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source: trunk/GSASIIIO.py @ 1156

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

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