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source: trunk/GSASIIIO.py @ 1165

Last change on this file since 1165 was 1165, checked in by vondreele, 9 years ago
image calibration much better now - works on transposed data
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
File size: 95.6 KB

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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2013-12-14 14:54:05 +0000 (Sat, 14 Dec 2013) $
4	# $Author: vondreele $
5	# $Revision: 1165 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 1165 2013-12-14 14:54:05Z vondreele $
8	########### SVN repository information ###################
9	'''
10	GSASIIIO: Misc I/O routines
11	=============================
12
13	Module with miscellaneous routines for input and output. Many
14	are GUI routines to interact with user.
15
16	Includes support for image reading.
17
18	Also includes base classes for data import routines.
19
20	'''
21	"""GSASIIIO: functions for IO of data
22	Copyright: 2008, Robert B. Von Dreele (Argonne National Laboratory)
23	"""
24	import wx
25	import math
26	import numpy as np
27	import cPickle
28	import sys
29	import re
30	import random as ran
31	import GSASIIpath
32	GSASIIpath.SetVersionNumber("$Revision: 1165 $")
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
46	def sfloat(S):
47	'Convert a string to float. An empty field is treated as zero'
48	if S.strip():
49	return float(S)
50	else:
51	return 0.0
52
53	def sint(S):
54	'Convert a string to int. An empty field is treated as zero'
55	if S.strip():
56	return int(S)
57	else:
58	return 0
59
60	def trim(val):
61	'''Simplify a string containing leading and trailing spaces
62	as well as newlines, tabs, repeated spaces etc. into a shorter and
63	more simple string, by replacing all ranges of whitespace
64	characters with a single space.
65
66	:param str val: the string to be simplified
67
68	:returns: the (usually) shortened version of the string
69	'''
70	return re.sub('\s+', ' ', val).strip()
71
72	def makeInstDict(names,data,codes):
73	inst = dict(zip(names,zip(data,data,codes)))
74	for item in inst:
75	inst[item] = list(inst[item])
76	return inst
77
78	def FileDlgFixExt(dlg,file):
79	'this is needed to fix a problem in linux wx.FileDialog'
80	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
81	if ext not in file:
82	file += ext
83	return file
84
85	def GetPowderPeaks(fileName):
86	'Read powder peaks from a file'
87	sind = lambda x: math.sin(x*math.pi/180.)
88	asind = lambda x: 180.*math.asin(x)/math.pi
89	Cuka = 1.54052
90	File = open(fileName,'Ur')
91	Comments = []
92	peaks = []
93	S = File.readline()
94	while S:
95	if S[:1] == '#':
96	Comments.append(S[:-1])
97	else:
98	item = S.split()
99	if len(item) == 1:
100	peaks.append([float(item[0]),1.0])
101	elif len(item) > 1:
102	peaks.append([float(item[0]),float(item[0])])
103	S = File.readline()
104	File.close()
105	if Comments:
106	print 'Comments on file:'
107	for Comment in Comments: print Comment
108	Peaks = []
109	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
110	for peak in peaks:
111	dsp = peak[0]
112	sth = Cuka/(2.0*dsp)
113	if sth < 1.0:
114	tth = 2.0*asind(sth)
115	else:
116	break
117	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
118	else: #2-thetas - assume Cuka (for now)
119	for peak in peaks:
120	tth = peak[0]
121	dsp = Cuka/(2.0*sind(tth/2.0))
122	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
123	return Comments,Peaks
124
125	def CheckImageFile(G2frame,imagefile):
126	'''Get an new image file name if the specified one does not
127	exist
128
129	:param wx.Frame G2frame: main GSAS-II Frame and data object
130
131	:param str imagefile: name of image file
132
133	:returns: imagefile, if it exists, or the name of a file
134	that does exist or False if the user presses Cancel
135
136	'''
137	if not ospath.exists(imagefile):
138	dlg = wx.FileDialog(G2frame, 'Bad image file name; choose name', '.', '',\
139	'Any image file (.edf;.tif;.tiff;.mar;.avg;.sum;.img)\
140	\|.edf;.tif;.tiff;.mar;.avg;.sum;.img\|\
141	European detector file (.edf)\|.edf\|\
142	Any detector tif (.tif;.tiff)\|.tif;.tiff\|\
143	MAR file (.mar)\|.mar\|\
144	GE Image (.avg;.sum)\|.avg;.sum\|\
145	ADSC Image (.img)\|.img\|\
146	All files (.)\|.',wx.OPEN\|wx.CHANGE_DIR)
147	try:
148	dlg.SetFilename(''+ospath.split(imagefile)[1])
149	if dlg.ShowModal() == wx.ID_OK:
150	imagefile = dlg.GetPath()
151	else:
152	imagefile = False
153	finally:
154	dlg.Destroy()
155	return imagefile
156
157	def GetImageData(G2frame,imagefile,imageOnly=False):
158	'''Read an image with the file reader keyed by the
159	file extension
160
161	:param wx.Frame G2frame: main GSAS-II Frame and data object. Note: not used!
162
163	:param str imagefile: name of image file
164
165	:param bool imageOnly: If True return only the image,
166	otherwise (default) return more (see below)
167
168	:returns: an image as a numpy array or a list of four items:
169	Comments, Data, Npix and the Image, as selected by imageOnly
170
171	'''
172	ext = ospath.splitext(imagefile)[1]
173	Comments = []
174	if ext == '.tif' or ext == '.tiff':
175	Comments,Data,Npix,Image = GetTifData(imagefile)
176	elif ext == '.edf':
177	Comments,Data,Npix,Image = GetEdfData(imagefile)
178	elif ext == '.img':
179	Comments,Data,Npix,Image = GetImgData(imagefile)
180	Image[0][0] = 0
181	elif ext == '.mar3450' or ext == '.mar2300':
182	Comments,Data,Npix,Image = GetMAR345Data(imagefile)
183	elif ext in ['.sum','.avg','']:
184	Comments,Data,Npix,Image = GetGEsumData(imagefile)
185	elif ext == '.G2img':
186	Comments,Data,Npix,Image = GetG2Image(imagefile)
187	if imageOnly:
188	if TRANSP:
189	return Image.T
190	else:
191	return Image
192	else:
193	if TRANSP:
194	return Comments,Data,Npix,Image.T
195	else:
196	return Comments,Data,Npix,Image
197
198	def PutG2Image(filename,Comments,Data,Npix,image):
199	'Write an image as a python pickle'
200	File = open(filename,'wb')
201	cPickle.dump([Comments,Data,Npix,image],File,1)
202	File.close()
203	return
204
205	def GetG2Image(filename):
206	'Read an image as a python pickle'
207	File = open(filename,'rb')
208	Comments,Data,Npix,image = cPickle.load(File)
209	File.close()
210	return Comments,Data,Npix,image
211
212	def GetEdfData(filename,imageOnly=False):
213	'Read European detector data edf file'
214	import struct as st
215	import array as ar
216	if not imageOnly:
217	print 'Read European detector data edf file: ',filename
218	File = open(filename,'rb')
219	fileSize = os.stat(filename).st_size
220	head = File.read(3072)
221	lines = head.split('\n')
222	sizexy = [0,0]
223	pixSize = [0,0]
224	cent = [0,0]
225	head = ['European detector data',]
226	for line in lines:
227	fields = line.split()
228	if 'Dim_1' in line:
229	sizexy[0] = int(fields[2])
230	elif 'Dim_2' in line:
231	sizexy[1] = int(fields[2])
232	elif 'DataType' in line:
233	dType = fields[2]
234	elif 'refined_wavelength' in line:
235	wave = float(fields[2])
236	elif 'Size' in line:
237	imSize = int(fields[2])
238	elif 'DataType' in lines:
239	dType = fields[2]
240	elif 'pixel_size_x' in line:
241	pixSize[0] = float(fields[2])
242	elif 'pixel_size_y' in line:
243	pixSize[1] = float(fields[2])
244	elif 'beam_center_x' in line:
245	cent[0] = float(fields[2])
246	elif 'beam_center_y' in line:
247	cent[1] = float(fields[2])
248	elif 'refined_distance' in line:
249	dist = float(fields[2])
250	if line:
251	head.append(line)
252	File.seek(fileSize-imSize)
253	if dType == 'UnsignedShort':
254	image = np.array(ar.array('H',File.read(imSize)),dtype=np.int32)
255	elif dType == 'UnsignedInt':
256	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
257	image = np.reshape(image,(sizexy[1],sizexy[0]))
258	data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'size':sizexy}
259	Npix = sizexy[0]*sizexy[1]
260	File.close()
261	if imageOnly:
262	return image
263	else:
264	return head,data,Npix,image
265
266	def GetGEsumData(filename,imageOnly=False):
267	'Read SUM file as produced at 1-ID from G.E. images'
268	import struct as st
269	import array as ar
270	if not imageOnly:
271	print 'Read GE sum file: ',filename
272	File = open(filename,'rb')
273	if '.sum' in filename:
274	head = ['GE detector sum data from APS 1-ID',]
275	sizexy = [2048,2048]
276	elif '.avg' in filename:
277	head = ['GE detector avg data from APS 1-ID',]
278	sizexy = [2048,2048]
279	else:
280	head = ['GE detector raw data from APS 1-ID',]
281	File.seek(18)
282	size,nframes = st.unpack('<ih',File.read(6))
283	sizexy = [2048,2048]
284	pos = 8192
285	File.seek(pos)
286	Npix = sizexy[0]*sizexy[1]
287	if '.sum' in filename:
288	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.int32)
289	elif '.avg' in filename:
290	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
291	else:
292	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
293	while nframes > 1:
294	image += np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
295	nframes -= 1
296	image = np.reshape(image,(sizexy[1],sizexy[0]))
297	data = {'pixelSize':(200,200),'wavelength':0.15,'distance':250.0,'center':[204.8,204.8],'size':sizexy}
298	File.close()
299	if imageOnly:
300	return image
301	else:
302	return head,data,Npix,image
303
304	def GetImgData(filename,imageOnly=False):
305	'Read an ADSC image file'
306	import struct as st
307	import array as ar
308	if not imageOnly:
309	print 'Read ADSC img file: ',filename
310	File = open(filename,'rb')
311	head = File.read(511)
312	lines = head.split('\n')
313	head = []
314	center = [0,0]
315	for line in lines[1:-2]:
316	line = line.strip()[:-1]
317	if line:
318	if 'SIZE1' in line:
319	size = int(line.split('=')[1])
320	Npix = size*size
321	elif 'WAVELENGTH' in line:
322	wave = float(line.split('=')[1])
323	elif 'BIN' in line:
324	if line.split('=')[1] == '2x2':
325	pixel=(102,102)
326	else:
327	pixel = (51,51)
328	elif 'DISTANCE' in line:
329	distance = float(line.split('=')[1])
330	elif 'CENTER_X' in line:
331	center[0] = float(line.split('=')[1])
332	elif 'CENTER_Y' in line:
333	center[1] = float(line.split('=')[1])
334	head.append(line)
335	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center,'size':[size,size]}
336	image = []
337	row = 0
338	pos = 512
339	File.seek(pos)
340	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
341	image = np.reshape(image,(sizexy[1],sizexy[0]))
342	# image = np.zeros(shape=(size,size),dtype=np.int32)
343	# while row < size:
344	# File.seek(pos)
345	# line = ar.array('H',File.read(2*size))
346	# image[row] = np.asarray(line)
347	# row += 1
348	# pos += 2*size
349	File.close()
350	if imageOnly:
351	return image
352	else:
353	return lines[1:-2],data,Npix,image
354
355	def GetMAR345Data(filename,imageOnly=False):
356	'Read a MAR-345 image plate image'
357	import array as ar
358	import struct as st
359	try:
360	import pack_f as pf
361	except:
362	msg = wx.MessageDialog(None, message="Unable to load the GSAS MAR image decompression, pack_f",
363	caption="Import Error",
364	style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
365	msg.ShowModal()
366	return None,None,None,None
367
368	if not imageOnly:
369	print 'Read Mar345 file: ',filename
370	File = open(filename,'rb')
371	head = File.read(4095)
372	numbers = st.unpack('<iiiiiiiiii',head[:40])
373	lines = head[128:].split('\n')
374	head = []
375	for line in lines:
376	line = line.strip()
377	if 'PIXEL' in line:
378	values = line.split()
379	pixel = (int(values[2]),int(values[4])) #in microns
380	elif 'WAVELENGTH' in line:
381	wave = float(line.split()[1])
382	elif 'DISTANCE' in line:
383	distance = float(line.split()[1]) #in mm
384	elif 'CENTER' in line:
385	values = line.split()
386	center = [float(values[2])/10.,float(values[4])/10.] #make in mm from pixels
387	if line:
388	head.append(line)
389	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center}
390	for line in head:
391	if 'FORMAT' in line[0:6]:
392	items = line.split()
393	size = int(items[1])
394	Npix = size*size
395	pos = 4096
396	data['size'] = [size,size]
397	File.seek(pos)
398	line = File.read(8)
399	while 'CCP4' not in line: #get past overflow list for now
400	line = File.read(8)
401	pos += 8
402	pos += 37
403	File.seek(pos)
404	raw = File.read()
405	File.close()
406	image = np.zeros(shape=(size,size),dtype=np.int32)
407	image = np.flipud(pf.pack_f(len(raw),raw,size,image).T) #transpose to get it right way around & flip
408	if imageOnly:
409	return image
410	else:
411	return head,data,Npix,image
412
413	def GetTifData(filename,imageOnly=False):
414	'''Read an image in a pseudo-tif format,
415	as produced by a wide variety of software, almost always
416	incorrectly in some way.
417	'''
418	import struct as st
419	import array as ar
420	import ReadMarCCDFrame as rmf
421	File = open(filename,'rb')
422	dataType = 5
423	center = [None,None]
424	wavelength = None
425	distance = None
426	try:
427	Meta = open(filename+'.metadata','Ur')
428	head = Meta.readlines()
429	for line in head:
430	line = line.strip()
431	if 'dataType=' in line:
432	dataType = int(line.split('=')[1])
433	Meta.close()
434	except IOError:
435	print 'no metadata file found - will try to read file anyway'
436	head = ['no metadata file found',]
437
438	tag = File.read(2)
439	byteOrd = '<'
440	if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
441	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
442	elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
443	byteOrd = '>'
444	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
445	else:
446	lines = ['not a detector tiff file',]
447	return lines,0,0,0
448	File.seek(IFD) #get number of directory entries
449	NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
450	IFD = {}
451	for ied in range(NED):
452	Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
453	nVal = st.unpack(byteOrd+'i',File.read(4))[0]
454	if Type == 1:
455	Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
456	elif Type == 2:
457	Value = st.unpack(byteOrd+'i',File.read(4))
458	elif Type == 3:
459	Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
460	x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
461	elif Type == 4:
462	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
463	elif Type == 5:
464	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
465	elif Type == 11:
466	Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
467	IFD[Tag] = [Type,nVal,Value]
468	if DEBUG: print Tag,IFD[Tag]
469	sizexy = [IFD[256][2][0],IFD[257][2][0]]
470	[nx,ny] = sizexy
471	Npix = nx*ny
472	if 34710 in IFD:
473	if not imageOnly:
474	print 'Read MAR CCD tiff file: ',filename
475	marFrame = rmf.marFrame(File,byteOrd,IFD)
476	image = np.flipud(np.array(np.asarray(marFrame.image),dtype=np.int32))
477	tifType = marFrame.filetitle
478	pixy = (marFrame.pixelsizeX/1000.0,marFrame.pixelsizeY/1000.0)
479	head = marFrame.outputHead()
480	# extract resonable wavelength from header
481	wavelength = marFrame.sourceWavelength*1e-5
482	wavelength = (marFrame.opticsWavelength > 0) and marFrame.opticsWavelength*1e-5 or wavelength
483	wavelength = (wavelength <= 0) and None or wavelength
484	# extract resonable distance from header
485	distance = (marFrame.startXtalToDetector+marFrame.endXtalToDetector)*5e-4
486	distance = (distance <= 0) and marFrame.xtalToDetector*1e-3 or distance
487	distance = (distance <= 0) and None or distance
488	# extract resonable center from header
489	center = [marFrame.beamXmarFrame.pixelsizeX1e-9,marFrame.beamYmarFrame.pixelsizeY1e-9]
490	center = (center[0] != 0 and center[1] != 0) and center or [None,None]
491	#print head,tifType,pixy
492	elif 272 in IFD:
493	ifd = IFD[272]
494	File.seek(ifd[2][0])
495	S = File.read(ifd[1])
496	if 'PILATUS' in S:
497	tifType = 'Pilatus'
498	dataType = 0
499	pixy = (172,172)
500	File.seek(4096)
501	if not imageOnly:
502	print 'Read Pilatus tiff file: ',filename
503	image = ar.array('L',File.read(4*Npix))
504	image = np.array(np.asarray(image),dtype=np.int32)
505	else:
506	if IFD[258][2][0] == 16:
507	print sizexy
508	tifType = 'GE'
509	pixy = (200,200)
510	File.seek(8)
511	if not imageOnly:
512	print 'Read GE-detector tiff file: ',filename
513	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
514	elif IFD[258][2][0] == 32:
515	print sizexy
516	tifType = 'CHESS'
517	pixy = (200,200)
518	File.seek(8)
519	if not imageOnly:
520	print 'Read CHESS-detector tiff file: ',filename
521	image = np.array(ar.array('L',File.read(4*Npix)),dtype=np.int32)
522
523	elif 262 in IFD and IFD[262][2][0] > 4:
524	tifType = 'DND'
525	pixy = (158,158)
526	File.seek(512)
527	if not imageOnly:
528	print 'Read DND SAX/WAX-detector tiff file: ',filename
529	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
530	elif sizexy == [1536,1536]:
531	tifType = 'APS Gold'
532	pixy = (150,150)
533	File.seek(64)
534	if not imageOnly:
535	print 'Read Gold tiff file:',filename
536	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
537	elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
538	if IFD[273][2][0] == 8:
539	if IFD[258][2][0] == 32:
540	tifType = 'PE'
541	pixy = (200,200)
542	File.seek(8)
543	if not imageOnly:
544	print 'Read APS PE-detector tiff file: ',filename
545	if dataType == 5:
546	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
547	else:
548	image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
549
550	elif IFD[273][2][0] == 4096:
551	if sizexy[0] == 3072:
552	pixy = (73,73)
553	tifType = 'MAR225'
554	else:
555	pixy = (158,158)
556	tifType = 'MAR325'
557	File.seek(4096)
558	if not imageOnly:
559	print 'Read MAR CCD tiff file: ',filename
560	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
561	elif IFD[273][2][0] == 512:
562	tiftype = '11-ID-C'
563	pixy = [200,200]
564	File.seek(512)
565	if not imageOnly:
566	print 'Read 11-ID-C tiff file: ',filename
567	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
568	elif sizexy == [4096,4096]:
569	if IFD[273][2][0] == 8:
570	if IFD[258][2][0] == 16:
571	tifType = 'scanCCD'
572	pixy = (9,9)
573	File.seek(8)
574	if not imageOnly:
575	print 'Read APS scanCCD tiff file: ',filename
576	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
577	elif IFD[273][2][0] == 4096:
578	tifType = 'Rayonix'
579	pixy = (73.242,73.242)
580	File.seek(4096)
581	if not imageOnly:
582	print 'Read Rayonix MX300HE tiff file: ',filename
583	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
584	# elif sizexy == [960,960]:
585	# tiftype = 'PE-BE'
586	# pixy = (200,200)
587	# File.seek(8)
588	# if not imageOnly:
589	# print 'Read Gold tiff file:',filename
590	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
591
592	else:
593	lines = ['not a known detector tiff file',]
594	return lines,0,0,0
595
596	image = np.reshape(image,(sizexy[1],sizexy[0]))
597	center = (not center[0]) and [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000] or center
598	wavelength = (not wavelength) and 0.10 or wavelength
599	distance = (not distance) and 100.0 or distance
600	data = {'pixelSize':pixy,'wavelength':wavelength,'distance':distance,'center':center,'size':sizexy}
601	File.close()
602	if imageOnly:
603	return image
604	else:
605	return head,data,Npix,image
606
607	#def GetTifData(filename,imageOnly=False):
608	# import struct as st
609	# import array as ar
610	# File = open(filename,'rb')
611	# dataType = 5
612	# try:
613	# Meta = open(filename+'.metadata','Ur')
614	# head = Meta.readlines()
615	# for line in head:
616	# line = line.strip()
617	# if 'dataType=' in line:
618	# dataType = int(line.split('=')[1])
619	# Meta.close()
620	# except IOError:
621	# print 'no metadata file found - will try to read file anyway'
622	# head = ['no metadata file found',]
623	#
624	# tag = File.read(2)
625	# byteOrd = '<'
626	# if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
627	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
628	# elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
629	# byteOrd = '>'
630	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
631	# else:
632	# lines = ['not a detector tiff file',]
633	# return lines,0,0,0
634	# File.seek(IFD) #get number of directory entries
635	# NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
636	# IFD = {}
637	# for ied in range(NED):
638	# Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
639	# nVal = st.unpack(byteOrd+'i',File.read(4))[0]
640	# if Type == 1:
641	# Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
642	# elif Type == 2:
643	# Value = st.unpack(byteOrd+'i',File.read(4))
644	# elif Type == 3:
645	# Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
646	# x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
647	# elif Type == 4:
648	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
649	# elif Type == 5:
650	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
651	# elif Type == 11:
652	# Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
653	# IFD[Tag] = [Type,nVal,Value]
654	## print Tag,IFD[Tag]
655	# sizexy = [IFD[256][2][0],IFD[257][2][0]]
656	# [nx,ny] = sizexy
657	# Npix = nx*ny
658	# if 272 in IFD:
659	# ifd = IFD[272]
660	# File.seek(ifd[2][0])
661	# S = File.read(ifd[1])
662	# if 'PILATUS' in S:
663	# tifType = 'Pilatus'
664	# dataType = 0
665	# pixy = (172,172)
666	# File.seek(4096)
667	# if not imageOnly:
668	# print 'Read Pilatus tiff file: ',filename
669	# image = ar.array('L',File.read(4*Npix))
670	# image = np.array(np.asarray(image),dtype=np.int32)
671	# elif 262 in IFD and IFD[262][2][0] > 4:
672	# tifType = 'DND'
673	# pixy = (158,158)
674	# File.seek(512)
675	# if not imageOnly:
676	# print 'Read DND SAX/WAX-detector tiff file: ',filename
677	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
678	# elif sizexy == [1536,1536]:
679	# tifType = 'APS Gold'
680	# pixy = (150,150)
681	# File.seek(64)
682	# if not imageOnly:
683	# print 'Read Gold tiff file:',filename
684	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
685	# elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
686	# if IFD[273][2][0] == 8:
687	# if IFD[258][2][0] == 32:
688	# tifType = 'PE'
689	# pixy = (200,200)
690	# File.seek(8)
691	# if not imageOnly:
692	# print 'Read APS PE-detector tiff file: ',filename
693	# if dataType == 5:
694	# image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
695	# else:
696	# image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
697	# elif IFD[273][2][0] == 4096:
698	# if sizexy[0] == 3072:
699	# pixy = (73,73)
700	# tifType = 'MAR225'
701	# else:
702	# pixy = (158,158)
703	# tifType = 'MAR325'
704	# File.seek(4096)
705	# if not imageOnly:
706	# print 'Read MAR CCD tiff file: ',filename
707	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
708	# elif IFD[273][2][0] == 512:
709	# tiftype = '11-ID-C'
710	# pixy = [200,200]
711	# File.seek(512)
712	# if not imageOnly:
713	# print 'Read 11-ID-C tiff file: ',filename
714	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
715	# elif sizexy == [4096,4096]:
716	# if IFD[273][2][0] == 8:
717	# if IFD[258][2][0] == 16:
718	# tifType = 'scanCCD'
719	# pixy = (9,9)
720	# File.seek(8)
721	# if not imageOnly:
722	# print 'Read APS scanCCD tiff file: ',filename
723	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
724	# elif IFD[273][2][0] == 4096:
725	# tifType = 'Rayonix'
726	# pixy = (73.242,73.242)
727	# File.seek(4096)
728	# if not imageOnly:
729	# print 'Read Rayonix MX300HE tiff file: ',filename
730	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
731	## elif sizexy == [960,960]:
732	## tiftype = 'PE-BE'
733	## pixy = (200,200)
734	## File.seek(8)
735	## if not imageOnly:
736	## print 'Read Gold tiff file:',filename
737	## image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
738	#
739	# else:
740	# lines = ['not a known detector tiff file',]
741	# return lines,0,0,0
742	#
743	# image = np.reshape(image,(sizexy[1],sizexy[0]))
744	# center = [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000]
745	# data = {'pixelSize':pixy,'wavelength':0.10,'distance':100.0,'center':center,'size':sizexy}
746	# File.close()
747	# if imageOnly:
748	# return image
749	# else:
750	# return head,data,Npix,image
751	#
752	def ProjFileOpen(G2frame):
753	'Read a GSAS-II project file and load into the G2 data tree'
754	file = open(G2frame.GSASprojectfile,'rb')
755	print 'load from file: ',G2frame.GSASprojectfile
756	G2frame.SetTitle("GSAS-II data tree: "+
757	os.path.split(G2frame.GSASprojectfile)[1])
758	wx.BeginBusyCursor()
759	try:
760	while True:
761	try:
762	data = cPickle.load(file)
763	except EOFError:
764	break
765	datum = data[0]
766
767	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=datum[0])
768	if 'PWDR' in datum[0]:
769	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
770	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
771	G2frame.PatternTree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
772	elif datum[0].startswith('HKLF'):
773	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
774	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
775	G2frame.PatternTree.SetItemPyData(Id,datum[1])
776	else:
777	G2frame.PatternTree.SetItemPyData(Id,datum[1])
778	for datus in data[1:]:
779	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
780	#patch
781	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
782	if 'PWDR' in datum[0]:
783	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
784	else:
785	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
786	for item in datus[1][0]: #zip makes tuples - now make lists!
787	datus[1][0][item] = list(datus[1][0][item])
788	#end patch
789	G2frame.PatternTree.SetItemPyData(sub,datus[1])
790	if 'IMG' in datum[0]: #retrieve image default flag & data if set
791	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
792	if Data['setDefault']:
793	G2frame.imageDefault = Data
794	file.close()
795	print('project load successful')
796	G2frame.NewPlot = True
797	except:
798	msg = wx.MessageDialog(G2frame,message="Error reading file "+
799	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
800	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
801	msg.ShowModal()
802	finally:
803	wx.EndBusyCursor()
804
805	def ProjFileSave(G2frame):
806	'Save a GSAS-II project file'
807	if not G2frame.PatternTree.IsEmpty():
808	file = open(G2frame.GSASprojectfile,'wb')
809	print 'save to file: ',G2frame.GSASprojectfile
810	wx.BeginBusyCursor()
811	try:
812	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
813	while item:
814	data = []
815	name = G2frame.PatternTree.GetItemText(item)
816	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
817	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
818	while item2:
819	name = G2frame.PatternTree.GetItemText(item2)
820	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
821	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
822	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
823	cPickle.dump(data,file,1)
824	file.close()
825	finally:
826	wx.EndBusyCursor()
827	print('project save successful')
828
829	def SaveIntegration(G2frame,PickId,data):
830	'Save image integration results as powder pattern(s)'
831	azms = G2frame.Integrate[1]
832	X = G2frame.Integrate[2][:-1]
833	Xminmax = [X[0],X[-1]]
834	N = len(X)
835	Id = G2frame.PatternTree.GetItemParent(PickId)
836	name = G2frame.PatternTree.GetItemText(Id)
837	name = name.replace('IMG ','PWDR ')
838	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
839	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
840	codes = [0 for i in range(12)]
841	LRazm = data['LRazimuth']
842	Azms = []
843	if data['fullIntegrate'] and data['outAzimuths'] == 1:
844	Azms = [45.0,] #a poor man's average?
845	else:
846	for i,azm in enumerate(azms[:-1]):
847	Azms.append((azms[i+1]+azm)/2.)
848	for i,azm in enumerate(azms[:-1]):
849	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
850	Id = 0
851	while item:
852	Name = G2frame.PatternTree.GetItemText(item)
853	if name == Name:
854	Id = item
855	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
856	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!
857	Y = G2frame.Integrate[0][i]
858	W = 1./Y #probably not true
859	Sample = G2pdG.SetDefaultSample()
860	Sample['Gonio. radius'] = data['distance']
861	Sample['Omega'] = data['GonioAngles'][0]
862	Sample['Chi'] = data['GonioAngles'][1]
863	Sample['Phi'] = data['GonioAngles'][2]
864	if Id:
865	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'),Comments)
866	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Limits'),[tuple(Xminmax),Xminmax])
867	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Background'),[['chebyschev',1,3,1.0,0.0,0.0],
868	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
869	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
870	for item in inst[0]:
871	inst[0][item] = list(inst[0][item])
872	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Instrument Parameters'),inst)
873	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Peak List'),[])
874	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Index Peak List'),[])
875	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Unit Cells List'),[])
876	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Reflection Lists'),{})
877	else:
878	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=name+" Azm= %.2f"%(Azms[i]))
879	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
880	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
881	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
882	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
883	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
884	for item in inst[0]:
885	inst[0][item] = list(inst[0][item])
886	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
887	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
888	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),[])
889	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[])
890	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
891	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
892	valuesdict = {
893	'wtFactor':1.0,
894	'Dummy':False,
895	'ranId':ran.randint(0,sys.maxint),
896	}
897	G2frame.PatternTree.SetItemPyData(
898	Id,[valuesdict,
899	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
900	G2frame.PatternTree.SelectItem(Id)
901	G2frame.PatternTree.Expand(Id)
902	G2frame.PatternId = Id
903
904	def powderFxyeSave(G2frame,exports,powderfile):
905	'Save a powder histogram as a GSAS FXYE file'
906	head,tail = ospath.split(powderfile)
907	name,ext = tail.split('.')
908	for i,export in enumerate(exports):
909	filename = ospath.join(head,name+'-%03d.'%(i)+ext)
910	prmname = filename.strip(ext)+'prm'
911	prm = open(prmname,'w') #old style GSAS parm file
912	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
913	Inst = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, \
914	PickId, 'Instrument Parameters'))[0]
915	prm.write( ' 123456789012345678901234567890123456789012345678901234567890 '+'\n')
916	prm.write( 'INS BANK 1 '+'\n')
917	prm.write(('INS HTYPE %sR '+'\n')%(Inst['Type'][0]))
918	if 'Lam1' in Inst: #Ka1 & Ka2
919	prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam1'][0],Inst['Lam2'][0]))
920	elif 'Lam' in Inst: #single wavelength
921	prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam'][1],0.0))
922	prm.write( 'INS 1 IRAD 0 '+'\n')
923	prm.write( 'INS 1I HEAD '+'\n')
924	prm.write( 'INS 1I ITYP 0 0.0000 180.0000 1 '+'\n')
925	prm.write(('INS 1DETAZM%10.3f '+'\n')%(Inst['Azimuth'][0]))
926	prm.write( 'INS 1PRCF1 3 8 0.00100 '+'\n')
927	prm.write(('INS 1PRCF11 %15.6g%15.6g%15.6g%15.6g '+'\n')%(Inst['U'][1],Inst['V'][1],Inst['W'][1],0.0))
928	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.))
929	prm.close()
930	file = open(filename,'w')
931	print 'save powder pattern to file: ',filename
932	x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
933	file.write(powderfile+'\n')
934	file.write('Instrument parameter file:'+ospath.split(prmname)[1]+'\n')
935	file.write('BANK 1 %d %d CONS %.2f %.2f 0 0 FXYE\n'%(len(x),len(x),\
936	100.x[0],100.(x[1]-x[0])))
937	s = list(np.sqrt(1./np.array(w)))
938	XYW = zip(x,y,s)
939	for X,Y,S in XYW:
940	file.write("%15.6g %15.6g %15.6g\n" % (100.*X,Y,max(S,1.0)))
941	file.close()
942	print 'powder pattern file '+filename+' written'
943
944	def powderXyeSave(G2frame,exports,powderfile):
945	'Save a powder histogram as a Topas XYE file'
946	head,tail = ospath.split(powderfile)
947	name,ext = tail.split('.')
948	for i,export in enumerate(exports):
949	filename = ospath.join(head,name+'-%03d.'%(i)+ext)
950	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
951	file = open(filename,'w')
952	file.write('#%s\n'%(export))
953	print 'save powder pattern to file: ',filename
954	x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
955	s = list(np.sqrt(1./np.array(w)))
956	XYW = zip(x,y,s)
957	for X,Y,W in XYW:
958	file.write("%15.6g %15.6g %15.6g\n" % (X,Y,W))
959	file.close()
960	print 'powder pattern file '+filename+' written'
961
962	def PDFSave(G2frame,exports):
963	'Save a PDF G(r) and S(Q) in column formats'
964	for export in exports:
965	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
966	SQname = 'S(Q)'+export[4:]
967	GRname = 'G(R)'+export[4:]
968	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
969	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
970	sqId = G2gd.GetPatternTreeItemId(G2frame, PickId, SQname)
971	grId = G2gd.GetPatternTreeItemId(G2frame, PickId, GRname)
972	sqdata = np.array(G2frame.PatternTree.GetItemPyData(sqId)[1][:2]).T
973	grdata = np.array(G2frame.PatternTree.GetItemPyData(grId)[1][:2]).T
974	sqfile = open(sqfilename,'w')
975	grfile = open(grfilename,'w')
976	sqfile.write('#T S(Q) %s\n'%(export))
977	grfile.write('#T G(R) %s\n'%(export))
978	sqfile.write('#L Q S(Q)\n')
979	grfile.write('#L R G(R)\n')
980	for q,sq in sqdata:
981	sqfile.write("%15.6g %15.6g\n" % (q,sq))
982	sqfile.close()
983	for r,gr in grdata:
984	grfile.write("%15.6g %15.6g\n" % (r,gr))
985	grfile.close()
986
987	def PeakListSave(G2frame,file,peaks):
988	'Save powder peaks to a data file'
989	print 'save peak list to file: ',G2frame.peaklistfile
990	if not peaks:
991	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
992	try:
993	result = dlg.ShowModal()
994	finally:
995	dlg.Destroy()
996	return
997	for peak in peaks:
998	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
999	(peak[0],peak[2],peak[4],peak[6]))
1000	print 'peak list saved'
1001
1002	def IndexPeakListSave(G2frame,peaks):
1003	'Save powder peaks from the indexing list'
1004	file = open(G2frame.peaklistfile,'wa')
1005	print 'save index peak list to file: ',G2frame.peaklistfile
1006	wx.BeginBusyCursor()
1007	try:
1008	if not peaks:
1009	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1010	try:
1011	result = dlg.ShowModal()
1012	finally:
1013	dlg.Destroy()
1014	return
1015	for peak in peaks:
1016	file.write("%12.6f\n" % (peak[7]))
1017	file.close()
1018	finally:
1019	wx.EndBusyCursor()
1020	print 'index peak list saved'
1021
1022	def SetNewPhase(Name='New Phase',SGData=None,cell=None):
1023	'''Create a new phase dict with default values for various parameters
1024
1025	:param str Name: Name for new Phase
1026
1027	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1028	defaults to data for P 1
1029
1030	:param list cell: unit cell parameter list; defaults to
1031	[1.0,1.0,1.0,90.,90,90.,1.]
1032
1033	'''
1034	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1035	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1036	phaseData = {
1037	'ranId':ran.randint(0,sys.maxint),
1038	'General':{
1039	'Name':Name,
1040	'Type':'nuclear',
1041	'AtomPtrs':[3,1,7,9],
1042	'SGData':SGData,
1043	'Cell':[False,]+cell,
1044	'Pawley dmin':1.0,
1045	'Data plot type':'None',
1046	'SH Texture':{
1047	'Order':0,
1048	'Model':'cylindrical',
1049	'Sample omega':[False,0.0],
1050	'Sample chi':[False,0.0],
1051	'Sample phi':[False,0.0],
1052	'SH Coeff':[False,{}],
1053	'SHShow':False,
1054	'PFhkl':[0,0,1],
1055	'PFxyz':[0,0,1],
1056	'PlotType':'Pole figure'}},
1057	'Atoms':[],
1058	'Drawing':{},
1059	'Histograms':{},
1060	'Pawley ref':[],
1061	'RBModels':{},
1062	}
1063	return phaseData
1064
1065	def ReadEXPPhase(G2frame,filename):
1066	'''Read a phase from a GSAS .EXP file.
1067	Called in the GSAS phase import routine (see imports/G2phase.py)
1068	'''
1069	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
1070	textureData = {'Order':0,'Model':'cylindrical','Sample omega':[False,0.0],
1071	'Sample chi':[False,0.0],'Sample phi':[False,0.0],'SH Coeff':[False,{}],
1072	'SHShow':False,'PFhkl':[0,0,1],'PFxyz':[0,0,1],'PlotType':'Pole figure'}
1073	shNcof = 0
1074	file = open(filename, 'Ur')
1075	S = 1
1076	Expr = [{},{},{},{},{},{},{},{},{}]
1077	while S:
1078	S = file.readline()
1079	if 'EXPR NPHAS' in S[:12]:
1080	Num = S[12:-1].count('0')
1081	NPhas = S[12:-1].split()
1082	if 'CRS' in S[:3]:
1083	N = int(S[3:4])-1
1084	Expr[N][S[:12]] = S[12:-1]
1085	file.close()
1086	PNames = []
1087	for n,N in enumerate(NPhas):
1088	if N != '0':
1089	result = n
1090	key = 'CRS'+str(n+1)+' PNAM'
1091	PNames.append(Expr[n][key])
1092	if Num < 8:
1093	dlg = wx.SingleChoiceDialog(G2frame, 'Which phase to read?', 'Read phase data', PNames, wx.CHOICEDLG_STYLE)
1094	try:
1095	if dlg.ShowModal() == wx.ID_OK:
1096	result = dlg.GetSelection()
1097	finally:
1098	dlg.Destroy()
1099	EXPphase = Expr[result]
1100	keyList = EXPphase.keys()
1101	keyList.sort()
1102	SGData = {}
1103	if NPhas[result] == '1':
1104	Ptype = 'nuclear'
1105	elif NPhas[result] in ['2','3']:
1106	Ptype = 'magnetic'
1107	elif NPhas[result] == '4':
1108	Ptype = 'macromolecular'
1109	elif NPhas[result] == '10':
1110	Ptype = 'Pawley'
1111	for key in keyList:
1112	if 'PNAM' in key:
1113	PhaseName = EXPphase[key].strip()
1114	elif 'ABC ' in key:
1115	abc = [float(EXPphase[key][:10]),float(EXPphase[key][10:20]),float(EXPphase[key][20:30])]
1116	elif 'ANGLES' in key:
1117	angles = [float(EXPphase[key][:10]),float(EXPphase[key][10:20]),float(EXPphase[key][20:30])]
1118	elif 'SG SYM' in key:
1119	SpGrp = EXPphase[key][:15].strip()
1120	E,SGData = G2spc.SpcGroup(SpGrp)
1121	if E:
1122	E,SGData = G2spc.SpcGroup('P 1') # unlikely to need this
1123	elif 'OD ' in key:
1124	SHdata = EXPphase[key].split() # may not have all 9 values
1125	SHvals = 9*[0]
1126	for i in range(9):
1127	try:
1128	float(SHdata[i])
1129	SHvals[i] = SHdata[i]
1130	except:
1131	pass
1132	textureData['Order'] = int(SHvals[0])
1133	textureData['Model'] = shModels[int(SHvals[2])]
1134	textureData['Sample omega'] = [False,float(SHvals[6])]
1135	textureData['Sample chi'] = [False,float(SHvals[7])]
1136	textureData['Sample phi'] = [False,float(SHvals[8])]
1137	shNcof = int(SHvals[1])
1138	Atoms = []
1139	if Ptype == 'nuclear':
1140	for key in keyList:
1141	if 'AT' in key:
1142	if key[11:] == 'A':
1143	S = EXPphase[key]
1144	elif key[11:] == 'B':
1145	S += EXPphase[key]
1146	Atom = [S[50:58].strip(),S[:10].strip().capitalize(),'',
1147	float(S[10:20]),float(S[20:30]),float(S[30:40]),
1148	float(S[40:50]),'',int(S[60:62]),S[130:131]]
1149	if Atom[9] == 'I':
1150	Atom += [float(S[68:78]),0.,0.,0.,0.,0.,0.]
1151	elif Atom[9] == 'A':
1152	Atom += [0.0,float(S[68:78]),float(S[78:88]),
1153	float(S[88:98]),float(S[98:108]),
1154	float(S[108:118]),float(S[118:128])]
1155	XYZ = Atom[3:6]
1156	Atom[7],Atom[8] = G2spc.SytSym(XYZ,SGData)
1157	Atom.append(ran.randint(0,sys.maxint))
1158	Atoms.append(Atom)
1159	elif Ptype == 'macromolecular':
1160	for key in keyList:
1161	if 'AT' in key[6:8]:
1162	S = EXPphase[key]
1163	Atom = [S[56:60],S[50:54].strip().upper(),S[54:56],
1164	S[46:51].strip(),S[:8].strip().capitalize(),'',
1165	float(S[16:24]),float(S[24:32]),float(S[32:40]),
1166	float(S[8:16]),'1',1,'I',float(S[40:46]),0,0,0,0,0,0]
1167	XYZ = Atom[6:9]
1168	Atom[10],Atom[11] = G2spc.SytSym(XYZ,SGData)
1169	Atom.append(ran.randint(0,sys.maxint))
1170	Atoms.append(Atom)
1171	Volume = G2lat.calc_V(G2lat.cell2A(abc+angles))
1172	if shNcof:
1173	shCoef = {}
1174	nRec = [i+1 for i in range((shNcof-1)/6+1)]
1175	for irec in nRec:
1176	ODkey = keyList[0][:6]+'OD'+'%3dA'%(irec)
1177	indx = EXPphase[ODkey].split()
1178	ODkey = ODkey[:-1]+'B'
1179	vals = EXPphase[ODkey].split()
1180	for i,val in enumerate(vals):
1181	key = 'C(%s,%s,%s)'%(indx[3i],indx[3i+1],indx[3*i+2])
1182	shCoef[key] = float(val)
1183	textureData['SH Coeff'] = [False,shCoef]
1184
1185	Phase = SetNewPhase(Name=PhaseName,SGData=SGData,cell=abc+angles+[Volume,])
1186	general = Phase['General']
1187	general['Type'] = Ptype
1188	if general['Type'] =='macromolecular':
1189	general['AtomPtrs'] = [6,4,10,12]
1190	else:
1191	general['AtomPtrs'] = [3,1,7,9]
1192	general['SH Texture'] = textureData
1193	Phase['Atoms'] = Atoms
1194	return Phase
1195
1196	def ReadPDBPhase(filename):
1197	'''Read a phase from a PDB file.
1198	Called in the PDB phase import routine (see imports/G2phase.py)
1199	'''
1200	EightPiSq = 8.math.pi*2
1201	file = open(filename, 'Ur')
1202	Phase = {}
1203	Title = ''
1204	Compnd = ''
1205	Atoms = []
1206	A = np.zeros(shape=(3,3))
1207	S = file.readline()
1208	while S:
1209	Atom = []
1210	if 'TITLE' in S[:5]:
1211	Title = S[10:72].strip()
1212	S = file.readline()
1213	elif 'COMPND ' in S[:10]:
1214	Compnd = S[10:72].strip()
1215	S = file.readline()
1216	elif 'CRYST' in S[:5]:
1217	abc = S[7:34].split()
1218	angles = S[34:55].split()
1219	cell=[float(abc[0]),float(abc[1]),float(abc[2]),
1220	float(angles[0]),float(angles[1]),float(angles[2])]
1221	Volume = G2lat.calc_V(G2lat.cell2A(cell))
1222	AA,AB = G2lat.cell2AB(cell)
1223	SpGrp = S[55:65]
1224	E,SGData = G2spc.SpcGroup(SpGrp)
1225	# space group processing failed, try to look up name in table
1226	if E:
1227	SpGrpNorm = G2spc.StandardizeSpcName(SpGrp)
1228	if SpGrpNorm:
1229	E,SGData = G2spc.SpcGroup(SpGrpNorm)
1230	while E:
1231	print G2spc.SGErrors(E)
1232	dlg = wx.TextEntryDialog(None,
1233	SpGrp[:-1]+' is invalid \nN.B.: make sure spaces separate axial fields in symbol',
1234	'ERROR in space group symbol','',style=wx.OK)
1235	if dlg.ShowModal() == wx.ID_OK:
1236	SpGrp = dlg.GetValue()
1237	E,SGData = G2spc.SpcGroup(SpGrp)
1238	else:
1239	return None
1240	dlg.Destroy()
1241	SGlines = G2spc.SGPrint(SGData)
1242	for line in SGlines: print line
1243	S = file.readline()
1244	elif 'SCALE' in S[:5]:
1245	V = (S[10:41].split())
1246	A[int(S[5])-1] = [float(V[0]),float(V[1]),float(V[2])]
1247	S = file.readline()
1248	elif 'ATOM' in S[:4] or 'HETATM' in S[:6]:
1249	XYZ = [float(S[31:39]),float(S[39:47]),float(S[47:55])]
1250	XYZ = np.inner(AB,XYZ)
1251	XYZ = np.where(abs(XYZ)<0.00001,0,XYZ)
1252	SytSym,Mult = G2spc.SytSym(XYZ,SGData)
1253	Uiso = float(S[61:67])/EightPiSq
1254	Type = S[12:14].lower()
1255	if Type[0] in '123456789':
1256	Type = Type[1:]
1257	Atom = [S[22:27].strip(),S[17:20].upper(),S[20:22],
1258	S[12:17].strip(),Type.strip().capitalize(),'',XYZ[0],XYZ[1],XYZ[2],
1259	float(S[55:61]),SytSym,Mult,'I',Uiso,0,0,0,0,0,0]
1260	S = file.readline()
1261	if 'ANISOU' in S[:6]:
1262	Uij = S[30:72].split()
1263	Uij = [float(Uij[0])/10000.,float(Uij[1])/10000.,float(Uij[2])/10000.,
1264	float(Uij[3])/10000.,float(Uij[4])/10000.,float(Uij[5])/10000.]
1265	Atom = Atom[:14]+Uij
1266	Atom[12] = 'A'
1267	S = file.readline()
1268	Atom.append(ran.randint(0,sys.maxint))
1269	Atoms.append(Atom)
1270	else:
1271	S = file.readline()
1272	file.close()
1273	if Title:
1274	PhaseName = Title
1275	elif Compnd:
1276	PhaseName = Compnd
1277	else:
1278	PhaseName = 'None'
1279	Phase = SetNewPhase(Name=PhaseName,SGData=SGData,cell=cell+[Volume,])
1280	Phase['General']['Type'] = 'macromolecular'
1281	Phase['General']['AtomPtrs'] = [6,4,10,12]
1282	Phase['Atoms'] = Atoms
1283	return Phase
1284
1285	class MultipleChoicesDialog(wx.Dialog):
1286	'''A dialog that offers a series of choices, each with a
1287	title and a wx.Choice widget. Intended to be used Modally.
1288	typical input:
1289
1290	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1291	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1292
1293	selections are placed in self.chosen when OK is pressed
1294	'''
1295	def __init__(self,choicelist,headinglist,
1296	head='Select options',
1297	title='Please select from options below',
1298	parent=None):
1299	self.chosen = []
1300	wx.Dialog.__init__(
1301	self,parent,wx.ID_ANY,head,
1302	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1303	panel = wx.Panel(self)
1304	mainSizer = wx.BoxSizer(wx.VERTICAL)
1305	mainSizer.Add((10,10),1)
1306	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1307	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1308	self.ChItems = []
1309	for choice,lbl in zip(choicelist,headinglist):
1310	mainSizer.Add((10,10),1)
1311	self.chosen.append(0)
1312	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1313	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1314	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1315	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1316
1317	OkBtn = wx.Button(panel,-1,"Ok")
1318	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1319	cancelBtn = wx.Button(panel,-1,"Cancel")
1320	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1321	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1322	btnSizer.Add((20,20),1)
1323	btnSizer.Add(OkBtn)
1324	btnSizer.Add((20,20),1)
1325	btnSizer.Add(cancelBtn)
1326	btnSizer.Add((20,20),1)
1327	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1328	panel.SetSizer(mainSizer)
1329	panel.Fit()
1330	self.Fit()
1331
1332	def OnOk(self,event):
1333	parent = self.GetParent()
1334	if parent is not None: parent.Raise()
1335	# save the results from the choice widgets
1336	self.chosen = []
1337	for w in self.ChItems:
1338	self.chosen.append(w.GetSelection())
1339	self.EndModal(wx.ID_OK)
1340
1341	def OnCancel(self,event):
1342	parent = self.GetParent()
1343	if parent is not None: parent.Raise()
1344	self.chosen = []
1345	self.EndModal(wx.ID_CANCEL)
1346
1347	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1348	confirmoverwrite=True, parent=None,
1349	multipleselect=False):
1350	'''If the filename is a zip file, extract a file from that
1351	archive.
1352
1353	:param list Selection: used to predefine the name of the file
1354	to be extracted. Filename case and zip directory name are
1355	ignored in selection; the first matching file is used.
1356
1357	:param bool confirmread: if True asks the user to confirm before expanding
1358	the only file in a zip
1359
1360	:param bool confirmoverwrite: if True asks the user to confirm
1361	before overwriting if the extracted file already exists
1362
1363	:param bool multipleselect: if True allows more than one zip
1364	file to be extracted, a list of file(s) is returned.
1365	If only one file is present, do not ask which one, otherwise
1366	offer a list of choices (unless selection is used).
1367
1368	:returns: the name of the file that has been created or a
1369	list of files (see multipleselect)
1370
1371	If the file is not a zipfile, return the name of the input file.
1372	If the zipfile is empty or no file has been selected, return None
1373	'''
1374	import zipfile # do this now, since we can save startup time by doing this only on need
1375	import shutil
1376	zloc = os.path.split(filename)[0]
1377	if not zipfile.is_zipfile(filename):
1378	#print("not zip")
1379	return filename
1380
1381	z = zipfile.ZipFile(filename,'r')
1382	zinfo = z.infolist()
1383
1384	if len(zinfo) == 0:
1385	#print('Zip has no files!')
1386	zlist = [-1]
1387	if selection:
1388	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1389	if selection.lower() in choices:
1390	zlist = [choices.index(selection.lower())]
1391	else:
1392	print('debug: file '+str(selection)+' was not found in '+str(filename))
1393	zlist = [-1]
1394	elif len(zinfo) == 1 and confirmread:
1395	result = wx.ID_NO
1396	dlg = wx.MessageDialog(
1397	parent,
1398	'Is file '+str(zinfo[0].filename)+
1399	' what you want to extract from '+
1400	str(os.path.split(filename)[1])+'?',
1401	'Confirm file',
1402	wx.YES_NO \| wx.ICON_QUESTION)
1403	try:
1404	result = dlg.ShowModal()
1405	finally:
1406	dlg.Destroy()
1407	if result == wx.ID_NO:
1408	zlist = [-1]
1409	else:
1410	zlist = [0]
1411	elif len(zinfo) == 1:
1412	zlist = [0]
1413	elif multipleselect:
1414	# select one or more from a from list
1415	choices = [i.filename for i in zinfo]
1416	dlg = wx.MultiChoiceDialog(parent,'Select file(s) to extract from zip file'+str(filename),
1417	'Choose file(s)',choices,wx.CHOICEDLG_STYLE,)
1418	if dlg.ShowModal() == wx.ID_OK:
1419	zlist = dlg.GetSelections()
1420	else:
1421	zlist = []
1422	dlg.Destroy()
1423	else:
1424	# select one from a from list
1425	choices = [i.filename for i in zinfo]
1426	dlg = wx.SingleChoiceDialog(parent,
1427	'Select file to extract from zip file'+str(filename),'Choose file',
1428	choices,)
1429	if dlg.ShowModal() == wx.ID_OK:
1430	zlist = [dlg.GetSelection()]
1431	else:
1432	zlist = [-1]
1433	dlg.Destroy()
1434
1435	outlist = []
1436	for zindex in zlist:
1437	if zindex >= 0:
1438	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1439	if os.path.exists(efil) and confirmoverwrite:
1440	result = wx.ID_NO
1441	dlg = wx.MessageDialog(parent,
1442	'File '+str(efil)+' already exists. OK to overwrite it?',
1443	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1444	try:
1445	result = dlg.ShowModal()
1446	finally:
1447	dlg.Destroy()
1448	if result == wx.ID_NO:
1449	zindex = -1
1450	if zindex >= 0:
1451	# extract the file to the current directory, regardless of it's original path
1452	#z.extract(zinfo[zindex],zloc)
1453	eloc,efil = os.path.split(zinfo[zindex].filename)
1454	outfile = os.path.join(zloc, efil)
1455	fpin = z.open(zinfo[zindex])
1456	fpout = file(outfile, "wb")
1457	shutil.copyfileobj(fpin, fpout)
1458	fpin.close()
1459	fpout.close()
1460	outlist.append(outfile)
1461	z.close()
1462	if multipleselect and len(outlist) >= 1:
1463	return outlist
1464	elif len(outlist) == 1:
1465	return outlist[0]
1466	else:
1467	return None
1468
1469	######################################################################
1470	# base classes for reading various types of data files
1471	# not used directly, only by subclassing
1472	######################################################################
1473	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1474	P1SGData = SGData
1475	class ImportBaseclass(object):
1476	'''Defines a base class for the reading of input files (diffraction
1477	data, coordinates,...
1478	'''
1479	def __init__(self,
1480	formatName,
1481	longFormatName=None,
1482	extensionlist=[],
1483	strictExtension=False,
1484	):
1485	self.formatName = formatName # short string naming file type
1486	if longFormatName: # longer string naming file type
1487	self.longFormatName = longFormatName
1488	else:
1489	self.longFormatName = formatName
1490	# define extensions that are allowed for the file type
1491	# for windows, remove any extensions that are duplicate, as case is ignored
1492	if sys.platform == 'windows' and extensionlist:
1493	extensionlist = list(set([s.lower() for s in extensionlist]))
1494	self.extensionlist = extensionlist
1495	# If strictExtension is True, the file will not be read, unless
1496	# the extension matches one in the extensionlist
1497	self.strictExtension = strictExtension
1498	self.warnings = ''
1499	# used for readers that will use multiple passes to read
1500	# more than one data block
1501	self.repeat = False
1502	self.repeatcount = 0
1503	#print 'created',self.__class__
1504
1505	def BlockSelector(self, ChoiceList, ParentFrame=None,
1506	title='Select a block',
1507	size=None, header='Block Selector',
1508	useCancel=True):
1509	''' Provide a wx dialog to select a block if the file contains more
1510	than one set of data and one must be selected
1511	'''
1512	if useCancel:
1513	dlg = wx.SingleChoiceDialog(
1514	ParentFrame,title, header,ChoiceList)
1515	else:
1516	dlg = wx.SingleChoiceDialog(
1517	ParentFrame,title, header,ChoiceList,
1518	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1519	if size: dlg.SetSize(size)
1520	dlg.CenterOnParent()
1521	if dlg.ShowModal() == wx.ID_OK:
1522	sel = dlg.GetSelection()
1523	return sel
1524	else:
1525	return None
1526	dlg.Destroy()
1527
1528	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1529	title='Select a block',size=None, header='Block Selector'):
1530	'''Provide a wx dialog to select a block of data if the
1531	file contains more than one set of data and one must be
1532	selected.
1533
1534	:returns: a list of the selected blocks
1535	'''
1536	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1537	wx.CHOICEDLG_STYLE)
1538	dlg.CenterOnParent()
1539	if size: dlg.SetSize(size)
1540	if dlg.ShowModal() == wx.ID_OK:
1541	sel = dlg.GetSelections()
1542	else:
1543	return []
1544	dlg.Destroy()
1545	selected = []
1546	if len(ChoiceList) in sel:
1547	return range(len(ChoiceList))
1548	else:
1549	return sel
1550	return selected
1551
1552	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1553	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1554	widget. Typical input:
1555
1556	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1557
1558	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1559
1560	optional keyword parameters are: head (window title) and title
1561	returns a list of selected indicies for each choice (or None)
1562	'''
1563	result = None
1564	dlg = MultipleChoicesDialog(choicelist,headinglist,
1565	parent=ParentFrame, **kwargs)
1566	dlg.CenterOnParent()
1567	if dlg.ShowModal() == wx.ID_OK:
1568	result = dlg.chosen
1569	dlg.Destroy()
1570	return result
1571
1572	def ShowBusy(self):
1573	wx.BeginBusyCursor()
1574
1575	def DoneBusy(self):
1576	wx.EndBusyCursor()
1577
1578	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1579	# '''This method must be supplied in the child class
1580	# it will read the file
1581	# '''
1582	# return True # if read OK
1583	# return False # if an error occurs
1584
1585	def ExtensionValidator(self, filename):
1586	'''This methods checks if the file has the correct extension
1587	Return False if this filename will not be supported by this reader
1588	Return True if the extension matches the list supplied by the reader
1589	Return None if the reader allows un-registered extensions
1590	'''
1591	if filename:
1592	ext = os.path.splitext(filename)[1]
1593	if sys.platform == 'windows': ext = ext.lower()
1594	if ext in self.extensionlist: return True
1595	if self.strictExtension: return False
1596	return None
1597
1598	def ContentsValidator(self, filepointer):
1599	'''This routine will attempt to determine if the file can be read
1600	with the current format.
1601	This will typically be overridden with a method that
1602	takes a quick scan of [some of]
1603	the file contents to do a "sanity" check if the file
1604	appears to match the selected format.
1605	Expected to be called via self.Validator()
1606	'''
1607	#filepointer.seek(0) # rewind the file pointer
1608	return True
1609
1610	class ImportPhase(ImportBaseclass):
1611	'''Defines a base class for the reading of files with coordinates
1612
1613	Objects constructed that subclass this (in import/G2phase_*.py) will be used
1614	in :meth:`GSASII.GSASII.OnImportPhase`
1615	'''
1616	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1617	strictExtension=False,):
1618	# call parent __init__
1619	ImportBaseclass.__init__(self,formatName,longFormatName,
1620	extensionlist,strictExtension)
1621	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1622	self.Constraints = None
1623
1624	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1625	title='Select a phase', size=None,header='Phase Selector'):
1626	''' Provide a wx dialog to select a phase if the file contains more
1627	than one phase
1628	'''
1629	return self.BlockSelector(ChoiceList,ParentFrame,title,
1630	size,header)
1631
1632	class ImportStructFactor(ImportBaseclass):
1633	'''Defines a base class for the reading of files with tables
1634	of structure factors
1635
1636	Note that the default controls are stored in self.Controls and the
1637	default instrument parameters are stored in self.Parameters.
1638	These can be changed, but any changes will be the defaults for all
1639	subsequent uses of the :class:`ImportStructFactor` derived classes
1640	until :meth:`InitControls` and :meth:`InitParameters` are
1641	called. Probably better to use :meth:`UpdateControls` and
1642	:meth:`UpdateControls` (adding new args if needed) to change
1643	values.
1644	'''
1645	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1646	strictExtension=False,):
1647	ImportBaseclass.__init__(self,formatName,longFormatName,
1648	extensionlist,strictExtension)
1649
1650	# define contents of Structure Factor entry
1651	self.InitParameters()
1652	self.InitControls()
1653	self.RefDict = {'RefList':[],'FF':[]}
1654
1655	def InitControls(self):
1656	'initialize the controls structure'
1657	self.Controls = { # dictionary with plotting controls
1658	'Type' : 'Fosq',
1659	'ifFc' : False, #
1660	'HKLmax' : [None,None,None],
1661	'HKLmin' : [None,None,None],
1662	'FoMax' : None, # maximum observed structure factor as Fo
1663	'Zone' : '001',
1664	'Layer' : 0,
1665	'Scale' : 1.0,
1666	'log-lin' : 'lin',
1667	}
1668
1669	def InitParameters(self):
1670	'initialize the instrument parameters structure'
1671	Lambda = 0.70926
1672	HistType = 'SXC'
1673	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1674	'Lam':[Lambda,Lambda]
1675	}, {}]
1676
1677	def UpdateParameters(self,Type=None,Wave=None):
1678	'Revise the instrument parameters'
1679	if Type is not None:
1680	self.Parameters[0]['Type'] = [Type,Type]
1681	if Wave is not None:
1682	self.Parameters[0]['Lam'] = [Wave,Wave]
1683
1684	def UpdateControls(self,Type='Fosq',FcalcPresent=False):
1685	'''Scan through the reflections to update the Controls dictionary
1686	'''
1687	self.Controls['Type'] = Type
1688	self.Controls['ifFc'] = FcalcPresent
1689	HKLmax = [None,None,None]
1690	HKLmin = [None,None,None]
1691	Fo2max = None
1692	for refl in self.RefDict['RefList']:
1693	HKL = refl[:3]
1694	if Fo2max is None:
1695	Fo2max = refl[8]
1696	else:
1697	Fo2max = max(Fo2max,refl[8])
1698	for i,hkl in enumerate(HKL):
1699	if HKLmax[i] is None:
1700	HKLmax[i] = hkl
1701	HKLmin[i] = hkl
1702	else:
1703	HKLmax[i] = max(HKLmax[i],hkl)
1704	HKLmin[i] = min(HKLmin[i],hkl)
1705	self.Controls['HKLmax'] = HKLmax
1706	self.Controls['HKLmin'] = HKLmin
1707	if Type == 'Fosq':
1708	self.Controls['FoMax'] = np.sqrt(Fo2max)
1709	elif Type == 'Fo':
1710	self.Controls['FoMax'] = Fo2max
1711	else:
1712	print "Unsupported Struct Fact type in ImportStructFactor.UpdateControls"
1713	raise Exception,"Unsupported Struct Fact type in ImportStructFactor.UpdateControls"
1714
1715	######################################################################
1716	class ImportPowderData(ImportBaseclass):
1717	'''Defines a base class for the reading of files with powder data
1718	'''
1719	# define some default instrument parameter files
1720	# just like GSAS, sigh
1721	defaultIparm_lbl = []
1722	defaultIparms = []
1723	defaultIparm_lbl.append('CuKa lab data')
1724	defaultIparms.append({
1725	'INS HTYPE ':'PXC ',
1726	'INS 1 ICONS':' 1.540500 1.544300 0.0 0 0.7 0 0.5 ',
1727	'INS 1PRCF1 ':' 3 8 0.01 ',
1728	'INS 1PRCF11':' 2.000000E+00 -2.000000E+00 5.000000E+00 0.000000E+00 ',
1729	'INS 1PRCF12':' 0.000000E+00 0.000000E+00 0.150000E-01 0.150000E-01 ',
1730	})
1731	defaultIparm_lbl.append('0.6A synch')
1732	defaultIparms.append({
1733	'INS HTYPE ':'PXC ',
1734	'INS 1 ICONS':' 0.600000 0.000000 0.0 0 0.99 0 0.5 ',
1735	'INS 1PRCF1 ':' 3 8 0.01 ',
1736	'INS 1PRCF11':' 1.000000E+00 -1.000000E+00 0.300000E+00 0.000000E+00 ',
1737	'INS 1PRCF12':' 0.000000E+00 0.000000E+00 0.100000E-01 0.100000E-01 ',
1738	})
1739	defaultIparm_lbl.append('1.5A CW neutron data')
1740	defaultIparms.append({
1741	'INS HTYPE ':'PNC',
1742	'INS 1 ICONS':' 1.54020 0.00000 0.04000 0',
1743	'INS 1PRCF1 ':' 3 8 0.005',
1744	'INS 1PRCF11':' 0.239700E+03 -0.298200E+03 0.180800E+03 0.000000E+00',
1745	'INS 1PRCF12':' 0.000000E+00 0.000000E+00 0.400000E-01 0.300000E-01',
1746	})
1747	defaultIparm_lbl.append('10m TOF backscattering bank')
1748	defaultIparms.append({
1749	'INS HTYPE ':'PNT',
1750	'INS 1 ICONS':' 5000.00 0.00 0.00',
1751	'INS 1BNKPAR':' 1.0000 150.000',
1752	'INS 1PRCF1 ':' 1 8 0.01000',
1753	'INS 1PRCF11':' 0.000000E+00 5.000000E+00 3.000000E-02 1.000000E-03',
1754	'INS 1PRCF12':' 0.000000E+00 4.000000E+01 0.000000E+00 0.000000E+00',
1755	})
1756	defaultIparm_lbl.append('10m TOF 90deg bank')
1757	defaultIparms.append({
1758	'INS HTYPE ':'PNT',
1759	'INS 1 ICONS':' 3500.00 0.00 0.00',
1760	'INS 1BNKPAR':' 1.0000 90.000',
1761	'INS 1PRCF1 ':' 1 8 0.01000',
1762	'INS 1PRCF11':' 0.000000E+00 5.000000E+00 3.000000E-02 4.000000E-03',
1763	'INS 1PRCF12':' 0.000000E+00 8.000000E+01 0.000000E+00 0.000000E+00',
1764	})
1765	defaultIparm_lbl.append('63m POWGEN 90deg bank')
1766	defaultIparms.append({
1767	'INS HTYPE ':'PNT',
1768	'INS 1 ICONS':' 22585.80 0.00 0.00',
1769	'INS 1BNKPAR':' 1.0000 90.000',
1770	'INS 1PRCF1 ':' 1 8 0.01000',
1771	'INS 1PRCF11':' 0.000000E+00 1.000000E+00 3.000000E-02 4.000000E-03',
1772	'INS 1PRCF12':' 0.000000E+00 8.000000E+01 0.000000E+00 0.000000E+00',
1773	})
1774	def __init__(self,
1775	formatName,
1776	longFormatName=None,
1777	extensionlist=[],
1778	strictExtension=False,
1779	):
1780	ImportBaseclass.__init__(self,formatName,
1781	longFormatName,
1782	extensionlist,
1783	strictExtension)
1784	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1785	self.powderdata = [] # Powder dataset
1786	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1787	np.array(x), # x-axis values
1788	np.array(y), # powder pattern intensities
1789	np.array(w), # 1/sig(intensity)^2 values (weights)
1790	np.array(yc), # calc. intensities (zero)
1791	np.array(yb), # calc. background (zero)
1792	np.array(yd), # obs-calc profiles
1793	'''
1794	self.comments = []
1795	self.idstring = ''
1796	self.Sample = G2pdG.SetDefaultSample()
1797	self.GSAS = None # used in TOF
1798	self.clockWd = None # used in TOF
1799	self.repeat_instparm = True # Should a parm file be
1800	# used for multiple histograms?
1801	self.instparm = None # name hint
1802	self.instfile = '' # full path name to instrument parameter file
1803	self.instbank = '' # inst parm bank number
1804	self.instmsg = '' # a label that gets printed to show
1805	# where instrument parameters are from
1806	self.numbanks = 1
1807	self.instdict = {} # place items here that will be transferred to the instrument parameters
1808	######################################################################
1809	class ExportBaseclass(object):
1810	'''Defines a base class for the exporting of GSAS-II results
1811	'''
1812	def __init__(self,
1813	G2frame,
1814	formatName,
1815	extension,
1816	longFormatName=None,
1817	):
1818	self.G2frame = G2frame
1819	self.formatName = formatName # short string naming file type
1820	self.extension = extension
1821	if longFormatName: # longer string naming file type
1822	self.longFormatName = longFormatName
1823	else:
1824	self.longFormatName = formatName
1825	self.OverallParms = {}
1826	self.Phases = {}
1827	self.Histograms = {}
1828	self.powderDict = {}
1829	self.xtalDict = {}
1830	self.parmDict = {}
1831	self.sigDict = {}
1832	# updated in InitExport:
1833	self.currentExportType = None # type of export that has been requested
1834	# updated in ExportSelect (when used):
1835	self.phasenam = None # a list of selected phases
1836	self.histnam = None # a list of selected histograms
1837	self.filename = None # name of file to be written
1838
1839	# items that should be defined in a subclass of this class
1840	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1841	# The following types are defined: 'project', "phase", "powder", "single"
1842	self.multiple = False # set as True if the class can export multiple phases or histograms
1843	# self.multiple is ignored for "project" exports
1844
1845	def InitExport(self,event):
1846	'''Determines the type of menu that called the Exporter.
1847	'''
1848	if event:
1849	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1850
1851	def ExportSelect(self,AskFile=True):
1852	'''Selects histograms or phases when needed. Sets a default file name.
1853
1854	:param bool AskFile: if AskFile is True (default) get the name of the file
1855	in a dialog
1856	:returns: True in case of an error
1857	'''
1858
1859	if self.currentExportType == 'phase':
1860	if len(self.Phases) == 0:
1861	self.G2frame.ErrorDialog(
1862	'Empty project',
1863	'Project does not contain any phases.')
1864	return True
1865	elif len(self.Phases) == 1:
1866	self.phasenam = self.Phases.keys()
1867	elif self.multiple:
1868	choices = sorted(self.Phases.keys())
1869	phasenum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1870	if phasenum is None: return True
1871	self.phasenam = [choices[i] for i in phasenum]
1872	if not self.phasenam: return True
1873	else:
1874	choices = sorted(self.Phases.keys())
1875	phasenum = G2gd.ItemSelector(choices,self.G2frame)
1876	if phasenum is None: return True
1877	self.phasenam = [choices[phasenum]]
1878	elif self.currentExportType == 'single':
1879	if len(self.xtalDict) == 0:
1880	self.G2frame.ErrorDialog(
1881	'Empty project',
1882	'Project does not contain any single crystal data.')
1883	return True
1884	elif len(self.xtalDict) == 1:
1885	self.histnam = self.xtalDict.values()
1886	elif self.multiple:
1887	choices = sorted(self.xtalDict.values())
1888	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1889	if not hnum: return True
1890	self.histnam = [choices[i] for i in hnum]
1891	else:
1892	choices = sorted(self.xtalDict.values())
1893	hnum = G2gd.ItemSelector(choices,self.G2frame)
1894	if hnum is None: return True
1895	self.histnam = [choices[hnum]]
1896	elif self.currentExportType == 'powder':
1897	if len(self.powderDict) == 0:
1898	self.G2frame.ErrorDialog(
1899	'Empty project',
1900	'Project does not contain any powder data.')
1901	return True
1902	elif len(self.powderDict) == 1:
1903	self.histnam = self.powderDict.values()
1904	elif self.multiple:
1905	choices = sorted(self.powderDict.values())
1906	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1907	if not hnum: return True
1908	self.histnam = [choices[i] for i in hnum]
1909	else:
1910	choices = sorted(self.powderDict.values())
1911	hnum = G2gd.ItemSelector(choices,self.G2frame)
1912	if hnum is None: return True
1913	self.histnam = [choices[hnum]]
1914	elif self.currentExportType == 'image':
1915	if len(self.Histograms) == 0:
1916	self.G2frame.ErrorDialog(
1917	'Empty project',
1918	'Project does not contain any images.')
1919	return True
1920	elif len(self.Histograms) == 1:
1921	self.histnam = self.Histograms.keys()
1922	else:
1923	choices = sorted(self.Histograms.keys())
1924	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1925	if self.multiple:
1926	if not hnum: return True
1927	self.histnam = [choices[i] for i in hnum]
1928	else:
1929	if hnum is None: return True
1930	self.histnam = [choices[hnum]]
1931	if self.currentExportType == 'map':
1932	# search for phases with maps
1933	mapPhases = []
1934	choices = []
1935	for phasenam in sorted(self.Phases):
1936	phasedict = self.Phases[phasenam] # pointer to current phase info
1937	if len(phasedict['General']['Map'].get('rho',[])):
1938	mapPhases.append(phasenam)
1939	if phasedict['General']['Map'].get('Flip'):
1940	choices.append('Charge flip map: '+str(phasenam))
1941	elif phasedict['General']['Map'].get('MapType'):
1942	choices.append(
1943	str(phasedict['General']['Map'].get('MapType'))
1944	+ ' map: ' + str(phasenam))
1945	else:
1946	choices.append('unknown map: '+str(phasenam))
1947	# select a map if needed
1948	if len(mapPhases) == 0:
1949	self.G2frame.ErrorDialog(
1950	'Empty project',
1951	'Project does not contain any maps.')
1952	return True
1953	elif len(mapPhases) == 1:
1954	self.phasenam = mapPhases
1955	else:
1956	phasenum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1957	if self.multiple:
1958	if not phasenum: return True
1959	self.phasenam = [mapPhases[i] for i in phasenum]
1960	else:
1961	if phasenum is None: return True
1962	self.phasenam = [mapPhases[phasenum]]
1963
1964	if AskFile:
1965	self.filename = self.askSaveFile()
1966	else:
1967	self.filename = self.defaultSaveFile()
1968	if not self.filename: return True
1969
1970	# def SetupExport(self,event,AskFile=True):
1971	# '''Determines the type of menu that called the Exporter. Selects histograms
1972	# or phases when needed. Better to replace with individual calls to
1973	# self.InitExport() and self.ExportSelect() so that the former can be called prior
1974	# to self.LoadTree()
1975
1976	# :param bool AskFile: if AskFile is True (default) get the name of the file
1977	# in a dialog
1978	# :returns: True in case of an error
1979	# '''
1980	# self.ExportInit(event)
1981	# return self.ExportSelect(AskFile)
1982
1983	def loadParmDict(self):
1984	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1985	refined values to those from the last cycle and set the uncertainties for the
1986	refined parameters in another dict (self.sigDict).
1987
1988	Expands the parm & sig dicts to include values derived from constraints.
1989	'''
1990	self.parmDict = {}
1991	self.sigDict = {}
1992	rigidbodyDict = {}
1993	covDict = {}
1994	consDict = {}
1995	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1996	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
1997	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
1998	while item:
1999	name = self.G2frame.PatternTree.GetItemText(item)
2000	if name == 'Rigid bodies':
2001	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
2002	elif name == 'Covariance':
2003	covDict = self.G2frame.PatternTree.GetItemPyData(item)
2004	elif name == 'Constraints':
2005	consDict = self.G2frame.PatternTree.GetItemPyData(item)
2006	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2007	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
2008	self.parmDict.update(rbDict)
2009	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
2010	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables = G2stIO.GetPhaseData(
2011	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
2012	self.parmDict.update(phaseDict)
2013	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
2014	Phases,Histograms,Print=False,resetRefList=False)
2015	self.parmDict.update(hapDict)
2016	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
2017	self.parmDict.update(histDict)
2018	self.parmDict.update(zip(
2019	covDict.get('varyList',[]),
2020	covDict.get('variables',[])))
2021	self.sigDict = dict(zip(
2022	covDict.get('varyList',[]),
2023	covDict.get('sig',[])))
2024	# expand to include constraints: first compile a list of constraints
2025	constList = []
2026	for item in consDict:
2027	if item.startswith('_'): continue
2028	constList += consDict[item]
2029	# now process the constraints
2030	G2mv.InitVars()
2031	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
2032	varyList = covDict.get('varyListStart')
2033	if varyList is None and len(constDict) == 0:
2034	# no constraints can use varyList
2035	varyList = covDict.get('varyList')
2036	elif varyList is None:
2037	# old GPX file from before pre-constraint varyList is saved
2038	print ' * Old refinement: Please use Calculate/Refine to redo *'
2039	raise Exception(' * Export aborted *')
2040	else:
2041	varyList = list(varyList)
2042	try:
2043	groups,parmlist = G2mv.GroupConstraints(constDict)
2044	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList)
2045	except:
2046	# this really should not happen
2047	print ' * ERROR - constraints are internally inconsistent *'
2048	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
2049	print 'Errors',errmsg
2050	if warnmsg: print 'Warnings',warnmsg
2051	raise Exception(' * CIF creation aborted *')
2052	# add the constrained values to the parameter dictionary
2053	G2mv.Dict2Map(self.parmDict,varyList)
2054	# and add their uncertainties into the esd dictionary (sigDict)
2055	if covDict.get('covMatrix') is not None:
2056	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
2057
2058	def loadTree(self):
2059	'''Load the contents of the data tree into a set of dicts
2060	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2061	& self.xtalDict)
2062
2063	* The childrenless data tree items are overall parameters/controls for the
2064	entire project and are placed in self.OverallParms
2065	* Phase items are placed in self.Phases
2066	* Data items are placed in self.Histogram. The key for these data items
2067	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2068	'''
2069	self.OverallParms = {}
2070	self.powderDict = {}
2071	self.xtalDict = {}
2072	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2073	histType = None
2074	if self.currentExportType == 'phase':
2075	# if exporting phases load them here
2076	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2077	if not sub:
2078	print 'no phases found'
2079	return True
2080	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2081	while item:
2082	phaseName = self.G2frame.PatternTree.GetItemText(item)
2083	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2084	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2085	return
2086	elif self.currentExportType == 'single':
2087	histType = 'HKLF'
2088	elif self.currentExportType == 'powder':
2089	histType = 'PWDR'
2090	elif self.currentExportType == 'image':
2091	histType = 'IMG'
2092
2093	if histType: # Loading just one kind of tree entry
2094	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2095	while item:
2096	name = self.G2frame.PatternTree.GetItemText(item)
2097	if name.startswith(histType):
2098	if self.Histograms.get(name): # there is already an item with this name
2099	if name[-1] == '9':
2100	name = name[:-1] + '10'
2101	elif name[-1] in '012345678':
2102	name = name[:-1] + str(int(name[:-1])+1)
2103	else:
2104	name += '-1'
2105	self.Histograms[name] = {}
2106	# the main info goes into Data, but the 0th
2107	# element contains refinement results, carry
2108	# that over too now.
2109	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2110	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2111	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2112	while item2:
2113	child = self.G2frame.PatternTree.GetItemText(item2)
2114	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2115	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2116	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2117	# index powder and single crystal histograms by number
2118	for hist in self.Histograms:
2119	if hist.startswith("PWDR"):
2120	d = self.powderDict
2121	elif hist.startswith("HKLF"):
2122	d = self.xtalDict
2123	else:
2124	return
2125	i = self.Histograms[hist].get('hId')
2126	if i is None and not d.keys():
2127	i = 0
2128	elif i is None or i in d.keys():
2129	i = max(d.keys())+1
2130	d[i] = hist
2131	return
2132	# else standard load: using all interlinked phases and histograms
2133	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2134	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2135	while item:
2136	name = self.G2frame.PatternTree.GetItemText(item)
2137	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2138	if not item2:
2139	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2140	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2141	# index powder and single crystal histograms
2142	for hist in self.Histograms:
2143	i = self.Histograms[hist]['hId']
2144	if hist.startswith("PWDR"):
2145	self.powderDict[i] = hist
2146	elif hist.startswith("HKLF"):
2147	self.xtalDict[i] = hist
2148
2149	def dumpTree(self,mode='type'):
2150	'''Print out information on the data tree dicts loaded in loadTree
2151	'''
2152	print '\nOverall'
2153	if mode == 'type':
2154	def Show(arg): return type(arg)
2155	else:
2156	def Show(arg): return arg
2157	for key in self.OverallParms:
2158	print ' ',key,Show(self.OverallParms[key])
2159	print 'Phases'
2160	for key1 in self.Phases:
2161	print ' ',key1,Show(self.Phases[key1])
2162	print 'Histogram'
2163	for key1 in self.Histograms:
2164	print ' ',key1,Show(self.Histograms[key1])
2165	for key2 in self.Histograms[key1]:
2166	print ' ',key2,Show(self.Histograms[key1][key2])
2167
2168	def defaultSaveFile(self):
2169	return os.path.abspath(
2170	os.path.splitext(self.G2frame.GSASprojectfile
2171	)[0]+self.extension)
2172
2173	def askSaveFile(self):
2174	'''Ask the user to supply a file name
2175
2176	:returns: a file name (str)
2177	'''
2178	defnam = os.path.splitext(
2179	os.path.split(self.G2frame.GSASprojectfile)[1]
2180	)[0]+self.extension
2181	dlg = wx.FileDialog(
2182	self.G2frame, 'Input name for file to write', '.', defnam,
2183	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2184	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2185	dlg.CenterOnParent()
2186	try:
2187	if dlg.ShowModal() == wx.ID_OK:
2188	filename = dlg.GetPath()
2189	# make sure extension is correct
2190	filename = os.path.splitext(filename)[0]+self.extension
2191	else:
2192	filename = None
2193	finally:
2194	dlg.Destroy()
2195	return filename
2196
2197	# Tools for file writing.
2198	def OpenFile(self,fil=None):
2199	'''Open the output file
2200
2201	:param str fil: The name of the file to open. If None (default)
2202	the name defaults to self.filename.
2203	:returns: the file object opened by the routine which is also
2204	saved as self.fp
2205	'''
2206	if not fil:
2207	fil = self.filename
2208	self.fp = open(fil,'w')
2209	return self.fp
2210	def Write(self,line):
2211	'''write a line of output, attaching a line-end character
2212
2213	:param str line: the text to be written.
2214	'''
2215	self.fp.write(line+'\n')
2216	def CloseFile(self,fp=None):
2217	'''Close a file opened in OpenFile
2218
2219	:param file fp: the file object to be closed. If None (default)
2220	file object self.fp is closed.
2221	'''
2222	if fp is None:
2223	fp = self.fp
2224	self.fp = None
2225	fp.close()
2226	# Tools to pull information out of the data arrays
2227	def GetCell(self,phasenam):
2228	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2229
2230	:param str phasenam: the name for the selected phase
2231	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2232	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2233	cell values and `cellSig` has their uncertainties.
2234	"""
2235	phasedict = self.Phases[phasenam] # pointer to current phase info
2236	try:
2237	pfx = str(phasedict['pId'])+'::'
2238	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2239	cellSig = G2stIO.getCellEsd(pfx,
2240	phasedict['General']['SGData'],A,
2241	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2242	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2243	return cellList,cellSig
2244	except KeyError:
2245	cell = phasedict['General']['Cell'][1:]
2246	return cell,7*[0]
2247
2248	def GetAtoms(self,phasenam):
2249	"""Gets the atoms associated with a phase. Can be used with standard
2250	or macromolecular phases
2251
2252	:param str phasenam: the name for the selected phase
2253	:returns: a list of items for eac atom where each item is a list containing:
2254	label, typ, mult, xyz, and td, where
2255
2256	* label and typ are the atom label and the scattering factor type (str)
2257	* mult is the site multiplicity (int)
2258	* xyz is contains a list with four pairs of numbers:
2259	x, y, z and fractional occupancy and
2260	their standard uncertainty (or a negative value)
2261	* td is contains a list with either one or six pairs of numbers:
2262	if one number it is U\ :sub:`iso` and with six numbers it is
2263	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2264	paired with their standard uncertainty (or a negative value)
2265	"""
2266	phasedict = self.Phases[phasenam] # pointer to current phase info
2267	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2268	cfrac = cx+3
2269	fpfx = str(phasedict['pId'])+'::Afrac:'
2270	atomslist = []
2271	for i,at in enumerate(phasedict['Atoms']):
2272	if phasedict['General']['Type'] == 'macromolecular':
2273	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2274	else:
2275	label = at[ct-1]
2276	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2277	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2278	mult = at[cs+1]
2279	typ = at[ct]
2280	xyz = []
2281	for j,v in enumerate(('x','y','z')):
2282	val = at[cx+j]
2283	pfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2284	sig = self.sigDict.get(pfx,-0.000009)
2285	xyz.append((val,sig))
2286	xyz.append((fval,fsig))
2287	td = []
2288	if at[cia] == 'I':
2289	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2290	val = self.parmDict.get(pfx,at[cia+1])
2291	sig = self.sigDict.get(pfx,-0.0009)
2292	td.append((val,sig))
2293	else:
2294	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2295	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2296	val = self.parmDict.get(pfx,at[cia+2+i])
2297	sig = self.sigDict.get(pfx,-0.0009)
2298	td.append((val,sig))
2299	atomslist.append((label,typ,mult,xyz,td))
2300	return atomslist
2301	######################################################################
2302
2303	def ReadCIF(URLorFile):
2304	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2305	(from James Hester).
2306	The open routine gets confused with DOS names that begin with a letter and colon
2307	"C:\dir\" so this routine will try to open the passed name as a file and if that
2308	fails, try it as a URL
2309
2310	:param str URLorFile: string containing a URL or a file name. Code will try first
2311	to open it as a file and then as a URL.
2312
2313	:returns: a PyCifRW CIF object.
2314	'''
2315	import CifFile as cif # PyCifRW from James Hester
2316
2317	# alternate approach:
2318	#import urllib
2319	#ciffile = 'file:'+urllib.pathname2url(filename)
2320
2321	try:
2322	fp = open(URLorFile,'r')
2323	cf = cif.ReadCif(fp)
2324	fp.close()
2325	return cf
2326	except IOError:
2327	return cif.ReadCif(URLorFile)
2328
2329	if __name__ == '__main__':
2330	app = wx.PySimpleApp()
2331	frm = wx.Frame(None) # create a frame
2332	frm.Show(True)
2333	filename = '/tmp/notzip.zip'
2334	filename = '/tmp/all.zip'
2335	#filename = '/tmp/11bmb_7652.zip'
2336
2337	#selection=None, confirmoverwrite=True, parent=None
2338	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2339	print ExtractFileFromZip(filename,multipleselect=True)
2340	#confirmread=False, confirmoverwrite=False)
2341
2342	# choicelist=[ ('a','b','c'),
2343	# ('test1','test2'),('no choice',)]
2344	# titles = [ 'a, b or c', 'tests', 'No option here']
2345	# dlg = MultipleChoicesDialog(
2346	# choicelist,titles,
2347	# parent=frm)
2348	# if dlg.ShowModal() == wx.ID_OK:
2349	# print 'Got OK'

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