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source: trunk/GSASIIIO.py @ 956

Last change on this file since 956 was 956, checked in by toby, 10 years ago
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2013-06-19 02:44:58 +0000 (Wed, 19 Jun 2013) $
4	# $Author: toby $
5	# $Revision: 956 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 956 2013-06-19 02:44:58Z 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 random as ran
30	import GSASIIpath
31	GSASIIpath.SetVersionNumber("$Revision: 956 $")
32	import GSASIIgrid as G2gd
33	import GSASIIspc as G2spc
34	import GSASIIlattice as G2lat
35	import GSASIIpwdGUI as G2pdG
36	import GSASIIElem as G2el
37	import GSASIIstrIO as G2stIO
38	import GSASIImapvars as G2mv
39	import os
40	import os.path as ospath
41
42	def sfloat(S):
43	'Convert a string to float. An empty field is treated as zero'
44	if S.strip():
45	return float(S)
46	else:
47	return 0.0
48
49	def sint(S):
50	'Convert a string to int. An empty field is treated as zero'
51	if S.strip():
52	return int(S)
53	else:
54	return 0
55
56	def makeInstDict(names,data,codes):
57	inst = dict(zip(names,zip(data,data,codes)))
58	for item in inst:
59	inst[item] = list(inst[item])
60	return inst
61
62	def FileDlgFixExt(dlg,file):
63	'this is needed to fix a problem in linux wx.FileDialog'
64	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
65	if ext not in file:
66	file += ext
67	return file
68
69	def GetPowderPeaks(fileName):
70	'Read powder peaks from a file'
71	sind = lambda x: math.sin(x*math.pi/180.)
72	asind = lambda x: 180.*math.asin(x)/math.pi
73	Cuka = 1.54052
74	File = open(fileName,'Ur')
75	Comments = []
76	peaks = []
77	S = File.readline()
78	while S:
79	if S[:1] == '#':
80	Comments.append(S[:-1])
81	else:
82	item = S.split()
83	if len(item) == 1:
84	peaks.append([float(item[0]),1.0])
85	elif len(item) > 1:
86	peaks.append([float(item[0]),float(item[0])])
87	S = File.readline()
88	File.close()
89	if Comments:
90	print 'Comments on file:'
91	for Comment in Comments: print Comment
92	Peaks = []
93	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
94	for peak in peaks:
95	dsp = peak[0]
96	sth = Cuka/(2.0*dsp)
97	if sth < 1.0:
98	tth = 2.0*asind(sth)
99	else:
100	break
101	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
102	else: #2-thetas - assume Cuka (for now)
103	for peak in peaks:
104	tth = peak[0]
105	dsp = Cuka/(2.0*sind(tth/2.0))
106	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
107	return Comments,Peaks
108
109	def CheckImageFile(G2frame,imagefile):
110	'''Get an new image file name if the specified one does not
111	exist
112
113	:param wx.Frame G2frame: main GSAS-II Frame and data object
114
115	:param str imagefile: name of image file
116
117	:returns: imagefile, if it exists, or the name of a file
118	that does exist or False if the user presses Cancel
119
120	'''
121	if not ospath.exists(imagefile):
122	dlg = wx.FileDialog(G2frame, 'Bad image file name; choose name', '.', '',\
123	'Any image file (.edf;.tif;.tiff;.mar;.avg;.sum;.img)\
124	\|.edf;.tif;.tiff;.mar;.avg;.sum;.img\|\
125	European detector file (.edf)\|.edf\|\
126	Any detector tif (.tif;.tiff)\|.tif;.tiff\|\
127	MAR file (.mar)\|.mar\|\
128	GE Image (.avg;.sum)\|.avg;.sum\|\
129	ADSC Image (.img)\|.img\|\
130	All files (.)\|.',wx.OPEN\|wx.CHANGE_DIR)
131	try:
132	dlg.SetFilename(''+ospath.split(imagefile)[1])
133	if dlg.ShowModal() == wx.ID_OK:
134	imagefile = dlg.GetPath()
135	else:
136	imagefile = False
137	finally:
138	dlg.Destroy()
139	return imagefile
140
141	def GetImageData(G2frame,imagefile,imageOnly=False):
142	'''Read an image with the file reader keyed by the
143	file extension
144
145	:param wx.Frame G2frame: main GSAS-II Frame and data object
146
147	:param str imagefile: name of image file
148
149	:param bool imageOnly: If True return only the image,
150	otherwise (default) return more (see below)
151
152	:returns: an image as a numpy array or a list of four items:
153	Comments, Data, Npix and the Image, as selected by imageOnly
154
155	'''
156	ext = ospath.splitext(imagefile)[1]
157	Comments = []
158	if ext == '.tif' or ext == '.tiff':
159	Comments,Data,Npix,Image = GetTifData(imagefile)
160	elif ext == '.edf':
161	Comments,Data,Npix,Image = GetEdfData(imagefile)
162	elif ext == '.img':
163	Comments,Data,Npix,Image = GetImgData(imagefile)
164	Image[0][0] = 0
165	elif ext == '.mar3450' or ext == '.mar2300':
166	Comments,Data,Npix,Image = GetMAR345Data(imagefile)
167	elif ext in ['.sum','.avg','']:
168	Comments,Data,Npix,Image = GetGEsumData(imagefile)
169	elif ext == '.G2img':
170	Comments,Data,Npix,Image = GetG2Image(imagefile)
171	if imageOnly:
172	return Image
173	else:
174	return Comments,Data,Npix,Image
175
176	def PutG2Image(filename,Comments,Data,Npix,image):
177	'Write an image as a python pickle'
178	File = open(filename,'wb')
179	cPickle.dump([Comments,Data,Npix,image],File,1)
180	File.close()
181	return
182
183	def GetG2Image(filename):
184	'Read an image as a python pickle'
185	File = open(filename,'rb')
186	Comments,Data,Npix,image = cPickle.load(File)
187	File.close()
188	return Comments,Data,Npix,image
189
190	def GetEdfData(filename,imageOnly=False):
191	'Read European detector data edf file'
192	import struct as st
193	import array as ar
194	if not imageOnly:
195	print 'Read European detector data edf file: ',filename
196	File = open(filename,'rb')
197	fileSize = os.stat(filename).st_size
198	head = File.read(3072)
199	lines = head.split('\n')
200	sizexy = [0,0]
201	pixSize = [0,0]
202	cent = [0,0]
203	head = ['European detector data',]
204	for line in lines:
205	fields = line.split()
206	if 'Dim_1' in line:
207	sizexy[0] = int(fields[2])
208	elif 'Dim_2' in line:
209	sizexy[1] = int(fields[2])
210	elif 'DataType' in line:
211	dType = fields[2]
212	elif 'refined_wavelength' in line:
213	wave = float(fields[2])
214	elif 'Size' in line:
215	imSize = int(fields[2])
216	elif 'DataType' in lines:
217	dType = fields[2]
218	elif 'pixel_size_x' in line:
219	pixSize[0] = float(fields[2])
220	elif 'pixel_size_y' in line:
221	pixSize[1] = float(fields[2])
222	elif 'beam_center_x' in line:
223	cent[0] = float(fields[2])
224	elif 'beam_center_y' in line:
225	cent[1] = float(fields[2])
226	elif 'refined_distance' in line:
227	dist = float(fields[2])
228	if line:
229	head.append(line)
230	File.seek(fileSize-imSize)
231	if dType == 'UnsignedShort':
232	image = np.array(ar.array('H',File.read(imSize)),dtype=np.int32)
233	image = np.reshape(image,(sizexy[1],sizexy[0]))
234	data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'size':sizexy}
235	Npix = sizexy[0]*sizexy[1]
236	File.close()
237	if imageOnly:
238	return image
239	else:
240	return head,data,Npix,image
241
242	def GetGEsumData(filename,imageOnly=False):
243	'Read SUM file as produced at 1-ID from G.E. images'
244	import struct as st
245	import array as ar
246	if not imageOnly:
247	print 'Read GE sum file: ',filename
248	File = open(filename,'rb')
249	if '.sum' in filename:
250	head = ['GE detector sum data from APS 1-ID',]
251	sizexy = [2048,2048]
252	elif '.avg' in filename:
253	head = ['GE detector avg data from APS 1-ID',]
254	sizexy = [2048,2048]
255	else:
256	head = ['GE detector raw data from APS 1-ID',]
257	File.seek(18)
258	size,nframes = st.unpack('<ih',File.read(6))
259	sizexy = [2048,2048]
260	pos = 8192
261	File.seek(pos)
262	Npix = sizexy[0]*sizexy[1]
263	if '.sum' in filename:
264	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.int32)
265	elif '.avg' in filename:
266	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
267	else:
268	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
269	while nframes > 1:
270	image += np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
271	nframes -= 1
272	image = np.reshape(image,(sizexy[1],sizexy[0]))
273	data = {'pixelSize':(200,200),'wavelength':0.15,'distance':250.0,'center':[204.8,204.8],'size':sizexy}
274	File.close()
275	if imageOnly:
276	return image
277	else:
278	return head,data,Npix,image
279
280	def GetImgData(filename,imageOnly=False):
281	'Read an ADSC image file'
282	import struct as st
283	import array as ar
284	if not imageOnly:
285	print 'Read ADSC img file: ',filename
286	File = open(filename,'rb')
287	head = File.read(511)
288	lines = head.split('\n')
289	head = []
290	center = [0,0]
291	for line in lines[1:-2]:
292	line = line.strip()[:-1]
293	if line:
294	if 'SIZE1' in line:
295	size = int(line.split('=')[1])
296	Npix = size*size
297	elif 'WAVELENGTH' in line:
298	wave = float(line.split('=')[1])
299	elif 'BIN' in line:
300	if line.split('=')[1] == '2x2':
301	pixel=(102,102)
302	else:
303	pixel = (51,51)
304	elif 'DISTANCE' in line:
305	distance = float(line.split('=')[1])
306	elif 'CENTER_X' in line:
307	center[0] = float(line.split('=')[1])
308	elif 'CENTER_Y' in line:
309	center[1] = float(line.split('=')[1])
310	head.append(line)
311	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center,'size':[size,size]}
312	image = []
313	row = 0
314	pos = 512
315	File.seek(pos)
316	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
317	image = np.reshape(image,(sizexy[1],sizexy[0]))
318	# image = np.zeros(shape=(size,size),dtype=np.int32)
319	# while row < size:
320	# File.seek(pos)
321	# line = ar.array('H',File.read(2*size))
322	# image[row] = np.asarray(line)
323	# row += 1
324	# pos += 2*size
325	File.close()
326	if imageOnly:
327	return image
328	else:
329	return lines[1:-2],data,Npix,image
330
331	def GetMAR345Data(filename,imageOnly=False):
332	'Read a MAR-345 image plate image'
333	import array as ar
334	import struct as st
335	try:
336	import pack_f as pf
337	except:
338	msg = wx.MessageDialog(None, message="Unable to load the GSAS MAR image decompression, pack_f",
339	caption="Import Error",
340	style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
341	msg.ShowModal()
342	return None,None,None,None
343
344	if not imageOnly:
345	print 'Read Mar345 file: ',filename
346	File = open(filename,'rb')
347	head = File.read(4095)
348	numbers = st.unpack('<iiiiiiiiii',head[:40])
349	lines = head[128:].split('\n')
350	head = []
351	for line in lines:
352	line = line.strip()
353	if 'PIXEL' in line:
354	values = line.split()
355	pixel = (int(values[2]),int(values[4])) #in microns
356	elif 'WAVELENGTH' in line:
357	wave = float(line.split()[1])
358	elif 'DISTANCE' in line:
359	distance = float(line.split()[1]) #in mm
360	elif 'CENTER' in line:
361	values = line.split()
362	center = [float(values[2])/10.,float(values[4])/10.] #make in mm from pixels
363	if line:
364	head.append(line)
365	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center}
366	for line in head:
367	if 'FORMAT' in line[0:6]:
368	items = line.split()
369	size = int(items[1])
370	Npix = size*size
371	pos = 4096
372	data['size'] = [size,size]
373	File.seek(pos)
374	line = File.read(8)
375	while 'CCP4' not in line: #get past overflow list for now
376	line = File.read(8)
377	pos += 8
378	pos += 37
379	File.seek(pos)
380	raw = File.read()
381	File.close()
382	image = np.zeros(shape=(size,size),dtype=np.int32)
383	image = np.flipud(pf.pack_f(len(raw),raw,size,image).T) #transpose to get it right way around & flip
384	if imageOnly:
385	return image
386	else:
387	return head,data,Npix,image
388
389	def GetTifData(filename,imageOnly=False):
390	'''Read an image in a pseudo-tif format,
391	as produced by a wide variety of software, almost always
392	incorrectly in some way.
393	'''
394	import struct as st
395	import array as ar
396	import ReadMarCCDFrame as rmf
397	File = open(filename,'rb')
398	dataType = 5
399	try:
400	Meta = open(filename+'.metadata','Ur')
401	head = Meta.readlines()
402	for line in head:
403	line = line.strip()
404	if 'dataType=' in line:
405	dataType = int(line.split('=')[1])
406	Meta.close()
407	except IOError:
408	print 'no metadata file found - will try to read file anyway'
409	head = ['no metadata file found',]
410
411	tag = File.read(2)
412	byteOrd = '<'
413	if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
414	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
415	elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
416	byteOrd = '>'
417	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
418	else:
419	lines = ['not a detector tiff file',]
420	return lines,0,0,0
421	File.seek(IFD) #get number of directory entries
422	NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
423	IFD = {}
424	for ied in range(NED):
425	Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
426	nVal = st.unpack(byteOrd+'i',File.read(4))[0]
427	if Type == 1:
428	Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
429	elif Type == 2:
430	Value = st.unpack(byteOrd+'i',File.read(4))
431	elif Type == 3:
432	Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
433	x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
434	elif Type == 4:
435	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
436	elif Type == 5:
437	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
438	elif Type == 11:
439	Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
440	IFD[Tag] = [Type,nVal,Value]
441	#print Tag,IFD[Tag]
442	sizexy = [IFD[256][2][0],IFD[257][2][0]]
443	[nx,ny] = sizexy
444	Npix = nx*ny
445	if 34710 in IFD:
446	if not imageOnly:
447	print 'Read MAR CCD tiff file: ',filename
448	marFrame = rmf.marFrame(File,byteOrd,IFD)
449	image = np.flipud(np.array(np.asarray(marFrame.image),dtype=np.int32))
450	tifType = marFrame.filetitle
451	pixy = (marFrame.pixelsizeX/1000.0,marFrame.pixelsizeY/1000.0)
452	head = marFrame.outputHead()
453	elif 272 in IFD:
454	ifd = IFD[272]
455	File.seek(ifd[2][0])
456	S = File.read(ifd[1])
457	if 'PILATUS' in S:
458	tifType = 'Pilatus'
459	dataType = 0
460	pixy = (172,172)
461	File.seek(4096)
462	if not imageOnly:
463	print 'Read Pilatus tiff file: ',filename
464	image = ar.array('L',File.read(4*Npix))
465	image = np.array(np.asarray(image),dtype=np.int32)
466	elif 262 in IFD and IFD[262][2][0] > 4:
467	tifType = 'DND'
468	pixy = (158,158)
469	File.seek(512)
470	if not imageOnly:
471	print 'Read DND SAX/WAX-detector tiff file: ',filename
472	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
473	elif sizexy == [1536,1536]:
474	tifType = 'APS Gold'
475	pixy = (150,150)
476	File.seek(64)
477	if not imageOnly:
478	print 'Read Gold tiff file:',filename
479	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
480	elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
481	if IFD[273][2][0] == 8:
482	if IFD[258][2][0] == 32:
483	tifType = 'PE'
484	pixy = (200,200)
485	File.seek(8)
486	if not imageOnly:
487	print 'Read APS PE-detector tiff file: ',filename
488	if dataType == 5:
489	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
490	else:
491	image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
492	elif IFD[273][2][0] == 4096:
493	if sizexy[0] == 3072:
494	pixy = (73,73)
495	tifType = 'MAR225'
496	else:
497	pixy = (158,158)
498	tifType = 'MAR325'
499	File.seek(4096)
500	if not imageOnly:
501	print 'Read MAR CCD tiff file: ',filename
502	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
503	elif IFD[273][2][0] == 512:
504	tiftype = '11-ID-C'
505	pixy = [200,200]
506	File.seek(512)
507	if not imageOnly:
508	print 'Read 11-ID-C tiff file: ',filename
509	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
510	elif sizexy == [4096,4096]:
511	if IFD[273][2][0] == 8:
512	if IFD[258][2][0] == 16:
513	tifType = 'scanCCD'
514	pixy = (9,9)
515	File.seek(8)
516	if not imageOnly:
517	print 'Read APS scanCCD tiff file: ',filename
518	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
519	elif IFD[273][2][0] == 4096:
520	tifType = 'Rayonix'
521	pixy = (73.242,73.242)
522	File.seek(4096)
523	if not imageOnly:
524	print 'Read Rayonix MX300HE tiff file: ',filename
525	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
526	# elif sizexy == [960,960]:
527	# tiftype = 'PE-BE'
528	# pixy = (200,200)
529	# File.seek(8)
530	# if not imageOnly:
531	# print 'Read Gold tiff file:',filename
532	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
533
534	else:
535	lines = ['not a known detector tiff file',]
536	return lines,0,0,0
537
538	image = np.reshape(image,(sizexy[1],sizexy[0]))
539	center = [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000]
540	data = {'pixelSize':pixy,'wavelength':0.10,'distance':100.0,'center':center,'size':sizexy}
541	File.close()
542	if imageOnly:
543	return image
544	else:
545	return head,data,Npix,image
546
547	#def GetTifData(filename,imageOnly=False):
548	# import struct as st
549	# import array as ar
550	# File = open(filename,'rb')
551	# dataType = 5
552	# try:
553	# Meta = open(filename+'.metadata','Ur')
554	# head = Meta.readlines()
555	# for line in head:
556	# line = line.strip()
557	# if 'dataType=' in line:
558	# dataType = int(line.split('=')[1])
559	# Meta.close()
560	# except IOError:
561	# print 'no metadata file found - will try to read file anyway'
562	# head = ['no metadata file found',]
563	#
564	# tag = File.read(2)
565	# byteOrd = '<'
566	# if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
567	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
568	# elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
569	# byteOrd = '>'
570	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
571	# else:
572	# lines = ['not a detector tiff file',]
573	# return lines,0,0,0
574	# File.seek(IFD) #get number of directory entries
575	# NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
576	# IFD = {}
577	# for ied in range(NED):
578	# Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
579	# nVal = st.unpack(byteOrd+'i',File.read(4))[0]
580	# if Type == 1:
581	# Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
582	# elif Type == 2:
583	# Value = st.unpack(byteOrd+'i',File.read(4))
584	# elif Type == 3:
585	# Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
586	# x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
587	# elif Type == 4:
588	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
589	# elif Type == 5:
590	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
591	# elif Type == 11:
592	# Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
593	# IFD[Tag] = [Type,nVal,Value]
594	## print Tag,IFD[Tag]
595	# sizexy = [IFD[256][2][0],IFD[257][2][0]]
596	# [nx,ny] = sizexy
597	# Npix = nx*ny
598	# if 272 in IFD:
599	# ifd = IFD[272]
600	# File.seek(ifd[2][0])
601	# S = File.read(ifd[1])
602	# if 'PILATUS' in S:
603	# tifType = 'Pilatus'
604	# dataType = 0
605	# pixy = (172,172)
606	# File.seek(4096)
607	# if not imageOnly:
608	# print 'Read Pilatus tiff file: ',filename
609	# image = ar.array('L',File.read(4*Npix))
610	# image = np.array(np.asarray(image),dtype=np.int32)
611	# elif 262 in IFD and IFD[262][2][0] > 4:
612	# tifType = 'DND'
613	# pixy = (158,158)
614	# File.seek(512)
615	# if not imageOnly:
616	# print 'Read DND SAX/WAX-detector tiff file: ',filename
617	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
618	# elif sizexy == [1536,1536]:
619	# tifType = 'APS Gold'
620	# pixy = (150,150)
621	# File.seek(64)
622	# if not imageOnly:
623	# print 'Read Gold tiff file:',filename
624	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
625	# elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
626	# if IFD[273][2][0] == 8:
627	# if IFD[258][2][0] == 32:
628	# tifType = 'PE'
629	# pixy = (200,200)
630	# File.seek(8)
631	# if not imageOnly:
632	# print 'Read APS PE-detector tiff file: ',filename
633	# if dataType == 5:
634	# image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
635	# else:
636	# image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
637	# elif IFD[273][2][0] == 4096:
638	# if sizexy[0] == 3072:
639	# pixy = (73,73)
640	# tifType = 'MAR225'
641	# else:
642	# pixy = (158,158)
643	# tifType = 'MAR325'
644	# File.seek(4096)
645	# if not imageOnly:
646	# print 'Read MAR CCD tiff file: ',filename
647	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
648	# elif IFD[273][2][0] == 512:
649	# tiftype = '11-ID-C'
650	# pixy = [200,200]
651	# File.seek(512)
652	# if not imageOnly:
653	# print 'Read 11-ID-C tiff file: ',filename
654	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
655	# elif sizexy == [4096,4096]:
656	# if IFD[273][2][0] == 8:
657	# if IFD[258][2][0] == 16:
658	# tifType = 'scanCCD'
659	# pixy = (9,9)
660	# File.seek(8)
661	# if not imageOnly:
662	# print 'Read APS scanCCD tiff file: ',filename
663	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
664	# elif IFD[273][2][0] == 4096:
665	# tifType = 'Rayonix'
666	# pixy = (73.242,73.242)
667	# File.seek(4096)
668	# if not imageOnly:
669	# print 'Read Rayonix MX300HE tiff file: ',filename
670	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
671	## elif sizexy == [960,960]:
672	## tiftype = 'PE-BE'
673	## pixy = (200,200)
674	## File.seek(8)
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	#
679	# else:
680	# lines = ['not a known detector tiff file',]
681	# return lines,0,0,0
682	#
683	# image = np.reshape(image,(sizexy[1],sizexy[0]))
684	# center = [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000]
685	# data = {'pixelSize':pixy,'wavelength':0.10,'distance':100.0,'center':center,'size':sizexy}
686	# File.close()
687	# if imageOnly:
688	# return image
689	# else:
690	# return head,data,Npix,image
691	#
692	def ProjFileOpen(G2frame):
693	'Read a GSAS-II project file'
694	file = open(G2frame.GSASprojectfile,'rb')
695	print 'load from file: ',G2frame.GSASprojectfile
696	G2frame.SetTitle("GSAS-II data tree: "+
697	os.path.split(G2frame.GSASprojectfile)[1])
698	wx.BeginBusyCursor()
699	try:
700	while True:
701	try:
702	data = cPickle.load(file)
703	except EOFError:
704	break
705	datum = data[0]
706
707	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=datum[0])
708	if 'PWDR' in datum[0]:
709	G2frame.PatternTree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk
710	else:
711	G2frame.PatternTree.SetItemPyData(Id,datum[1])
712	for datus in data[1:]:
713	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
714	#patch
715	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
716	if 'PWDR' in datum[0]:
717	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
718	else:
719	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
720	for item in datus[1][0]: #zip makes tuples - now make lists!
721	datus[1][0][item] = list(datus[1][0][item])
722	#end patch
723	G2frame.PatternTree.SetItemPyData(sub,datus[1])
724	if 'IMG' in datum[0]: #retrieve image default flag & data if set
725	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
726	if Data['setDefault']:
727	G2frame.imageDefault = Data
728	file.close()
729	print 'project load successful'
730	G2frame.NewPlot = True
731	except:
732	msg = wx.MessageDialog(G2frame,message="Error reading file "+
733	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
734	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
735	msg.ShowModal()
736	finally:
737	wx.EndBusyCursor()
738
739	def ProjFileSave(G2frame):
740	'Save a GSAS-II project file'
741	if not G2frame.PatternTree.IsEmpty():
742	file = open(G2frame.GSASprojectfile,'wb')
743	print 'save to file: ',G2frame.GSASprojectfile
744	wx.BeginBusyCursor()
745	try:
746	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
747	while item:
748	data = []
749	name = G2frame.PatternTree.GetItemText(item)
750	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
751	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
752	while item2:
753	name = G2frame.PatternTree.GetItemText(item2)
754	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
755	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
756	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
757	cPickle.dump(data,file,1)
758	file.close()
759	finally:
760	wx.EndBusyCursor()
761	print 'project save successful'
762
763	def SaveIntegration(G2frame,PickId,data):
764	'Save image integration results as powder pattern(s)'
765	azms = G2frame.Integrate[1]
766	X = G2frame.Integrate[2][:-1]
767	Xminmax = [X[0],X[-1]]
768	N = len(X)
769	Id = G2frame.PatternTree.GetItemParent(PickId)
770	name = G2frame.PatternTree.GetItemText(Id)
771	name = name.replace('IMG ','PWDR ')
772	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
773	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
774	codes = [0 for i in range(12)]
775	LRazm = data['LRazimuth']
776	Azms = []
777	if data['fullIntegrate'] and data['outAzimuths'] == 1:
778	Azms = [45.0,] #a poor man's average?
779	else:
780	for i,azm in enumerate(azms[:-1]):
781	Azms.append((azms[i+1]+azm)/2.)
782	for i,azm in enumerate(azms[:-1]):
783	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
784	Id = 0
785	while item:
786	Name = G2frame.PatternTree.GetItemText(item)
787	if name == Name:
788	Id = item
789	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
790	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!
791	Y = G2frame.Integrate[0][i]
792	W = 1./Y #probably not true
793	Sample = G2pdG.SetDefaultSample()
794	Sample['Gonio. radius'] = data['distance']
795	Sample['Omega'] = data['GonioAngles'][0]
796	Sample['Chi'] = data['GonioAngles'][1]
797	Sample['Phi'] = data['GonioAngles'][2]
798	if Id:
799	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'),Comments)
800	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Limits'),[tuple(Xminmax),Xminmax])
801	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Background'),[['chebyschev',1,3,1.0,0.0,0.0],
802	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
803	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
804	for item in inst[0]:
805	inst[0][item] = list(inst[0][item])
806	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Instrument Parameters'),inst)
807	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Peak List'),[])
808	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Index Peak List'),[])
809	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Unit Cells List'),[])
810	G2frame.PatternTree.SetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Reflection Lists'),{})
811	else:
812	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=name+" Azm= %.2f"%(Azms[i]))
813	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
814	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
815	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
816	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
817	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
818	for item in inst[0]:
819	inst[0][item] = list(inst[0][item])
820	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
821	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
822	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),[])
823	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[])
824	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
825	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
826	G2frame.PatternTree.SetItemPyData(Id,[[''],[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
827	G2frame.PatternTree.SelectItem(Id)
828	G2frame.PatternTree.Expand(Id)
829	G2frame.PatternId = Id
830
831	def powderFxyeSave(G2frame,exports,powderfile):
832	'Save a powder histogram as a GSAS FXYE file'
833	head,tail = ospath.split(powderfile)
834	name,ext = tail.split('.')
835	for i,export in enumerate(exports):
836	filename = ospath.join(head,name+'-%03d.'%(i)+ext)
837	prmname = filename.strip(ext)+'prm'
838	prm = open(prmname,'w') #old style GSAS parm file
839	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
840	Inst = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, \
841	PickId, 'Instrument Parameters'))[0]
842	prm.write( ' 123456789012345678901234567890123456789012345678901234567890 '+'\n')
843	prm.write( 'INS BANK 1 '+'\n')
844	prm.write(('INS HTYPE %sR '+'\n')%(Inst['Type'][0]))
845	if 'Lam1' in Inst: #Ka1 & Ka2
846	prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam1'][0],Inst['Lam2'][0]))
847	elif 'Lam' in Inst: #single wavelength
848	prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam'][1],0.0))
849	prm.write( 'INS 1 IRAD 0 '+'\n')
850	prm.write( 'INS 1I HEAD '+'\n')
851	prm.write( 'INS 1I ITYP 0 0.0000 180.0000 1 '+'\n')
852	prm.write(('INS 1DETAZM%10.3f '+'\n')%(Inst['Azimuth'][0]))
853	prm.write( 'INS 1PRCF1 3 8 0.00100 '+'\n')
854	prm.write(('INS 1PRCF11 %15.6g%15.6g%15.6g%15.6g '+'\n')%(Inst['U'][1],Inst['V'][1],Inst['W'][1],0.0))
855	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.))
856	prm.close()
857	file = open(filename,'w')
858	print 'save powder pattern to file: ',filename
859	x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
860	file.write(powderfile+'\n')
861	file.write('Instrument parameter file:'+ospath.split(prmname)[1]+'\n')
862	file.write('BANK 1 %d %d CONS %.2f %.2f 0 0 FXYE\n'%(len(x),len(x),\
863	100.x[0],100.(x[1]-x[0])))
864	s = list(np.sqrt(1./np.array(w)))
865	XYW = zip(x,y,s)
866	for X,Y,S in XYW:
867	file.write("%15.6g %15.6g %15.6g\n" % (100.*X,Y,max(S,1.0)))
868	file.close()
869	print 'powder pattern file '+filename+' written'
870
871	def powderXyeSave(G2frame,exports,powderfile):
872	'Save a powder histogram as a Topas XYE file'
873	head,tail = ospath.split(powderfile)
874	name,ext = tail.split('.')
875	for i,export in enumerate(exports):
876	filename = ospath.join(head,name+'-%03d.'%(i)+ext)
877	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
878	file = open(filename,'w')
879	file.write('#%s\n'%(export))
880	print 'save powder pattern to file: ',filename
881	x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
882	s = list(np.sqrt(1./np.array(w)))
883	XYW = zip(x,y,s)
884	for X,Y,W in XYW:
885	file.write("%15.6g %15.6g %15.6g\n" % (X,Y,W))
886	file.close()
887	print 'powder pattern file '+filename+' written'
888
889	def PDFSave(G2frame,exports):
890	'Save a PDF G(r) and S(Q) in column formats'
891	for export in exports:
892	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
893	SQname = 'S(Q)'+export[4:]
894	GRname = 'G(R)'+export[4:]
895	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
896	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
897	sqId = G2gd.GetPatternTreeItemId(G2frame, PickId, SQname)
898	grId = G2gd.GetPatternTreeItemId(G2frame, PickId, GRname)
899	sqdata = np.array(G2frame.PatternTree.GetItemPyData(sqId)[1][:2]).T
900	grdata = np.array(G2frame.PatternTree.GetItemPyData(grId)[1][:2]).T
901	sqfile = open(sqfilename,'w')
902	grfile = open(grfilename,'w')
903	sqfile.write('#T S(Q) %s\n'%(export))
904	grfile.write('#T G(R) %s\n'%(export))
905	sqfile.write('#L Q S(Q)\n')
906	grfile.write('#L R G(R)\n')
907	for q,sq in sqdata:
908	sqfile.write("%15.6g %15.6g\n" % (q,sq))
909	sqfile.close()
910	for r,gr in grdata:
911	grfile.write("%15.6g %15.6g\n" % (r,gr))
912	grfile.close()
913
914	def PeakListSave(G2frame,file,peaks):
915	'Save powder peaks to a data file'
916	print 'save peak list to file: ',G2frame.peaklistfile
917	if not peaks:
918	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
919	try:
920	result = dlg.ShowModal()
921	finally:
922	dlg.Destroy()
923	return
924	for peak in peaks:
925	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
926	(peak[0],peak[2],peak[4],peak[6]))
927	print 'peak list saved'
928
929	def IndexPeakListSave(G2frame,peaks):
930	'Save powder peaks from the indexing list'
931	file = open(G2frame.peaklistfile,'wa')
932	print 'save index peak list to file: ',G2frame.peaklistfile
933	wx.BeginBusyCursor()
934	try:
935	if not peaks:
936	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
937	try:
938	result = dlg.ShowModal()
939	finally:
940	dlg.Destroy()
941	return
942	for peak in peaks:
943	file.write("%12.6f\n" % (peak[7]))
944	file.close()
945	finally:
946	wx.EndBusyCursor()
947	print 'index peak list saved'
948
949	def SetNewPhase(Name='New Phase',SGData=None,cell=None):
950	'''Create a new phase with default values for various parameters
951
952	:param str Name: Name for new Phase
953
954	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
955	defaults to data for P 1
956
957	:param list cell: unit cell parameter list; defaults to
958	[1.0,1.0,1.0,90.,90,90.,1.]
959
960	'''
961	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
962	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
963	phaseData = {
964	'ranId':ran.randint(0,sys.maxint),
965	'General':{
966	'Name':Name,
967	'Type':'nuclear',
968	'SGData':SGData,
969	'Cell':[False,]+cell,
970	'Pawley dmin':1.0,
971	'Data plot type':'None',
972	'SH Texture':{
973	'Order':0,
974	'Model':'cylindrical',
975	'Sample omega':[False,0.0],
976	'Sample chi':[False,0.0],
977	'Sample phi':[False,0.0],
978	'SH Coeff':[False,{}],
979	'SHShow':False,
980	'PFhkl':[0,0,1],
981	'PFxyz':[0,0,1],
982	'PlotType':'Pole figure'}},
983	'Atoms':[],
984	'Drawing':{},
985	'Histograms':{},
986	'Pawley ref':[],
987	'RBModels':{},
988	}
989	return phaseData
990
991	def ReadEXPPhase(G2frame,filename):
992	'''Read a phase from a GSAS .EXP file.
993	Called in the GSAS phase import routine (see imports/G2phase.py)
994	'''
995	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
996	textureData = {'Order':0,'Model':'cylindrical','Sample omega':[False,0.0],
997	'Sample chi':[False,0.0],'Sample phi':[False,0.0],'SH Coeff':[False,{}],
998	'SHShow':False,'PFhkl':[0,0,1],'PFxyz':[0,0,1],'PlotType':'Pole figure'}
999	shNcof = 0
1000	file = open(filename, 'Ur')
1001	S = 1
1002	Expr = [{},{},{},{},{},{},{},{},{}]
1003	while S:
1004	S = file.readline()
1005	if 'EXPR NPHAS' in S[:12]:
1006	Num = S[12:-1].count('0')
1007	NPhas = S[12:-1].split()
1008	if 'CRS' in S[:3]:
1009	N = int(S[3:4])-1
1010	Expr[N][S[:12]] = S[12:-1]
1011	file.close()
1012	PNames = []
1013	for n,N in enumerate(NPhas):
1014	if N != '0':
1015	result = n
1016	key = 'CRS'+str(n+1)+' PNAM'
1017	PNames.append(Expr[n][key])
1018	if Num < 8:
1019	dlg = wx.SingleChoiceDialog(G2frame, 'Which phase to read?', 'Read phase data', PNames, wx.CHOICEDLG_STYLE)
1020	try:
1021	if dlg.ShowModal() == wx.ID_OK:
1022	result = dlg.GetSelection()
1023	finally:
1024	dlg.Destroy()
1025	EXPphase = Expr[result]
1026	keyList = EXPphase.keys()
1027	keyList.sort()
1028	SGData = {}
1029	if NPhas[result] == '1':
1030	Ptype = 'nuclear'
1031	elif NPhas[result] in ['2','3']:
1032	Ptype = 'magnetic'
1033	elif NPhas[result] == '4':
1034	Ptype = 'macromolecular'
1035	elif NPhas[result] == '10':
1036	Ptype = 'Pawley'
1037	for key in keyList:
1038	if 'PNAM' in key:
1039	PhaseName = EXPphase[key].strip()
1040	elif 'ABC ' in key:
1041	abc = [float(EXPphase[key][:10]),float(EXPphase[key][10:20]),float(EXPphase[key][20:30])]
1042	elif 'ANGLES' in key:
1043	angles = [float(EXPphase[key][:10]),float(EXPphase[key][10:20]),float(EXPphase[key][20:30])]
1044	elif 'SG SYM' in key:
1045	SpGrp = EXPphase[key][:15].strip()
1046	E,SGData = G2spc.SpcGroup(SpGrp)
1047	if E:
1048	E,SGData = G2spc.SpcGroup('P 1') # unlikely to need this
1049	elif 'OD ' in key:
1050	SHdata = EXPphase[key].split() # may not have all 9 values
1051	SHvals = 9*[0]
1052	for i in range(9):
1053	try:
1054	float(SHdata[i])
1055	SHvals[i] = SHdata[i]
1056	except:
1057	pass
1058	textureData['Order'] = int(SHvals[0])
1059	textureData['Model'] = shModels[int(SHvals[2])]
1060	textureData['Sample omega'] = [False,float(SHvals[6])]
1061	textureData['Sample chi'] = [False,float(SHvals[7])]
1062	textureData['Sample phi'] = [False,float(SHvals[8])]
1063	shNcof = int(SHvals[1])
1064	Atoms = []
1065	if Ptype == 'nuclear':
1066	for key in keyList:
1067	if 'AT' in key:
1068	if key[11:] == 'A':
1069	S = EXPphase[key]
1070	elif key[11:] == 'B':
1071	S += EXPphase[key]
1072	Atom = [S[50:58].strip(),S[:10].strip(),'',
1073	float(S[10:20]),float(S[20:30]),float(S[30:40]),
1074	float(S[40:50]),'',int(S[60:62]),S[130:131]]
1075	if Atom[9] == 'I':
1076	Atom += [float(S[68:78]),0.,0.,0.,0.,0.,0.]
1077	elif Atom[9] == 'A':
1078	Atom += [0.0,float(S[68:78]),float(S[78:88]),
1079	float(S[88:98]),float(S[98:108]),
1080	float(S[108:118]),float(S[118:128])]
1081	XYZ = Atom[3:6]
1082	Atom[7],Atom[8] = G2spc.SytSym(XYZ,SGData)
1083	Atom.append(ran.randint(0,sys.maxint))
1084	Atoms.append(Atom)
1085	elif Ptype == 'macromolecular':
1086	for key in keyList:
1087	if 'AT' in key[6:8]:
1088	S = EXPphase[key]
1089	Atom = [S[56:60],S[50:54].strip().upper(),S[54:56],
1090	S[46:51].strip(),S[:8].strip(),'',
1091	float(S[16:24]),float(S[24:32]),float(S[32:40]),
1092	float(S[8:16]),'1',1,'I',float(S[40:46]),0,0,0,0,0,0]
1093	XYZ = Atom[6:9]
1094	Atom[10],Atom[11] = G2spc.SytSym(XYZ,SGData)
1095	Atom.append(ran.randint(0,sys.maxint))
1096	Atoms.append(Atom)
1097	Volume = G2lat.calc_V(G2lat.cell2A(abc+angles))
1098	if shNcof:
1099	shCoef = {}
1100	nRec = [i+1 for i in range((shNcof-1)/6+1)]
1101	for irec in nRec:
1102	ODkey = keyList[0][:6]+'OD'+'%3dA'%(irec)
1103	indx = EXPphase[ODkey].split()
1104	ODkey = ODkey[:-1]+'B'
1105	vals = EXPphase[ODkey].split()
1106	for i,val in enumerate(vals):
1107	key = 'C(%s,%s,%s)'%(indx[3i],indx[3i+1],indx[3*i+2])
1108	shCoef[key] = float(val)
1109	textureData['SH Coeff'] = [False,shCoef]
1110
1111	Phase = SetNewPhase(Name=PhaseName,SGData=SGData,cell=abc+angles+[Volume,])
1112	general = Phase['General']
1113	general['Type'] = Ptype
1114	general['SH Texture'] = textureData
1115	Phase['Atoms'] = Atoms
1116	return Phase
1117
1118	def ReadPDBPhase(filename):
1119	'''Read a phase from a PDB file.
1120	Called in the PDB phase import routine (see imports/G2phase.py)
1121	'''
1122	EightPiSq = 8.math.pi*2
1123	file = open(filename, 'Ur')
1124	Phase = {}
1125	Title = ''
1126	Compnd = ''
1127	Atoms = []
1128	A = np.zeros(shape=(3,3))
1129	S = file.readline()
1130	while S:
1131	Atom = []
1132	if 'TITLE' in S[:5]:
1133	Title = S[10:72].strip()
1134	S = file.readline()
1135	elif 'COMPND ' in S[:10]:
1136	Compnd = S[10:72].strip()
1137	S = file.readline()
1138	elif 'CRYST' in S[:5]:
1139	abc = S[7:34].split()
1140	angles = S[34:55].split()
1141	cell=[float(abc[0]),float(abc[1]),float(abc[2]),
1142	float(angles[0]),float(angles[1]),float(angles[2])]
1143	Volume = G2lat.calc_V(G2lat.cell2A(cell))
1144	AA,AB = G2lat.cell2AB(cell)
1145	SpGrp = S[55:65]
1146	E,SGData = G2spc.SpcGroup(SpGrp)
1147	# space group processing failed, try to look up name in table
1148	if E:
1149	SpGrpNorm = G2spc.StandardizeSpcName(SpGrp)
1150	if SpGrpNorm:
1151	E,SGData = G2spc.SpcGroup(SpGrpNorm)
1152	while E:
1153	print G2spc.SGErrors(E)
1154	dlg = wx.TextEntryDialog(None,
1155	SpGrp[:-1]+' is invalid \nN.B.: make sure spaces separate axial fields in symbol',
1156	'ERROR in space group symbol','',style=wx.OK)
1157	if dlg.ShowModal() == wx.ID_OK:
1158	SpGrp = dlg.GetValue()
1159	E,SGData = G2spc.SpcGroup(SpGrp)
1160	else:
1161	return None
1162	dlg.Destroy()
1163	SGlines = G2spc.SGPrint(SGData)
1164	for line in SGlines: print line
1165	S = file.readline()
1166	elif 'SCALE' in S[:5]:
1167	V = (S[10:41].split())
1168	A[int(S[5])-1] = [float(V[0]),float(V[1]),float(V[2])]
1169	S = file.readline()
1170	elif 'ATOM' in S[:4] or 'HETATM' in S[:6]:
1171	XYZ = [float(S[31:39]),float(S[39:47]),float(S[47:55])]
1172	XYZ = np.inner(AB,XYZ)
1173	XYZ = np.where(abs(XYZ)<0.00001,0,XYZ)
1174	SytSym,Mult = G2spc.SytSym(XYZ,SGData)
1175	Uiso = float(S[61:67])/EightPiSq
1176	Type = S[12:14].upper()
1177	if Type[0] in '123456789':
1178	Type = Type[1:]
1179	Atom = [S[22:27].strip(),S[17:20].upper(),S[20:22],
1180	S[12:17].strip(),Type.strip(),'',XYZ[0],XYZ[1],XYZ[2],
1181	float(S[55:61]),SytSym,Mult,'I',Uiso,0,0,0,0,0,0]
1182	S = file.readline()
1183	if 'ANISOU' in S[:6]:
1184	Uij = S[30:72].split()
1185	Uij = [float(Uij[0])/10000.,float(Uij[1])/10000.,float(Uij[2])/10000.,
1186	float(Uij[3])/10000.,float(Uij[4])/10000.,float(Uij[5])/10000.]
1187	Atom = Atom[:14]+Uij
1188	Atom[12] = 'A'
1189	S = file.readline()
1190	Atom.append(ran.randint(0,sys.maxint))
1191	Atoms.append(Atom)
1192	else:
1193	S = file.readline()
1194	file.close()
1195	if Title:
1196	PhaseName = Title
1197	elif Compnd:
1198	PhaseName = Compnd
1199	else:
1200	PhaseName = 'None'
1201	Phase = SetNewPhase(Name=PhaseName,SGData=SGData,cell=cell+[Volume,])
1202	Phase['General']['Type'] = 'macromolecular'
1203	Phase['Atoms'] = Atoms
1204
1205	return Phase
1206
1207	class MultipleChoicesDialog(wx.Dialog):
1208	'''A dialog that offers a series of choices, each with a
1209	title and a wx.Choice widget. Intended to be used Modally.
1210	typical input:
1211
1212	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1213	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1214
1215	selections are placed in self.chosen when OK is pressed
1216	'''
1217	def __init__(self,choicelist,headinglist,
1218	head='Select options',
1219	title='Please select from options below',
1220	parent=None):
1221	self.chosen = []
1222	wx.Dialog.__init__(
1223	self,parent,wx.ID_ANY,head,
1224	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1225	panel = wx.Panel(self)
1226	mainSizer = wx.BoxSizer(wx.VERTICAL)
1227	mainSizer.Add((10,10),1)
1228	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1229	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1230	self.ChItems = []
1231	for choice,lbl in zip(choicelist,headinglist):
1232	mainSizer.Add((10,10),1)
1233	self.chosen.append(0)
1234	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1235	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1236	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1237	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1238
1239	OkBtn = wx.Button(panel,-1,"Ok")
1240	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1241	cancelBtn = wx.Button(panel,-1,"Cancel")
1242	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1243	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1244	btnSizer.Add((20,20),1)
1245	btnSizer.Add(OkBtn)
1246	btnSizer.Add((20,20),1)
1247	btnSizer.Add(cancelBtn)
1248	btnSizer.Add((20,20),1)
1249	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1250	panel.SetSizer(mainSizer)
1251	panel.Fit()
1252	self.Fit()
1253
1254	def OnOk(self,event):
1255	parent = self.GetParent()
1256	if parent is not None: parent.Raise()
1257	# save the results from the choice widgets
1258	self.chosen = []
1259	for w in self.ChItems:
1260	self.chosen.append(w.GetSelection())
1261	self.EndModal(wx.ID_OK)
1262
1263	def OnCancel(self,event):
1264	parent = self.GetParent()
1265	if parent is not None: parent.Raise()
1266	self.chosen = []
1267	self.EndModal(wx.ID_CANCEL)
1268
1269	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1270	confirmoverwrite=True, parent=None,
1271	multipleselect=False):
1272	'''If the filename is a zip file, extract a file from that
1273	archive.
1274
1275	:param list Selection: used to predefine the name of the file
1276	to be extracted. Filename case and zip directory name are
1277	ignored in selection; the first matching file is used.
1278
1279	:param bool confirmread: if True asks the user to confirm before expanding
1280	the only file in a zip
1281
1282	:param bool confirmoverwrite: if True asks the user to confirm
1283	before overwriting if the extracted file already exists
1284
1285	:param bool multipleselect: if True allows more than one zip
1286	file to be extracted, a list of file(s) is returned.
1287	If only one file is present, do not ask which one, otherwise
1288	offer a list of choices (unless selection is used).
1289
1290	:returns: the name of the file that has been created or a
1291	list of files (see multipleselect)
1292
1293	If the file is not a zipfile, return the name of the input file.
1294	If the zipfile is empty or no file has been selected, return None
1295	'''
1296	import zipfile # do this now, since we can save startup time by doing this only on need
1297	import shutil
1298	zloc = os.path.split(filename)[0]
1299	if not zipfile.is_zipfile(filename):
1300	#print("not zip")
1301	return filename
1302
1303	z = zipfile.ZipFile(filename,'r')
1304	zinfo = z.infolist()
1305
1306	if len(zinfo) == 0:
1307	#print('Zip has no files!')
1308	zlist = [-1]
1309	if selection:
1310	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1311	if selection.lower() in choices:
1312	zlist = [choices.index(selection.lower())]
1313	else:
1314	print('debug: file '+str(selection)+' was not found in '+str(filename))
1315	zlist = [-1]
1316	elif len(zinfo) == 1 and confirmread:
1317	result = wx.ID_NO
1318	dlg = wx.MessageDialog(
1319	parent,
1320	'Is file '+str(zinfo[0].filename)+
1321	' what you want to extract from '+
1322	str(os.path.split(filename)[1])+'?',
1323	'Confirm file',
1324	wx.YES_NO \| wx.ICON_QUESTION)
1325	try:
1326	result = dlg.ShowModal()
1327	finally:
1328	dlg.Destroy()
1329	if result == wx.ID_NO:
1330	zlist = [-1]
1331	else:
1332	zlist = [0]
1333	elif len(zinfo) == 1:
1334	zlist = [0]
1335	elif multipleselect:
1336	# select one or more from a from list
1337	choices = [i.filename for i in zinfo]
1338	dlg = wx.MultiChoiceDialog(parent,'Select file(s) to extract from zip file'+str(filename),
1339	'Choose file(s)',choices,wx.CHOICEDLG_STYLE,)
1340	if dlg.ShowModal() == wx.ID_OK:
1341	zlist = dlg.GetSelections()
1342	else:
1343	zlist = []
1344	dlg.Destroy()
1345	else:
1346	# select one from a from list
1347	choices = [i.filename for i in zinfo]
1348	dlg = wx.SingleChoiceDialog(parent,
1349	'Select file to extract from zip file'+str(filename),'Choose file',
1350	choices,)
1351	if dlg.ShowModal() == wx.ID_OK:
1352	zlist = [dlg.GetSelection()]
1353	else:
1354	zlist = [-1]
1355	dlg.Destroy()
1356
1357	outlist = []
1358	for zindex in zlist:
1359	if zindex >= 0:
1360	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1361	if os.path.exists(efil) and confirmoverwrite:
1362	result = wx.ID_NO
1363	dlg = wx.MessageDialog(parent,
1364	'File '+str(efil)+' already exists. OK to overwrite it?',
1365	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1366	try:
1367	result = dlg.ShowModal()
1368	finally:
1369	dlg.Destroy()
1370	if result == wx.ID_NO:
1371	zindex = -1
1372	if zindex >= 0:
1373	# extract the file to the current directory, regardless of it's original path
1374	#z.extract(zinfo[zindex],zloc)
1375	eloc,efil = os.path.split(zinfo[zindex].filename)
1376	outfile = os.path.join(zloc, efil)
1377	fpin = z.open(zinfo[zindex])
1378	fpout = file(outfile, "wb")
1379	shutil.copyfileobj(fpin, fpout)
1380	fpin.close()
1381	fpout.close()
1382	outlist.append(outfile)
1383	z.close()
1384	if multipleselect and len(outlist) >= 1:
1385	return outlist
1386	elif len(outlist) == 1:
1387	return outlist[0]
1388	else:
1389	return None
1390
1391	######################################################################
1392	# base classes for reading various types of data files
1393	# not used directly, only by subclassing
1394	######################################################################
1395	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1396	class ImportBaseclass(object):
1397	'''Defines a base class for the importing of data files (diffraction
1398	data, coordinates,...
1399	'''
1400	def __init__(self,
1401	formatName,
1402	longFormatName=None,
1403	extensionlist=[],
1404	strictExtension=False,
1405	):
1406	self.formatName = formatName # short string naming file type
1407	if longFormatName: # longer string naming file type
1408	self.longFormatName = longFormatName
1409	else:
1410	self.longFormatName = formatName
1411	# define extensions that are allowed for the file type
1412	# for windows, remove any extensions that are duplicate, as case is ignored
1413	if sys.platform == 'windows' and extensionlist:
1414	extensionlist = list(set([s.lower() for s in extensionlist]))
1415	self.extensionlist = extensionlist
1416	# If strictExtension is True, the file will not be read, unless
1417	# the extension matches one in the extensionlist
1418	self.strictExtension = strictExtension
1419	self.warnings = ''
1420	# used for readers that will use multiple passes to read
1421	# more than one data block
1422	self.repeat = False
1423	self.repeatcount = 0
1424	#print 'created',self.__class__
1425
1426	def BlockSelector(self, ChoiceList, ParentFrame=None,
1427	title='Select a block',
1428	size=None, header='Block Selector',
1429	useCancel=True):
1430	''' Provide a wx dialog to select a block if the file contains more
1431	than one set of data and one must be selected
1432	'''
1433	if useCancel:
1434	dlg = wx.SingleChoiceDialog(
1435	ParentFrame,title, header,ChoiceList)
1436	else:
1437	dlg = wx.SingleChoiceDialog(
1438	ParentFrame,title, header,ChoiceList,
1439	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1440	if size: dlg.SetSize(size)
1441	if dlg.ShowModal() == wx.ID_OK:
1442	sel = dlg.GetSelection()
1443	return sel
1444	else:
1445	return None
1446	dlg.Destroy()
1447
1448	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1449	title='Select a block',size=None, header='Block Selector'):
1450	'''Provide a wx dialog to select a block of data if the
1451	file contains more than one set of data and one must be
1452	selected.
1453
1454	:returns: a list of the selected blocks
1455	'''
1456	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1457	wx.CHOICEDLG_STYLE)
1458	if size: dlg.SetSize(size)
1459	if dlg.ShowModal() == wx.ID_OK:
1460	sel = dlg.GetSelections()
1461	else:
1462	return []
1463	dlg.Destroy()
1464	selected = []
1465	if len(ChoiceList) in sel:
1466	return range(len(ChoiceList))
1467	else:
1468	return sel
1469	return selected
1470
1471	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1472	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1473	widget. Typical input:
1474
1475	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1476
1477	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1478
1479	optional keyword parameters are: head (window title) and title
1480	returns a list of selected indicies for each choice (or None)
1481	'''
1482	result = None
1483	dlg = MultipleChoicesDialog(choicelist,headinglist,
1484	parent=ParentFrame, **kwargs)
1485	if dlg.ShowModal() == wx.ID_OK:
1486	result = dlg.chosen
1487	dlg.Destroy()
1488	return result
1489
1490	def ShowBusy(self):
1491	wx.BeginBusyCursor()
1492
1493	def DoneBusy(self):
1494	wx.EndBusyCursor()
1495
1496	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1497	# '''This method must be supplied in the child class
1498	# it will read the file
1499	# '''
1500	# return True # if read OK
1501	# return False # if an error occurs
1502
1503	def ExtensionValidator(self, filename):
1504	'''This methods checks if the file has the correct extension
1505	Return False if this filename will not be supported by this reader
1506	Return True if the extension matches the list supplied by the reader
1507	Return None if the reader allows un-registered extensions
1508	'''
1509	if filename:
1510	ext = os.path.splitext(filename)[1]
1511	if sys.platform == 'windows': ext = ext.lower()
1512	if ext in self.extensionlist: return True
1513	if self.strictExtension: return False
1514	return None
1515
1516	def ContentsValidator(self, filepointer):
1517	'''This routine will attempt to determine if the file can be read
1518	with the current format.
1519	This will typically be overridden with a method that
1520	takes a quick scan of [some of]
1521	the file contents to do a "sanity" check if the file
1522	appears to match the selected format.
1523	Expected to be called via self.Validator()
1524	'''
1525	#filepointer.seek(0) # rewind the file pointer
1526	return True
1527
1528	class ImportPhase(ImportBaseclass):
1529	'''Defines a base class for the reading of files with coordinates
1530	'''
1531	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1532	strictExtension=False,):
1533	# call parent __init__
1534	ImportBaseclass.__init__(self,formatName,longFormatName,
1535	extensionlist,strictExtension)
1536	# define a default Phase structure
1537	self.Phase = SetNewPhase(Name='new phase',SGData=SGData)
1538
1539	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1540	title='Select a phase', size=None,header='Phase Selector'):
1541	''' Provide a wx dialog to select a phase if the file contains more
1542	than one phase
1543	'''
1544	return self.BlockSelector(ChoiceList,ParentFrame,title,
1545	size,header)
1546
1547	######################################################################
1548	class ExportBaseclass(object):
1549	'''Defines a base class for the exporting of GSAS-II results
1550	'''
1551	def __init__(self,
1552	G2frame,
1553	formatName,
1554	longFormatName=None,
1555	):
1556	self.G2frame = G2frame
1557	self.formatName = formatName # short string naming file type
1558	if longFormatName: # longer string naming file type
1559	self.longFormatName = longFormatName
1560	else:
1561	self.longFormatName = formatName
1562	self.OverallParms = {}
1563	self.Phases = {}
1564	self.Histograms = {}
1565
1566	def loadParmDict(self):
1567	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1568	refined values to those from the last cycle and set the uncertainties for the
1569	refined parameters in another dict (self.sigDict).
1570
1571	Expands the parm & sig dicts to include values derived from constraints.
1572	'''
1573	self.parmDict = {}
1574	self.sigDict = {}
1575	rigidbodyDict = {}
1576	covDict = {}
1577	consDict = {}
1578	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1579	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
1580	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
1581	while item:
1582	name = self.G2frame.PatternTree.GetItemText(item)
1583	if name == 'Rigid bodies':
1584	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
1585	elif name == 'Covariance':
1586	covDict = self.G2frame.PatternTree.GetItemPyData(item)
1587	elif name == 'Constraints':
1588	consDict = self.G2frame.PatternTree.GetItemPyData(item)
1589	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
1590	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1591	self.parmDict.update(rbDict)
1592	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1593	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables = G2stIO.GetPhaseData(
1594	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1595	self.parmDict.update(phaseDict)
1596	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(Phases,Histograms,Print=False)
1597	self.parmDict.update(hapDict)
1598	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1599	self.parmDict.update(histDict)
1600	self.parmDict.update(zip(
1601	covDict.get('varyList',[]),
1602	covDict.get('variables',[])))
1603	self.sigDict = dict(zip(
1604	covDict.get('varyList',[]),
1605	covDict.get('sig',[])))
1606	# expand to include constraints: first compile a list of constraints
1607	constList = []
1608	for item in consDict:
1609	constList += consDict[item]
1610	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
1611	# now process the constraints
1612	G2mv.InitVars()
1613	varyList = covDict.get('varyList',[])
1614	try:
1615	groups,parmlist = G2mv.GroupConstraints(constDict)
1616	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList)
1617	except:
1618	# this really should not happen
1619	print ' * ERROR - constraints are internally inconsistent *'
1620	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
1621	print 'Errors',errmsg
1622	if warnmsg: print 'Warnings',warnmsg
1623	raise Exception(' * CIF creation aborted *')
1624	# add the constrained values to the parameter dictionary
1625	G2mv.Dict2Map(self.parmDict,varyList)
1626	# and add their uncertainties into the esd dictionary (sigDict)
1627	if covDict.get('covMatrix') is not None:
1628	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],varyList,self.parmDict))
1629
1630	def loadTree(self):
1631	'''Load the contents of the data tree into a set of dicts
1632	(self.OverallParms, self.Phases and self.Histogram)
1633
1634	* The childrenless data tree items are overall parameters/controls for the
1635	entire project and are placed in self.OverallParms
1636	* Phase items are placed in self.Phases
1637	* Data items are placed in self.Histogram. The key for these data items
1638	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
1639	'''
1640	self.OverallParms = {}
1641	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1642	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
1643	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
1644	while item:
1645	name = self.G2frame.PatternTree.GetItemText(item)
1646	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
1647	if not item2:
1648	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
1649	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
1650
1651	def dumpTree(self,mode='type'):
1652	'''Print out information on the data tree dicts loaded in loadTree
1653	'''
1654	print '\nOverall'
1655	if mode == 'type':
1656	def Show(arg): return type(arg)
1657	else:
1658	def Show(arg): return arg
1659	for key in self.OverallParms:
1660	print ' ',key,Show(self.OverallParms[key])
1661	print 'Phases'
1662	for key1 in self.Phases:
1663	print ' ',key1,Show(self.Phases[key1])
1664	print 'Histogram'
1665	for key1 in self.Histograms:
1666	print ' ',key1,Show(self.Histograms[key1])
1667	for key2 in self.Histograms[key1]:
1668	print ' ',key2,Show(self.Histograms[key1][key2])
1669
1670	######################################################################
1671	class ImportStructFactor(ImportBaseclass):
1672	'''Defines a base class for the reading of files with tables
1673	of structure factors
1674	'''
1675	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1676	strictExtension=False,):
1677	ImportBaseclass.__init__(self,formatName,longFormatName,
1678	extensionlist,strictExtension)
1679
1680	# define contents of Structure Factor entry
1681	self.Controls = { # dictionary with plotting controls
1682	'Type' : 'Fosq',
1683	'ifFc' : False, #
1684	'HKLmax' : [None,None,None],
1685	'HKLmin' : [None,None,None],
1686	'FoMax' : None, # maximum observed structure factor as Fo
1687	'Zone' : '001',
1688	'Layer' : 0,
1689	'Scale' : 1.0,
1690	'log-lin' : 'lin',
1691	}
1692	self.Parameters = [ # list with data collection parameters
1693	('SXC',0.70926),
1694	['SXC',0.70926],
1695	['Type','Lam']
1696	]
1697	self.RefList = []
1698
1699	def UpdateParameters(self,Type=None,Wave=None):
1700	HistType = self.Parameters[0][0]
1701	HistWave = self.Parameters[0][1]
1702	if Type is not None:
1703	HistType = Type
1704	if Wave is not None:
1705	HistWave = Wave
1706	self.Parameters = [{'Type':[HistType,HistType],'Lam':[HistWave,HistWave]},{}] # overwrite entire list
1707
1708	def UpdateControls(self,Type='Fosq',FcalcPresent=False):
1709	'''Scan through the reflections to update the Controls dictionary
1710	'''
1711	self.Controls['Type'] = Type
1712	self.Controls['ifFc'] = FcalcPresent
1713	HKLmax = [None,None,None]
1714	HKLmin = [None,None,None]
1715	Fo2max = None
1716	for refl in self.RefList:
1717	HKL = refl[:3]
1718	if Fo2max is None:
1719	Fo2max = refl[8]
1720	else:
1721	Fo2max = max(Fo2max,refl[8])
1722	for i,hkl in enumerate(HKL):
1723	if HKLmax[i] is None:
1724	HKLmax[i] = hkl
1725	HKLmin[i] = hkl
1726	else:
1727	HKLmax[i] = max(HKLmax[i],hkl)
1728	HKLmin[i] = min(HKLmin[i],hkl)
1729	self.Controls['HKLmax'] = HKLmax
1730	self.Controls['HKLmin'] = HKLmin
1731	if Type == 'Fosq':
1732	self.Controls['FoMax'] = np.sqrt(Fo2max)
1733	elif Type == 'Fo':
1734	self.Controls['FoMax'] = Fo2max
1735	else:
1736	print "Unsupported Struct Fact type in ImportStructFactor.UpdateControls"
1737	raise Exception,"Unsupported Struct Fact type in ImportStructFactor.UpdateControls"
1738
1739	######################################################################
1740	class ImportPowderData(ImportBaseclass):
1741	'''Defines a base class for the reading of files with powder data
1742	'''
1743	# define some default instrument parameter files
1744	# just like GSAS, sigh
1745	defaultIparm_lbl = []
1746	defaultIparms = []
1747	defaultIparm_lbl.append('CuKa lab data')
1748	defaultIparms.append({
1749	'INS HTYPE ':'PXC ',
1750	'INS 1 ICONS':' 1.540500 1.544300 0.0 0 0.7 0 0.5 ',
1751	'INS 1PRCF1 ':' 3 8 0.01 ',
1752	'INS 1PRCF11':' 2.000000E+00 -2.000000E+00 5.000000E+00 0.000000E+00 ',
1753	'INS 1PRCF12':' 0.000000E+00 0.000000E+00 0.150000E-01 0.150000E-01 ',
1754	})
1755	defaultIparm_lbl.append('0.6A synch')
1756	defaultIparms.append({
1757	'INS HTYPE ':'PXC ',
1758	'INS 1 ICONS':' 0.600000 0.000000 0.0 0 0.99 0 0.5 ',
1759	'INS 1PRCF1 ':' 3 8 0.01 ',
1760	'INS 1PRCF11':' 1.000000E+00 -1.000000E+00 0.300000E+00 0.000000E+00 ',
1761	'INS 1PRCF12':' 0.000000E+00 0.000000E+00 0.100000E-01 0.100000E-01 ',
1762	})
1763	defaultIparm_lbl.append('1.5A CW neutron data')
1764	defaultIparms.append({
1765	'INS HTYPE ':'PNC',
1766	'INS 1 ICONS':' 1.54020 0.00000 0.04000 0',
1767	'INS 1PRCF1 ':' 3 8 0.005',
1768	'INS 1PRCF11':' 0.239700E+03 -0.298200E+03 0.180800E+03 0.000000E+00',
1769	'INS 1PRCF12':' 0.000000E+00 0.000000E+00 0.400000E-01 0.300000E-01',
1770	})
1771	defaultIparm_lbl.append('10m TOF backscattering bank')
1772	defaultIparms.append({
1773	'INS HTYPE ':'PNT',
1774	'INS 1 ICONS':' 5000.00 0.00 0.00',
1775	'INS 1BNKPAR':' 1.0000 150.000',
1776	'INS 1PRCF1 ':' 1 8 0.01000',
1777	'INS 1PRCF11':' 0.000000E+00 5.000000E+00 3.000000E-02 1.000000E-03',
1778	'INS 1PRCF12':' 0.000000E+00 4.000000E+01 0.000000E+00 0.000000E+00',
1779	})
1780	defaultIparm_lbl.append('10m TOF 90deg bank')
1781	defaultIparms.append({
1782	'INS HTYPE ':'PNT',
1783	'INS 1 ICONS':' 3500.00 0.00 0.00',
1784	'INS 1BNKPAR':' 1.0000 90.000',
1785	'INS 1PRCF1 ':' 1 8 0.01000',
1786	'INS 1PRCF11':' 0.000000E+00 5.000000E+00 3.000000E-02 4.000000E-03',
1787	'INS 1PRCF12':' 0.000000E+00 8.000000E+01 0.000000E+00 0.000000E+00',
1788	})
1789	defaultIparm_lbl.append('63m POWGEN 90deg bank')
1790	defaultIparms.append({
1791	'INS HTYPE ':'PNT',
1792	'INS 1 ICONS':' 22585.80 0.00 0.00',
1793	'INS 1BNKPAR':' 1.0000 90.000',
1794	'INS 1PRCF1 ':' 1 8 0.01000',
1795	'INS 1PRCF11':' 0.000000E+00 1.000000E+00 3.000000E-02 4.000000E-03',
1796	'INS 1PRCF12':' 0.000000E+00 8.000000E+01 0.000000E+00 0.000000E+00',
1797	})
1798	def __init__(self,
1799	formatName,
1800	longFormatName=None,
1801	extensionlist=[],
1802	strictExtension=False,
1803	):
1804	ImportBaseclass.__init__(self,formatName,
1805	longFormatName,
1806	extensionlist,
1807	strictExtension)
1808	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1809	self.powderdata = [] # Powder dataset
1810	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1811	np.array(x), # x-axis values
1812	np.array(y), # powder pattern intensities
1813	np.array(w), # 1/sig(intensity)^2 values (weights)
1814	np.array(yc), # calc. intensities (zero)
1815	np.array(yb), # calc. background (zero)
1816	np.array(yd), # obs-calc profiles
1817	'''
1818	self.comments = []
1819	self.idstring = ''
1820	self.Sample = G2pdG.SetDefaultSample()
1821	self.GSAS = None # used in TOF
1822	self.clockWd = None # used in TOF
1823	self.repeat_instparm = True # Should a parm file be
1824	# used for multiple histograms?
1825	self.instparm = None # name hint
1826	self.instfile = '' # full path name to instrument parameter file
1827	self.instbank = '' # inst parm bank number
1828	self.instmsg = '' # a label that gets printed to show
1829	# where instrument parameters are from
1830	self.numbanks = 1
1831	self.instdict = {} # place items here that will be transferred to the instrument parameters
1832
1833	if __name__ == '__main__':
1834	app = wx.PySimpleApp()
1835	frm = wx.Frame(None) # create a frame
1836	frm.Show(True)
1837	filename = '/tmp/notzip.zip'
1838	filename = '/tmp/all.zip'
1839	#filename = '/tmp/11bmb_7652.zip'
1840
1841	#selection=None, confirmoverwrite=True, parent=None
1842	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
1843	print ExtractFileFromZip(filename,multipleselect=True)
1844	#confirmread=False, confirmoverwrite=False)
1845
1846	# choicelist=[ ('a','b','c'),
1847	# ('test1','test2'),('no choice',)]
1848	# titles = [ 'a, b or c', 'tests', 'No option here']
1849	# dlg = MultipleChoicesDialog(
1850	# choicelist,titles,
1851	# parent=frm)
1852	# if dlg.ShowModal() == wx.ID_OK:
1853	# print 'Got OK'

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