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source: trunk/GSASIIIO.py @ 1572

Last change on this file since 1572 was 1572, checked in by vondreele, 8 years ago
complete SS indexing, apply hklm extinction rules cleanup indexing, cell refine, load cell, make new phase, calibration, etc.
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2014-11-17 22:37:02 +0000 (Mon, 17 Nov 2014) $
4	# $Author: vondreele $
5	# $Revision: 1572 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 1572 2014-11-17 22:37:02Z 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: 1572 $")
33	import GSASIIgrid as G2gd
34	import GSASIIspc as G2spc
35	import GSASIIlattice as G2lat
36	import GSASIIpwdGUI as G2pdG
37	import GSASIIElem as G2el
38	import GSASIIstrIO as G2stIO
39	import GSASIImapvars as G2mv
40	import os
41	import os.path as ospath
42
43	DEBUG = False #=True for various prints
44	TRANSP = False #=true to transpose images for testing
45	npsind = lambda x: np.sin(x*np.pi/180.)
46
47	def sfloat(S):
48	'Convert a string to float. An empty field is treated as zero'
49	if S.strip():
50	return float(S)
51	else:
52	return 0.0
53
54	def sint(S):
55	'Convert a string to int. An empty field is treated as zero'
56	if S.strip():
57	return int(S)
58	else:
59	return 0
60
61	def trim(val):
62	'''Simplify a string containing leading and trailing spaces
63	as well as newlines, tabs, repeated spaces etc. into a shorter and
64	more simple string, by replacing all ranges of whitespace
65	characters with a single space.
66
67	:param str val: the string to be simplified
68
69	:returns: the (usually) shortened version of the string
70	'''
71	return re.sub('\s+', ' ', val).strip()
72
73	def makeInstDict(names,data,codes):
74	inst = dict(zip(names,zip(data,data,codes)))
75	for item in inst:
76	inst[item] = list(inst[item])
77	return inst
78
79	def FileDlgFixExt(dlg,file):
80	'this is needed to fix a problem in linux wx.FileDialog'
81	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
82	if ext not in file:
83	file += ext
84	return file
85
86	def GetPowderPeaks(fileName):
87	'Read powder peaks from a file'
88	sind = lambda x: math.sin(x*math.pi/180.)
89	asind = lambda x: 180.*math.asin(x)/math.pi
90	Cuka = 1.54052
91	File = open(fileName,'Ur')
92	Comments = []
93	peaks = []
94	S = File.readline()
95	while S:
96	if S[:1] == '#':
97	Comments.append(S[:-1])
98	else:
99	item = S.split()
100	if len(item) == 1:
101	peaks.append([float(item[0]),1.0])
102	elif len(item) > 1:
103	peaks.append([float(item[0]),float(item[0])])
104	S = File.readline()
105	File.close()
106	if Comments:
107	print 'Comments on file:'
108	for Comment in Comments: print Comment
109	Peaks = []
110	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
111	for peak in peaks:
112	dsp = peak[0]
113	sth = Cuka/(2.0*dsp)
114	if sth < 1.0:
115	tth = 2.0*asind(sth)
116	else:
117	break
118	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
119	else: #2-thetas - assume Cuka (for now)
120	for peak in peaks:
121	tth = peak[0]
122	dsp = Cuka/(2.0*sind(tth/2.0))
123	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
124	return Comments,Peaks
125
126	def CheckImageFile(G2frame,imagefile):
127	'''Get an new image file name if the specified one does not
128	exist
129
130	:param wx.Frame G2frame: main GSAS-II Frame and data object
131
132	:param str imagefile: name of image file
133
134	:returns: imagefile, if it exists, or the name of a file
135	that does exist or False if the user presses Cancel
136
137	'''
138	if not ospath.exists(imagefile):
139	dlg = wx.FileDialog(G2frame, 'Bad image file name; choose name', '.', '',\
140	'Any image file (.edf;.tif;.tiff;.mar;.ge;.avg;.sum;.img)\
141	\|.edf;.tif;.tiff;.mar;.ge;.avg;.sum;.img\|\
142	European detector file (.edf)\|.edf\|\
143	Any detector tif (.tif;.tiff)\|.tif;.tiff\|\
144	MAR file (.mar)\|.mar\|\
145	GE Image (.ge;.avg;.sum)\|.ge;.avg;.sum\|\
146	ADSC Image (.img)\|.img\|\
147	All files (.)\|.',wx.OPEN\|wx.CHANGE_DIR)
148	try:
149	dlg.SetFilename(''+ospath.split(imagefile)[1])
150	if dlg.ShowModal() == wx.ID_OK:
151	imagefile = dlg.GetPath()
152	else:
153	imagefile = False
154	finally:
155	dlg.Destroy()
156	return imagefile
157
158	def EditImageParms(parent,Data,Comments,Image,filename):
159	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
160	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
161	def onClose(event):
162	dlg.EndModal(wx.ID_OK)
163	mainsizer = wx.BoxSizer(wx.VERTICAL)
164	h,w = Image.shape[:2]
165	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,
166	'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
167	0,wx.ALIGN_LEFT\|wx.ALL, 2)
168
169	vsizer = wx.BoxSizer(wx.HORIZONTAL)
170	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
171	0,wx.ALIGN_LEFT\|wx.ALL, 2)
172	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data,'wavelength')
173	vsizer.Add(wdgt)
174	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
175
176	vsizer = wx.BoxSizer(wx.HORIZONTAL)
177	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
178	0,wx.ALIGN_LEFT\|wx.ALL, 2)
179	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
180	size=(50,-1))
181	vsizer.Add(wdgt)
182	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),
183	wx.ALIGN_LEFT\|wx.ALL, 2)
184	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,
185	size=(50,-1))
186	vsizer.Add(wdgt)
187	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
188
189	vsizer = wx.BoxSizer(wx.HORIZONTAL)
190	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
191	0,wx.ALIGN_LEFT\|wx.ALL, 2)
192	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data,'distance')
193	vsizer.Add(wdgt)
194	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
195
196	vsizer = wx.BoxSizer(wx.HORIZONTAL)
197	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
198	0,wx.ALIGN_LEFT\|wx.ALL, 2)
199	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data['center'],0,
200	size=(75,-1))
201	vsizer.Add(wdgt)
202	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),
203	wx.ALIGN_LEFT\|wx.ALL, 2)
204	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data['center'],1,
205	size=(75,-1))
206	vsizer.Add(wdgt)
207	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
208
209	vsizer = wx.BoxSizer(wx.HORIZONTAL)
210	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
211	0,wx.ALIGN_LEFT\|wx.ALL, 2)
212	wdgt = G2gd.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
213	vsizer.Add(wdgt)
214	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
215
216	btnsizer = wx.StdDialogButtonSizer()
217	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
218	OKbtn.SetDefault()
219	OKbtn.Bind(wx.EVT_BUTTON,onClose)
220	btnsizer.AddButton(OKbtn) # not sure why this is needed
221	btnsizer.Realize()
222	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
223	dlg.SetSizer(mainsizer)
224	dlg.CenterOnParent()
225	dlg.ShowModal()
226
227	def GetImageData(G2frame,imagefile,imageOnly=False):
228	'''Read an image with the file reader keyed by the
229	file extension
230
231	:param wx.Frame G2frame: main GSAS-II Frame and data object.
232
233	:param str imagefile: name of image file
234
235	:param bool imageOnly: If True return only the image,
236	otherwise (default) return more (see below)
237
238	:returns: an image as a numpy array or a list of four items:
239	Comments, Data, Npix and the Image, as selected by imageOnly
240
241	'''
242	ext = ospath.splitext(imagefile)[1]
243	Comments = []
244	if ext == '.tif' or ext == '.tiff':
245	Comments,Data,Npix,Image = GetTifData(imagefile)
246	if Npix == 0:
247	print("GetTifData failed to read "+str(filename)+" Trying PIL")
248	import scipy.misc
249	Image = scipy.misc.imread(imagefile,flatten=True)
250	Npix = Image.size
251	Comments = ['no metadata']
252	Data = {'wavelength': 0.1, 'pixelSize': [200, 200], 'distance': 100.0}
253	Data['size'] = list(Image.shape)
254	Data['center'] = [int(i/2) for i in Image.shape]
255	if not imageOnly:
256	EditImageParms(G2frame,Data,Comments,Image,imagefile)
257	elif ext == '.edf':
258	Comments,Data,Npix,Image = GetEdfData(imagefile)
259	elif ext == '.img':
260	Comments,Data,Npix,Image = GetImgData(imagefile)
261	Image[0][0] = 0
262	elif ext == '.mar3450' or ext == '.mar2300':
263	Comments,Data,Npix,Image = GetMAR345Data(imagefile)
264	elif ext in ['.sum','.avg'] or 'ge' in ext:
265	Comments,Data,Npix,Image = GetGEsumData(imagefile)
266	elif ext == '.G2img':
267	Comments,Data,Npix,Image = GetG2Image(imagefile)
268	elif ext == '.png':
269	Comments,Data,Npix,Image = GetPNGData(imagefile)
270	if not imageOnly:
271	EditImageParms(G2frame,Data,Comments,Image,imagefile)
272	if imageOnly:
273	if TRANSP:
274	return Image.T
275	else:
276	return Image
277	else:
278	if TRANSP:
279	return Comments,Data,Npix,Image.T
280	else:
281	return Comments,Data,Npix,Image
282
283	def PutG2Image(filename,Comments,Data,Npix,image):
284	'Write an image as a python pickle - might be better as an .edf file?'
285	File = open(filename,'wb')
286	cPickle.dump([Comments,Data,Npix,image],File,1)
287	File.close()
288	return
289
290	def GetG2Image(filename):
291	'Read an image as a python pickle'
292	File = open(filename,'rb')
293	Comments,Data,Npix,image = cPickle.load(File)
294	File.close()
295	return Comments,Data,Npix,image
296
297	def GetEdfData(filename,imageOnly=False):
298	'Read European detector data edf file'
299	import struct as st
300	import array as ar
301	if not imageOnly:
302	print 'Read European detector data edf file: ',filename
303	File = open(filename,'rb')
304	fileSize = os.stat(filename).st_size
305	head = File.read(3072)
306	lines = head.split('\n')
307	sizexy = [0,0]
308	pixSize = [154,154] #Pixium4700?
309	cent = [0,0]
310	wave = 1.54187 #default <CuKa>
311	dist = 1000.
312	head = ['European detector data',]
313	for line in lines:
314	line = line.replace(';',' ').strip()
315	fields = line.split()
316	if 'Dim_1' in line:
317	sizexy[0] = int(fields[2])
318	elif 'Dim_2' in line:
319	sizexy[1] = int(fields[2])
320	elif 'DataType' in line:
321	dType = fields[2]
322	elif 'wavelength' in line:
323	wave = float(fields[2])
324	elif 'Size' in line:
325	imSize = int(fields[2])
326	elif 'DataType' in lines:
327	dType = fields[2]
328	elif 'pixel_size_x' in line:
329	pixSize[0] = float(fields[2])
330	elif 'pixel_size_y' in line:
331	pixSize[1] = float(fields[2])
332	elif 'beam_center_x' in line:
333	cent[0] = float(fields[2])
334	elif 'beam_center_y' in line:
335	cent[1] = float(fields[2])
336	elif 'refined_distance' in line:
337	dist = float(fields[2])
338	if line:
339	head.append(line)
340	else: #blank line at end of header
341	break
342	File.seek(fileSize-imSize)
343	if dType == 'UnsignedShort':
344	image = np.array(ar.array('H',File.read(imSize)),dtype=np.int32)
345	elif dType == 'UnsignedInt':
346	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
347	elif dType == 'UnsignedLong':
348	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
349	image = np.reshape(image,(sizexy[1],sizexy[0]))
350	data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'size':sizexy}
351	Npix = sizexy[0]*sizexy[1]
352	File.close()
353	if imageOnly:
354	return image
355	else:
356	return head,data,Npix,image
357
358	def GetGEsumData(filename,imageOnly=False):
359	'Read SUM file as produced at 1-ID from G.E. images'
360	import struct as st
361	import array as ar
362	if not imageOnly:
363	print 'Read GE sum file: ',filename
364	File = open(filename,'rb')
365	if '.sum' in filename:
366	head = ['GE detector sum data from APS 1-ID',]
367	sizexy = [2048,2048]
368	elif '.avg' in filename or '.ge' in filename:
369	head = ['GE detector avg or ge* data from APS 1-ID',]
370	sizexy = [2048,2048]
371	else:
372	head = ['GE detector raw data from APS 1-ID',]
373	File.seek(18)
374	size,nframes = st.unpack('<ih',File.read(6))
375	sizexy = [2048,2048]
376	pos = 8192
377	File.seek(pos)
378	Npix = sizexy[0]*sizexy[1]
379	if '.sum' in filename:
380	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.int32)
381	elif '.avg' in filename or '.ge' in filename:
382	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
383	else:
384	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
385	while nframes > 1:
386	image += np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
387	nframes -= 1
388	image = np.reshape(image,(sizexy[1],sizexy[0]))
389	data = {'pixelSize':[200,200],'wavelength':0.15,'distance':250.0,'center':[204.8,204.8],'size':sizexy}
390	File.close()
391	if imageOnly:
392	return image
393	else:
394	return head,data,Npix,image
395
396	def GetImgData(filename,imageOnly=False):
397	'Read an ADSC image file'
398	import struct as st
399	import array as ar
400	if not imageOnly:
401	print 'Read ADSC img file: ',filename
402	File = open(filename,'rb')
403	head = File.read(511)
404	lines = head.split('\n')
405	head = []
406	center = [0,0]
407	for line in lines[1:-2]:
408	line = line.strip()[:-1]
409	if line:
410	if 'SIZE1' in line:
411	size = int(line.split('=')[1])
412	Npix = size*size
413	elif 'WAVELENGTH' in line:
414	wave = float(line.split('=')[1])
415	elif 'BIN' in line:
416	if line.split('=')[1] == '2x2':
417	pixel=(102,102)
418	else:
419	pixel = (51,51)
420	elif 'DISTANCE' in line:
421	distance = float(line.split('=')[1])
422	elif 'CENTER_X' in line:
423	center[0] = float(line.split('=')[1])
424	elif 'CENTER_Y' in line:
425	center[1] = float(line.split('=')[1])
426	head.append(line)
427	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center,'size':[size,size]}
428	image = []
429	row = 0
430	pos = 512
431	File.seek(pos)
432	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
433	image = np.reshape(image,(sizexy[1],sizexy[0]))
434	# image = np.zeros(shape=(size,size),dtype=np.int32)
435	# while row < size:
436	# File.seek(pos)
437	# line = ar.array('H',File.read(2*size))
438	# image[row] = np.asarray(line)
439	# row += 1
440	# pos += 2*size
441	File.close()
442	if imageOnly:
443	return image
444	else:
445	return lines[1:-2],data,Npix,image
446
447	def GetMAR345Data(filename,imageOnly=False):
448	'Read a MAR-345 image plate image'
449	import array as ar
450	import struct as st
451	try:
452	import pack_f as pf
453	except:
454	msg = wx.MessageDialog(None, message="Unable to load the GSAS MAR image decompression, pack_f",
455	caption="Import Error",
456	style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
457	msg.ShowModal()
458	return None,None,None,None
459
460	if not imageOnly:
461	print 'Read Mar345 file: ',filename
462	File = open(filename,'rb')
463	head = File.read(4095)
464	numbers = st.unpack('<iiiiiiiiii',head[:40])
465	lines = head[128:].split('\n')
466	head = []
467	for line in lines:
468	line = line.strip()
469	if 'PIXEL' in line:
470	values = line.split()
471	pixel = (int(values[2]),int(values[4])) #in microns
472	elif 'WAVELENGTH' in line:
473	wave = float(line.split()[1])
474	elif 'DISTANCE' in line:
475	distance = float(line.split()[1]) #in mm
476	elif 'CENTER' in line:
477	values = line.split()
478	center = [float(values[2])/10.,float(values[4])/10.] #make in mm from pixels
479	if line:
480	head.append(line)
481	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center}
482	for line in head:
483	if 'FORMAT' in line[0:6]:
484	items = line.split()
485	size = int(items[1])
486	Npix = size*size
487	pos = 4096
488	data['size'] = [size,size]
489	File.seek(pos)
490	line = File.read(8)
491	while 'CCP4' not in line: #get past overflow list for now
492	line = File.read(8)
493	pos += 8
494	pos += 37
495	File.seek(pos)
496	raw = File.read()
497	File.close()
498	image = np.zeros(shape=(size,size),dtype=np.int32)
499	image = np.flipud(pf.pack_f(len(raw),raw,size,image).T) #transpose to get it right way around & flip
500	if imageOnly:
501	return image
502	else:
503	return head,data,Npix,image
504
505	def GetPNGData(filename,imageOnly=False):
506	'''Read an image in a png format, assumes image is converted from CheMin tif file
507	so default parameters are that machine.
508	'''
509	import scipy.misc
510	Image = scipy.misc.imread(filename,flatten=True)
511	Npix = Image.size
512	Comments = ['no metadata']
513	pixy = list(Image.shape)
514	sizexy = [40,40]
515	Data = {'wavelength': 1.78892, 'pixelSize': sizexy, 'distance': 18.0,'size':pixy}
516	Data['center'] = [pixy[0]sizexy[0]/1000,pixy[1]sizexy[1]/2000]
517	if imageOnly:
518	return Image.T
519	else:
520	return Comments,Data,Npix,Image.T
521
522	def GetTifData(filename,imageOnly=False):
523	'''Read an image in a pseudo-tif format,
524	as produced by a wide variety of software, almost always
525	incorrectly in some way.
526	'''
527	import struct as st
528	try:
529	import Image as Im
530	except ImportError:
531	try:
532	from PIL import Image as Im
533	except ImportError:
534	print "PIL/pillow Image module not present. TIFs cannot be read without this"
535	raise Exception("PIL/pillow Image module not found")
536	import array as ar
537	import ReadMarCCDFrame as rmf
538	File = open(filename,'rb')
539	dataType = 5
540	center = [None,None]
541	wavelength = None
542	distance = None
543	try:
544	Meta = open(filename+'.metadata','Ur')
545	head = Meta.readlines()
546	for line in head:
547	line = line.strip()
548	if 'dataType=' in line:
549	dataType = int(line.split('=')[1])
550	Meta.close()
551	except IOError:
552	print 'no metadata file found - will try to read file anyway'
553	head = ['no metadata file found',]
554
555	tag = File.read(2)
556	byteOrd = '<'
557	if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
558	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
559	elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
560	byteOrd = '>'
561	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
562	else:
563	lines = ['not a detector tiff file',]
564	return lines,0,0,0
565	File.seek(IFD) #get number of directory entries
566	NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
567	IFD = {}
568	nSlice = 1
569	for ied in range(NED):
570	Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
571	nVal = st.unpack(byteOrd+'i',File.read(4))[0]
572	if DEBUG: print 'Try:',Tag,Type,nVal
573	if Type == 1:
574	Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
575	elif Type == 2:
576	Value = st.unpack(byteOrd+'i',File.read(4))
577	elif Type == 3:
578	Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
579	x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
580	elif Type == 4:
581	if Tag in [273,279]:
582	nSlice = nVal
583	nVal = 1
584	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
585	elif Type == 5:
586	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
587	elif Type == 11:
588	Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
589	IFD[Tag] = [Type,nVal,Value]
590	if DEBUG: print Tag,IFD[Tag]
591	sizexy = [IFD[256][2][0],IFD[257][2][0]]
592	[nx,ny] = sizexy
593	Npix = nx*ny
594	if 34710 in IFD:
595	if not imageOnly:
596	print 'Read MAR CCD tiff file: ',filename
597	marFrame = rmf.marFrame(File,byteOrd,IFD)
598	image = np.flipud(np.array(np.asarray(marFrame.image),dtype=np.int32))
599	tifType = marFrame.filetitle
600	pixy = [marFrame.pixelsizeX/1000.0,marFrame.pixelsizeY/1000.0]
601	head = marFrame.outputHead()
602	# extract resonable wavelength from header
603	wavelength = marFrame.sourceWavelength*1e-5
604	wavelength = (marFrame.opticsWavelength > 0) and marFrame.opticsWavelength*1e-5 or wavelength
605	wavelength = (wavelength <= 0) and None or wavelength
606	# extract resonable distance from header
607	distance = (marFrame.startXtalToDetector+marFrame.endXtalToDetector)*5e-4
608	distance = (distance <= 0) and marFrame.xtalToDetector*1e-3 or distance
609	distance = (distance <= 0) and None or distance
610	# extract resonable center from header
611	center = [marFrame.beamXmarFrame.pixelsizeX1e-9,marFrame.beamYmarFrame.pixelsizeY1e-9]
612	center = (center[0] != 0 and center[1] != 0) and center or [None,None]
613	#print head,tifType,pixy
614	elif nSlice > 1: #CheMin multislice tif file!
615	tifType = 'CheMin'
616	pixy = [40,40]
617	image = np.flipud(np.array(Im.open(filename)))*10.
618	distance = 18.0
619	center = [pixy[0]*sizexy[0]/2000,0] #the CheMin beam stop is here
620	wavelength = 1.78892
621	elif 272 in IFD:
622	ifd = IFD[272]
623	File.seek(ifd[2][0])
624	S = File.read(ifd[1])
625	if 'PILATUS' in S:
626	tifType = 'Pilatus'
627	dataType = 0
628	pixy = [172,172]
629	File.seek(4096)
630	if not imageOnly:
631	print 'Read Pilatus tiff file: ',filename
632	image = ar.array('L',File.read(4*Npix))
633	image = np.array(np.asarray(image),dtype=np.int32)
634	else:
635	if IFD[258][2][0] == 16:
636	tifType = 'GE'
637	pixy = [200,200]
638	File.seek(8)
639	if not imageOnly:
640	print 'Read GE-detector tiff file: ',filename
641	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
642	elif IFD[258][2][0] == 32:
643	tifType = 'CHESS'
644	pixy = [200,200]
645	File.seek(8)
646	if not imageOnly:
647	print 'Read CHESS-detector tiff file: ',filename
648	image = np.array(ar.array('L',File.read(4*Npix)),dtype=np.int32)
649
650	elif 262 in IFD and IFD[262][2][0] > 4:
651	tifType = 'DND'
652	pixy = [158,158]
653	File.seek(512)
654	if not imageOnly:
655	print 'Read DND SAX/WAX-detector tiff file: ',filename
656	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
657	elif sizexy == [1536,1536]:
658	tifType = 'APS Gold'
659	pixy = [150,150]
660	File.seek(64)
661	if not imageOnly:
662	print 'Read Gold tiff file:',filename
663	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
664	elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
665	if IFD[273][2][0] == 8:
666	if IFD[258][2][0] == 32:
667	tifType = 'PE'
668	pixy = [200,200]
669	File.seek(8)
670	if not imageOnly:
671	print 'Read APS PE-detector tiff file: ',filename
672	if dataType == 5:
673	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
674	else:
675	image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
676
677	elif IFD[273][2][0] == 4096:
678	if sizexy[0] == 3072:
679	pixy = [73,73]
680	tifType = 'MAR225'
681	else:
682	pixy = [158,158]
683	tifType = 'MAR325'
684	File.seek(4096)
685	if not imageOnly:
686	print 'Read MAR CCD tiff file: ',filename
687	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
688	elif IFD[273][2][0] == 512:
689	tiftype = '11-ID-C'
690	pixy = [200,200]
691	File.seek(512)
692	if not imageOnly:
693	print 'Read 11-ID-C tiff file: ',filename
694	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
695	elif sizexy == [4096,4096]:
696	if IFD[273][2][0] == 8:
697	if IFD[258][2][0] == 16:
698	tifType = 'scanCCD'
699	pixy = [9,9]
700	File.seek(8)
701	if not imageOnly:
702	print 'Read APS scanCCD tiff file: ',filename
703	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
704	elif IFD[273][2][0] == 4096:
705	tifType = 'Rayonix'
706	pixy = [73.242,73.242]
707	File.seek(4096)
708	if not imageOnly:
709	print 'Read Rayonix MX300HE tiff file: ',filename
710	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
711	# elif sizexy == [960,960]:
712	# tiftype = 'PE-BE'
713	# pixy = (200,200)
714	# File.seek(8)
715	# if not imageOnly:
716	# print 'Read Gold tiff file:',filename
717	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
718
719	else:
720	lines = ['not a known detector tiff file',]
721	return lines,0,0,0
722
723	image = np.reshape(image,(sizexy[1],sizexy[0]))
724	center = (not center[0]) and [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000] or center
725	wavelength = (not wavelength) and 0.10 or wavelength
726	distance = (not distance) and 100.0 or distance
727	data = {'pixelSize':pixy,'wavelength':wavelength,'distance':distance,'center':center,'size':sizexy}
728	File.close()
729	if imageOnly:
730	return image
731	else:
732	return head,data,Npix,image
733
734	#def GetTifData(filename,imageOnly=False):
735	# import struct as st
736	# import array as ar
737	# File = open(filename,'rb')
738	# dataType = 5
739	# try:
740	# Meta = open(filename+'.metadata','Ur')
741	# head = Meta.readlines()
742	# for line in head:
743	# line = line.strip()
744	# if 'dataType=' in line:
745	# dataType = int(line.split('=')[1])
746	# Meta.close()
747	# except IOError:
748	# print 'no metadata file found - will try to read file anyway'
749	# head = ['no metadata file found',]
750	#
751	# tag = File.read(2)
752	# byteOrd = '<'
753	# if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
754	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
755	# elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
756	# byteOrd = '>'
757	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
758	# else:
759	# lines = ['not a detector tiff file',]
760	# return lines,0,0,0
761	# File.seek(IFD) #get number of directory entries
762	# NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
763	# IFD = {}
764	# for ied in range(NED):
765	# Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
766	# nVal = st.unpack(byteOrd+'i',File.read(4))[0]
767	# if Type == 1:
768	# Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
769	# elif Type == 2:
770	# Value = st.unpack(byteOrd+'i',File.read(4))
771	# elif Type == 3:
772	# Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
773	# x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
774	# elif Type == 4:
775	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
776	# elif Type == 5:
777	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
778	# elif Type == 11:
779	# Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
780	# IFD[Tag] = [Type,nVal,Value]
781	## print Tag,IFD[Tag]
782	# sizexy = [IFD[256][2][0],IFD[257][2][0]]
783	# [nx,ny] = sizexy
784	# Npix = nx*ny
785	# if 272 in IFD:
786	# ifd = IFD[272]
787	# File.seek(ifd[2][0])
788	# S = File.read(ifd[1])
789	# if 'PILATUS' in S:
790	# tifType = 'Pilatus'
791	# dataType = 0
792	# pixy = (172,172)
793	# File.seek(4096)
794	# if not imageOnly:
795	# print 'Read Pilatus tiff file: ',filename
796	# image = ar.array('L',File.read(4*Npix))
797	# image = np.array(np.asarray(image),dtype=np.int32)
798	# elif 262 in IFD and IFD[262][2][0] > 4:
799	# tifType = 'DND'
800	# pixy = (158,158)
801	# File.seek(512)
802	# if not imageOnly:
803	# print 'Read DND SAX/WAX-detector tiff file: ',filename
804	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
805	# elif sizexy == [1536,1536]:
806	# tifType = 'APS Gold'
807	# pixy = (150,150)
808	# File.seek(64)
809	# if not imageOnly:
810	# print 'Read Gold tiff file:',filename
811	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
812	# elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
813	# if IFD[273][2][0] == 8:
814	# if IFD[258][2][0] == 32:
815	# tifType = 'PE'
816	# pixy = (200,200)
817	# File.seek(8)
818	# if not imageOnly:
819	# print 'Read APS PE-detector tiff file: ',filename
820	# if dataType == 5:
821	# image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
822	# else:
823	# image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
824	# elif IFD[273][2][0] == 4096:
825	# if sizexy[0] == 3072:
826	# pixy = (73,73)
827	# tifType = 'MAR225'
828	# else:
829	# pixy = (158,158)
830	# tifType = 'MAR325'
831	# File.seek(4096)
832	# if not imageOnly:
833	# print 'Read MAR CCD tiff file: ',filename
834	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
835	# elif IFD[273][2][0] == 512:
836	# tiftype = '11-ID-C'
837	# pixy = [200,200]
838	# File.seek(512)
839	# if not imageOnly:
840	# print 'Read 11-ID-C tiff file: ',filename
841	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
842	# elif sizexy == [4096,4096]:
843	# if IFD[273][2][0] == 8:
844	# if IFD[258][2][0] == 16:
845	# tifType = 'scanCCD'
846	# pixy = (9,9)
847	# File.seek(8)
848	# if not imageOnly:
849	# print 'Read APS scanCCD tiff file: ',filename
850	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
851	# elif IFD[273][2][0] == 4096:
852	# tifType = 'Rayonix'
853	# pixy = (73.242,73.242)
854	# File.seek(4096)
855	# if not imageOnly:
856	# print 'Read Rayonix MX300HE tiff file: ',filename
857	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
858	## elif sizexy == [960,960]:
859	## tiftype = 'PE-BE'
860	## pixy = (200,200)
861	## File.seek(8)
862	## if not imageOnly:
863	## print 'Read Gold tiff file:',filename
864	## image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
865	#
866	# else:
867	# lines = ['not a known detector tiff file',]
868	# return lines,0,0,0
869	#
870	# image = np.reshape(image,(sizexy[1],sizexy[0]))
871	# center = [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000]
872	# data = {'pixelSize':pixy,'wavelength':0.10,'distance':100.0,'center':center,'size':sizexy}
873	# File.close()
874	# if imageOnly:
875	# return image
876	# else:
877	# return head,data,Npix,image
878	#
879	def ProjFileOpen(G2frame):
880	'Read a GSAS-II project file and load into the G2 data tree'
881	if not os.path.exists(G2frame.GSASprojectfile):
882	print ('\n*** Error attempt to open project file that does not exist:\n '+
883	str(G2frame.GSASprojectfile))
884	return
885	file = open(G2frame.GSASprojectfile,'rb')
886	print 'load from file: ',G2frame.GSASprojectfile
887	G2frame.SetTitle("GSAS-II data tree: "+
888	os.path.split(G2frame.GSASprojectfile)[1])
889	wx.BeginBusyCursor()
890	try:
891	while True:
892	try:
893	data = cPickle.load(file)
894	except EOFError:
895	break
896	datum = data[0]
897
898	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=datum[0])
899	if 'PWDR' in datum[0]:
900	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
901	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
902	G2frame.PatternTree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
903	elif datum[0].startswith('HKLF'):
904	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
905	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
906	G2frame.PatternTree.SetItemPyData(Id,datum[1])
907	else:
908	G2frame.PatternTree.SetItemPyData(Id,datum[1])
909	for datus in data[1:]:
910	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
911	#patch
912	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
913	if 'PWDR' in datum[0]:
914	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
915	else:
916	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
917	for item in datus[1][0]: #zip makes tuples - now make lists!
918	datus[1][0][item] = list(datus[1][0][item])
919	#end patch
920	G2frame.PatternTree.SetItemPyData(sub,datus[1])
921	if 'IMG' in datum[0]: #retrieve image default flag & data if set
922	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
923	if Data['setDefault']:
924	G2frame.imageDefault = Data
925	file.close()
926	print('project load successful')
927	G2frame.NewPlot = True
928	except:
929	msg = wx.MessageDialog(G2frame,message="Error reading file "+
930	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
931	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
932	msg.ShowModal()
933	finally:
934	wx.EndBusyCursor()
935	G2frame.Status.SetStatusText('To reorder tree items, use mouse RB to drag/drop them')
936
937	def ProjFileSave(G2frame):
938	'Save a GSAS-II project file'
939	if not G2frame.PatternTree.IsEmpty():
940	file = open(G2frame.GSASprojectfile,'wb')
941	print 'save to file: ',G2frame.GSASprojectfile
942	wx.BeginBusyCursor()
943	try:
944	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
945	while item:
946	data = []
947	name = G2frame.PatternTree.GetItemText(item)
948	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
949	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
950	while item2:
951	name = G2frame.PatternTree.GetItemText(item2)
952	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
953	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
954	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
955	cPickle.dump(data,file,1)
956	file.close()
957	finally:
958	wx.EndBusyCursor()
959	print('project save successful')
960
961	def SaveIntegration(G2frame,PickId,data):
962	'Save image integration results as powder pattern(s)'
963	azms = G2frame.Integrate[1]
964	X = G2frame.Integrate[2][:-1]
965	N = len(X)
966	Id = G2frame.PatternTree.GetItemParent(PickId)
967	name = G2frame.PatternTree.GetItemText(Id)
968	name = name.replace('IMG ',data['type']+' ')
969	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
970	if 'PWDR' in name:
971	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
972	codes = [0 for i in range(11)]
973	elif 'SASD' in name:
974	names = ['Type','Lam','Zero','Azimuth']
975	codes = [0 for i in range(4)]
976	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
977	Xminmax = [X[0],X[-1]]
978	LRazm = data['LRazimuth']
979	Azms = []
980	if data['fullIntegrate'] and data['outAzimuths'] == 1:
981	Azms = [45.0,] #a poor man's average?
982	else:
983	for i,azm in enumerate(azms[:-1]):
984	Azms.append((azms[i+1]+azm)/2.)
985	for i,azm in enumerate(azms[:-1]):
986	Aname = name+" Azm= %.2f"%(Azms[i])
987	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
988	nOcc = 0
989	while item:
990	Name = G2frame.PatternTree.GetItemText(item)
991	if Aname in Name:
992	nOcc += 1
993	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
994	if nOcc:
995	Aname += '(%d)'%(nOcc)
996	Sample = G2pdG.SetDefaultSample()
997	Sample['Gonio. radius'] = data['distance']
998	Sample['Omega'] = data['GonioAngles'][0]
999	Sample['Chi'] = data['GonioAngles'][1]
1000	Sample['Phi'] = data['GonioAngles'][2]
1001	if 'PWDR' in Aname:
1002	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!
1003	elif 'SASD' in Aname:
1004	Sample['Trans'] = data['SampleAbs'][0]
1005	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
1006	Y = G2frame.Integrate[0][i]
1007	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
1008	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=Aname)
1009	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
1010	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
1011	if 'PWDR' in Aname:
1012	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
1013	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
1014	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
1015	for item in inst[0]:
1016	inst[0][item] = list(inst[0][item])
1017	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
1018	if 'PWDR' in Aname:
1019	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1020	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
1021	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),{'sigDict':{},'peaks':[]})
1022	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
1023	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
1024	elif 'SASD' in Aname:
1025	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
1026	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1027	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
1028	valuesdict = {
1029	'wtFactor':1.0,
1030	'Dummy':False,
1031	'ranId':ran.randint(0,sys.maxint),
1032	}
1033	G2frame.PatternTree.SetItemPyData(
1034	Id,[valuesdict,
1035	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
1036	return Id #last powder pattern generated
1037
1038	# def powderFxyeSave(G2frame,exports,powderfile):
1039	# 'Save a powder histogram as a GSAS FXYE file'
1040	# head,tail = ospath.split(powderfile)
1041	# name,ext = tail.split('.')
1042	# for i,export in enumerate(exports):
1043	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1044	# prmname = filename.strip(ext)+'prm'
1045	# prm = open(prmname,'w') #old style GSAS parm file
1046	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1047	# Inst = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, \
1048	# PickId, 'Instrument Parameters'))[0]
1049	# prm.write( ' 123456789012345678901234567890123456789012345678901234567890 '+'\n')
1050	# prm.write( 'INS BANK 1 '+'\n')
1051	# prm.write(('INS HTYPE %sR '+'\n')%(Inst['Type'][0]))
1052	# if 'Lam1' in Inst: #Ka1 & Ka2
1053	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam1'][0],Inst['Lam2'][0]))
1054	# elif 'Lam' in Inst: #single wavelength
1055	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam'][1],0.0))
1056	# prm.write( 'INS 1 IRAD 0 '+'\n')
1057	# prm.write( 'INS 1I HEAD '+'\n')
1058	# prm.write( 'INS 1I ITYP 0 0.0000 180.0000 1 '+'\n')
1059	# prm.write(('INS 1DETAZM%10.3f '+'\n')%(Inst['Azimuth'][0]))
1060	# prm.write( 'INS 1PRCF1 3 8 0.00100 '+'\n')
1061	# prm.write(('INS 1PRCF11 %15.6g%15.6g%15.6g%15.6g '+'\n')%(Inst['U'][1],Inst['V'][1],Inst['W'][1],0.0))
1062	# 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.))
1063	# prm.close()
1064	# file = open(filename,'w')
1065	# print 'save powder pattern to file: ',filename
1066	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1067	# file.write(powderfile+'\n')
1068	# file.write('Instrument parameter file:'+ospath.split(prmname)[1]+'\n')
1069	# file.write('BANK 1 %d %d CONS %.2f %.2f 0 0 FXYE\n'%(len(x),len(x),\
1070	# 100.x[0],100.(x[1]-x[0])))
1071	# s = list(np.sqrt(1./np.array(w)))
1072	# XYW = zip(x,y,s)
1073	# for X,Y,S in XYW:
1074	# file.write("%15.6g %15.6g %15.6g\n" % (100.*X,Y,max(S,1.0)))
1075	# file.close()
1076	# print 'powder pattern file '+filename+' written'
1077
1078	# def powderXyeSave(G2frame,exports,powderfile):
1079	# 'Save a powder histogram as a Topas XYE file'
1080	# head,tail = ospath.split(powderfile)
1081	# name,ext = tail.split('.')
1082	# for i,export in enumerate(exports):
1083	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1084	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1085	# file = open(filename,'w')
1086	# file.write('#%s\n'%(export))
1087	# print 'save powder pattern to file: ',filename
1088	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1089	# s = list(np.sqrt(1./np.array(w)))
1090	# XYW = zip(x,y,s)
1091	# for X,Y,W in XYW:
1092	# file.write("%15.6g %15.6g %15.6g\n" % (X,Y,W))
1093	# file.close()
1094	# print 'powder pattern file '+filename+' written'
1095
1096	def PDFSave(G2frame,exports):
1097	'Save a PDF G(r) and S(Q) in column formats'
1098	for export in exports:
1099	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1100	SQname = 'S(Q)'+export[4:]
1101	GRname = 'G(R)'+export[4:]
1102	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
1103	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
1104	sqId = G2gd.GetPatternTreeItemId(G2frame, PickId, SQname)
1105	grId = G2gd.GetPatternTreeItemId(G2frame, PickId, GRname)
1106	sqdata = np.array(G2frame.PatternTree.GetItemPyData(sqId)[1][:2]).T
1107	grdata = np.array(G2frame.PatternTree.GetItemPyData(grId)[1][:2]).T
1108	sqfile = open(sqfilename,'w')
1109	grfile = open(grfilename,'w')
1110	sqfile.write('#T S(Q) %s\n'%(export))
1111	grfile.write('#T G(R) %s\n'%(export))
1112	sqfile.write('#L Q S(Q)\n')
1113	grfile.write('#L R G(R)\n')
1114	for q,sq in sqdata:
1115	sqfile.write("%15.6g %15.6g\n" % (q,sq))
1116	sqfile.close()
1117	for r,gr in grdata:
1118	grfile.write("%15.6g %15.6g\n" % (r,gr))
1119	grfile.close()
1120
1121	def PeakListSave(G2frame,file,peaks):
1122	'Save powder peaks to a data file'
1123	print 'save peak list to file: ',G2frame.peaklistfile
1124	if not peaks:
1125	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1126	try:
1127	result = dlg.ShowModal()
1128	finally:
1129	dlg.Destroy()
1130	return
1131	for peak in peaks:
1132	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1133	(peak[0],peak[2],peak[4],peak[6]))
1134	print 'peak list saved'
1135
1136	def IndexPeakListSave(G2frame,peaks):
1137	'Save powder peaks from the indexing list'
1138	file = open(G2frame.peaklistfile,'wa')
1139	print 'save index peak list to file: ',G2frame.peaklistfile
1140	wx.BeginBusyCursor()
1141	try:
1142	if not peaks:
1143	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1144	try:
1145	result = dlg.ShowModal()
1146	finally:
1147	dlg.Destroy()
1148	return
1149	for peak in peaks:
1150	file.write("%12.6f\n" % (peak[7]))
1151	file.close()
1152	finally:
1153	wx.EndBusyCursor()
1154	print 'index peak list saved'
1155
1156	def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1157	'''Create a new phase dict with default values for various parameters
1158
1159	:param str Name: Name for new Phase
1160
1161	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1162	defaults to data for P 1
1163
1164	:param list cell: unit cell parameter list; defaults to
1165	[1.0,1.0,1.0,90.,90,90.,1.]
1166
1167	'''
1168	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1169	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1170	phaseData = {
1171	'ranId':ran.randint(0,sys.maxint),
1172	'General':{
1173	'Name':Name,
1174	'Type':'nuclear',
1175	'AtomPtrs':[3,1,7,9],
1176	'SGData':SGData,
1177	'Cell':[False,]+cell,
1178	'Pawley dmin':1.0,
1179	'Data plot type':'None',
1180	'SH Texture':{
1181	'Order':0,
1182	'Model':'cylindrical',
1183	'Sample omega':[False,0.0],
1184	'Sample chi':[False,0.0],
1185	'Sample phi':[False,0.0],
1186	'SH Coeff':[False,{}],
1187	'SHShow':False,
1188	'PFhkl':[0,0,1],
1189	'PFxyz':[0,0,1],
1190	'PlotType':'Pole figure'}},
1191	'Atoms':[],
1192	'Drawing':{},
1193	'Histograms':{},
1194	'Pawley ref':[],
1195	'RBModels':{},
1196	}
1197	if Super.get('Use',False):
1198	phaseData['General'].update({'Type':'modulated','Super':1,'SuperSg':Super['ssSymb']})
1199	phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])
1200	phaseData['General']['SuperVec'] = [[Super['ModVec'],False,Super['maxH']],
1201	[[0,0,.1],False,4],[[0.,0.,.1],False,4]]
1202
1203	return phaseData
1204
1205	class MultipleChoicesDialog(wx.Dialog):
1206	'''A dialog that offers a series of choices, each with a
1207	title and a wx.Choice widget. Intended to be used Modally.
1208	typical input:
1209
1210	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1211	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1212
1213	selections are placed in self.chosen when OK is pressed
1214	'''
1215	def __init__(self,choicelist,headinglist,
1216	head='Select options',
1217	title='Please select from options below',
1218	parent=None):
1219	self.chosen = []
1220	wx.Dialog.__init__(
1221	self,parent,wx.ID_ANY,head,
1222	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1223	panel = wx.Panel(self)
1224	mainSizer = wx.BoxSizer(wx.VERTICAL)
1225	mainSizer.Add((10,10),1)
1226	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1227	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1228	self.ChItems = []
1229	for choice,lbl in zip(choicelist,headinglist):
1230	mainSizer.Add((10,10),1)
1231	self.chosen.append(0)
1232	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1233	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1234	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1235	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1236
1237	OkBtn = wx.Button(panel,-1,"Ok")
1238	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1239	cancelBtn = wx.Button(panel,-1,"Cancel")
1240	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1241	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1242	btnSizer.Add((20,20),1)
1243	btnSizer.Add(OkBtn)
1244	btnSizer.Add((20,20),1)
1245	btnSizer.Add(cancelBtn)
1246	btnSizer.Add((20,20),1)
1247	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1248	panel.SetSizer(mainSizer)
1249	panel.Fit()
1250	self.Fit()
1251
1252	def OnOk(self,event):
1253	parent = self.GetParent()
1254	if parent is not None: parent.Raise()
1255	# save the results from the choice widgets
1256	self.chosen = []
1257	for w in self.ChItems:
1258	self.chosen.append(w.GetSelection())
1259	self.EndModal(wx.ID_OK)
1260
1261	def OnCancel(self,event):
1262	parent = self.GetParent()
1263	if parent is not None: parent.Raise()
1264	self.chosen = []
1265	self.EndModal(wx.ID_CANCEL)
1266
1267	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1268	confirmoverwrite=True, parent=None,
1269	multipleselect=False):
1270	'''If the filename is a zip file, extract a file from that
1271	archive.
1272
1273	:param list Selection: used to predefine the name of the file
1274	to be extracted. Filename case and zip directory name are
1275	ignored in selection; the first matching file is used.
1276
1277	:param bool confirmread: if True asks the user to confirm before expanding
1278	the only file in a zip
1279
1280	:param bool confirmoverwrite: if True asks the user to confirm
1281	before overwriting if the extracted file already exists
1282
1283	:param bool multipleselect: if True allows more than one zip
1284	file to be extracted, a list of file(s) is returned.
1285	If only one file is present, do not ask which one, otherwise
1286	offer a list of choices (unless selection is used).
1287
1288	:returns: the name of the file that has been created or a
1289	list of files (see multipleselect)
1290
1291	If the file is not a zipfile, return the name of the input file.
1292	If the zipfile is empty or no file has been selected, return None
1293	'''
1294	import zipfile # do this now, since we can save startup time by doing this only on need
1295	import shutil
1296	zloc = os.path.split(filename)[0]
1297	if not zipfile.is_zipfile(filename):
1298	#print("not zip")
1299	return filename
1300
1301	z = zipfile.ZipFile(filename,'r')
1302	zinfo = z.infolist()
1303
1304	if len(zinfo) == 0:
1305	#print('Zip has no files!')
1306	zlist = [-1]
1307	if selection:
1308	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1309	if selection.lower() in choices:
1310	zlist = [choices.index(selection.lower())]
1311	else:
1312	print('debug: file '+str(selection)+' was not found in '+str(filename))
1313	zlist = [-1]
1314	elif len(zinfo) == 1 and confirmread:
1315	result = wx.ID_NO
1316	dlg = wx.MessageDialog(
1317	parent,
1318	'Is file '+str(zinfo[0].filename)+
1319	' what you want to extract from '+
1320	str(os.path.split(filename)[1])+'?',
1321	'Confirm file',
1322	wx.YES_NO \| wx.ICON_QUESTION)
1323	try:
1324	result = dlg.ShowModal()
1325	finally:
1326	dlg.Destroy()
1327	if result == wx.ID_NO:
1328	zlist = [-1]
1329	else:
1330	zlist = [0]
1331	elif len(zinfo) == 1:
1332	zlist = [0]
1333	elif multipleselect:
1334	# select one or more from a from list
1335	choices = [i.filename for i in zinfo]
1336	dlg = G2gd.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1337	'Choose file(s)',choices)
1338	if dlg.ShowModal() == wx.ID_OK:
1339	zlist = dlg.GetSelections()
1340	else:
1341	zlist = []
1342	dlg.Destroy()
1343	else:
1344	# select one from a from list
1345	choices = [i.filename for i in zinfo]
1346	dlg = wx.SingleChoiceDialog(parent,
1347	'Select file to extract from zip file'+str(filename),'Choose file',
1348	choices,)
1349	if dlg.ShowModal() == wx.ID_OK:
1350	zlist = [dlg.GetSelection()]
1351	else:
1352	zlist = [-1]
1353	dlg.Destroy()
1354
1355	outlist = []
1356	for zindex in zlist:
1357	if zindex >= 0:
1358	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1359	if os.path.exists(efil) and confirmoverwrite:
1360	result = wx.ID_NO
1361	dlg = wx.MessageDialog(parent,
1362	'File '+str(efil)+' already exists. OK to overwrite it?',
1363	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1364	try:
1365	result = dlg.ShowModal()
1366	finally:
1367	dlg.Destroy()
1368	if result == wx.ID_NO:
1369	zindex = -1
1370	if zindex >= 0:
1371	# extract the file to the current directory, regardless of it's original path
1372	#z.extract(zinfo[zindex],zloc)
1373	eloc,efil = os.path.split(zinfo[zindex].filename)
1374	outfile = os.path.join(zloc, efil)
1375	fpin = z.open(zinfo[zindex])
1376	fpout = file(outfile, "wb")
1377	shutil.copyfileobj(fpin, fpout)
1378	fpin.close()
1379	fpout.close()
1380	outlist.append(outfile)
1381	z.close()
1382	if multipleselect and len(outlist) >= 1:
1383	return outlist
1384	elif len(outlist) == 1:
1385	return outlist[0]
1386	else:
1387	return None
1388
1389	######################################################################
1390	# base classes for reading various types of data files
1391	# not used directly, only by subclassing
1392	######################################################################
1393	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1394	P1SGData = SGData
1395	class ImportBaseclass(object):
1396	'''Defines a base class for the reading of input files (diffraction
1397	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1398	for an explanation on how to use a subclass of this class.
1399	'''
1400	class ImportException(Exception):
1401	'''Defines an Exception that is used when an import routine hits an expected error,
1402	usually in .Reader.
1403
1404	Good practice is that the Reader should define a value in self.errors that
1405	tells the user some information about what is wrong with their file.
1406	'''
1407	pass
1408
1409	def __init__(self,
1410	formatName,
1411	longFormatName=None,
1412	extensionlist=[],
1413	strictExtension=False,
1414	):
1415	self.formatName = formatName # short string naming file type
1416	if longFormatName: # longer string naming file type
1417	self.longFormatName = longFormatName
1418	else:
1419	self.longFormatName = formatName
1420	# define extensions that are allowed for the file type
1421	# for windows, remove any extensions that are duplicate, as case is ignored
1422	if sys.platform == 'windows' and extensionlist:
1423	extensionlist = list(set([s.lower() for s in extensionlist]))
1424	self.extensionlist = extensionlist
1425	# If strictExtension is True, the file will not be read, unless
1426	# the extension matches one in the extensionlist
1427	self.strictExtension = strictExtension
1428	self.errors = ''
1429	self.warnings = ''
1430	# used for readers that will use multiple passes to read
1431	# more than one data block
1432	self.repeat = False
1433	self.selections = []
1434	self.repeatcount = 0
1435	self.readfilename = '?'
1436	#print 'created',self.__class__
1437
1438	def ReInitialize(self):
1439	'Reinitialize the Reader to initial settings'
1440	self.errors = ''
1441	self.warnings = ''
1442	self.repeat = False
1443	self.repeatcount = 0
1444	self.readfilename = '?'
1445
1446	def BlockSelector(self, ChoiceList, ParentFrame=None,
1447	title='Select a block',
1448	size=None, header='Block Selector',
1449	useCancel=True):
1450	''' Provide a wx dialog to select a block if the file contains more
1451	than one set of data and one must be selected
1452	'''
1453	if useCancel:
1454	dlg = wx.SingleChoiceDialog(
1455	ParentFrame,title, header,ChoiceList)
1456	else:
1457	dlg = wx.SingleChoiceDialog(
1458	ParentFrame,title, header,ChoiceList,
1459	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1460	if size: dlg.SetSize(size)
1461	dlg.CenterOnParent()
1462	if dlg.ShowModal() == wx.ID_OK:
1463	sel = dlg.GetSelection()
1464	return sel
1465	else:
1466	return None
1467	dlg.Destroy()
1468
1469	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1470	title='Select a block',size=None, header='Block Selector'):
1471	'''Provide a wx dialog to select a block of data if the
1472	file contains more than one set of data and one must be
1473	selected.
1474
1475	:returns: a list of the selected blocks
1476	'''
1477	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1478	wx.CHOICEDLG_STYLE)
1479	dlg.CenterOnParent()
1480	if size: dlg.SetSize(size)
1481	if dlg.ShowModal() == wx.ID_OK:
1482	sel = dlg.GetSelections()
1483	else:
1484	return []
1485	dlg.Destroy()
1486	selected = []
1487	if len(ChoiceList) in sel:
1488	return range(len(ChoiceList))
1489	else:
1490	return sel
1491	return selected
1492
1493	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1494	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1495	widget. Typical input:
1496
1497	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1498
1499	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1500
1501	optional keyword parameters are: head (window title) and title
1502	returns a list of selected indicies for each choice (or None)
1503	'''
1504	result = None
1505	dlg = MultipleChoicesDialog(choicelist,headinglist,
1506	parent=ParentFrame, **kwargs)
1507	dlg.CenterOnParent()
1508	if dlg.ShowModal() == wx.ID_OK:
1509	result = dlg.chosen
1510	dlg.Destroy()
1511	return result
1512
1513	def ShowBusy(self):
1514	wx.BeginBusyCursor()
1515	wx.Yield() # make it happen now!
1516
1517	def DoneBusy(self):
1518	wx.EndBusyCursor()
1519	wx.Yield() # make it happen now!
1520
1521	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1522	# '''This method must be supplied in the child class to read the file.
1523	# if the read fails either return False or raise an Exception
1524	# preferably of type ImportException.
1525	# '''
1526	# #start reading
1527	# raise ImportException("Error occurred while...")
1528	# self.errors += "Hint for user on why the error occur
1529	# return False # if an error occurs
1530	# return True # if read OK
1531
1532	def ExtensionValidator(self, filename):
1533	'''This methods checks if the file has the correct extension
1534	Return False if this filename will not be supported by this reader
1535	Return True if the extension matches the list supplied by the reader
1536	Return None if the reader allows un-registered extensions
1537	'''
1538	if filename:
1539	ext = os.path.splitext(filename)[1]
1540	if sys.platform == 'windows': ext = ext.lower()
1541	if ext in self.extensionlist: return True
1542	if self.strictExtension: return False
1543	return None
1544
1545	def ContentsValidator(self, filepointer):
1546	'''This routine will attempt to determine if the file can be read
1547	with the current format.
1548	This will typically be overridden with a method that
1549	takes a quick scan of [some of]
1550	the file contents to do a "sanity" check if the file
1551	appears to match the selected format.
1552	Expected to be called via self.Validator()
1553	'''
1554	#filepointer.seek(0) # rewind the file pointer
1555	return True
1556
1557	def CIFValidator(self, filepointer):
1558	'''A :meth:`ContentsValidator` for use to validate CIF files.
1559	'''
1560	for i,l in enumerate(filepointer):
1561	if i >= 1000: return True
1562	'''Encountered only blank lines or comments in first 1000
1563	lines. This is unlikely, but assume it is CIF anyway, since we are
1564	even less likely to find a file with nothing but hashes and
1565	blank lines'''
1566	line = l.strip()
1567	if len(line) == 0: # ignore blank lines
1568	continue
1569	elif line.startswith('#'): # ignore comments
1570	continue
1571	elif line.startswith('data_'): # on the right track, accept this file
1572	return True
1573	else: # found something invalid
1574	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1575	self.errors += ' '+str(l)
1576	self.errors += ' Note: a CIF should only have blank lines or comments before'
1577	self.errors += ' a data_ statement begins a block.'
1578	return False
1579
1580	class ImportPhase(ImportBaseclass):
1581	'''Defines a base class for the reading of files with coordinates
1582
1583	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1584	in :meth:`GSASII.GSASII.OnImportPhase`.
1585	See :ref:`Writing a Import Routine<Import_Routines>`
1586	for an explanation on how to use this class.
1587
1588	'''
1589	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1590	strictExtension=False,):
1591	# call parent __init__
1592	ImportBaseclass.__init__(self,formatName,longFormatName,
1593	extensionlist,strictExtension)
1594	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1595	self.Constraints = None
1596
1597	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1598	title='Select a phase', size=None,header='Phase Selector'):
1599	''' Provide a wx dialog to select a phase if the file contains more
1600	than one phase
1601	'''
1602	return self.BlockSelector(ChoiceList,ParentFrame,title,
1603	size,header)
1604
1605	class ImportStructFactor(ImportBaseclass):
1606	'''Defines a base class for the reading of files with tables
1607	of structure factors.
1608
1609	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1610	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1611	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1612	:meth:`Reader`.
1613
1614	See :ref:`Writing a Import Routine<Import_Routines>`
1615	for an explanation on how to use import classes in general. The specifics
1616	for reading a structure factor histogram require that
1617	the ``Reader()`` routine in the import
1618	class need to do only a few things: It
1619	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1620	and set :attr:`Parameters` with the instrument parameters
1621	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1622	'''
1623	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1624	strictExtension=False,):
1625	ImportBaseclass.__init__(self,formatName,longFormatName,
1626	extensionlist,strictExtension)
1627
1628	# define contents of Structure Factor entry
1629	self.Parameters = []
1630	'self.Parameters is a list with two dicts for data parameter settings'
1631	self.InitParameters()
1632	self.RefDict = {'RefList':[],'FF':[],'Super':0}
1633	self.Banks = [] #for multi bank data (usually TOF)
1634	'''self.RefDict is a dict containing the reflection information, as read from the file.
1635	Item 'RefList' contains the reflection information. See the
1636	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1637	for the contents of each row. Dict element 'FF'
1638	contains the form factor values for each element type; if this entry
1639	is left as initialized (an empty list) it will be initialized as needed later.
1640	'''
1641	def ReInitialize(self):
1642	'Reinitialize the Reader to initial settings'
1643	ImportBaseclass.ReInitialize(self)
1644	self.InitParameters()
1645	self.Banks = [] #for multi bank data (usually TOF)
1646	self.RefDict = {'RefList':[],'FF':[],'Super':0}
1647
1648	def InitParameters(self):
1649	'initialize the instrument parameters structure'
1650	Lambda = 0.70926
1651	HistType = 'SXC'
1652	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1653	'Lam':[Lambda,Lambda]
1654	}, {}]
1655	'Parameters is a list with two dicts for data parameter settings'
1656
1657	def UpdateParameters(self,Type=None,Wave=None):
1658	'Revise the instrument parameters'
1659	if Type is not None:
1660	self.Parameters[0]['Type'] = [Type,Type]
1661	if Wave is not None:
1662	self.Parameters[0]['Lam'] = [Wave,Wave]
1663
1664	######################################################################
1665	class ImportPowderData(ImportBaseclass):
1666	'''Defines a base class for the reading of files with powder data.
1667
1668	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1669	in :meth:`GSASII.GSASII.OnImportPowder`.
1670	See :ref:`Writing a Import Routine<Import_Routines>`
1671	for an explanation on how to use this class.
1672	'''
1673	def __init__(self,
1674	formatName,
1675	longFormatName=None,
1676	extensionlist=[],
1677	strictExtension=False,
1678	):
1679	ImportBaseclass.__init__(self,formatName,
1680	longFormatName,
1681	extensionlist,
1682	strictExtension)
1683	self.clockWd = None # used in TOF
1684	self.ReInitialize()
1685
1686	def ReInitialize(self):
1687	'Reinitialize the Reader to initial settings'
1688	ImportBaseclass.ReInitialize(self)
1689	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1690	self.powderdata = [] # Powder dataset
1691	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1692	np.array(x), # x-axis values
1693	np.array(y), # powder pattern intensities
1694	np.array(w), # 1/sig(intensity)^2 values (weights)
1695	np.array(yc), # calc. intensities (zero)
1696	np.array(yb), # calc. background (zero)
1697	np.array(yd), # obs-calc profiles
1698	'''
1699	self.comments = []
1700	self.idstring = ''
1701	self.Sample = G2pdG.SetDefaultSample()
1702	self.GSAS = None # used in TOF
1703	self.repeat_instparm = True # Should a parm file be
1704	# used for multiple histograms?
1705	self.instparm = None # name hint from file of instparm to use
1706	self.instfile = '' # full path name to instrument parameter file
1707	self.instbank = '' # inst parm bank number
1708	self.instmsg = '' # a label that gets printed to show
1709	# where instrument parameters are from
1710	self.numbanks = 1
1711	self.instdict = {} # place items here that will be transferred to the instrument parameters
1712	######################################################################
1713	class ImportSmallAngleData(ImportBaseclass):
1714	'''Defines a base class for the reading of files with small angle data.
1715	See :ref:`Writing a Import Routine<Import_Routines>`
1716	for an explanation on how to use this class.
1717	'''
1718	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1719	strictExtension=False,):
1720
1721	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1722	strictExtension)
1723	self.ReInitialize()
1724
1725	def ReInitialize(self):
1726	'Reinitialize the Reader to initial settings'
1727	ImportBaseclass.ReInitialize(self)
1728	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1729	self.smallangledata = [] # SASD dataset
1730	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1731	np.array(x), # x-axis values
1732	np.array(y), # powder pattern intensities
1733	np.array(w), # 1/sig(intensity)^2 values (weights)
1734	np.array(yc), # calc. intensities (zero)
1735	np.array(yd), # obs-calc profiles
1736	np.array(yb), # preset bkg
1737	'''
1738	self.comments = []
1739	self.idstring = ''
1740	self.Sample = G2pdG.SetDefaultSample()
1741	self.GSAS = None # used in TOF
1742	self.clockWd = None # used in TOF
1743	self.numbanks = 1
1744	self.instdict = {} # place items here that will be transferred to the instrument parameters
1745	######################################################################
1746	class ExportBaseclass(object):
1747	'''Defines a base class for the exporting of GSAS-II results.
1748
1749	This class is subclassed in the various exports/G2export_*.py files. Those files
1750	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
1751	appropriate menu items for each one and the .Exporter method is called
1752	directly from the menu item.
1753
1754	'''
1755	def __init__(self,
1756	G2frame,
1757	formatName,
1758	extension,
1759	longFormatName=None,
1760	):
1761	self.G2frame = G2frame
1762	self.formatName = formatName # short string naming file type
1763	self.extension = extension
1764	if longFormatName: # longer string naming file type
1765	self.longFormatName = longFormatName
1766	else:
1767	self.longFormatName = formatName
1768	self.OverallParms = {}
1769	self.Phases = {}
1770	self.Histograms = {}
1771	self.powderDict = {}
1772	self.xtalDict = {}
1773	self.parmDict = {}
1774	self.sigDict = {}
1775	# updated in InitExport:
1776	self.currentExportType = None # type of export that has been requested
1777	# updated in ExportSelect (when used):
1778	self.phasenam = None # a list of selected phases
1779	self.histnam = None # a list of selected histograms
1780	self.filename = None # name of file to be written (single export) or template (multiple files)
1781	self.dirname = '' # name of directory where file(s) will be written
1782	self.fullpath = '' # name of file being written -- full path
1783
1784	# items that should be defined in a subclass of this class
1785	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1786	# The following types are defined: 'project', "phase", "powder", "single"
1787	self.multiple = False # set as True if the class can export multiple phases or histograms
1788	# self.multiple is ignored for "project" exports
1789
1790	def InitExport(self,event):
1791	'''Determines the type of menu that called the Exporter and
1792	misc initialization.
1793	'''
1794	self.filename = None # name of file to be written (single export)
1795	self.dirname = '' # name of file to be written (multiple export)
1796	if event:
1797	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1798
1799	def MakePWDRfilename(self,hist):
1800	'''Make a filename root (no extension) from a PWDR histogram name
1801
1802	:param str hist: the histogram name in data tree (starts with "PWDR ")
1803	'''
1804	file0 = ''
1805	file1 = hist[5:]
1806	# replace repeated blanks
1807	while file1 != file0:
1808	file0 = file1
1809	file1 = file0.replace(' ',' ').strip()
1810	file0 = file1.replace('Azm= ','A')
1811	# if angle has unneeded decimal places on aziumuth, remove them
1812	if file0[-3:] == '.00': file0 = file0[:-3]
1813	file0 = file0.replace('.','_')
1814	file0 = file0.replace(' ','_')
1815	return file0
1816
1817	def ExportSelect(self,AskFile='ask'):
1818	'''Selects histograms or phases when needed. Sets a default file name when
1819	requested in self.filename; always sets a default directory in self.dirname.
1820
1821	:param bool AskFile: Determines how this routine processes getting a
1822	location to store the current export(s).
1823
1824	* if AskFile is 'ask' (default option), get the name of the file to be written;
1825	self.filename and self.dirname are always set. In the case where
1826	multiple files must be generated, the export routine should do this
1827	based on self.filename as a template.
1828	* if AskFile is 'dir', get the name of the directory to be used;
1829	self.filename is not used, but self.dirname is always set. The export routine
1830	will always generate the file name.
1831	* if AskFile is 'single', get only the name of the directory to be used when
1832	multiple items will be written (as multiple files) are used
1833	or a complete file name is requested when a single file
1834	name is selected. self.dirname is always set and self.filename used
1835	only when a single file is selected.
1836	* if AskFile is 'default', creates a name of the file to be used from
1837	the name of the project (.gpx) file. If the project has not been saved,
1838	then the name of file is requested.
1839	self.filename and self.dirname are always set. In the case where
1840	multiple file names must be generated, the export routine should do this
1841	based on self.filename.
1842	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1843	file. If the project has not been saved, then a directory is requested.
1844	self.filename is not used.
1845
1846	:returns: True in case of an error
1847	'''
1848
1849	numselected = 1
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	numselected = len(self.phasenam)
1865	else:
1866	choices = sorted(self.Phases.keys())
1867	phasenum = G2gd.ItemSelector(choices,self.G2frame)
1868	if phasenum is None: return True
1869	self.phasenam = [choices[phasenum]]
1870	numselected = len(self.phasenam)
1871	elif self.currentExportType == 'single':
1872	if len(self.xtalDict) == 0:
1873	self.G2frame.ErrorDialog(
1874	'Empty project',
1875	'Project does not contain any single crystal data.')
1876	return True
1877	elif len(self.xtalDict) == 1:
1878	self.histnam = self.xtalDict.values()
1879	elif self.multiple:
1880	choices = sorted(self.xtalDict.values())
1881	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1882	if not hnum: return True
1883	self.histnam = [choices[i] for i in hnum]
1884	numselected = len(self.histnam)
1885	else:
1886	choices = sorted(self.xtalDict.values())
1887	hnum = G2gd.ItemSelector(choices,self.G2frame)
1888	if hnum is None: return True
1889	self.histnam = [choices[hnum]]
1890	numselected = len(self.histnam)
1891	elif self.currentExportType == 'powder':
1892	if len(self.powderDict) == 0:
1893	self.G2frame.ErrorDialog(
1894	'Empty project',
1895	'Project does not contain any powder data.')
1896	return True
1897	elif len(self.powderDict) == 1:
1898	self.histnam = self.powderDict.values()
1899	elif self.multiple:
1900	choices = sorted(self.powderDict.values())
1901	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1902	if not hnum: return True
1903	self.histnam = [choices[i] for i in hnum]
1904	numselected = len(self.histnam)
1905	else:
1906	choices = sorted(self.powderDict.values())
1907	hnum = G2gd.ItemSelector(choices,self.G2frame)
1908	if hnum is None: return True
1909	self.histnam = [choices[hnum]]
1910	numselected = len(self.histnam)
1911	elif self.currentExportType == 'image':
1912	if len(self.Histograms) == 0:
1913	self.G2frame.ErrorDialog(
1914	'Empty project',
1915	'Project does not contain any images.')
1916	return True
1917	elif len(self.Histograms) == 1:
1918	self.histnam = self.Histograms.keys()
1919	else:
1920	choices = sorted(self.Histograms.keys())
1921	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1922	if self.multiple:
1923	if not hnum: return True
1924	self.histnam = [choices[i] for i in hnum]
1925	else:
1926	if hnum is None: return True
1927	self.histnam = [choices[hnum]]
1928	numselected = len(self.histnam)
1929	if self.currentExportType == 'map':
1930	# search for phases with maps
1931	mapPhases = []
1932	choices = []
1933	for phasenam in sorted(self.Phases):
1934	phasedict = self.Phases[phasenam] # pointer to current phase info
1935	if len(phasedict['General']['Map'].get('rho',[])):
1936	mapPhases.append(phasenam)
1937	if phasedict['General']['Map'].get('Flip'):
1938	choices.append('Charge flip map: '+str(phasenam))
1939	elif phasedict['General']['Map'].get('MapType'):
1940	choices.append(
1941	str(phasedict['General']['Map'].get('MapType'))
1942	+ ' map: ' + str(phasenam))
1943	else:
1944	choices.append('unknown map: '+str(phasenam))
1945	# select a map if needed
1946	if len(mapPhases) == 0:
1947	self.G2frame.ErrorDialog(
1948	'Empty project',
1949	'Project does not contain any maps.')
1950	return True
1951	elif len(mapPhases) == 1:
1952	self.phasenam = mapPhases
1953	else:
1954	phasenum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1955	if self.multiple:
1956	if not phasenum: return True
1957	self.phasenam = [mapPhases[i] for i in phasenum]
1958	else:
1959	if phasenum is None: return True
1960	self.phasenam = [mapPhases[phasenum]]
1961	numselected = len(self.phasenam)
1962
1963	# items selected, now set self.dirname and usually self.filename
1964	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1965	AskFile == 'default' and not self.G2frame.GSASprojectfile
1966	):
1967	filename = self.askSaveFile()
1968	if not filename: return True
1969	self.dirname,self.filename = os.path.split(filename)
1970	elif AskFile == 'dir' or AskFile == 'single' or (
1971	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1972	):
1973	self.dirname = self.askSaveDirectory()
1974	if not self.dirname: return True
1975	elif AskFile == 'default-dir' or AskFile == 'default':
1976	self.dirname,self.filename = os.path.split(
1977	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1978	)
1979	else:
1980	raise Exception('This should not happen!')
1981
1982	def loadParmDict(self):
1983	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1984	refined values to those from the last cycle and set the uncertainties for the
1985	refined parameters in another dict (self.sigDict).
1986
1987	Expands the parm & sig dicts to include values derived from constraints.
1988	'''
1989	self.parmDict = {}
1990	self.sigDict = {}
1991	rigidbodyDict = {}
1992	covDict = {}
1993	consDict = {}
1994	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1995	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
1996	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
1997	while item:
1998	name = self.G2frame.PatternTree.GetItemText(item)
1999	if name == 'Rigid bodies':
2000	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
2001	elif name == 'Covariance':
2002	covDict = self.G2frame.PatternTree.GetItemPyData(item)
2003	elif name == 'Constraints':
2004	consDict = self.G2frame.PatternTree.GetItemPyData(item)
2005	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2006	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
2007	self.parmDict.update(rbDict)
2008	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
2009	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables = G2stIO.GetPhaseData(
2010	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
2011	self.parmDict.update(phaseDict)
2012	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
2013	Phases,Histograms,Print=False,resetRefList=False)
2014	self.parmDict.update(hapDict)
2015	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
2016	self.parmDict.update(histDict)
2017	self.parmDict.update(zip(
2018	covDict.get('varyList',[]),
2019	covDict.get('variables',[])))
2020	self.sigDict = dict(zip(
2021	covDict.get('varyList',[]),
2022	covDict.get('sig',[])))
2023	# expand to include constraints: first compile a list of constraints
2024	constList = []
2025	for item in consDict:
2026	if item.startswith('_'): continue
2027	constList += consDict[item]
2028	# now process the constraints
2029	G2mv.InitVars()
2030	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
2031	varyList = covDict.get('varyListStart')
2032	if varyList is None and len(constDict) == 0:
2033	# no constraints can use varyList
2034	varyList = covDict.get('varyList')
2035	elif varyList is None:
2036	# old GPX file from before pre-constraint varyList is saved
2037	print ' * Old refinement: Please use Calculate/Refine to redo *'
2038	raise Exception(' * Export aborted *')
2039	else:
2040	varyList = list(varyList)
2041	try:
2042	groups,parmlist = G2mv.GroupConstraints(constDict)
2043	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
2044	except:
2045	# this really should not happen
2046	print ' * ERROR - constraints are internally inconsistent *'
2047	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
2048	print 'Errors',errmsg
2049	if warnmsg: print 'Warnings',warnmsg
2050	raise Exception(' * CIF creation aborted *')
2051	# add the constrained values to the parameter dictionary
2052	G2mv.Dict2Map(self.parmDict,varyList)
2053	# and add their uncertainties into the esd dictionary (sigDict)
2054	if covDict.get('covMatrix') is not None:
2055	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
2056
2057	def loadTree(self):
2058	'''Load the contents of the data tree into a set of dicts
2059	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2060	& self.xtalDict)
2061
2062	* The childrenless data tree items are overall parameters/controls for the
2063	entire project and are placed in self.OverallParms
2064	* Phase items are placed in self.Phases
2065	* Data items are placed in self.Histogram. The key for these data items
2066	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2067	'''
2068	self.OverallParms = {}
2069	self.powderDict = {}
2070	self.xtalDict = {}
2071	self.Phases = {}
2072	self.Histograms = {}
2073	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2074	histType = None
2075	if self.currentExportType == 'phase':
2076	# if exporting phases load them here
2077	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2078	if not sub:
2079	print 'no phases found'
2080	return True
2081	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2082	while item:
2083	phaseName = self.G2frame.PatternTree.GetItemText(item)
2084	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2085	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2086	return
2087	elif self.currentExportType == 'single':
2088	histType = 'HKLF'
2089	elif self.currentExportType == 'powder':
2090	histType = 'PWDR'
2091	elif self.currentExportType == 'image':
2092	histType = 'IMG'
2093
2094	if histType: # Loading just one kind of tree entry
2095	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2096	while item:
2097	name = self.G2frame.PatternTree.GetItemText(item)
2098	if name.startswith(histType):
2099	if self.Histograms.get(name): # there is already an item with this name
2100	print('Histogram name '+str(name)+' is repeated. Renaming')
2101	if name[-1] == '9':
2102	name = name[:-1] + '10'
2103	elif name[-1] in '012345678':
2104	name = name[:-1] + str(int(name[-1])+1)
2105	else:
2106	name += '-1'
2107	self.Histograms[name] = {}
2108	# the main info goes into Data, but the 0th
2109	# element contains refinement results, carry
2110	# that over too now.
2111	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2112	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2113	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2114	while item2:
2115	child = self.G2frame.PatternTree.GetItemText(item2)
2116	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2117	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2118	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2119	# index powder and single crystal histograms by number
2120	for hist in self.Histograms:
2121	if hist.startswith("PWDR"):
2122	d = self.powderDict
2123	elif hist.startswith("HKLF"):
2124	d = self.xtalDict
2125	else:
2126	return
2127	i = self.Histograms[hist].get('hId')
2128	if i is None and not d.keys():
2129	i = 0
2130	elif i is None or i in d.keys():
2131	i = max(d.keys())+1
2132	d[i] = hist
2133	return
2134	# else standard load: using all interlinked phases and histograms
2135	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2136	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2137	while item:
2138	name = self.G2frame.PatternTree.GetItemText(item)
2139	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2140	if not item2:
2141	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2142	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2143	# index powder and single crystal histograms
2144	for hist in self.Histograms:
2145	i = self.Histograms[hist]['hId']
2146	if hist.startswith("PWDR"):
2147	self.powderDict[i] = hist
2148	elif hist.startswith("HKLF"):
2149	self.xtalDict[i] = hist
2150
2151	def dumpTree(self,mode='type'):
2152	'''Print out information on the data tree dicts loaded in loadTree
2153	'''
2154	print '\nOverall'
2155	if mode == 'type':
2156	def Show(arg): return type(arg)
2157	else:
2158	def Show(arg): return arg
2159	for key in self.OverallParms:
2160	print ' ',key,Show(self.OverallParms[key])
2161	print 'Phases'
2162	for key1 in self.Phases:
2163	print ' ',key1,Show(self.Phases[key1])
2164	print 'Histogram'
2165	for key1 in self.Histograms:
2166	print ' ',key1,Show(self.Histograms[key1])
2167	for key2 in self.Histograms[key1]:
2168	print ' ',key2,Show(self.Histograms[key1][key2])
2169
2170	def defaultSaveFile(self):
2171	return os.path.abspath(
2172	os.path.splitext(self.G2frame.GSASprojectfile
2173	)[0]+self.extension)
2174
2175	def askSaveFile(self):
2176	'''Ask the user to supply a file name
2177
2178	:returns: a file name (str) or None if Cancel is pressed
2179	'''
2180	defnam = os.path.splitext(
2181	os.path.split(self.G2frame.GSASprojectfile)[1]
2182	)[0]+self.extension
2183	dlg = wx.FileDialog(
2184	self.G2frame, 'Input name for file to write', '.', defnam,
2185	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2186	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2187	dlg.CenterOnParent()
2188	try:
2189	if dlg.ShowModal() == wx.ID_OK:
2190	filename = dlg.GetPath()
2191	# make sure extension is correct
2192	filename = os.path.splitext(filename)[0]+self.extension
2193	else:
2194	filename = None
2195	finally:
2196	dlg.Destroy()
2197	return filename
2198
2199	def askSaveDirectory(self):
2200	'''Ask the user to supply a directory name. Path name is used as the
2201	starting point for the next export path search.
2202
2203	:returns: a directory name (str) or None if Cancel is pressed
2204	'''
2205	if self.G2frame.exportDir:
2206	startdir = self.G2frame.exportDir
2207	elif self.G2frame.GSASprojectfile:
2208	startdir = os.path.split(self.G2frame.GSASprojectfile)[0]
2209	elif self.G2frame.dirname:
2210	startdir = self.G2frame.dirname
2211	else:
2212	startdir = ''
2213	dlg = wx.DirDialog(
2214	self.G2frame, 'Input directory where file(s) will be written', startdir,
2215	wx.DD_DEFAULT_STYLE)
2216	dlg.CenterOnParent()
2217	try:
2218	if dlg.ShowModal() == wx.ID_OK:
2219	filename = dlg.GetPath()
2220	self.G2frame.exportDir = filename
2221	else:
2222	filename = None
2223	finally:
2224	dlg.Destroy()
2225	return filename
2226
2227	# Tools for file writing.
2228	def OpenFile(self,fil=None,mode='w'):
2229	'''Open the output file
2230
2231	:param str fil: The name of the file to open. If None (default)
2232	the name defaults to self.dirname + self.filename.
2233	If an extension is supplied, it is not overridded,
2234	but if not, the default extension is used.
2235	:returns: the file object opened by the routine which is also
2236	saved as self.fp
2237	'''
2238	if not fil:
2239	if not os.path.splitext(self.filename)[1]:
2240	self.filename += self.extension
2241	fil = os.path.join(self.dirname,self.filename)
2242	self.fullpath = fil
2243	self.fp = open(fil,mode)
2244	return self.fp
2245
2246	def Write(self,line):
2247	'''write a line of output, attaching a line-end character
2248
2249	:param str line: the text to be written.
2250	'''
2251	self.fp.write(line+'\n')
2252	def CloseFile(self,fp=None):
2253	'''Close a file opened in OpenFile
2254
2255	:param file fp: the file object to be closed. If None (default)
2256	file object self.fp is closed.
2257	'''
2258	if fp is None:
2259	fp = self.fp
2260	self.fp = None
2261	fp.close()
2262	# Tools to pull information out of the data arrays
2263	def GetCell(self,phasenam):
2264	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2265
2266	:param str phasenam: the name for the selected phase
2267	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2268	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2269	cell values and `cellSig` has their uncertainties.
2270	"""
2271	phasedict = self.Phases[phasenam] # pointer to current phase info
2272	try:
2273	pfx = str(phasedict['pId'])+'::'
2274	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2275	cellSig = G2stIO.getCellEsd(pfx,
2276	phasedict['General']['SGData'],A,
2277	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2278	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2279	return cellList,cellSig
2280	except KeyError:
2281	cell = phasedict['General']['Cell'][1:]
2282	return cell,7*[0]
2283
2284	def GetAtoms(self,phasenam):
2285	"""Gets the atoms associated with a phase. Can be used with standard
2286	or macromolecular phases
2287
2288	:param str phasenam: the name for the selected phase
2289	:returns: a list of items for eac atom where each item is a list containing:
2290	label, typ, mult, xyz, and td, where
2291
2292	* label and typ are the atom label and the scattering factor type (str)
2293	* mult is the site multiplicity (int)
2294	* xyz is contains a list with four pairs of numbers:
2295	x, y, z and fractional occupancy and
2296	their standard uncertainty (or a negative value)
2297	* td is contains a list with either one or six pairs of numbers:
2298	if one number it is U\ :sub:`iso` and with six numbers it is
2299	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2300	paired with their standard uncertainty (or a negative value)
2301	"""
2302	phasedict = self.Phases[phasenam] # pointer to current phase info
2303	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2304	cfrac = cx+3
2305	fpfx = str(phasedict['pId'])+'::Afrac:'
2306	atomslist = []
2307	for i,at in enumerate(phasedict['Atoms']):
2308	if phasedict['General']['Type'] == 'macromolecular':
2309	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2310	else:
2311	label = at[ct-1]
2312	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2313	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2314	mult = at[cs+1]
2315	typ = at[ct]
2316	xyz = []
2317	for j,v in enumerate(('x','y','z')):
2318	val = at[cx+j]
2319	pfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2320	sig = self.sigDict.get(pfx,-0.000009)
2321	xyz.append((val,sig))
2322	xyz.append((fval,fsig))
2323	td = []
2324	if at[cia] == 'I':
2325	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2326	val = self.parmDict.get(pfx,at[cia+1])
2327	sig = self.sigDict.get(pfx,-0.0009)
2328	td.append((val,sig))
2329	else:
2330	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2331	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2332	val = self.parmDict.get(pfx,at[cia+2+i])
2333	sig = self.sigDict.get(pfx,-0.0009)
2334	td.append((val,sig))
2335	atomslist.append((label,typ,mult,xyz,td))
2336	return atomslist
2337	######################################################################
2338
2339	def ReadCIF(URLorFile):
2340	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2341	(from James Hester).
2342	The open routine gets confused with DOS names that begin with a letter and colon
2343	"C:\dir\" so this routine will try to open the passed name as a file and if that
2344	fails, try it as a URL
2345
2346	:param str URLorFile: string containing a URL or a file name. Code will try first
2347	to open it as a file and then as a URL.
2348
2349	:returns: a PyCifRW CIF object.
2350	'''
2351	import CifFile as cif # PyCifRW from James Hester
2352
2353	# alternate approach:
2354	#import urllib
2355	#ciffile = 'file:'+urllib.pathname2url(filename)
2356
2357	try:
2358	fp = open(URLorFile,'r')
2359	cf = cif.ReadCif(fp)
2360	fp.close()
2361	return cf
2362	except IOError:
2363	return cif.ReadCif(URLorFile)
2364
2365	if __name__ == '__main__':
2366	app = wx.PySimpleApp()
2367	frm = wx.Frame(None) # create a frame
2368	frm.Show(True)
2369	filename = '/tmp/notzip.zip'
2370	filename = '/tmp/all.zip'
2371	#filename = '/tmp/11bmb_7652.zip'
2372
2373	#selection=None, confirmoverwrite=True, parent=None
2374	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2375	print ExtractFileFromZip(filename,multipleselect=True)
2376	#confirmread=False, confirmoverwrite=False)
2377
2378	# choicelist=[ ('a','b','c'),
2379	# ('test1','test2'),('no choice',)]
2380	# titles = [ 'a, b or c', 'tests', 'No option here']
2381	# dlg = MultipleChoicesDialog(
2382	# choicelist,titles,
2383	# parent=frm)
2384	# if dlg.ShowModal() == wx.ID_OK:
2385	# print 'Got OK'

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