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source: trunk/GSASIIIO.py @ 1160

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

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