]))
824	# center = [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000]
825	# data = {'pixelSize':pixy,'wavelength':0.10,'distance':100.0,'center':center,'size':sizexy}
826	# File.close()
827	# if imageOnly:
828	# return image
829	# else:
830	# return head,data,Npix,image
831	#
832	def ProjFileOpen(G2frame):
833	'Read a GSAS-II project file and load into the G2 data tree'
834	file = open(G2frame.GSASprojectfile,'rb')
835	print 'load from file: ',G2frame.GSASprojectfile
836	G2frame.SetTitle("GSAS-II data tree: "+
837	os.path.split(G2frame.GSASprojectfile)[1])
838	wx.BeginBusyCursor()
839	try:
840	while True:
841	try:
842	data = cPickle.load(file)
843	except EOFError:
844	break
845	datum = data[0]
846
847	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=datum[0])
848	if 'PWDR' in datum[0]:
849	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
850	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
851	G2frame.PatternTree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
852	elif datum[0].startswith('HKLF'):
853	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
854	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
855	G2frame.PatternTree.SetItemPyData(Id,datum[1])
856	else:
857	G2frame.PatternTree.SetItemPyData(Id,datum[1])
858	for datus in data[1:]:
859	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
860	#patch
861	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
862	if 'PWDR' in datum[0]:
863	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
864	else:
865	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
866	for item in datus[1][0]: #zip makes tuples - now make lists!
867	datus[1][0][item] = list(datus[1][0][item])
868	#end patch
869	G2frame.PatternTree.SetItemPyData(sub,datus[1])
870	if 'IMG' in datum[0]: #retrieve image default flag & data if set
871	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
872	if Data['setDefault']:
873	G2frame.imageDefault = Data
874	file.close()
875	print('project load successful')
876	G2frame.NewPlot = True
877	except:
878	msg = wx.MessageDialog(G2frame,message="Error reading file "+
879	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
880	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
881	msg.ShowModal()
882	finally:
883	wx.EndBusyCursor()
884
885	def ProjFileSave(G2frame):
886	'Save a GSAS-II project file'
887	if not G2frame.PatternTree.IsEmpty():
888	file = open(G2frame.GSASprojectfile,'wb')
889	print 'save to file: ',G2frame.GSASprojectfile
890	wx.BeginBusyCursor()
891	try:
892	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
893	while item:
894	data = []
895	name = G2frame.PatternTree.GetItemText(item)
896	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
897	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
898	while item2:
899	name = G2frame.PatternTree.GetItemText(item2)
900	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
901	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
902	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
903	cPickle.dump(data,file,1)
904	file.close()
905	finally:
906	wx.EndBusyCursor()
907	print('project save successful')
908
909	def SaveIntegration(G2frame,PickId,data):
910	'Save image integration results as powder pattern(s)'
911	azms = G2frame.Integrate[1]
912	X = G2frame.Integrate[2][:-1]
913	N = len(X)
914	Id = G2frame.PatternTree.GetItemParent(PickId)
915	name = G2frame.PatternTree.GetItemText(Id)
916	name = name.replace('IMG ',data['type']+' ')
917	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
918	if 'PWDR' in name:
919	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
920	codes = [0 for i in range(11)]
921	elif 'SASD' in name:
922	names = ['Type','Lam','Zero','Azimuth']
923	codes = [0 for i in range(4)]
924	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
925	Xminmax = [X[0],X[-1]]
926	LRazm = data['LRazimuth']
927	Azms = []
928	if data['fullIntegrate'] and data['outAzimuths'] == 1:
929	Azms = [45.0,] #a poor man's average?
930	else:
931	for i,azm in enumerate(azms[:-1]):
932	Azms.append((azms[i+1]+azm)/2.)
933	for i,azm in enumerate(azms[:-1]):
934	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
935	Id = 0
936	while item:
937	Name = G2frame.PatternTree.GetItemText(item)
938	if name == Name:
939	Id = item
940	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
941	Sample = G2pdG.SetDefaultSample()
942	Sample['Gonio. radius'] = data['distance']
943	Sample['Omega'] = data['GonioAngles'][0]
944	Sample['Chi'] = data['GonioAngles'][1]
945	Sample['Phi'] = data['GonioAngles'][2]
946	if 'PWDR' in name:
947	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!
948	elif 'SASD' in name:
949	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
950	Y = G2frame.Integrate[0][i]
951	W = 1./Y #probably not true
952	if Id:
953	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'),Comments)
954	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Limits'),[tuple(Xminmax),Xminmax])
955	if 'PWDR' in name:
956	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Background'),[['chebyschev',1,3,1.0,0.0,0.0],
957	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
958	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
959	for item in inst[0]:
960	inst[0][item] = list(inst[0][item])
961	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Instrument Parameters'),inst)
962	if 'PWDR' in name:
963	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Peak List'),[])
964	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Index Peak List'),[])
965	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Unit Cells List'),[])
966	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Reflection Lists'),{})
967	elif 'SASD' in name:
968	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Substances'),G2pdG.SetDefaultSubstances())
969	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Models'),G2pdG.SetDefaultSASDModel())
970	else:
971	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=name+" Azm= %.2f"%(Azms[i]))
972	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
973	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
974	if 'PWDR' in name:
975	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
976	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
977	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
978	for item in inst[0]:
979	inst[0][item] = list(inst[0][item])
980	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
981	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
982	if 'PWDR' in name:
983	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),[])
984	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[])
985	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
986	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
987	elif 'SASD' in name:
988	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
989	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
990	valuesdict = {
991	'wtFactor':1.0,
992	'Dummy':False,
993	'ranId':ran.randint(0,sys.maxint),
994	}
995	G2frame.PatternTree.SetItemPyData(
996	Id,[valuesdict,
997	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
998	G2frame.PatternTree.SelectItem(Id)
999	G2frame.PatternTree.Expand(Id)
1000	G2frame.PatternId = Id
1001
1002	def powderFxyeSave(G2frame,exports,powderfile):
1003	'Save a powder histogram as a GSAS FXYE file'
1004	head,tail = ospath.split(powderfile)
1005	name,ext = tail.split('.')
1006	for i,export in enumerate(exports):
1007	filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1008	prmname = filename.strip(ext)+'prm'
1009	prm = open(prmname,'w') #old style GSAS parm file
1010	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1011	Inst = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, \
1012	PickId, 'Instrument Parameters'))[0]
1013	prm.write( ' 123456789012345678901234567890123456789012345678901234567890 '+'\n')
1014	prm.write( 'INS BANK 1 '+'\n')
1015	prm.write(('INS HTYPE %sR '+'\n')%(Inst['Type'][0]))
1016	if 'Lam1' in Inst: #Ka1 & Ka2
1017	prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam1'][0],Inst['Lam2'][0]))
1018	elif 'Lam' in Inst: #single wavelength
1019	prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam'][1],0.0))
1020	prm.write( 'INS 1 IRAD 0 '+'\n')
1021	prm.write( 'INS 1I HEAD '+'\n')
1022	prm.write( 'INS 1I ITYP 0 0.0000 180.0000 1 '+'\n')
1023	prm.write(('INS 1DETAZM%10.3f '+'\n')%(Inst['Azimuth'][0]))
1024	prm.write( 'INS 1PRCF1 3 8 0.00100 '+'\n')
1025	prm.write(('INS 1PRCF11 %15.6g%15.6g%15.6g%15.6g '+'\n')%(Inst['U'][1],Inst['V'][1],Inst['W'][1],0.0))
1026	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.))
1027	prm.close()
1028	file = open(filename,'w')
1029	print 'save powder pattern to file: ',filename
1030	x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1031	file.write(powderfile+'\n')
1032	file.write('Instrument parameter file:'+ospath.split(prmname)[1]+'\n')
1033	file.write('BANK 1 %d %d CONS %.2f %.2f 0 0 FXYE\n'%(len(x),len(x),\
1034	100.x[0],100.(x[1]-x[0])))
1035	s = list(np.sqrt(1./np.array(w)))
1036	XYW = zip(x,y,s)
1037	for X,Y,S in XYW:
1038	file.write("%15.6g %15.6g %15.6g\n" % (100.*X,Y,max(S,1.0)))
1039	file.close()
1040	print 'powder pattern file '+filename+' written'
1041
1042	def powderXyeSave(G2frame,exports,powderfile):
1043	'Save a powder histogram as a Topas XYE file'
1044	head,tail = ospath.split(powderfile)
1045	name,ext = tail.split('.')
1046	for i,export in enumerate(exports):
1047	filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1048	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1049	file = open(filename,'w')
1050	file.write('#%s\n'%(export))
1051	print 'save powder pattern to file: ',filename
1052	x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1053	s = list(np.sqrt(1./np.array(w)))
1054	XYW = zip(x,y,s)
1055	for X,Y,W in XYW:
1056	file.write("%15.6g %15.6g %15.6g\n" % (X,Y,W))
1057	file.close()
1058	print 'powder pattern file '+filename+' written'
1059
1060	def PDFSave(G2frame,exports):
1061	'Save a PDF G(r) and S(Q) in column formats'
1062	for export in exports:
1063	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1064	SQname = 'S(Q)'+export[4:]
1065	GRname = 'G(R)'+export[4:]
1066	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
1067	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
1068	sqId = G2gd.GetPatternTreeItemId(G2frame, PickId, SQname)
1069	grId = G2gd.GetPatternTreeItemId(G2frame, PickId, GRname)
1070	sqdata = np.array(G2frame.PatternTree.GetItemPyData(sqId)[1][:2]).T
1071	grdata = np.array(G2frame.PatternTree.GetItemPyData(grId)[1][:2]).T
1072	sqfile = open(sqfilename,'w')
1073	grfile = open(grfilename,'w')
1074	sqfile.write('#T S(Q) %s\n'%(export))
1075	grfile.write('#T G(R) %s\n'%(export))
1076	sqfile.write('#L Q S(Q)\n')
1077	grfile.write('#L R G(R)\n')
1078	for q,sq in sqdata:
1079	sqfile.write("%15.6g %15.6g\n" % (q,sq))
1080	sqfile.close()
1081	for r,gr in grdata:
1082	grfile.write("%15.6g %15.6g\n" % (r,gr))
1083	grfile.close()
1084
1085	def PeakListSave(G2frame,file,peaks):
1086	'Save powder peaks to a data file'
1087	print 'save peak list to file: ',G2frame.peaklistfile
1088	if not peaks:
1089	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1090	try:
1091	result = dlg.ShowModal()
1092	finally:
1093	dlg.Destroy()
1094	return
1095	for peak in peaks:
1096	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1097	(peak[0],peak[2],peak[4],peak[6]))
1098	print 'peak list saved'
1099
1100	def IndexPeakListSave(G2frame,peaks):
1101	'Save powder peaks from the indexing list'
1102	file = open(G2frame.peaklistfile,'wa')
1103	print 'save index peak list to file: ',G2frame.peaklistfile
1104	wx.BeginBusyCursor()
1105	try:
1106	if not peaks:
1107	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1108	try:
1109	result = dlg.ShowModal()
1110	finally:
1111	dlg.Destroy()
1112	return
1113	for peak in peaks:
1114	file.write("%12.6f\n" % (peak[7]))
1115	file.close()
1116	finally:
1117	wx.EndBusyCursor()
1118	print 'index peak list saved'
1119
1120	def SetNewPhase(Name='New Phase',SGData=None,cell=None):
1121	'''Create a new phase dict with default values for various parameters
1122
1123	:param str Name: Name for new Phase
1124
1125	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1126	defaults to data for P 1
1127
1128	:param list cell: unit cell parameter list; defaults to
1129	[1.0,1.0,1.0,90.,90,90.,1.]
1130
1131	'''
1132	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1133	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1134	phaseData = {
1135	'ranId':ran.randint(0,sys.maxint),
1136	'General':{
1137	'Name':Name,
1138	'Type':'nuclear',
1139	'AtomPtrs':[3,1,7,9],
1140	'SGData':SGData,
1141	'Cell':[False,]+cell,
1142	'Pawley dmin':1.0,
1143	'Data plot type':'None',
1144	'SH Texture':{
1145	'Order':0,
1146	'Model':'cylindrical',
1147	'Sample omega':[False,0.0],
1148	'Sample chi':[False,0.0],
1149	'Sample phi':[False,0.0],
1150	'SH Coeff':[False,{}],
1151	'SHShow':False,
1152	'PFhkl':[0,0,1],
1153	'PFxyz':[0,0,1],
1154	'PlotType':'Pole figure'}},
1155	'Atoms':[],
1156	'Drawing':{},
1157	'Histograms':{},
1158	'Pawley ref':[],
1159	'RBModels':{},
1160	}
1161	return phaseData
1162
1163	class MultipleChoicesDialog(wx.Dialog):
1164	'''A dialog that offers a series of choices, each with a
1165	title and a wx.Choice widget. Intended to be used Modally.
1166	typical input:
1167
1168	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1169	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1170
1171	selections are placed in self.chosen when OK is pressed
1172	'''
1173	def __init__(self,choicelist,headinglist,
1174	head='Select options',
1175	title='Please select from options below',
1176	parent=None):
1177	self.chosen = []
1178	wx.Dialog.__init__(
1179	self,parent,wx.ID_ANY,head,
1180	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1181	panel = wx.Panel(self)
1182	mainSizer = wx.BoxSizer(wx.VERTICAL)
1183	mainSizer.Add((10,10),1)
1184	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1185	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1186	self.ChItems = []
1187	for choice,lbl in zip(choicelist,headinglist):
1188	mainSizer.Add((10,10),1)
1189	self.chosen.append(0)
1190	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1191	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1192	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1193	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1194
1195	OkBtn = wx.Button(panel,-1,"Ok")
1196	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1197	cancelBtn = wx.Button(panel,-1,"Cancel")
1198	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1199	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1200	btnSizer.Add((20,20),1)
1201	btnSizer.Add(OkBtn)
1202	btnSizer.Add((20,20),1)
1203	btnSizer.Add(cancelBtn)
1204	btnSizer.Add((20,20),1)
1205	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1206	panel.SetSizer(mainSizer)
1207	panel.Fit()
1208	self.Fit()
1209
1210	def OnOk(self,event):
1211	parent = self.GetParent()
1212	if parent is not None: parent.Raise()
1213	# save the results from the choice widgets
1214	self.chosen = []
1215	for w in self.ChItems:
1216	self.chosen.append(w.GetSelection())
1217	self.EndModal(wx.ID_OK)
1218
1219	def OnCancel(self,event):
1220	parent = self.GetParent()
1221	if parent is not None: parent.Raise()
1222	self.chosen = []
1223	self.EndModal(wx.ID_CANCEL)
1224
1225	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1226	confirmoverwrite=True, parent=None,
1227	multipleselect=False):
1228	'''If the filename is a zip file, extract a file from that
1229	archive.
1230
1231	:param list Selection: used to predefine the name of the file
1232	to be extracted. Filename case and zip directory name are
1233	ignored in selection; the first matching file is used.
1234
1235	:param bool confirmread: if True asks the user to confirm before expanding
1236	the only file in a zip
1237
1238	:param bool confirmoverwrite: if True asks the user to confirm
1239	before overwriting if the extracted file already exists
1240
1241	:param bool multipleselect: if True allows more than one zip
1242	file to be extracted, a list of file(s) is returned.
1243	If only one file is present, do not ask which one, otherwise
1244	offer a list of choices (unless selection is used).
1245
1246	:returns: the name of the file that has been created or a
1247	list of files (see multipleselect)
1248
1249	If the file is not a zipfile, return the name of the input file.
1250	If the zipfile is empty or no file has been selected, return None
1251	'''
1252	import zipfile # do this now, since we can save startup time by doing this only on need
1253	import shutil
1254	zloc = os.path.split(filename)[0]
1255	if not zipfile.is_zipfile(filename):
1256	#print("not zip")
1257	return filename
1258
1259	z = zipfile.ZipFile(filename,'r')
1260	zinfo = z.infolist()
1261
1262	if len(zinfo) == 0:
1263	#print('Zip has no files!')
1264	zlist = [-1]
1265	if selection:
1266	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1267	if selection.lower() in choices:
1268	zlist = [choices.index(selection.lower())]
1269	else:
1270	print('debug: file '+str(selection)+' was not found in '+str(filename))
1271	zlist = [-1]
1272	elif len(zinfo) == 1 and confirmread:
1273	result = wx.ID_NO
1274	dlg = wx.MessageDialog(
1275	parent,
1276	'Is file '+str(zinfo[0].filename)+
1277	' what you want to extract from '+
1278	str(os.path.split(filename)[1])+'?',
1279	'Confirm file',
1280	wx.YES_NO \| wx.ICON_QUESTION)
1281	try:
1282	result = dlg.ShowModal()
1283	finally:
1284	dlg.Destroy()
1285	if result == wx.ID_NO:
1286	zlist = [-1]
1287	else:
1288	zlist = [0]
1289	elif len(zinfo) == 1:
1290	zlist = [0]
1291	elif multipleselect:
1292	# select one or more from a from list
1293	choices = [i.filename for i in zinfo]
1294	dlg = wx.MultiChoiceDialog(parent,'Select file(s) to extract from zip file'+str(filename),
1295	'Choose file(s)',choices,wx.CHOICEDLG_STYLE,)
1296	if dlg.ShowModal() == wx.ID_OK:
1297	zlist = dlg.GetSelections()
1298	else:
1299	zlist = []
1300	dlg.Destroy()
1301	else:
1302	# select one from a from list
1303	choices = [i.filename for i in zinfo]
1304	dlg = wx.SingleChoiceDialog(parent,
1305	'Select file to extract from zip file'+str(filename),'Choose file',
1306	choices,)
1307	if dlg.ShowModal() == wx.ID_OK:
1308	zlist = [dlg.GetSelection()]
1309	else:
1310	zlist = [-1]
1311	dlg.Destroy()
1312
1313	outlist = []
1314	for zindex in zlist:
1315	if zindex >= 0:
1316	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1317	if os.path.exists(efil) and confirmoverwrite:
1318	result = wx.ID_NO
1319	dlg = wx.MessageDialog(parent,
1320	'File '+str(efil)+' already exists. OK to overwrite it?',
1321	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1322	try:
1323	result = dlg.ShowModal()
1324	finally:
1325	dlg.Destroy()
1326	if result == wx.ID_NO:
1327	zindex = -1
1328	if zindex >= 0:
1329	# extract the file to the current directory, regardless of it's original path
1330	#z.extract(zinfo[zindex],zloc)
1331	eloc,efil = os.path.split(zinfo[zindex].filename)
1332	outfile = os.path.join(zloc, efil)
1333	fpin = z.open(zinfo[zindex])
1334	fpout = file(outfile, "wb")
1335	shutil.copyfileobj(fpin, fpout)
1336	fpin.close()
1337	fpout.close()
1338	outlist.append(outfile)
1339	z.close()
1340	if multipleselect and len(outlist) >= 1:
1341	return outlist
1342	elif len(outlist) == 1:
1343	return outlist[0]
1344	else:
1345	return None
1346
1347	######################################################################
1348	# base classes for reading various types of data files
1349	# not used directly, only by subclassing
1350	######################################################################
1351	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1352	P1SGData = SGData
1353	class ImportBaseclass(object):
1354	'''Defines a base class for the reading of input files (diffraction
1355	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1356	for an explanation on how to use a subclass of this class.
1357	'''
1358	class ImportException(Exception):
1359	'''Defines an Exception that is used when an import routine hits an expected error,
1360	usually in .Reader.
1361
1362	Good practice is that the Reader should define a value in self.errors that
1363	tells the user some information about what is wrong with their file.
1364	'''
1365	pass
1366
1367	def __init__(self,
1368	formatName,
1369	longFormatName=None,
1370	extensionlist=[],
1371	strictExtension=False,
1372	):
1373	self.formatName = formatName # short string naming file type
1374	if longFormatName: # longer string naming file type
1375	self.longFormatName = longFormatName
1376	else:
1377	self.longFormatName = formatName
1378	# define extensions that are allowed for the file type
1379	# for windows, remove any extensions that are duplicate, as case is ignored
1380	if sys.platform == 'windows' and extensionlist:
1381	extensionlist = list(set([s.lower() for s in extensionlist]))
1382	self.extensionlist = extensionlist
1383	# If strictExtension is True, the file will not be read, unless
1384	# the extension matches one in the extensionlist
1385	self.strictExtension = strictExtension
1386	self.errors = ''
1387	self.warnings = ''
1388	# used for readers that will use multiple passes to read
1389	# more than one data block
1390	self.repeat = False
1391	self.repeatcount = 0
1392	#print 'created',self.__class__
1393
1394	def ReInitialize(self):
1395	'Reinitialize the Reader to initital settings'
1396	self.errors = ''
1397	self.warnings = ''
1398	self.repeat = False
1399	self.repeatcount = 0
1400
1401	def BlockSelector(self, ChoiceList, ParentFrame=None,
1402	title='Select a block',
1403	size=None, header='Block Selector',
1404	useCancel=True):
1405	''' Provide a wx dialog to select a block if the file contains more
1406	than one set of data and one must be selected
1407	'''
1408	if useCancel:
1409	dlg = wx.SingleChoiceDialog(
1410	ParentFrame,title, header,ChoiceList)
1411	else:
1412	dlg = wx.SingleChoiceDialog(
1413	ParentFrame,title, header,ChoiceList,
1414	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1415	if size: dlg.SetSize(size)
1416	dlg.CenterOnParent()
1417	if dlg.ShowModal() == wx.ID_OK:
1418	sel = dlg.GetSelection()
1419	return sel
1420	else:
1421	return None
1422	dlg.Destroy()
1423
1424	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1425	title='Select a block',size=None, header='Block Selector'):
1426	'''Provide a wx dialog to select a block of data if the
1427	file contains more than one set of data and one must be
1428	selected.
1429
1430	:returns: a list of the selected blocks
1431	'''
1432	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1433	wx.CHOICEDLG_STYLE)
1434	dlg.CenterOnParent()
1435	if size: dlg.SetSize(size)
1436	if dlg.ShowModal() == wx.ID_OK:
1437	sel = dlg.GetSelections()
1438	else:
1439	return []
1440	dlg.Destroy()
1441	selected = []
1442	if len(ChoiceList) in sel:
1443	return range(len(ChoiceList))
1444	else:
1445	return sel
1446	return selected
1447
1448	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1449	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1450	widget. Typical input:
1451
1452	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1453
1454	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1455
1456	optional keyword parameters are: head (window title) and title
1457	returns a list of selected indicies for each choice (or None)
1458	'''
1459	result = None
1460	dlg = MultipleChoicesDialog(choicelist,headinglist,
1461	parent=ParentFrame, **kwargs)
1462	dlg.CenterOnParent()
1463	if dlg.ShowModal() == wx.ID_OK:
1464	result = dlg.chosen
1465	dlg.Destroy()
1466	return result
1467
1468	def ShowBusy(self):
1469	wx.BeginBusyCursor()
1470	wx.Yield() # make it happen now!
1471
1472	def DoneBusy(self):
1473	wx.EndBusyCursor()
1474	wx.Yield() # make it happen now!
1475
1476	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1477	# '''This method must be supplied in the child class to read the file.
1478	# if the read fails either return False or raise an Exception
1479	# preferably of type ImportException.
1480	# '''
1481	# #start reading
1482	# raise ImportException("Error occurred while...")
1483	# self.errors += "Hint for user on why the error occur
1484	# return False # if an error occurs
1485	# return True # if read OK
1486
1487	def ExtensionValidator(self, filename):
1488	'''This methods checks if the file has the correct extension
1489	Return False if this filename will not be supported by this reader
1490	Return True if the extension matches the list supplied by the reader
1491	Return None if the reader allows un-registered extensions
1492	'''
1493	if filename:
1494	ext = os.path.splitext(filename)[1]
1495	if sys.platform == 'windows': ext = ext.lower()
1496	if ext in self.extensionlist: return True
1497	if self.strictExtension: return False
1498	return None
1499
1500	def ContentsValidator(self, filepointer):
1501	'''This routine will attempt to determine if the file can be read
1502	with the current format.
1503	This will typically be overridden with a method that
1504	takes a quick scan of [some of]
1505	the file contents to do a "sanity" check if the file
1506	appears to match the selected format.
1507	Expected to be called via self.Validator()
1508	'''
1509	#filepointer.seek(0) # rewind the file pointer
1510	return True
1511
1512	def CIFValidator(self, filepointer):
1513	'''A :meth:`ContentsValidator` for use to validate CIF files.
1514	'''
1515	for i,l in enumerate(filepointer):
1516	if i >= 1000: return True
1517	'''Encountered only blank lines or comments in first 1000
1518	lines. This is unlikely, but assume it is CIF anyway, since we are
1519	even less likely to find a file with nothing but hashes and
1520	blank lines'''
1521	line = l.strip()
1522	if len(line) == 0: # ignore blank lines
1523	continue
1524	elif line.startswith('#'): # ignore comments
1525	continue
1526	elif line.startswith('data_'): # on the right track, accept this file
1527	return True
1528	else: # found something invalid
1529	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1530	self.errors += ' '+str(l)
1531	self.errors += ' Note: a CIF should only have blank lines or comments before'
1532	self.errors += ' a data_ statement begins a block.'
1533	return False
1534
1535	class ImportPhase(ImportBaseclass):
1536	'''Defines a base class for the reading of files with coordinates
1537
1538	Objects constructed that subclass this (in import/G2phase_*.py) will be used
1539	in :meth:`GSASII.GSASII.OnImportPhase`.
1540	See :ref:`Writing a Import Routine<Import_Routines>`
1541	for an explanation on how to use this class.
1542
1543	'''
1544	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1545	strictExtension=False,):
1546	# call parent __init__
1547	ImportBaseclass.__init__(self,formatName,longFormatName,
1548	extensionlist,strictExtension)
1549	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1550	self.Constraints = None
1551
1552	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1553	title='Select a phase', size=None,header='Phase Selector'):
1554	''' Provide a wx dialog to select a phase if the file contains more
1555	than one phase
1556	'''
1557	return self.BlockSelector(ChoiceList,ParentFrame,title,
1558	size,header)
1559
1560	class ImportStructFactor(ImportBaseclass):
1561	'''Defines a base class for the reading of files with tables
1562	of structure factors.
1563
1564	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1565	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1566	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1567	:meth:`Reader`.
1568
1569	See :ref:`Writing a Import Routine<Import_Routines>`
1570	for an explanation on how to use import classes in general. The specifics
1571	for reading a structure factor histogram require that
1572	the ``Reader()`` routine in the import
1573	class need to do only a few things: It
1574	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1575	and set :attr:`Parameters` with the instrument parameters
1576	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1577	Also, set :attr:`Controls`,
1578	which specifies how the histogram is plotted
1579	(initialized with :meth:`InitControls` and set with :meth:`UpdateControls`).
1580	'''
1581	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1582	strictExtension=False,):
1583	ImportBaseclass.__init__(self,formatName,longFormatName,
1584	extensionlist,strictExtension)
1585
1586	# define contents of Structure Factor entry
1587	self.Parameters = []
1588	'self.Parameters is a list with two dicts for data parameter settings'
1589	self.InitParameters()
1590	self.Controls = {}
1591	'self.Controls is a dict with plotting controls'
1592	self.InitControls() # initialize the above
1593	self.RefDict = {'RefList':[],'FF':[]}
1594	'''self.RefDict is a dict containing the reflection information, as read from the file.
1595	Item 'RefList' contains the reflection information. See the
1596	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1597	for the contents of each row. Dict element 'FF'
1598	contains the form factor values for each element type; if this entry
1599	is left as initialized (an empty list) it will be initialized as needed later.
1600	'''
1601	def ReInitialize(self):
1602	'Reinitialize the Reader to initital settings'
1603	ImportBaseclass.ReInitialize(self)
1604	self.InitParameters()
1605	self.InitControls()
1606	self.RefDict = {'RefList':[],'FF':[]}
1607
1608
1609	def InitControls(self):
1610	'initialize the controls structure'
1611	self.Controls = { # dictionary with plotting controls
1612	'Type' : 'Fosq',
1613	'ifFc' : False, #
1614	'HKLmax' : [None,None,None],
1615	'HKLmin' : [None,None,None],
1616	'FoMax' : None, # maximum observed structure factor as Fo
1617	'Zone' : '001',
1618	'Layer' : 0,
1619	'Scale' : 1.0,
1620	'log-lin' : 'lin',
1621	}
1622
1623	def InitParameters(self):
1624	'initialize the instrument parameters structure'
1625	Lambda = 0.70926
1626	HistType = 'SXC'
1627	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1628	'Lam':[Lambda,Lambda]
1629	}, {}]
1630	'Parameters is a list with two dicts for data parameter settings'
1631
1632	def UpdateParameters(self,Type=None,Wave=None):
1633	'Revise the instrument parameters'
1634	if Type is not None:
1635	self.Parameters[0]['Type'] = [Type,Type]
1636	if Wave is not None:
1637	self.Parameters[0]['Lam'] = [Wave,Wave]
1638
1639	def UpdateControls(self,Type='Fosq',FcalcPresent=False):
1640	'''Scan through the reflections to update the Controls dictionary
1641	'''
1642	self.Controls['Type'] = Type
1643	self.Controls['ifFc'] = FcalcPresent
1644	HKLmax = [None,None,None]
1645	HKLmin = [None,None,None]
1646	Fo2max = None
1647	for refl in self.RefDict['RefList']:
1648	HKL = refl[:3]
1649	if Fo2max is None:
1650	Fo2max = refl[8]
1651	else:
1652	Fo2max = max(Fo2max,refl[8])
1653	for i,hkl in enumerate(HKL):
1654	if HKLmax[i] is None:
1655	HKLmax[i] = hkl
1656	HKLmin[i] = hkl
1657	else:
1658	HKLmax[i] = max(HKLmax[i],hkl)
1659	HKLmin[i] = min(HKLmin[i],hkl)
1660	self.Controls['HKLmax'] = HKLmax
1661	self.Controls['HKLmin'] = HKLmin
1662	if Type == 'Fosq':
1663	self.Controls['FoMax'] = np.sqrt(Fo2max)
1664	elif Type == 'Fo':
1665	self.Controls['FoMax'] = Fo2max
1666	else:
1667	print "Unsupported Struct Fact type in ImportStructFactor.UpdateControls"
1668	raise Exception,"Unsupported Struct Fact type in ImportStructFactor.UpdateControls"
1669
1670	######################################################################
1671	class ImportPowderData(ImportBaseclass):
1672	'''Defines a base class for the reading of files with powder data.
1673	See :ref:`Writing a Import Routine<Import_Routines>`
1674	for an explanation on how to use this class.
1675	'''
1676	# define some default instrument parameter files
1677	# just like GSAS, sigh
1678	defaultIparm_lbl = []
1679	defaultIparms = []
1680	defaultIparm_lbl.append('CuKa lab data')
1681	defaultIparms.append({
1682	'INS HTYPE ':'PXC ',
1683	'INS 1 ICONS':' 1.540500 1.544300 0.0 0 0.7 0 0.5 ',
1684	'INS 1PRCF1 ':' 3 8 0.01 ',
1685	'INS 1PRCF11':' 2.000000E+00 -2.000000E+00 5.000000E+00 0.000000E+00 ',
1686	'INS 1PRCF12':' 0.000000E+00 0.000000E+00 0.150000E-01 0.150000E-01 ',
1687	})
1688	defaultIparm_lbl.append('0.6A synch')
1689	defaultIparms.append({
1690	'INS HTYPE ':'PXC ',
1691	'INS 1 ICONS':' 0.600000 0.000000 0.0 0 0.99 0 0.5 ',
1692	'INS 1PRCF1 ':' 3 8 0.01 ',
1693	'INS 1PRCF11':' 1.000000E+00 -1.000000E+00 0.300000E+00 0.000000E+00 ',
1694	'INS 1PRCF12':' 0.000000E+00 0.000000E+00 0.100000E-01 0.100000E-01 ',
1695	})
1696	defaultIparm_lbl.append('1.5A CW neutron data')
1697	defaultIparms.append({
1698	'INS HTYPE ':'PNC',
1699	'INS 1 ICONS':' 1.54020 0.00000 0.04000 0',
1700	'INS 1PRCF1 ':' 3 8 0.005',
1701	'INS 1PRCF11':' 0.239700E+03 -0.298200E+03 0.180800E+03 0.000000E+00',
1702	'INS 1PRCF12':' 0.000000E+00 0.000000E+00 0.400000E-01 0.300000E-01',
1703	})
1704	defaultIparm_lbl.append('10m TOF backscattering bank')
1705	defaultIparms.append({
1706	'INS HTYPE ':'PNT',
1707	'INS 1 ICONS':' 5000.00 0.00 0.00',
1708	'INS 1BNKPAR':' 1.0000 150.000',
1709	'INS 1PRCF1 ':' 1 8 0.01000',
1710	'INS 1PRCF11':' 0.000000E+00 5.000000E+00 3.000000E-02 1.000000E-03',
1711	'INS 1PRCF12':' 0.000000E+00 4.000000E+01 0.000000E+00 0.000000E+00',
1712	})
1713	defaultIparm_lbl.append('10m TOF 90deg bank')
1714	defaultIparms.append({
1715	'INS HTYPE ':'PNT',
1716	'INS 1 ICONS':' 3500.00 0.00 0.00',
1717	'INS 1BNKPAR':' 1.0000 90.000',
1718	'INS 1PRCF1 ':' 1 8 0.01000',
1719	'INS 1PRCF11':' 0.000000E+00 5.000000E+00 3.000000E-02 4.000000E-03',
1720	'INS 1PRCF12':' 0.000000E+00 8.000000E+01 0.000000E+00 0.000000E+00',
1721	})
1722	defaultIparm_lbl.append('63m POWGEN 90deg bank')
1723	defaultIparms.append({
1724	'INS HTYPE ':'PNT',
1725	'INS 1 ICONS':' 22585.80 0.00 0.00',
1726	'INS 1BNKPAR':' 1.0000 90.000',
1727	'INS 1PRCF1 ':' 1 8 0.01000',
1728	'INS 1PRCF11':' 0.000000E+00 1.000000E+00 3.000000E-02 4.000000E-03',
1729	'INS 1PRCF12':' 0.000000E+00 8.000000E+01 0.000000E+00 0.000000E+00',
1730	})
1731	def __init__(self,
1732	formatName,
1733	longFormatName=None,
1734	extensionlist=[],
1735	strictExtension=False,
1736	):
1737	ImportBaseclass.__init__(self,formatName,
1738	longFormatName,
1739	extensionlist,
1740	strictExtension)
1741	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1742	self.powderdata = [] # Powder dataset
1743	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1744	np.array(x), # x-axis values
1745	np.array(y), # powder pattern intensities
1746	np.array(w), # 1/sig(intensity)^2 values (weights)
1747	np.array(yc), # calc. intensities (zero)
1748	np.array(yb), # calc. background (zero)
1749	np.array(yd), # obs-calc profiles
1750	'''
1751	self.comments = []
1752	self.idstring = ''
1753	self.Sample = G2pdG.SetDefaultSample()
1754	self.GSAS = None # used in TOF
1755	self.clockWd = None # used in TOF
1756	self.repeat_instparm = True # Should a parm file be
1757	# used for multiple histograms?
1758	self.instparm = None # name hint
1759	self.instfile = '' # full path name to instrument parameter file
1760	self.instbank = '' # inst parm bank number
1761	self.instmsg = '' # a label that gets printed to show
1762	# where instrument parameters are from
1763	self.numbanks = 1
1764	self.instdict = {} # place items here that will be transferred to the instrument parameters
1765	######################################################################
1766	class ImportSmallAngleData(ImportBaseclass):
1767	'''Defines a base class for the reading of files with small angle data.
1768	See :ref:`Writing a Import Routine<Import_Routines>`
1769	for an explanation on how to use this class.
1770	'''
1771	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1772	strictExtension=False,):
1773
1774	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1775	strictExtension)
1776	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1777	self.smallangledata = [] # SASD dataset
1778	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1779	np.array(x), # x-axis values
1780	np.array(y), # powder pattern intensities
1781	np.array(w), # 1/sig(intensity)^2 values (weights)
1782	np.array(yc), # calc. intensities (zero)
1783	np.array(yd), # obs-calc profiles
1784	'''
1785	self.comments = []
1786	self.idstring = ''
1787	self.Sample = G2pdG.SetDefaultSample()
1788	self.GSAS = None # used in TOF
1789	self.clockWd = None # used in TOF
1790	self.numbanks = 1
1791	self.instdict = {} # place items here that will be transferred to the instrument parameters
1792	######################################################################
1793	class ExportBaseclass(object):
1794	'''Defines a base class for the exporting of GSAS-II results
1795	'''
1796	def __init__(self,
1797	G2frame,
1798	formatName,
1799	extension,
1800	longFormatName=None,
1801	):
1802	self.G2frame = G2frame
1803	self.formatName = formatName # short string naming file type
1804	self.extension = extension
1805	if longFormatName: # longer string naming file type
1806	self.longFormatName = longFormatName
1807	else:
1808	self.longFormatName = formatName
1809	self.OverallParms = {}
1810	self.Phases = {}
1811	self.Histograms = {}
1812	self.powderDict = {}
1813	self.xtalDict = {}
1814	self.parmDict = {}
1815	self.sigDict = {}
1816	# updated in InitExport:
1817	self.currentExportType = None # type of export that has been requested
1818	# updated in ExportSelect (when used):
1819	self.phasenam = None # a list of selected phases
1820	self.histnam = None # a list of selected histograms
1821	self.filename = None # name of file to be written
1822
1823	# items that should be defined in a subclass of this class
1824	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1825	# The following types are defined: 'project', "phase", "powder", "single"
1826	self.multiple = False # set as True if the class can export multiple phases or histograms
1827	# self.multiple is ignored for "project" exports
1828
1829	def InitExport(self,event):
1830	'''Determines the type of menu that called the Exporter.
1831	'''
1832	if event:
1833	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1834
1835	def ExportSelect(self,AskFile=True):
1836	'''Selects histograms or phases when needed. Sets a default file name.
1837
1838	:param bool AskFile: if AskFile is True (default) get the name of the file
1839	in a dialog
1840	:returns: True in case of an error
1841	'''
1842
1843	if self.currentExportType == 'phase':
1844	if len(self.Phases) == 0:
1845	self.G2frame.ErrorDialog(
1846	'Empty project',
1847	'Project does not contain any phases.')
1848	return True
1849	elif len(self.Phases) == 1:
1850	self.phasenam = self.Phases.keys()
1851	elif self.multiple:
1852	choices = sorted(self.Phases.keys())
1853	phasenum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1854	if phasenum is None: return True
1855	self.phasenam = [choices[i] for i in phasenum]
1856	if not self.phasenam: return True
1857	else:
1858	choices = sorted(self.Phases.keys())
1859	phasenum = G2gd.ItemSelector(choices,self.G2frame)
1860	if phasenum is None: return True
1861	self.phasenam = [choices[phasenum]]
1862	elif self.currentExportType == 'single':
1863	if len(self.xtalDict) == 0:
1864	self.G2frame.ErrorDialog(
1865	'Empty project',
1866	'Project does not contain any single crystal data.')
1867	return True
1868	elif len(self.xtalDict) == 1:
1869	self.histnam = self.xtalDict.values()
1870	elif self.multiple:
1871	choices = sorted(self.xtalDict.values())
1872	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1873	if not hnum: return True
1874	self.histnam = [choices[i] for i in hnum]
1875	else:
1876	choices = sorted(self.xtalDict.values())
1877	hnum = G2gd.ItemSelector(choices,self.G2frame)
1878	if hnum is None: return True
1879	self.histnam = [choices[hnum]]
1880	elif self.currentExportType == 'powder':
1881	if len(self.powderDict) == 0:
1882	self.G2frame.ErrorDialog(
1883	'Empty project',
1884	'Project does not contain any powder data.')
1885	return True
1886	elif len(self.powderDict) == 1:
1887	self.histnam = self.powderDict.values()
1888	elif self.multiple:
1889	choices = sorted(self.powderDict.values())
1890	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1891	if not hnum: return True
1892	self.histnam = [choices[i] for i in hnum]
1893	else:
1894	choices = sorted(self.powderDict.values())
1895	hnum = G2gd.ItemSelector(choices,self.G2frame)
1896	if hnum is None: return True
1897	self.histnam = [choices[hnum]]
1898	elif self.currentExportType == 'image':
1899	if len(self.Histograms) == 0:
1900	self.G2frame.ErrorDialog(
1901	'Empty project',
1902	'Project does not contain any images.')
1903	return True
1904	elif len(self.Histograms) == 1:
1905	self.histnam = self.Histograms.keys()
1906	else:
1907	choices = sorted(self.Histograms.keys())
1908	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1909	if self.multiple:
1910	if not hnum: return True
1911	self.histnam = [choices[i] for i in hnum]
1912	else:
1913	if hnum is None: return True
1914	self.histnam = [choices[hnum]]
1915	if self.currentExportType == 'map':
1916	# search for phases with maps
1917	mapPhases = []
1918	choices = []
1919	for phasenam in sorted(self.Phases):
1920	phasedict = self.Phases[phasenam] # pointer to current phase info
1921	if len(phasedict['General']['Map'].get('rho',[])):
1922	mapPhases.append(phasenam)
1923	if phasedict['General']['Map'].get('Flip'):
1924	choices.append('Charge flip map: '+str(phasenam))
1925	elif phasedict['General']['Map'].get('MapType'):
1926	choices.append(
1927	str(phasedict['General']['Map'].get('MapType'))
1928	+ ' map: ' + str(phasenam))
1929	else:
1930	choices.append('unknown map: '+str(phasenam))
1931	# select a map if needed
1932	if len(mapPhases) == 0:
1933	self.G2frame.ErrorDialog(
1934	'Empty project',
1935	'Project does not contain any maps.')
1936	return True
1937	elif len(mapPhases) == 1:
1938	self.phasenam = mapPhases
1939	else:
1940	phasenum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1941	if self.multiple:
1942	if not phasenum: return True
1943	self.phasenam = [mapPhases[i] for i in phasenum]
1944	else:
1945	if phasenum is None: return True
1946	self.phasenam = [mapPhases[phasenum]]
1947
1948	if AskFile:
1949	self.filename = self.askSaveFile()
1950	else:
1951	self.filename = self.defaultSaveFile()
1952	if not self.filename: return True
1953
1954	# def SetupExport(self,event,AskFile=True):
1955	# '''Determines the type of menu that called the Exporter. Selects histograms
1956	# or phases when needed. Better to replace with individual calls to
1957	# self.InitExport() and self.ExportSelect() so that the former can be called prior
1958	# to self.LoadTree()
1959
1960	# :param bool AskFile: if AskFile is True (default) get the name of the file
1961	# in a dialog
1962	# :returns: True in case of an error
1963	# '''
1964	# self.ExportInit(event)
1965	# return self.ExportSelect(AskFile)
1966
1967	def loadParmDict(self):
1968	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1969	refined values to those from the last cycle and set the uncertainties for the
1970	refined parameters in another dict (self.sigDict).
1971
1972	Expands the parm & sig dicts to include values derived from constraints.
1973	'''
1974	self.parmDict = {}
1975	self.sigDict = {}
1976	rigidbodyDict = {}
1977	covDict = {}
1978	consDict = {}
1979	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1980	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
1981	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
1982	while item:
1983	name = self.G2frame.PatternTree.GetItemText(item)
1984	if name == 'Rigid bodies':
1985	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
1986	elif name == 'Covariance':
1987	covDict = self.G2frame.PatternTree.GetItemPyData(item)
1988	elif name == 'Constraints':
1989	consDict = self.G2frame.PatternTree.GetItemPyData(item)
1990	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
1991	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1992	self.parmDict.update(rbDict)
1993	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1994	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables = G2stIO.GetPhaseData(
1995	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1996	self.parmDict.update(phaseDict)
1997	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
1998	Phases,Histograms,Print=False,resetRefList=False)
1999	self.parmDict.update(hapDict)
2000	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
2001	self.parmDict.update(histDict)
2002	self.parmDict.update(zip(
2003	covDict.get('varyList',[]),
2004	covDict.get('variables',[])))
2005	self.sigDict = dict(zip(
2006	covDict.get('varyList',[]),
2007	covDict.get('sig',[])))
2008	# expand to include constraints: first compile a list of constraints
2009	constList = []
2010	for item in consDict:
2011	if item.startswith('_'): continue
2012	constList += consDict[item]
2013	# now process the constraints
2014	G2mv.InitVars()
2015	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
2016	varyList = covDict.get('varyListStart')
2017	if varyList is None and len(constDict) == 0:
2018	# no constraints can use varyList
2019	varyList = covDict.get('varyList')
2020	elif varyList is None:
2021	# old GPX file from before pre-constraint varyList is saved
2022	print ' * Old refinement: Please use Calculate/Refine to redo *'
2023	raise Exception(' * Export aborted *')
2024	else:
2025	varyList = list(varyList)
2026	try:
2027	groups,parmlist = G2mv.GroupConstraints(constDict)
2028	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList)
2029	except:
2030	# this really should not happen
2031	print ' * ERROR - constraints are internally inconsistent *'
2032	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
2033	print 'Errors',errmsg
2034	if warnmsg: print 'Warnings',warnmsg
2035	raise Exception(' * CIF creation aborted *')
2036	# add the constrained values to the parameter dictionary
2037	G2mv.Dict2Map(self.parmDict,varyList)
2038	# and add their uncertainties into the esd dictionary (sigDict)
2039	if covDict.get('covMatrix') is not None:
2040	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
2041
2042	def loadTree(self):
2043	'''Load the contents of the data tree into a set of dicts
2044	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2045	& self.xtalDict)
2046
2047	* The childrenless data tree items are overall parameters/controls for the
2048	entire project and are placed in self.OverallParms
2049	* Phase items are placed in self.Phases
2050	* Data items are placed in self.Histogram. The key for these data items
2051	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2052	'''
2053	self.OverallParms = {}
2054	self.powderDict = {}
2055	self.xtalDict = {}
2056	self.Phases = {}
2057	self.Histograms = {}
2058	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2059	histType = None
2060	if self.currentExportType == 'phase':
2061	# if exporting phases load them here
2062	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2063	if not sub:
2064	print 'no phases found'
2065	return True
2066	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2067	while item:
2068	phaseName = self.G2frame.PatternTree.GetItemText(item)
2069	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2070	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2071	return
2072	elif self.currentExportType == 'single':
2073	histType = 'HKLF'
2074	elif self.currentExportType == 'powder':
2075	histType = 'PWDR'
2076	elif self.currentExportType == 'image':
2077	histType = 'IMG'
2078
2079	if histType: # Loading just one kind of tree entry
2080	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2081	while item:
2082	name = self.G2frame.PatternTree.GetItemText(item)
2083	if name.startswith(histType):
2084	if self.Histograms.get(name): # there is already an item with this name
2085	print('Histogram name '+str(name)+' is repeated. Renaming')
2086	if name[-1] == '9':
2087	name = name[:-1] + '10'
2088	elif name[-1] in '012345678':
2089	name = name[:-1] + str(int(name[-1])+1)
2090	else:
2091	name += '-1'
2092	self.Histograms[name] = {}
2093	# the main info goes into Data, but the 0th
2094	# element contains refinement results, carry
2095	# that over too now.
2096	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2097	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2098	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2099	while item2:
2100	child = self.G2frame.PatternTree.GetItemText(item2)
2101	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2102	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2103	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2104	# index powder and single crystal histograms by number
2105	for hist in self.Histograms:
2106	if hist.startswith("PWDR"):
2107	d = self.powderDict
2108	elif hist.startswith("HKLF"):
2109	d = self.xtalDict
2110	else:
2111	return
2112	i = self.Histograms[hist].get('hId')
2113	if i is None and not d.keys():
2114	i = 0
2115	elif i is None or i in d.keys():
2116	i = max(d.keys())+1
2117	d[i] = hist
2118	return
2119	# else standard load: using all interlinked phases and histograms
2120	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2121	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2122	while item:
2123	name = self.G2frame.PatternTree.GetItemText(item)
2124	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2125	if not item2:
2126	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2127	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2128	# index powder and single crystal histograms
2129	for hist in self.Histograms:
2130	i = self.Histograms[hist]['hId']
2131	if hist.startswith("PWDR"):
2132	self.powderDict[i] = hist
2133	elif hist.startswith("HKLF"):
2134	self.xtalDict[i] = hist
2135
2136	def dumpTree(self,mode='type'):
2137	'''Print out information on the data tree dicts loaded in loadTree
2138	'''
2139	print '\nOverall'
2140	if mode == 'type':
2141	def Show(arg): return type(arg)
2142	else:
2143	def Show(arg): return arg
2144	for key in self.OverallParms:
2145	print ' ',key,Show(self.OverallParms[key])
2146	print 'Phases'
2147	for key1 in self.Phases:
2148	print ' ',key1,Show(self.Phases[key1])
2149	print 'Histogram'
2150	for key1 in self.Histograms:
2151	print ' ',key1,Show(self.Histograms[key1])
2152	for key2 in self.Histograms[key1]:
2153	print ' ',key2,Show(self.Histograms[key1][key2])
2154
2155	def defaultSaveFile(self):
2156	return os.path.abspath(
2157	os.path.splitext(self.G2frame.GSASprojectfile
2158	)[0]+self.extension)
2159
2160	def askSaveFile(self):
2161	'''Ask the user to supply a file name
2162
2163	:returns: a file name (str)
2164	'''
2165	defnam = os.path.splitext(
2166	os.path.split(self.G2frame.GSASprojectfile)[1]
2167	)[0]+self.extension
2168	dlg = wx.FileDialog(
2169	self.G2frame, 'Input name for file to write', '.', defnam,
2170	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2171	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2172	dlg.CenterOnParent()
2173	try:
2174	if dlg.ShowModal() == wx.ID_OK:
2175	filename = dlg.GetPath()
2176	# make sure extension is correct
2177	filename = os.path.splitext(filename)[0]+self.extension
2178	else:
2179	filename = None
2180	finally:
2181	dlg.Destroy()
2182	return filename
2183
2184	# Tools for file writing.
2185	def OpenFile(self,fil=None):
2186	'''Open the output file
2187
2188	:param str fil: The name of the file to open. If None (default)
2189	the name defaults to self.filename.
2190	:returns: the file object opened by the routine which is also
2191	saved as self.fp
2192	'''
2193	if not fil:
2194	fil = self.filename
2195	self.fp = open(fil,'w')
2196	return self.fp
2197	def Write(self,line):
2198	'''write a line of output, attaching a line-end character
2199
2200	:param str line: the text to be written.
2201	'''
2202	self.fp.write(line+'\n')
2203	def CloseFile(self,fp=None):
2204	'''Close a file opened in OpenFile
2205
2206	:param file fp: the file object to be closed. If None (default)
2207	file object self.fp is closed.
2208	'''
2209	if fp is None:
2210	fp = self.fp
2211	self.fp = None
2212	fp.close()
2213	# Tools to pull information out of the data arrays
2214	def GetCell(self,phasenam):
2215	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2216
2217	:param str phasenam: the name for the selected phase
2218	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2219	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2220	cell values and `cellSig` has their uncertainties.
2221	"""
2222	phasedict = self.Phases[phasenam] # pointer to current phase info
2223	try:
2224	pfx = str(phasedict['pId'])+'::'
2225	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2226	cellSig = G2stIO.getCellEsd(pfx,
2227	phasedict['General']['SGData'],A,
2228	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2229	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2230	return cellList,cellSig
2231	except KeyError:
2232	cell = phasedict['General']['Cell'][1:]
2233	return cell,7*[0]
2234
2235	def GetAtoms(self,phasenam):
2236	"""Gets the atoms associated with a phase. Can be used with standard
2237	or macromolecular phases
2238
2239	:param str phasenam: the name for the selected phase
2240	:returns: a list of items for eac atom where each item is a list containing:
2241	label, typ, mult, xyz, and td, where
2242
2243	* label and typ are the atom label and the scattering factor type (str)
2244	* mult is the site multiplicity (int)
2245	* xyz is contains a list with four pairs of numbers:
2246	x, y, z and fractional occupancy and
2247	their standard uncertainty (or a negative value)
2248	* td is contains a list with either one or six pairs of numbers:
2249	if one number it is U\ :sub:`iso` and with six numbers it is
2250	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2251	paired with their standard uncertainty (or a negative value)
2252	"""
2253	phasedict = self.Phases[phasenam] # pointer to current phase info
2254	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2255	cfrac = cx+3
2256	fpfx = str(phasedict['pId'])+'::Afrac:'
2257	atomslist = []
2258	for i,at in enumerate(phasedict['Atoms']):
2259	if phasedict['General']['Type'] == 'macromolecular':
2260	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2261	else:
2262	label = at[ct-1]
2263	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2264	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2265	mult = at[cs+1]
2266	typ = at[ct]
2267	xyz = []
2268	for j,v in enumerate(('x','y','z')):
2269	val = at[cx+j]
2270	pfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2271	sig = self.sigDict.get(pfx,-0.000009)
2272	xyz.append((val,sig))
2273	xyz.append((fval,fsig))
2274	td = []
2275	if at[cia] == 'I':
2276	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2277	val = self.parmDict.get(pfx,at[cia+1])
2278	sig = self.sigDict.get(pfx,-0.0009)
2279	td.append((val,sig))
2280	else:
2281	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2282	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2283	val = self.parmDict.get(pfx,at[cia+2+i])
2284	sig = self.sigDict.get(pfx,-0.0009)
2285	td.append((val,sig))
2286	atomslist.append((label,typ,mult,xyz,td))
2287	return atomslist
2288	######################################################################
2289
2290	def ReadCIF(URLorFile):
2291	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2292	(from James Hester).
2293	The open routine gets confused with DOS names that begin with a letter and colon
2294	"C:\dir\" so this routine will try to open the passed name as a file and if that
2295	fails, try it as a URL
2296
2297	:param str URLorFile: string containing a URL or a file name. Code will try first
2298	to open it as a file and then as a URL.
2299
2300	:returns: a PyCifRW CIF object.
2301	'''
2302	import CifFile as cif # PyCifRW from James Hester
2303
2304	# alternate approach:
2305	#import urllib
2306	#ciffile = 'file:'+urllib.pathname2url(filename)
2307
2308	try:
2309	fp = open(URLorFile,'r')
2310	cf = cif.ReadCif(fp)
2311	fp.close()
2312	return cf
2313	except IOError:
2314	return cif.ReadCif(URLorFile)
2315
2316	if __name__ == '__main__':
2317	app = wx.PySimpleApp()
2318	frm = wx.Frame(None) # create a frame
2319	frm.Show(True)
2320	filename = '/tmp/notzip.zip'
2321	filename = '/tmp/all.zip'
2322	#filename = '/tmp/11bmb_7652.zip'
2323
2324	#selection=None, confirmoverwrite=True, parent=None
2325	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2326	print ExtractFileFromZip(filename,multipleselect=True)
2327	#confirmread=False, confirmoverwrite=False)
2328
2329	# choicelist=[ ('a','b','c'),
2330	# ('test1','test2'),('no choice',)]
2331	# titles = [ 'a, b or c', 'tests', 'No option here']
2332	# dlg = MultipleChoicesDialog(
2333	# choicelist,titles,
2334	# parent=frm)
2335	# if dlg.ShowModal() == wx.ID_OK:
2336	# print 'Got OK'

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