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source: trunk/GSASIIIO.py @ 1446

Last change on this file since 1446 was 1446, checked in by vondreele, 9 years ago
add new import routine for JANA2000 single xtal files from ISIS
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2014-07-30 16:36:23 +0000 (Wed, 30 Jul 2014) $
4	# $Author: vondreele $
5	# $Revision: 1446 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 1446 2014-07-30 16:36:23Z 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: 1446 $")
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
936	def ProjFileSave(G2frame):
937	'Save a GSAS-II project file'
938	if not G2frame.PatternTree.IsEmpty():
939	file = open(G2frame.GSASprojectfile,'wb')
940	print 'save to file: ',G2frame.GSASprojectfile
941	wx.BeginBusyCursor()
942	try:
943	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
944	while item:
945	data = []
946	name = G2frame.PatternTree.GetItemText(item)
947	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
948	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
949	while item2:
950	name = G2frame.PatternTree.GetItemText(item2)
951	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
952	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
953	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
954	cPickle.dump(data,file,1)
955	file.close()
956	finally:
957	wx.EndBusyCursor()
958	print('project save successful')
959
960	def SaveIntegration(G2frame,PickId,data):
961	'Save image integration results as powder pattern(s)'
962	azms = G2frame.Integrate[1]
963	X = G2frame.Integrate[2][:-1]
964	N = len(X)
965	Id = G2frame.PatternTree.GetItemParent(PickId)
966	name = G2frame.PatternTree.GetItemText(Id)
967	name = name.replace('IMG ',data['type']+' ')
968	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
969	if 'PWDR' in name:
970	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
971	codes = [0 for i in range(11)]
972	elif 'SASD' in name:
973	names = ['Type','Lam','Zero','Azimuth']
974	codes = [0 for i in range(4)]
975	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
976	Xminmax = [X[0],X[-1]]
977	LRazm = data['LRazimuth']
978	Azms = []
979	if data['fullIntegrate'] and data['outAzimuths'] == 1:
980	Azms = [45.0,] #a poor man's average?
981	else:
982	for i,azm in enumerate(azms[:-1]):
983	Azms.append((azms[i+1]+azm)/2.)
984	for i,azm in enumerate(azms[:-1]):
985	Aname = name+" Azm= %.2f"%(Azms[i])
986	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
987	nOcc = 0
988	while item:
989	Name = G2frame.PatternTree.GetItemText(item)
990	if Aname in Name:
991	nOcc += 1
992	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
993	if nOcc:
994	Aname += '(%d)'%(nOcc)
995	Sample = G2pdG.SetDefaultSample()
996	Sample['Gonio. radius'] = data['distance']
997	Sample['Omega'] = data['GonioAngles'][0]
998	Sample['Chi'] = data['GonioAngles'][1]
999	Sample['Phi'] = data['GonioAngles'][2]
1000	if 'PWDR' in Aname:
1001	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!
1002	elif 'SASD' in Aname:
1003	Sample['Trans'] = data['SampleAbs'][0]
1004	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
1005	Y = G2frame.Integrate[0][i]
1006	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
1007	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=Aname)
1008	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
1009	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
1010	if 'PWDR' in Aname:
1011	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
1012	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
1013	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
1014	for item in inst[0]:
1015	inst[0][item] = list(inst[0][item])
1016	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
1017	if 'PWDR' in Aname:
1018	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1019	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),[])
1020	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[])
1021	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
1022	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
1023	elif 'SASD' in Aname:
1024	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
1025	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1026	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
1027	valuesdict = {
1028	'wtFactor':1.0,
1029	'Dummy':False,
1030	'ranId':ran.randint(0,sys.maxint),
1031	}
1032	G2frame.PatternTree.SetItemPyData(
1033	Id,[valuesdict,
1034	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
1035	return Id #last powder pattern generated
1036
1037	# def powderFxyeSave(G2frame,exports,powderfile):
1038	# 'Save a powder histogram as a GSAS FXYE file'
1039	# head,tail = ospath.split(powderfile)
1040	# name,ext = tail.split('.')
1041	# for i,export in enumerate(exports):
1042	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1043	# prmname = filename.strip(ext)+'prm'
1044	# prm = open(prmname,'w') #old style GSAS parm file
1045	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1046	# Inst = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, \
1047	# PickId, 'Instrument Parameters'))[0]
1048	# prm.write( ' 123456789012345678901234567890123456789012345678901234567890 '+'\n')
1049	# prm.write( 'INS BANK 1 '+'\n')
1050	# prm.write(('INS HTYPE %sR '+'\n')%(Inst['Type'][0]))
1051	# if 'Lam1' in Inst: #Ka1 & Ka2
1052	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam1'][0],Inst['Lam2'][0]))
1053	# elif 'Lam' in Inst: #single wavelength
1054	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam'][1],0.0))
1055	# prm.write( 'INS 1 IRAD 0 '+'\n')
1056	# prm.write( 'INS 1I HEAD '+'\n')
1057	# prm.write( 'INS 1I ITYP 0 0.0000 180.0000 1 '+'\n')
1058	# prm.write(('INS 1DETAZM%10.3f '+'\n')%(Inst['Azimuth'][0]))
1059	# prm.write( 'INS 1PRCF1 3 8 0.00100 '+'\n')
1060	# prm.write(('INS 1PRCF11 %15.6g%15.6g%15.6g%15.6g '+'\n')%(Inst['U'][1],Inst['V'][1],Inst['W'][1],0.0))
1061	# 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.))
1062	# prm.close()
1063	# file = open(filename,'w')
1064	# print 'save powder pattern to file: ',filename
1065	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1066	# file.write(powderfile+'\n')
1067	# file.write('Instrument parameter file:'+ospath.split(prmname)[1]+'\n')
1068	# file.write('BANK 1 %d %d CONS %.2f %.2f 0 0 FXYE\n'%(len(x),len(x),\
1069	# 100.x[0],100.(x[1]-x[0])))
1070	# s = list(np.sqrt(1./np.array(w)))
1071	# XYW = zip(x,y,s)
1072	# for X,Y,S in XYW:
1073	# file.write("%15.6g %15.6g %15.6g\n" % (100.*X,Y,max(S,1.0)))
1074	# file.close()
1075	# print 'powder pattern file '+filename+' written'
1076
1077	# def powderXyeSave(G2frame,exports,powderfile):
1078	# 'Save a powder histogram as a Topas XYE file'
1079	# head,tail = ospath.split(powderfile)
1080	# name,ext = tail.split('.')
1081	# for i,export in enumerate(exports):
1082	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1083	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1084	# file = open(filename,'w')
1085	# file.write('#%s\n'%(export))
1086	# print 'save powder pattern to file: ',filename
1087	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1088	# s = list(np.sqrt(1./np.array(w)))
1089	# XYW = zip(x,y,s)
1090	# for X,Y,W in XYW:
1091	# file.write("%15.6g %15.6g %15.6g\n" % (X,Y,W))
1092	# file.close()
1093	# print 'powder pattern file '+filename+' written'
1094
1095	def PDFSave(G2frame,exports):
1096	'Save a PDF G(r) and S(Q) in column formats'
1097	for export in exports:
1098	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1099	SQname = 'S(Q)'+export[4:]
1100	GRname = 'G(R)'+export[4:]
1101	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
1102	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
1103	sqId = G2gd.GetPatternTreeItemId(G2frame, PickId, SQname)
1104	grId = G2gd.GetPatternTreeItemId(G2frame, PickId, GRname)
1105	sqdata = np.array(G2frame.PatternTree.GetItemPyData(sqId)[1][:2]).T
1106	grdata = np.array(G2frame.PatternTree.GetItemPyData(grId)[1][:2]).T
1107	sqfile = open(sqfilename,'w')
1108	grfile = open(grfilename,'w')
1109	sqfile.write('#T S(Q) %s\n'%(export))
1110	grfile.write('#T G(R) %s\n'%(export))
1111	sqfile.write('#L Q S(Q)\n')
1112	grfile.write('#L R G(R)\n')
1113	for q,sq in sqdata:
1114	sqfile.write("%15.6g %15.6g\n" % (q,sq))
1115	sqfile.close()
1116	for r,gr in grdata:
1117	grfile.write("%15.6g %15.6g\n" % (r,gr))
1118	grfile.close()
1119
1120	def PeakListSave(G2frame,file,peaks):
1121	'Save powder peaks to a data file'
1122	print 'save peak list to file: ',G2frame.peaklistfile
1123	if not peaks:
1124	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1125	try:
1126	result = dlg.ShowModal()
1127	finally:
1128	dlg.Destroy()
1129	return
1130	for peak in peaks:
1131	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1132	(peak[0],peak[2],peak[4],peak[6]))
1133	print 'peak list saved'
1134
1135	def IndexPeakListSave(G2frame,peaks):
1136	'Save powder peaks from the indexing list'
1137	file = open(G2frame.peaklistfile,'wa')
1138	print 'save index peak list to file: ',G2frame.peaklistfile
1139	wx.BeginBusyCursor()
1140	try:
1141	if not peaks:
1142	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1143	try:
1144	result = dlg.ShowModal()
1145	finally:
1146	dlg.Destroy()
1147	return
1148	for peak in peaks:
1149	file.write("%12.6f\n" % (peak[7]))
1150	file.close()
1151	finally:
1152	wx.EndBusyCursor()
1153	print 'index peak list saved'
1154
1155	def SetNewPhase(Name='New Phase',SGData=None,cell=None):
1156	'''Create a new phase dict with default values for various parameters
1157
1158	:param str Name: Name for new Phase
1159
1160	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1161	defaults to data for P 1
1162
1163	:param list cell: unit cell parameter list; defaults to
1164	[1.0,1.0,1.0,90.,90,90.,1.]
1165
1166	'''
1167	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1168	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1169	phaseData = {
1170	'ranId':ran.randint(0,sys.maxint),
1171	'General':{
1172	'Name':Name,
1173	'Type':'nuclear',
1174	'AtomPtrs':[3,1,7,9],
1175	'SGData':SGData,
1176	'Cell':[False,]+cell,
1177	'Pawley dmin':1.0,
1178	'Data plot type':'None',
1179	'SH Texture':{
1180	'Order':0,
1181	'Model':'cylindrical',
1182	'Sample omega':[False,0.0],
1183	'Sample chi':[False,0.0],
1184	'Sample phi':[False,0.0],
1185	'SH Coeff':[False,{}],
1186	'SHShow':False,
1187	'PFhkl':[0,0,1],
1188	'PFxyz':[0,0,1],
1189	'PlotType':'Pole figure'}},
1190	'Atoms':[],
1191	'Drawing':{},
1192	'Histograms':{},
1193	'Pawley ref':[],
1194	'RBModels':{},
1195	}
1196	return phaseData
1197
1198	class MultipleChoicesDialog(wx.Dialog):
1199	'''A dialog that offers a series of choices, each with a
1200	title and a wx.Choice widget. Intended to be used Modally.
1201	typical input:
1202
1203	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1204	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1205
1206	selections are placed in self.chosen when OK is pressed
1207	'''
1208	def __init__(self,choicelist,headinglist,
1209	head='Select options',
1210	title='Please select from options below',
1211	parent=None):
1212	self.chosen = []
1213	wx.Dialog.__init__(
1214	self,parent,wx.ID_ANY,head,
1215	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1216	panel = wx.Panel(self)
1217	mainSizer = wx.BoxSizer(wx.VERTICAL)
1218	mainSizer.Add((10,10),1)
1219	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1220	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1221	self.ChItems = []
1222	for choice,lbl in zip(choicelist,headinglist):
1223	mainSizer.Add((10,10),1)
1224	self.chosen.append(0)
1225	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1226	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1227	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1228	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1229
1230	OkBtn = wx.Button(panel,-1,"Ok")
1231	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1232	cancelBtn = wx.Button(panel,-1,"Cancel")
1233	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1234	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1235	btnSizer.Add((20,20),1)
1236	btnSizer.Add(OkBtn)
1237	btnSizer.Add((20,20),1)
1238	btnSizer.Add(cancelBtn)
1239	btnSizer.Add((20,20),1)
1240	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1241	panel.SetSizer(mainSizer)
1242	panel.Fit()
1243	self.Fit()
1244
1245	def OnOk(self,event):
1246	parent = self.GetParent()
1247	if parent is not None: parent.Raise()
1248	# save the results from the choice widgets
1249	self.chosen = []
1250	for w in self.ChItems:
1251	self.chosen.append(w.GetSelection())
1252	self.EndModal(wx.ID_OK)
1253
1254	def OnCancel(self,event):
1255	parent = self.GetParent()
1256	if parent is not None: parent.Raise()
1257	self.chosen = []
1258	self.EndModal(wx.ID_CANCEL)
1259
1260	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1261	confirmoverwrite=True, parent=None,
1262	multipleselect=False):
1263	'''If the filename is a zip file, extract a file from that
1264	archive.
1265
1266	:param list Selection: used to predefine the name of the file
1267	to be extracted. Filename case and zip directory name are
1268	ignored in selection; the first matching file is used.
1269
1270	:param bool confirmread: if True asks the user to confirm before expanding
1271	the only file in a zip
1272
1273	:param bool confirmoverwrite: if True asks the user to confirm
1274	before overwriting if the extracted file already exists
1275
1276	:param bool multipleselect: if True allows more than one zip
1277	file to be extracted, a list of file(s) is returned.
1278	If only one file is present, do not ask which one, otherwise
1279	offer a list of choices (unless selection is used).
1280
1281	:returns: the name of the file that has been created or a
1282	list of files (see multipleselect)
1283
1284	If the file is not a zipfile, return the name of the input file.
1285	If the zipfile is empty or no file has been selected, return None
1286	'''
1287	import zipfile # do this now, since we can save startup time by doing this only on need
1288	import shutil
1289	zloc = os.path.split(filename)[0]
1290	if not zipfile.is_zipfile(filename):
1291	#print("not zip")
1292	return filename
1293
1294	z = zipfile.ZipFile(filename,'r')
1295	zinfo = z.infolist()
1296
1297	if len(zinfo) == 0:
1298	#print('Zip has no files!')
1299	zlist = [-1]
1300	if selection:
1301	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1302	if selection.lower() in choices:
1303	zlist = [choices.index(selection.lower())]
1304	else:
1305	print('debug: file '+str(selection)+' was not found in '+str(filename))
1306	zlist = [-1]
1307	elif len(zinfo) == 1 and confirmread:
1308	result = wx.ID_NO
1309	dlg = wx.MessageDialog(
1310	parent,
1311	'Is file '+str(zinfo[0].filename)+
1312	' what you want to extract from '+
1313	str(os.path.split(filename)[1])+'?',
1314	'Confirm file',
1315	wx.YES_NO \| wx.ICON_QUESTION)
1316	try:
1317	result = dlg.ShowModal()
1318	finally:
1319	dlg.Destroy()
1320	if result == wx.ID_NO:
1321	zlist = [-1]
1322	else:
1323	zlist = [0]
1324	elif len(zinfo) == 1:
1325	zlist = [0]
1326	elif multipleselect:
1327	# select one or more from a from list
1328	choices = [i.filename for i in zinfo]
1329	dlg = G2gd.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1330	'Choose file(s)',choices)
1331	if dlg.ShowModal() == wx.ID_OK:
1332	zlist = dlg.GetSelections()
1333	else:
1334	zlist = []
1335	dlg.Destroy()
1336	else:
1337	# select one from a from list
1338	choices = [i.filename for i in zinfo]
1339	dlg = wx.SingleChoiceDialog(parent,
1340	'Select file to extract from zip file'+str(filename),'Choose file',
1341	choices,)
1342	if dlg.ShowModal() == wx.ID_OK:
1343	zlist = [dlg.GetSelection()]
1344	else:
1345	zlist = [-1]
1346	dlg.Destroy()
1347
1348	outlist = []
1349	for zindex in zlist:
1350	if zindex >= 0:
1351	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1352	if os.path.exists(efil) and confirmoverwrite:
1353	result = wx.ID_NO
1354	dlg = wx.MessageDialog(parent,
1355	'File '+str(efil)+' already exists. OK to overwrite it?',
1356	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1357	try:
1358	result = dlg.ShowModal()
1359	finally:
1360	dlg.Destroy()
1361	if result == wx.ID_NO:
1362	zindex = -1
1363	if zindex >= 0:
1364	# extract the file to the current directory, regardless of it's original path
1365	#z.extract(zinfo[zindex],zloc)
1366	eloc,efil = os.path.split(zinfo[zindex].filename)
1367	outfile = os.path.join(zloc, efil)
1368	fpin = z.open(zinfo[zindex])
1369	fpout = file(outfile, "wb")
1370	shutil.copyfileobj(fpin, fpout)
1371	fpin.close()
1372	fpout.close()
1373	outlist.append(outfile)
1374	z.close()
1375	if multipleselect and len(outlist) >= 1:
1376	return outlist
1377	elif len(outlist) == 1:
1378	return outlist[0]
1379	else:
1380	return None
1381
1382	######################################################################
1383	# base classes for reading various types of data files
1384	# not used directly, only by subclassing
1385	######################################################################
1386	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1387	P1SGData = SGData
1388	class ImportBaseclass(object):
1389	'''Defines a base class for the reading of input files (diffraction
1390	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1391	for an explanation on how to use a subclass of this class.
1392	'''
1393	class ImportException(Exception):
1394	'''Defines an Exception that is used when an import routine hits an expected error,
1395	usually in .Reader.
1396
1397	Good practice is that the Reader should define a value in self.errors that
1398	tells the user some information about what is wrong with their file.
1399	'''
1400	pass
1401
1402	def __init__(self,
1403	formatName,
1404	longFormatName=None,
1405	extensionlist=[],
1406	strictExtension=False,
1407	):
1408	self.formatName = formatName # short string naming file type
1409	if longFormatName: # longer string naming file type
1410	self.longFormatName = longFormatName
1411	else:
1412	self.longFormatName = formatName
1413	# define extensions that are allowed for the file type
1414	# for windows, remove any extensions that are duplicate, as case is ignored
1415	if sys.platform == 'windows' and extensionlist:
1416	extensionlist = list(set([s.lower() for s in extensionlist]))
1417	self.extensionlist = extensionlist
1418	# If strictExtension is True, the file will not be read, unless
1419	# the extension matches one in the extensionlist
1420	self.strictExtension = strictExtension
1421	self.errors = ''
1422	self.warnings = ''
1423	# used for readers that will use multiple passes to read
1424	# more than one data block
1425	self.repeat = False
1426	self.selections = []
1427	self.repeatcount = 0
1428	self.readfilename = '?'
1429	#print 'created',self.__class__
1430
1431	def ReInitialize(self):
1432	'Reinitialize the Reader to initial settings'
1433	self.errors = ''
1434	self.warnings = ''
1435	self.repeat = False
1436	self.repeatcount = 0
1437	self.readfilename = '?'
1438
1439	def BlockSelector(self, ChoiceList, ParentFrame=None,
1440	title='Select a block',
1441	size=None, header='Block Selector',
1442	useCancel=True):
1443	''' Provide a wx dialog to select a block if the file contains more
1444	than one set of data and one must be selected
1445	'''
1446	if useCancel:
1447	dlg = wx.SingleChoiceDialog(
1448	ParentFrame,title, header,ChoiceList)
1449	else:
1450	dlg = wx.SingleChoiceDialog(
1451	ParentFrame,title, header,ChoiceList,
1452	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1453	if size: dlg.SetSize(size)
1454	dlg.CenterOnParent()
1455	if dlg.ShowModal() == wx.ID_OK:
1456	sel = dlg.GetSelection()
1457	return sel
1458	else:
1459	return None
1460	dlg.Destroy()
1461
1462	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1463	title='Select a block',size=None, header='Block Selector'):
1464	'''Provide a wx dialog to select a block of data if the
1465	file contains more than one set of data and one must be
1466	selected.
1467
1468	:returns: a list of the selected blocks
1469	'''
1470	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1471	wx.CHOICEDLG_STYLE)
1472	dlg.CenterOnParent()
1473	if size: dlg.SetSize(size)
1474	if dlg.ShowModal() == wx.ID_OK:
1475	sel = dlg.GetSelections()
1476	else:
1477	return []
1478	dlg.Destroy()
1479	selected = []
1480	if len(ChoiceList) in sel:
1481	return range(len(ChoiceList))
1482	else:
1483	return sel
1484	return selected
1485
1486	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1487	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1488	widget. Typical input:
1489
1490	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1491
1492	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1493
1494	optional keyword parameters are: head (window title) and title
1495	returns a list of selected indicies for each choice (or None)
1496	'''
1497	result = None
1498	dlg = MultipleChoicesDialog(choicelist,headinglist,
1499	parent=ParentFrame, **kwargs)
1500	dlg.CenterOnParent()
1501	if dlg.ShowModal() == wx.ID_OK:
1502	result = dlg.chosen
1503	dlg.Destroy()
1504	return result
1505
1506	def ShowBusy(self):
1507	wx.BeginBusyCursor()
1508	wx.Yield() # make it happen now!
1509
1510	def DoneBusy(self):
1511	wx.EndBusyCursor()
1512	wx.Yield() # make it happen now!
1513
1514	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1515	# '''This method must be supplied in the child class to read the file.
1516	# if the read fails either return False or raise an Exception
1517	# preferably of type ImportException.
1518	# '''
1519	# #start reading
1520	# raise ImportException("Error occurred while...")
1521	# self.errors += "Hint for user on why the error occur
1522	# return False # if an error occurs
1523	# return True # if read OK
1524
1525	def ExtensionValidator(self, filename):
1526	'''This methods checks if the file has the correct extension
1527	Return False if this filename will not be supported by this reader
1528	Return True if the extension matches the list supplied by the reader
1529	Return None if the reader allows un-registered extensions
1530	'''
1531	if filename:
1532	ext = os.path.splitext(filename)[1]
1533	if sys.platform == 'windows': ext = ext.lower()
1534	if ext in self.extensionlist: return True
1535	if self.strictExtension: return False
1536	return None
1537
1538	def ContentsValidator(self, filepointer):
1539	'''This routine will attempt to determine if the file can be read
1540	with the current format.
1541	This will typically be overridden with a method that
1542	takes a quick scan of [some of]
1543	the file contents to do a "sanity" check if the file
1544	appears to match the selected format.
1545	Expected to be called via self.Validator()
1546	'''
1547	#filepointer.seek(0) # rewind the file pointer
1548	return True
1549
1550	def CIFValidator(self, filepointer):
1551	'''A :meth:`ContentsValidator` for use to validate CIF files.
1552	'''
1553	for i,l in enumerate(filepointer):
1554	if i >= 1000: return True
1555	'''Encountered only blank lines or comments in first 1000
1556	lines. This is unlikely, but assume it is CIF anyway, since we are
1557	even less likely to find a file with nothing but hashes and
1558	blank lines'''
1559	line = l.strip()
1560	if len(line) == 0: # ignore blank lines
1561	continue
1562	elif line.startswith('#'): # ignore comments
1563	continue
1564	elif line.startswith('data_'): # on the right track, accept this file
1565	return True
1566	else: # found something invalid
1567	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1568	self.errors += ' '+str(l)
1569	self.errors += ' Note: a CIF should only have blank lines or comments before'
1570	self.errors += ' a data_ statement begins a block.'
1571	return False
1572
1573	class ImportPhase(ImportBaseclass):
1574	'''Defines a base class for the reading of files with coordinates
1575
1576	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1577	in :meth:`GSASII.GSASII.OnImportPhase`.
1578	See :ref:`Writing a Import Routine<Import_Routines>`
1579	for an explanation on how to use this class.
1580
1581	'''
1582	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1583	strictExtension=False,):
1584	# call parent __init__
1585	ImportBaseclass.__init__(self,formatName,longFormatName,
1586	extensionlist,strictExtension)
1587	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1588	self.Constraints = None
1589
1590	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1591	title='Select a phase', size=None,header='Phase Selector'):
1592	''' Provide a wx dialog to select a phase if the file contains more
1593	than one phase
1594	'''
1595	return self.BlockSelector(ChoiceList,ParentFrame,title,
1596	size,header)
1597
1598	class ImportStructFactor(ImportBaseclass):
1599	'''Defines a base class for the reading of files with tables
1600	of structure factors.
1601
1602	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1603	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1604	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1605	:meth:`Reader`.
1606
1607	See :ref:`Writing a Import Routine<Import_Routines>`
1608	for an explanation on how to use import classes in general. The specifics
1609	for reading a structure factor histogram require that
1610	the ``Reader()`` routine in the import
1611	class need to do only a few things: It
1612	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1613	and set :attr:`Parameters` with the instrument parameters
1614	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1615	'''
1616	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1617	strictExtension=False,):
1618	ImportBaseclass.__init__(self,formatName,longFormatName,
1619	extensionlist,strictExtension)
1620
1621	# define contents of Structure Factor entry
1622	self.Parameters = []
1623	'self.Parameters is a list with two dicts for data parameter settings'
1624	self.InitParameters()
1625	self.RefDict = {'RefList':[],'FF':[]}
1626	self.Banks = [] #for multi bank data (usually TOF)
1627	'''self.RefDict is a dict containing the reflection information, as read from the file.
1628	Item 'RefList' contains the reflection information. See the
1629	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1630	for the contents of each row. Dict element 'FF'
1631	contains the form factor values for each element type; if this entry
1632	is left as initialized (an empty list) it will be initialized as needed later.
1633	'''
1634	def ReInitialize(self):
1635	'Reinitialize the Reader to initial settings'
1636	ImportBaseclass.ReInitialize(self)
1637	self.InitParameters()
1638	self.Banks = [] #for multi bank data (usually TOF)
1639	self.RefDict = {'RefList':[],'FF':[]}
1640
1641	def InitParameters(self):
1642	'initialize the instrument parameters structure'
1643	Lambda = 0.70926
1644	HistType = 'SXC'
1645	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1646	'Lam':[Lambda,Lambda]
1647	}, {}]
1648	'Parameters is a list with two dicts for data parameter settings'
1649
1650	def UpdateParameters(self,Type=None,Wave=None):
1651	'Revise the instrument parameters'
1652	if Type is not None:
1653	self.Parameters[0]['Type'] = [Type,Type]
1654	if Wave is not None:
1655	self.Parameters[0]['Lam'] = [Wave,Wave]
1656
1657	######################################################################
1658	class ImportPowderData(ImportBaseclass):
1659	'''Defines a base class for the reading of files with powder data.
1660
1661	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1662	in :meth:`GSASII.GSASII.OnImportPowder`.
1663	See :ref:`Writing a Import Routine<Import_Routines>`
1664	for an explanation on how to use this class.
1665	'''
1666	# define some default instrument parameter files
1667	# just like GSAS, sigh
1668	defaultIparm_lbl = []
1669	defaultIparms = []
1670	defaultIparm_lbl.append('CuKa lab data')
1671	defaultIparms.append({
1672	'INS HTYPE ':'PXC ',
1673	'INS 1 ICONS':' 1.540500 1.544300 0.0 0 0.7 0 0.5 ',
1674	'INS 1PRCF1 ':' 3 8 0.01 ',
1675	'INS 1PRCF11':' 2.000000E+00 -2.000000E+00 5.000000E+00 0.000000E+00 ',
1676	'INS 1PRCF12':' 0.000000E+00 0.000000E+00 0.150000E-01 0.150000E-01 ',
1677	})
1678	defaultIparm_lbl.append('0.6A synch')
1679	defaultIparms.append({
1680	'INS HTYPE ':'PXC ',
1681	'INS 1 ICONS':' 0.600000 0.000000 0.0 0 0.99 0 0.5 ',
1682	'INS 1PRCF1 ':' 3 8 0.01 ',
1683	'INS 1PRCF11':' 1.000000E+00 -1.000000E+00 0.300000E+00 0.000000E+00 ',
1684	'INS 1PRCF12':' 0.000000E+00 0.000000E+00 0.100000E-01 0.100000E-01 ',
1685	})
1686	defaultIparm_lbl.append('1.5A CW neutron data')
1687	defaultIparms.append({
1688	'INS HTYPE ':'PNC',
1689	'INS 1 ICONS':' 1.54020 0.00000 0.04000 0',
1690	'INS 1PRCF1 ':' 3 8 0.005',
1691	'INS 1PRCF11':' 0.239700E+03 -0.298200E+03 0.180800E+03 0.000000E+00',
1692	'INS 1PRCF12':' 0.000000E+00 0.000000E+00 0.400000E-01 0.300000E-01',
1693	})
1694	defaultIparm_lbl.append('10m TOF backscattering bank')
1695	defaultIparms.append({
1696	'INS HTYPE ':'PNT',
1697	'INS 1 ICONS':' 5000.00 0.00 0.00',
1698	'INS 1BNKPAR':' 1.0000 150.000',
1699	'INS 1PRCF1 ':' 1 8 0.01000',
1700	'INS 1PRCF11':' 0.000000E+00 5.000000E+00 3.000000E-02 1.000000E-03',
1701	'INS 1PRCF12':' 0.000000E+00 4.000000E+01 0.000000E+00 0.000000E+00',
1702	})
1703	defaultIparm_lbl.append('10m TOF 90deg bank')
1704	defaultIparms.append({
1705	'INS HTYPE ':'PNT',
1706	'INS 1 ICONS':' 3500.00 0.00 0.00',
1707	'INS 1BNKPAR':' 1.0000 90.000',
1708	'INS 1PRCF1 ':' 1 8 0.01000',
1709	'INS 1PRCF11':' 0.000000E+00 5.000000E+00 3.000000E-02 4.000000E-03',
1710	'INS 1PRCF12':' 0.000000E+00 8.000000E+01 0.000000E+00 0.000000E+00',
1711	})
1712	defaultIparm_lbl.append('63m POWGEN 90deg bank')
1713	defaultIparms.append({
1714	'INS HTYPE ':'PNT',
1715	'INS 1 ICONS':' 22585.80 0.00 0.00',
1716	'INS 1BNKPAR':' 1.0000 90.000',
1717	'INS 1PRCF1 ':' 1 8 0.01000',
1718	'INS 1PRCF11':' 0.000000E+00 1.000000E+00 3.000000E-02 4.000000E-03',
1719	'INS 1PRCF12':' 0.000000E+00 8.000000E+01 0.000000E+00 0.000000E+00',
1720	})
1721	def __init__(self,
1722	formatName,
1723	longFormatName=None,
1724	extensionlist=[],
1725	strictExtension=False,
1726	):
1727	ImportBaseclass.__init__(self,formatName,
1728	longFormatName,
1729	extensionlist,
1730	strictExtension)
1731	self.clockWd = None # used in TOF
1732	self.ReInitialize()
1733
1734	def ReInitialize(self):
1735	'Reinitialize the Reader to initial settings'
1736	ImportBaseclass.ReInitialize(self)
1737	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1738	self.powderdata = [] # Powder dataset
1739	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1740	np.array(x), # x-axis values
1741	np.array(y), # powder pattern intensities
1742	np.array(w), # 1/sig(intensity)^2 values (weights)
1743	np.array(yc), # calc. intensities (zero)
1744	np.array(yb), # calc. background (zero)
1745	np.array(yd), # obs-calc profiles
1746	'''
1747	self.comments = []
1748	self.idstring = ''
1749	self.Sample = G2pdG.SetDefaultSample()
1750	self.GSAS = None # used in TOF
1751	self.repeat_instparm = True # Should a parm file be
1752	# used for multiple histograms?
1753	self.instparm = None # name hint from file of instparm to use
1754	self.instfile = '' # full path name to instrument parameter file
1755	self.instbank = '' # inst parm bank number
1756	self.instmsg = '' # a label that gets printed to show
1757	# where instrument parameters are from
1758	self.numbanks = 1
1759	self.instdict = {} # place items here that will be transferred to the instrument parameters
1760	######################################################################
1761	class ImportSmallAngleData(ImportBaseclass):
1762	'''Defines a base class for the reading of files with small angle data.
1763	See :ref:`Writing a Import Routine<Import_Routines>`
1764	for an explanation on how to use this class.
1765	'''
1766	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1767	strictExtension=False,):
1768
1769	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1770	strictExtension)
1771	self.ReInitialize()
1772
1773	def ReInitialize(self):
1774	'Reinitialize the Reader to initial settings'
1775	ImportBaseclass.ReInitialize(self)
1776	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1777	self.smallangledata = [] # SASD dataset
1778	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1779	np.array(x), # x-axis values
1780	np.array(y), # powder pattern intensities
1781	np.array(w), # 1/sig(intensity)^2 values (weights)
1782	np.array(yc), # calc. intensities (zero)
1783	np.array(yd), # obs-calc profiles
1784	np.array(yb), # preset bkg
1785	'''
1786	self.comments = []
1787	self.idstring = ''
1788	self.Sample = G2pdG.SetDefaultSample()
1789	self.GSAS = None # used in TOF
1790	self.clockWd = None # used in TOF
1791	self.numbanks = 1
1792	self.instdict = {} # place items here that will be transferred to the instrument parameters
1793	######################################################################
1794	class ExportBaseclass(object):
1795	'''Defines a base class for the exporting of GSAS-II results.
1796
1797	This class is subclassed in the various exports/G2export_*.py files. Those files
1798	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
1799	appropriate menu items for each one and the .Exporter method is called
1800	directly from the menu item.
1801
1802	'''
1803	def __init__(self,
1804	G2frame,
1805	formatName,
1806	extension,
1807	longFormatName=None,
1808	):
1809	self.G2frame = G2frame
1810	self.formatName = formatName # short string naming file type
1811	self.extension = extension
1812	if longFormatName: # longer string naming file type
1813	self.longFormatName = longFormatName
1814	else:
1815	self.longFormatName = formatName
1816	self.OverallParms = {}
1817	self.Phases = {}
1818	self.Histograms = {}
1819	self.powderDict = {}
1820	self.xtalDict = {}
1821	self.parmDict = {}
1822	self.sigDict = {}
1823	# updated in InitExport:
1824	self.currentExportType = None # type of export that has been requested
1825	# updated in ExportSelect (when used):
1826	self.phasenam = None # a list of selected phases
1827	self.histnam = None # a list of selected histograms
1828	self.filename = None # name of file to be written (single export) or template (multiple files)
1829	self.dirname = '' # name of directory where file(s) will be written
1830	self.fullpath = '' # name of file being written -- full path
1831
1832	# items that should be defined in a subclass of this class
1833	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1834	# The following types are defined: 'project', "phase", "powder", "single"
1835	self.multiple = False # set as True if the class can export multiple phases or histograms
1836	# self.multiple is ignored for "project" exports
1837
1838	def InitExport(self,event):
1839	'''Determines the type of menu that called the Exporter and
1840	misc initialization.
1841	'''
1842	self.filename = None # name of file to be written (single export)
1843	self.dirname = '' # name of file to be written (multiple export)
1844	if event:
1845	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1846
1847	def MakePWDRfilename(self,hist):
1848	'''Make a filename root (no extension) from a PWDR histogram name
1849
1850	:param str hist: the histogram name in data tree (starts with "PWDR ")
1851	'''
1852	file0 = ''
1853	file1 = hist[5:]
1854	# replace repeated blanks
1855	while file1 != file0:
1856	file0 = file1
1857	file1 = file0.replace(' ',' ').strip()
1858	file0 = file1.replace('Azm= ','A')
1859	# if angle has unneeded decimal places on aziumuth, remove them
1860	if file0[-3:] == '.00': file0 = file0[:-3]
1861	file0 = file0.replace('.','_')
1862	file0 = file0.replace(' ','_')
1863	return file0
1864
1865	def ExportSelect(self,AskFile='ask'):
1866	'''Selects histograms or phases when needed. Sets a default file name when
1867	requested in self.filename; always sets a default directory in self.dirname.
1868
1869	:param bool AskFile: Determines how this routine processes getting a
1870	location to store the current export(s).
1871
1872	* if AskFile is 'ask' (default option), get the name of the file to be written;
1873	self.filename and self.dirname are always set. In the case where
1874	multiple files must be generated, the export routine should do this
1875	based on self.filename as a template.
1876	* if AskFile is 'dir', get the name of the directory to be used;
1877	self.filename is not used, but self.dirname is always set. The export routine
1878	will always generate the file name.
1879	* if AskFile is 'single', get only the name of the directory to be used when
1880	multiple items will be written (as multiple files) are used
1881	or a complete file name is requested when a single file
1882	name is selected. self.dirname is always set and self.filename used
1883	only when a single file is selected.
1884	* if AskFile is 'default', creates a name of the file to be used from
1885	the name of the project (.gpx) file. If the project has not been saved,
1886	then the name of file is requested.
1887	self.filename and self.dirname are always set. In the case where
1888	multiple file names must be generated, the export routine should do this
1889	based on self.filename.
1890	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1891	file. If the project has not been saved, then a directory is requested.
1892	self.filename is not used.
1893
1894	:returns: True in case of an error
1895	'''
1896
1897	numselected = 1
1898	if self.currentExportType == 'phase':
1899	if len(self.Phases) == 0:
1900	self.G2frame.ErrorDialog(
1901	'Empty project',
1902	'Project does not contain any phases.')
1903	return True
1904	elif len(self.Phases) == 1:
1905	self.phasenam = self.Phases.keys()
1906	elif self.multiple:
1907	choices = sorted(self.Phases.keys())
1908	phasenum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1909	if phasenum is None: return True
1910	self.phasenam = [choices[i] for i in phasenum]
1911	if not self.phasenam: return True
1912	numselected = len(self.phasenam)
1913	else:
1914	choices = sorted(self.Phases.keys())
1915	phasenum = G2gd.ItemSelector(choices,self.G2frame)
1916	if phasenum is None: return True
1917	self.phasenam = [choices[phasenum]]
1918	numselected = len(self.phasenam)
1919	elif self.currentExportType == 'single':
1920	if len(self.xtalDict) == 0:
1921	self.G2frame.ErrorDialog(
1922	'Empty project',
1923	'Project does not contain any single crystal data.')
1924	return True
1925	elif len(self.xtalDict) == 1:
1926	self.histnam = self.xtalDict.values()
1927	elif self.multiple:
1928	choices = sorted(self.xtalDict.values())
1929	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1930	if not hnum: return True
1931	self.histnam = [choices[i] for i in hnum]
1932	numselected = len(self.histnam)
1933	else:
1934	choices = sorted(self.xtalDict.values())
1935	hnum = G2gd.ItemSelector(choices,self.G2frame)
1936	if hnum is None: return True
1937	self.histnam = [choices[hnum]]
1938	numselected = len(self.histnam)
1939	elif self.currentExportType == 'powder':
1940	if len(self.powderDict) == 0:
1941	self.G2frame.ErrorDialog(
1942	'Empty project',
1943	'Project does not contain any powder data.')
1944	return True
1945	elif len(self.powderDict) == 1:
1946	self.histnam = self.powderDict.values()
1947	elif self.multiple:
1948	choices = sorted(self.powderDict.values())
1949	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1950	if not hnum: return True
1951	self.histnam = [choices[i] for i in hnum]
1952	numselected = len(self.histnam)
1953	else:
1954	choices = sorted(self.powderDict.values())
1955	hnum = G2gd.ItemSelector(choices,self.G2frame)
1956	if hnum is None: return True
1957	self.histnam = [choices[hnum]]
1958	numselected = len(self.histnam)
1959	elif self.currentExportType == 'image':
1960	if len(self.Histograms) == 0:
1961	self.G2frame.ErrorDialog(
1962	'Empty project',
1963	'Project does not contain any images.')
1964	return True
1965	elif len(self.Histograms) == 1:
1966	self.histnam = self.Histograms.keys()
1967	else:
1968	choices = sorted(self.Histograms.keys())
1969	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1970	if self.multiple:
1971	if not hnum: return True
1972	self.histnam = [choices[i] for i in hnum]
1973	else:
1974	if hnum is None: return True
1975	self.histnam = [choices[hnum]]
1976	numselected = len(self.histnam)
1977	if self.currentExportType == 'map':
1978	# search for phases with maps
1979	mapPhases = []
1980	choices = []
1981	for phasenam in sorted(self.Phases):
1982	phasedict = self.Phases[phasenam] # pointer to current phase info
1983	if len(phasedict['General']['Map'].get('rho',[])):
1984	mapPhases.append(phasenam)
1985	if phasedict['General']['Map'].get('Flip'):
1986	choices.append('Charge flip map: '+str(phasenam))
1987	elif phasedict['General']['Map'].get('MapType'):
1988	choices.append(
1989	str(phasedict['General']['Map'].get('MapType'))
1990	+ ' map: ' + str(phasenam))
1991	else:
1992	choices.append('unknown map: '+str(phasenam))
1993	# select a map if needed
1994	if len(mapPhases) == 0:
1995	self.G2frame.ErrorDialog(
1996	'Empty project',
1997	'Project does not contain any maps.')
1998	return True
1999	elif len(mapPhases) == 1:
2000	self.phasenam = mapPhases
2001	else:
2002	phasenum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
2003	if self.multiple:
2004	if not phasenum: return True
2005	self.phasenam = [mapPhases[i] for i in phasenum]
2006	else:
2007	if phasenum is None: return True
2008	self.phasenam = [mapPhases[phasenum]]
2009	numselected = len(self.phasenam)
2010
2011	# items selected, now set self.dirname and usually self.filename
2012	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
2013	AskFile == 'default' and not self.G2frame.GSASprojectfile
2014	):
2015	filename = self.askSaveFile()
2016	if not filename: return True
2017	self.dirname,self.filename = os.path.split(filename)
2018	elif AskFile == 'dir' or AskFile == 'single' or (
2019	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
2020	):
2021	self.dirname = self.askSaveDirectory()
2022	if not self.dirname: return True
2023	elif AskFile == 'default-dir' or AskFile == 'default':
2024	self.dirname,self.filename = os.path.split(
2025	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
2026	)
2027	else:
2028	raise Exception('This should not happen!')
2029
2030	def loadParmDict(self):
2031	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
2032	refined values to those from the last cycle and set the uncertainties for the
2033	refined parameters in another dict (self.sigDict).
2034
2035	Expands the parm & sig dicts to include values derived from constraints.
2036	'''
2037	self.parmDict = {}
2038	self.sigDict = {}
2039	rigidbodyDict = {}
2040	covDict = {}
2041	consDict = {}
2042	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2043	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2044	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2045	while item:
2046	name = self.G2frame.PatternTree.GetItemText(item)
2047	if name == 'Rigid bodies':
2048	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
2049	elif name == 'Covariance':
2050	covDict = self.G2frame.PatternTree.GetItemPyData(item)
2051	elif name == 'Constraints':
2052	consDict = self.G2frame.PatternTree.GetItemPyData(item)
2053	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2054	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
2055	self.parmDict.update(rbDict)
2056	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
2057	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables = G2stIO.GetPhaseData(
2058	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
2059	self.parmDict.update(phaseDict)
2060	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
2061	Phases,Histograms,Print=False,resetRefList=False)
2062	self.parmDict.update(hapDict)
2063	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
2064	self.parmDict.update(histDict)
2065	self.parmDict.update(zip(
2066	covDict.get('varyList',[]),
2067	covDict.get('variables',[])))
2068	self.sigDict = dict(zip(
2069	covDict.get('varyList',[]),
2070	covDict.get('sig',[])))
2071	# expand to include constraints: first compile a list of constraints
2072	constList = []
2073	for item in consDict:
2074	if item.startswith('_'): continue
2075	constList += consDict[item]
2076	# now process the constraints
2077	G2mv.InitVars()
2078	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
2079	varyList = covDict.get('varyListStart')
2080	if varyList is None and len(constDict) == 0:
2081	# no constraints can use varyList
2082	varyList = covDict.get('varyList')
2083	elif varyList is None:
2084	# old GPX file from before pre-constraint varyList is saved
2085	print ' * Old refinement: Please use Calculate/Refine to redo *'
2086	raise Exception(' * Export aborted *')
2087	else:
2088	varyList = list(varyList)
2089	try:
2090	groups,parmlist = G2mv.GroupConstraints(constDict)
2091	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
2092	except:
2093	# this really should not happen
2094	print ' * ERROR - constraints are internally inconsistent *'
2095	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
2096	print 'Errors',errmsg
2097	if warnmsg: print 'Warnings',warnmsg
2098	raise Exception(' * CIF creation aborted *')
2099	# add the constrained values to the parameter dictionary
2100	G2mv.Dict2Map(self.parmDict,varyList)
2101	# and add their uncertainties into the esd dictionary (sigDict)
2102	if covDict.get('covMatrix') is not None:
2103	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
2104
2105	def loadTree(self):
2106	'''Load the contents of the data tree into a set of dicts
2107	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2108	& self.xtalDict)
2109
2110	* The childrenless data tree items are overall parameters/controls for the
2111	entire project and are placed in self.OverallParms
2112	* Phase items are placed in self.Phases
2113	* Data items are placed in self.Histogram. The key for these data items
2114	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2115	'''
2116	self.OverallParms = {}
2117	self.powderDict = {}
2118	self.xtalDict = {}
2119	self.Phases = {}
2120	self.Histograms = {}
2121	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2122	histType = None
2123	if self.currentExportType == 'phase':
2124	# if exporting phases load them here
2125	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2126	if not sub:
2127	print 'no phases found'
2128	return True
2129	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2130	while item:
2131	phaseName = self.G2frame.PatternTree.GetItemText(item)
2132	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2133	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2134	return
2135	elif self.currentExportType == 'single':
2136	histType = 'HKLF'
2137	elif self.currentExportType == 'powder':
2138	histType = 'PWDR'
2139	elif self.currentExportType == 'image':
2140	histType = 'IMG'
2141
2142	if histType: # Loading just one kind of tree entry
2143	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2144	while item:
2145	name = self.G2frame.PatternTree.GetItemText(item)
2146	if name.startswith(histType):
2147	if self.Histograms.get(name): # there is already an item with this name
2148	print('Histogram name '+str(name)+' is repeated. Renaming')
2149	if name[-1] == '9':
2150	name = name[:-1] + '10'
2151	elif name[-1] in '012345678':
2152	name = name[:-1] + str(int(name[-1])+1)
2153	else:
2154	name += '-1'
2155	self.Histograms[name] = {}
2156	# the main info goes into Data, but the 0th
2157	# element contains refinement results, carry
2158	# that over too now.
2159	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2160	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2161	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2162	while item2:
2163	child = self.G2frame.PatternTree.GetItemText(item2)
2164	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2165	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2166	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2167	# index powder and single crystal histograms by number
2168	for hist in self.Histograms:
2169	if hist.startswith("PWDR"):
2170	d = self.powderDict
2171	elif hist.startswith("HKLF"):
2172	d = self.xtalDict
2173	else:
2174	return
2175	i = self.Histograms[hist].get('hId')
2176	if i is None and not d.keys():
2177	i = 0
2178	elif i is None or i in d.keys():
2179	i = max(d.keys())+1
2180	d[i] = hist
2181	return
2182	# else standard load: using all interlinked phases and histograms
2183	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2184	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2185	while item:
2186	name = self.G2frame.PatternTree.GetItemText(item)
2187	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2188	if not item2:
2189	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2190	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2191	# index powder and single crystal histograms
2192	for hist in self.Histograms:
2193	i = self.Histograms[hist]['hId']
2194	if hist.startswith("PWDR"):
2195	self.powderDict[i] = hist
2196	elif hist.startswith("HKLF"):
2197	self.xtalDict[i] = hist
2198
2199	def dumpTree(self,mode='type'):
2200	'''Print out information on the data tree dicts loaded in loadTree
2201	'''
2202	print '\nOverall'
2203	if mode == 'type':
2204	def Show(arg): return type(arg)
2205	else:
2206	def Show(arg): return arg
2207	for key in self.OverallParms:
2208	print ' ',key,Show(self.OverallParms[key])
2209	print 'Phases'
2210	for key1 in self.Phases:
2211	print ' ',key1,Show(self.Phases[key1])
2212	print 'Histogram'
2213	for key1 in self.Histograms:
2214	print ' ',key1,Show(self.Histograms[key1])
2215	for key2 in self.Histograms[key1]:
2216	print ' ',key2,Show(self.Histograms[key1][key2])
2217
2218	def defaultSaveFile(self):
2219	return os.path.abspath(
2220	os.path.splitext(self.G2frame.GSASprojectfile
2221	)[0]+self.extension)
2222
2223	def askSaveFile(self):
2224	'''Ask the user to supply a file name
2225
2226	:returns: a file name (str) or None if Cancel is pressed
2227	'''
2228	defnam = os.path.splitext(
2229	os.path.split(self.G2frame.GSASprojectfile)[1]
2230	)[0]+self.extension
2231	dlg = wx.FileDialog(
2232	self.G2frame, 'Input name for file to write', '.', defnam,
2233	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2234	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2235	dlg.CenterOnParent()
2236	try:
2237	if dlg.ShowModal() == wx.ID_OK:
2238	filename = dlg.GetPath()
2239	# make sure extension is correct
2240	filename = os.path.splitext(filename)[0]+self.extension
2241	else:
2242	filename = None
2243	finally:
2244	dlg.Destroy()
2245	return filename
2246
2247	def askSaveDirectory(self):
2248	'''Ask the user to supply a directory name. Path name is used as the
2249	starting point for the next export path search.
2250
2251	:returns: a directory name (str) or None if Cancel is pressed
2252	'''
2253	if self.G2frame.exportDir:
2254	startdir = self.G2frame.exportDir
2255	elif self.G2frame.GSASprojectfile:
2256	startdir = os.path.split(self.G2frame.GSASprojectfile)[0]
2257	elif self.G2frame.dirname:
2258	startdir = self.G2frame.dirname
2259	else:
2260	startdir = ''
2261	dlg = wx.DirDialog(
2262	self.G2frame, 'Input directory where file(s) will be written', startdir,
2263	wx.DD_DEFAULT_STYLE)
2264	dlg.CenterOnParent()
2265	try:
2266	if dlg.ShowModal() == wx.ID_OK:
2267	filename = dlg.GetPath()
2268	self.G2frame.exportDir = filename
2269	else:
2270	filename = None
2271	finally:
2272	dlg.Destroy()
2273	return filename
2274
2275	# Tools for file writing.
2276	def OpenFile(self,fil=None,mode='w'):
2277	'''Open the output file
2278
2279	:param str fil: The name of the file to open. If None (default)
2280	the name defaults to self.dirname + self.filename.
2281	If an extension is supplied, it is not overridded,
2282	but if not, the default extension is used.
2283	:returns: the file object opened by the routine which is also
2284	saved as self.fp
2285	'''
2286	if not fil:
2287	if not os.path.splitext(self.filename)[1]:
2288	self.filename += self.extension
2289	fil = os.path.join(self.dirname,self.filename)
2290	self.fullpath = fil
2291	self.fp = open(fil,mode)
2292	return self.fp
2293
2294	def Write(self,line):
2295	'''write a line of output, attaching a line-end character
2296
2297	:param str line: the text to be written.
2298	'''
2299	self.fp.write(line+'\n')
2300	def CloseFile(self,fp=None):
2301	'''Close a file opened in OpenFile
2302
2303	:param file fp: the file object to be closed. If None (default)
2304	file object self.fp is closed.
2305	'''
2306	if fp is None:
2307	fp = self.fp
2308	self.fp = None
2309	fp.close()
2310	# Tools to pull information out of the data arrays
2311	def GetCell(self,phasenam):
2312	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2313
2314	:param str phasenam: the name for the selected phase
2315	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2316	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2317	cell values and `cellSig` has their uncertainties.
2318	"""
2319	phasedict = self.Phases[phasenam] # pointer to current phase info
2320	try:
2321	pfx = str(phasedict['pId'])+'::'
2322	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2323	cellSig = G2stIO.getCellEsd(pfx,
2324	phasedict['General']['SGData'],A,
2325	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2326	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2327	return cellList,cellSig
2328	except KeyError:
2329	cell = phasedict['General']['Cell'][1:]
2330	return cell,7*[0]
2331
2332	def GetAtoms(self,phasenam):
2333	"""Gets the atoms associated with a phase. Can be used with standard
2334	or macromolecular phases
2335
2336	:param str phasenam: the name for the selected phase
2337	:returns: a list of items for eac atom where each item is a list containing:
2338	label, typ, mult, xyz, and td, where
2339
2340	* label and typ are the atom label and the scattering factor type (str)
2341	* mult is the site multiplicity (int)
2342	* xyz is contains a list with four pairs of numbers:
2343	x, y, z and fractional occupancy and
2344	their standard uncertainty (or a negative value)
2345	* td is contains a list with either one or six pairs of numbers:
2346	if one number it is U\ :sub:`iso` and with six numbers it is
2347	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2348	paired with their standard uncertainty (or a negative value)
2349	"""
2350	phasedict = self.Phases[phasenam] # pointer to current phase info
2351	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2352	cfrac = cx+3
2353	fpfx = str(phasedict['pId'])+'::Afrac:'
2354	atomslist = []
2355	for i,at in enumerate(phasedict['Atoms']):
2356	if phasedict['General']['Type'] == 'macromolecular':
2357	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2358	else:
2359	label = at[ct-1]
2360	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2361	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2362	mult = at[cs+1]
2363	typ = at[ct]
2364	xyz = []
2365	for j,v in enumerate(('x','y','z')):
2366	val = at[cx+j]
2367	pfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2368	sig = self.sigDict.get(pfx,-0.000009)
2369	xyz.append((val,sig))
2370	xyz.append((fval,fsig))
2371	td = []
2372	if at[cia] == 'I':
2373	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2374	val = self.parmDict.get(pfx,at[cia+1])
2375	sig = self.sigDict.get(pfx,-0.0009)
2376	td.append((val,sig))
2377	else:
2378	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2379	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2380	val = self.parmDict.get(pfx,at[cia+2+i])
2381	sig = self.sigDict.get(pfx,-0.0009)
2382	td.append((val,sig))
2383	atomslist.append((label,typ,mult,xyz,td))
2384	return atomslist
2385	######################################################################
2386
2387	def ReadCIF(URLorFile):
2388	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2389	(from James Hester).
2390	The open routine gets confused with DOS names that begin with a letter and colon
2391	"C:\dir\" so this routine will try to open the passed name as a file and if that
2392	fails, try it as a URL
2393
2394	:param str URLorFile: string containing a URL or a file name. Code will try first
2395	to open it as a file and then as a URL.
2396
2397	:returns: a PyCifRW CIF object.
2398	'''
2399	import CifFile as cif # PyCifRW from James Hester
2400
2401	# alternate approach:
2402	#import urllib
2403	#ciffile = 'file:'+urllib.pathname2url(filename)
2404
2405	try:
2406	fp = open(URLorFile,'r')
2407	cf = cif.ReadCif(fp)
2408	fp.close()
2409	return cf
2410	except IOError:
2411	return cif.ReadCif(URLorFile)
2412
2413	if __name__ == '__main__':
2414	app = wx.PySimpleApp()
2415	frm = wx.Frame(None) # create a frame
2416	frm.Show(True)
2417	filename = '/tmp/notzip.zip'
2418	filename = '/tmp/all.zip'
2419	#filename = '/tmp/11bmb_7652.zip'
2420
2421	#selection=None, confirmoverwrite=True, parent=None
2422	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2423	print ExtractFileFromZip(filename,multipleselect=True)
2424	#confirmread=False, confirmoverwrite=False)
2425
2426	# choicelist=[ ('a','b','c'),
2427	# ('test1','test2'),('no choice',)]
2428	# titles = [ 'a, b or c', 'tests', 'No option here']
2429	# dlg = MultipleChoicesDialog(
2430	# choicelist,titles,
2431	# parent=frm)
2432	# if dlg.ShowModal() == wx.ID_OK:
2433	# print 'Got OK'

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