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source: trunk/GSASIIIO.py @ 1528

Last change on this file since 1528 was 1528, checked in by toby, 8 years ago
missing quotes on PWDR init.
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2014-10-17 14:51:16 +0000 (Fri, 17 Oct 2014) $
4	# $Author: toby $
5	# $Revision: 1528 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 1528 2014-10-17 14:51:16Z toby $
8	########### SVN repository information ###################
9	'''
10	GSASIIIO: Misc I/O routines
11	=============================
12
13	Module with miscellaneous routines for input and output. Many
14	are GUI routines to interact with user.
15
16	Includes support for image reading.
17
18	Also includes base classes for data import routines.
19
20	'''
21	"""GSASIIIO: functions for IO of data
22	Copyright: 2008, Robert B. Von Dreele (Argonne National Laboratory)
23	"""
24	import wx
25	import math
26	import numpy as np
27	import cPickle
28	import sys
29	import re
30	import random as ran
31	import GSASIIpath
32	GSASIIpath.SetVersionNumber("$Revision: 1528 $")
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):
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	return phaseData
1198
1199	class MultipleChoicesDialog(wx.Dialog):
1200	'''A dialog that offers a series of choices, each with a
1201	title and a wx.Choice widget. Intended to be used Modally.
1202	typical input:
1203
1204	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1205	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1206
1207	selections are placed in self.chosen when OK is pressed
1208	'''
1209	def __init__(self,choicelist,headinglist,
1210	head='Select options',
1211	title='Please select from options below',
1212	parent=None):
1213	self.chosen = []
1214	wx.Dialog.__init__(
1215	self,parent,wx.ID_ANY,head,
1216	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1217	panel = wx.Panel(self)
1218	mainSizer = wx.BoxSizer(wx.VERTICAL)
1219	mainSizer.Add((10,10),1)
1220	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1221	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1222	self.ChItems = []
1223	for choice,lbl in zip(choicelist,headinglist):
1224	mainSizer.Add((10,10),1)
1225	self.chosen.append(0)
1226	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1227	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1228	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1229	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1230
1231	OkBtn = wx.Button(panel,-1,"Ok")
1232	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1233	cancelBtn = wx.Button(panel,-1,"Cancel")
1234	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1235	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1236	btnSizer.Add((20,20),1)
1237	btnSizer.Add(OkBtn)
1238	btnSizer.Add((20,20),1)
1239	btnSizer.Add(cancelBtn)
1240	btnSizer.Add((20,20),1)
1241	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1242	panel.SetSizer(mainSizer)
1243	panel.Fit()
1244	self.Fit()
1245
1246	def OnOk(self,event):
1247	parent = self.GetParent()
1248	if parent is not None: parent.Raise()
1249	# save the results from the choice widgets
1250	self.chosen = []
1251	for w in self.ChItems:
1252	self.chosen.append(w.GetSelection())
1253	self.EndModal(wx.ID_OK)
1254
1255	def OnCancel(self,event):
1256	parent = self.GetParent()
1257	if parent is not None: parent.Raise()
1258	self.chosen = []
1259	self.EndModal(wx.ID_CANCEL)
1260
1261	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1262	confirmoverwrite=True, parent=None,
1263	multipleselect=False):
1264	'''If the filename is a zip file, extract a file from that
1265	archive.
1266
1267	:param list Selection: used to predefine the name of the file
1268	to be extracted. Filename case and zip directory name are
1269	ignored in selection; the first matching file is used.
1270
1271	:param bool confirmread: if True asks the user to confirm before expanding
1272	the only file in a zip
1273
1274	:param bool confirmoverwrite: if True asks the user to confirm
1275	before overwriting if the extracted file already exists
1276
1277	:param bool multipleselect: if True allows more than one zip
1278	file to be extracted, a list of file(s) is returned.
1279	If only one file is present, do not ask which one, otherwise
1280	offer a list of choices (unless selection is used).
1281
1282	:returns: the name of the file that has been created or a
1283	list of files (see multipleselect)
1284
1285	If the file is not a zipfile, return the name of the input file.
1286	If the zipfile is empty or no file has been selected, return None
1287	'''
1288	import zipfile # do this now, since we can save startup time by doing this only on need
1289	import shutil
1290	zloc = os.path.split(filename)[0]
1291	if not zipfile.is_zipfile(filename):
1292	#print("not zip")
1293	return filename
1294
1295	z = zipfile.ZipFile(filename,'r')
1296	zinfo = z.infolist()
1297
1298	if len(zinfo) == 0:
1299	#print('Zip has no files!')
1300	zlist = [-1]
1301	if selection:
1302	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1303	if selection.lower() in choices:
1304	zlist = [choices.index(selection.lower())]
1305	else:
1306	print('debug: file '+str(selection)+' was not found in '+str(filename))
1307	zlist = [-1]
1308	elif len(zinfo) == 1 and confirmread:
1309	result = wx.ID_NO
1310	dlg = wx.MessageDialog(
1311	parent,
1312	'Is file '+str(zinfo[0].filename)+
1313	' what you want to extract from '+
1314	str(os.path.split(filename)[1])+'?',
1315	'Confirm file',
1316	wx.YES_NO \| wx.ICON_QUESTION)
1317	try:
1318	result = dlg.ShowModal()
1319	finally:
1320	dlg.Destroy()
1321	if result == wx.ID_NO:
1322	zlist = [-1]
1323	else:
1324	zlist = [0]
1325	elif len(zinfo) == 1:
1326	zlist = [0]
1327	elif multipleselect:
1328	# select one or more from a from list
1329	choices = [i.filename for i in zinfo]
1330	dlg = G2gd.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1331	'Choose file(s)',choices)
1332	if dlg.ShowModal() == wx.ID_OK:
1333	zlist = dlg.GetSelections()
1334	else:
1335	zlist = []
1336	dlg.Destroy()
1337	else:
1338	# select one from a from list
1339	choices = [i.filename for i in zinfo]
1340	dlg = wx.SingleChoiceDialog(parent,
1341	'Select file to extract from zip file'+str(filename),'Choose file',
1342	choices,)
1343	if dlg.ShowModal() == wx.ID_OK:
1344	zlist = [dlg.GetSelection()]
1345	else:
1346	zlist = [-1]
1347	dlg.Destroy()
1348
1349	outlist = []
1350	for zindex in zlist:
1351	if zindex >= 0:
1352	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1353	if os.path.exists(efil) and confirmoverwrite:
1354	result = wx.ID_NO
1355	dlg = wx.MessageDialog(parent,
1356	'File '+str(efil)+' already exists. OK to overwrite it?',
1357	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1358	try:
1359	result = dlg.ShowModal()
1360	finally:
1361	dlg.Destroy()
1362	if result == wx.ID_NO:
1363	zindex = -1
1364	if zindex >= 0:
1365	# extract the file to the current directory, regardless of it's original path
1366	#z.extract(zinfo[zindex],zloc)
1367	eloc,efil = os.path.split(zinfo[zindex].filename)
1368	outfile = os.path.join(zloc, efil)
1369	fpin = z.open(zinfo[zindex])
1370	fpout = file(outfile, "wb")
1371	shutil.copyfileobj(fpin, fpout)
1372	fpin.close()
1373	fpout.close()
1374	outlist.append(outfile)
1375	z.close()
1376	if multipleselect and len(outlist) >= 1:
1377	return outlist
1378	elif len(outlist) == 1:
1379	return outlist[0]
1380	else:
1381	return None
1382
1383	######################################################################
1384	# base classes for reading various types of data files
1385	# not used directly, only by subclassing
1386	######################################################################
1387	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1388	P1SGData = SGData
1389	class ImportBaseclass(object):
1390	'''Defines a base class for the reading of input files (diffraction
1391	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1392	for an explanation on how to use a subclass of this class.
1393	'''
1394	class ImportException(Exception):
1395	'''Defines an Exception that is used when an import routine hits an expected error,
1396	usually in .Reader.
1397
1398	Good practice is that the Reader should define a value in self.errors that
1399	tells the user some information about what is wrong with their file.
1400	'''
1401	pass
1402
1403	def __init__(self,
1404	formatName,
1405	longFormatName=None,
1406	extensionlist=[],
1407	strictExtension=False,
1408	):
1409	self.formatName = formatName # short string naming file type
1410	if longFormatName: # longer string naming file type
1411	self.longFormatName = longFormatName
1412	else:
1413	self.longFormatName = formatName
1414	# define extensions that are allowed for the file type
1415	# for windows, remove any extensions that are duplicate, as case is ignored
1416	if sys.platform == 'windows' and extensionlist:
1417	extensionlist = list(set([s.lower() for s in extensionlist]))
1418	self.extensionlist = extensionlist
1419	# If strictExtension is True, the file will not be read, unless
1420	# the extension matches one in the extensionlist
1421	self.strictExtension = strictExtension
1422	self.errors = ''
1423	self.warnings = ''
1424	# used for readers that will use multiple passes to read
1425	# more than one data block
1426	self.repeat = False
1427	self.selections = []
1428	self.repeatcount = 0
1429	self.readfilename = '?'
1430	#print 'created',self.__class__
1431
1432	def ReInitialize(self):
1433	'Reinitialize the Reader to initial settings'
1434	self.errors = ''
1435	self.warnings = ''
1436	self.repeat = False
1437	self.repeatcount = 0
1438	self.readfilename = '?'
1439
1440	def BlockSelector(self, ChoiceList, ParentFrame=None,
1441	title='Select a block',
1442	size=None, header='Block Selector',
1443	useCancel=True):
1444	''' Provide a wx dialog to select a block if the file contains more
1445	than one set of data and one must be selected
1446	'''
1447	if useCancel:
1448	dlg = wx.SingleChoiceDialog(
1449	ParentFrame,title, header,ChoiceList)
1450	else:
1451	dlg = wx.SingleChoiceDialog(
1452	ParentFrame,title, header,ChoiceList,
1453	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1454	if size: dlg.SetSize(size)
1455	dlg.CenterOnParent()
1456	if dlg.ShowModal() == wx.ID_OK:
1457	sel = dlg.GetSelection()
1458	return sel
1459	else:
1460	return None
1461	dlg.Destroy()
1462
1463	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1464	title='Select a block',size=None, header='Block Selector'):
1465	'''Provide a wx dialog to select a block of data if the
1466	file contains more than one set of data and one must be
1467	selected.
1468
1469	:returns: a list of the selected blocks
1470	'''
1471	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1472	wx.CHOICEDLG_STYLE)
1473	dlg.CenterOnParent()
1474	if size: dlg.SetSize(size)
1475	if dlg.ShowModal() == wx.ID_OK:
1476	sel = dlg.GetSelections()
1477	else:
1478	return []
1479	dlg.Destroy()
1480	selected = []
1481	if len(ChoiceList) in sel:
1482	return range(len(ChoiceList))
1483	else:
1484	return sel
1485	return selected
1486
1487	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1488	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1489	widget. Typical input:
1490
1491	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1492
1493	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1494
1495	optional keyword parameters are: head (window title) and title
1496	returns a list of selected indicies for each choice (or None)
1497	'''
1498	result = None
1499	dlg = MultipleChoicesDialog(choicelist,headinglist,
1500	parent=ParentFrame, **kwargs)
1501	dlg.CenterOnParent()
1502	if dlg.ShowModal() == wx.ID_OK:
1503	result = dlg.chosen
1504	dlg.Destroy()
1505	return result
1506
1507	def ShowBusy(self):
1508	wx.BeginBusyCursor()
1509	wx.Yield() # make it happen now!
1510
1511	def DoneBusy(self):
1512	wx.EndBusyCursor()
1513	wx.Yield() # make it happen now!
1514
1515	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1516	# '''This method must be supplied in the child class to read the file.
1517	# if the read fails either return False or raise an Exception
1518	# preferably of type ImportException.
1519	# '''
1520	# #start reading
1521	# raise ImportException("Error occurred while...")
1522	# self.errors += "Hint for user on why the error occur
1523	# return False # if an error occurs
1524	# return True # if read OK
1525
1526	def ExtensionValidator(self, filename):
1527	'''This methods checks if the file has the correct extension
1528	Return False if this filename will not be supported by this reader
1529	Return True if the extension matches the list supplied by the reader
1530	Return None if the reader allows un-registered extensions
1531	'''
1532	if filename:
1533	ext = os.path.splitext(filename)[1]
1534	if sys.platform == 'windows': ext = ext.lower()
1535	if ext in self.extensionlist: return True
1536	if self.strictExtension: return False
1537	return None
1538
1539	def ContentsValidator(self, filepointer):
1540	'''This routine will attempt to determine if the file can be read
1541	with the current format.
1542	This will typically be overridden with a method that
1543	takes a quick scan of [some of]
1544	the file contents to do a "sanity" check if the file
1545	appears to match the selected format.
1546	Expected to be called via self.Validator()
1547	'''
1548	#filepointer.seek(0) # rewind the file pointer
1549	return True
1550
1551	def CIFValidator(self, filepointer):
1552	'''A :meth:`ContentsValidator` for use to validate CIF files.
1553	'''
1554	for i,l in enumerate(filepointer):
1555	if i >= 1000: return True
1556	'''Encountered only blank lines or comments in first 1000
1557	lines. This is unlikely, but assume it is CIF anyway, since we are
1558	even less likely to find a file with nothing but hashes and
1559	blank lines'''
1560	line = l.strip()
1561	if len(line) == 0: # ignore blank lines
1562	continue
1563	elif line.startswith('#'): # ignore comments
1564	continue
1565	elif line.startswith('data_'): # on the right track, accept this file
1566	return True
1567	else: # found something invalid
1568	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1569	self.errors += ' '+str(l)
1570	self.errors += ' Note: a CIF should only have blank lines or comments before'
1571	self.errors += ' a data_ statement begins a block.'
1572	return False
1573
1574	class ImportPhase(ImportBaseclass):
1575	'''Defines a base class for the reading of files with coordinates
1576
1577	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1578	in :meth:`GSASII.GSASII.OnImportPhase`.
1579	See :ref:`Writing a Import Routine<Import_Routines>`
1580	for an explanation on how to use this class.
1581
1582	'''
1583	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1584	strictExtension=False,):
1585	# call parent __init__
1586	ImportBaseclass.__init__(self,formatName,longFormatName,
1587	extensionlist,strictExtension)
1588	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1589	self.Constraints = None
1590
1591	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1592	title='Select a phase', size=None,header='Phase Selector'):
1593	''' Provide a wx dialog to select a phase if the file contains more
1594	than one phase
1595	'''
1596	return self.BlockSelector(ChoiceList,ParentFrame,title,
1597	size,header)
1598
1599	class ImportStructFactor(ImportBaseclass):
1600	'''Defines a base class for the reading of files with tables
1601	of structure factors.
1602
1603	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1604	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1605	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1606	:meth:`Reader`.
1607
1608	See :ref:`Writing a Import Routine<Import_Routines>`
1609	for an explanation on how to use import classes in general. The specifics
1610	for reading a structure factor histogram require that
1611	the ``Reader()`` routine in the import
1612	class need to do only a few things: It
1613	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1614	and set :attr:`Parameters` with the instrument parameters
1615	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1616	'''
1617	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1618	strictExtension=False,):
1619	ImportBaseclass.__init__(self,formatName,longFormatName,
1620	extensionlist,strictExtension)
1621
1622	# define contents of Structure Factor entry
1623	self.Parameters = []
1624	'self.Parameters is a list with two dicts for data parameter settings'
1625	self.InitParameters()
1626	self.RefDict = {'RefList':[],'FF':[],'Super':0}
1627	self.Banks = [] #for multi bank data (usually TOF)
1628	'''self.RefDict is a dict containing the reflection information, as read from the file.
1629	Item 'RefList' contains the reflection information. See the
1630	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1631	for the contents of each row. Dict element 'FF'
1632	contains the form factor values for each element type; if this entry
1633	is left as initialized (an empty list) it will be initialized as needed later.
1634	'''
1635	def ReInitialize(self):
1636	'Reinitialize the Reader to initial settings'
1637	ImportBaseclass.ReInitialize(self)
1638	self.InitParameters()
1639	self.Banks = [] #for multi bank data (usually TOF)
1640	self.RefDict = {'RefList':[],'FF':[],'Super':0}
1641
1642	def InitParameters(self):
1643	'initialize the instrument parameters structure'
1644	Lambda = 0.70926
1645	HistType = 'SXC'
1646	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1647	'Lam':[Lambda,Lambda]
1648	}, {}]
1649	'Parameters is a list with two dicts for data parameter settings'
1650
1651	def UpdateParameters(self,Type=None,Wave=None):
1652	'Revise the instrument parameters'
1653	if Type is not None:
1654	self.Parameters[0]['Type'] = [Type,Type]
1655	if Wave is not None:
1656	self.Parameters[0]['Lam'] = [Wave,Wave]
1657
1658	######################################################################
1659	class ImportPowderData(ImportBaseclass):
1660	'''Defines a base class for the reading of files with powder data.
1661
1662	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1663	in :meth:`GSASII.GSASII.OnImportPowder`.
1664	See :ref:`Writing a Import Routine<Import_Routines>`
1665	for an explanation on how to use this class.
1666	'''
1667	def __init__(self,
1668	formatName,
1669	longFormatName=None,
1670	extensionlist=[],
1671	strictExtension=False,
1672	):
1673	ImportBaseclass.__init__(self,formatName,
1674	longFormatName,
1675	extensionlist,
1676	strictExtension)
1677	self.clockWd = None # used in TOF
1678	self.ReInitialize()
1679
1680	def ReInitialize(self):
1681	'Reinitialize the Reader to initial settings'
1682	ImportBaseclass.ReInitialize(self)
1683	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1684	self.powderdata = [] # Powder dataset
1685	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1686	np.array(x), # x-axis values
1687	np.array(y), # powder pattern intensities
1688	np.array(w), # 1/sig(intensity)^2 values (weights)
1689	np.array(yc), # calc. intensities (zero)
1690	np.array(yb), # calc. background (zero)
1691	np.array(yd), # obs-calc profiles
1692	'''
1693	self.comments = []
1694	self.idstring = ''
1695	self.Sample = G2pdG.SetDefaultSample()
1696	self.GSAS = None # used in TOF
1697	self.repeat_instparm = True # Should a parm file be
1698	# used for multiple histograms?
1699	self.instparm = None # name hint from file of instparm to use
1700	self.instfile = '' # full path name to instrument parameter file
1701	self.instbank = '' # inst parm bank number
1702	self.instmsg = '' # a label that gets printed to show
1703	# where instrument parameters are from
1704	self.numbanks = 1
1705	self.instdict = {} # place items here that will be transferred to the instrument parameters
1706	######################################################################
1707	class ImportSmallAngleData(ImportBaseclass):
1708	'''Defines a base class for the reading of files with small angle data.
1709	See :ref:`Writing a Import Routine<Import_Routines>`
1710	for an explanation on how to use this class.
1711	'''
1712	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1713	strictExtension=False,):
1714
1715	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1716	strictExtension)
1717	self.ReInitialize()
1718
1719	def ReInitialize(self):
1720	'Reinitialize the Reader to initial settings'
1721	ImportBaseclass.ReInitialize(self)
1722	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1723	self.smallangledata = [] # SASD dataset
1724	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1725	np.array(x), # x-axis values
1726	np.array(y), # powder pattern intensities
1727	np.array(w), # 1/sig(intensity)^2 values (weights)
1728	np.array(yc), # calc. intensities (zero)
1729	np.array(yd), # obs-calc profiles
1730	np.array(yb), # preset bkg
1731	'''
1732	self.comments = []
1733	self.idstring = ''
1734	self.Sample = G2pdG.SetDefaultSample()
1735	self.GSAS = None # used in TOF
1736	self.clockWd = None # used in TOF
1737	self.numbanks = 1
1738	self.instdict = {} # place items here that will be transferred to the instrument parameters
1739	######################################################################
1740	class ExportBaseclass(object):
1741	'''Defines a base class for the exporting of GSAS-II results.
1742
1743	This class is subclassed in the various exports/G2export_*.py files. Those files
1744	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
1745	appropriate menu items for each one and the .Exporter method is called
1746	directly from the menu item.
1747
1748	'''
1749	def __init__(self,
1750	G2frame,
1751	formatName,
1752	extension,
1753	longFormatName=None,
1754	):
1755	self.G2frame = G2frame
1756	self.formatName = formatName # short string naming file type
1757	self.extension = extension
1758	if longFormatName: # longer string naming file type
1759	self.longFormatName = longFormatName
1760	else:
1761	self.longFormatName = formatName
1762	self.OverallParms = {}
1763	self.Phases = {}
1764	self.Histograms = {}
1765	self.powderDict = {}
1766	self.xtalDict = {}
1767	self.parmDict = {}
1768	self.sigDict = {}
1769	# updated in InitExport:
1770	self.currentExportType = None # type of export that has been requested
1771	# updated in ExportSelect (when used):
1772	self.phasenam = None # a list of selected phases
1773	self.histnam = None # a list of selected histograms
1774	self.filename = None # name of file to be written (single export) or template (multiple files)
1775	self.dirname = '' # name of directory where file(s) will be written
1776	self.fullpath = '' # name of file being written -- full path
1777
1778	# items that should be defined in a subclass of this class
1779	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1780	# The following types are defined: 'project', "phase", "powder", "single"
1781	self.multiple = False # set as True if the class can export multiple phases or histograms
1782	# self.multiple is ignored for "project" exports
1783
1784	def InitExport(self,event):
1785	'''Determines the type of menu that called the Exporter and
1786	misc initialization.
1787	'''
1788	self.filename = None # name of file to be written (single export)
1789	self.dirname = '' # name of file to be written (multiple export)
1790	if event:
1791	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1792
1793	def MakePWDRfilename(self,hist):
1794	'''Make a filename root (no extension) from a PWDR histogram name
1795
1796	:param str hist: the histogram name in data tree (starts with "PWDR ")
1797	'''
1798	file0 = ''
1799	file1 = hist[5:]
1800	# replace repeated blanks
1801	while file1 != file0:
1802	file0 = file1
1803	file1 = file0.replace(' ',' ').strip()
1804	file0 = file1.replace('Azm= ','A')
1805	# if angle has unneeded decimal places on aziumuth, remove them
1806	if file0[-3:] == '.00': file0 = file0[:-3]
1807	file0 = file0.replace('.','_')
1808	file0 = file0.replace(' ','_')
1809	return file0
1810
1811	def ExportSelect(self,AskFile='ask'):
1812	'''Selects histograms or phases when needed. Sets a default file name when
1813	requested in self.filename; always sets a default directory in self.dirname.
1814
1815	:param bool AskFile: Determines how this routine processes getting a
1816	location to store the current export(s).
1817
1818	* if AskFile is 'ask' (default option), get the name of the file to be written;
1819	self.filename and self.dirname are always set. In the case where
1820	multiple files must be generated, the export routine should do this
1821	based on self.filename as a template.
1822	* if AskFile is 'dir', get the name of the directory to be used;
1823	self.filename is not used, but self.dirname is always set. The export routine
1824	will always generate the file name.
1825	* if AskFile is 'single', get only the name of the directory to be used when
1826	multiple items will be written (as multiple files) are used
1827	or a complete file name is requested when a single file
1828	name is selected. self.dirname is always set and self.filename used
1829	only when a single file is selected.
1830	* if AskFile is 'default', creates a name of the file to be used from
1831	the name of the project (.gpx) file. If the project has not been saved,
1832	then the name of file is requested.
1833	self.filename and self.dirname are always set. In the case where
1834	multiple file names must be generated, the export routine should do this
1835	based on self.filename.
1836	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1837	file. If the project has not been saved, then a directory is requested.
1838	self.filename is not used.
1839
1840	:returns: True in case of an error
1841	'''
1842
1843	numselected = 1
1844	if self.currentExportType == 'phase':
1845	if len(self.Phases) == 0:
1846	self.G2frame.ErrorDialog(
1847	'Empty project',
1848	'Project does not contain any phases.')
1849	return True
1850	elif len(self.Phases) == 1:
1851	self.phasenam = self.Phases.keys()
1852	elif self.multiple:
1853	choices = sorted(self.Phases.keys())
1854	phasenum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1855	if phasenum is None: return True
1856	self.phasenam = [choices[i] for i in phasenum]
1857	if not self.phasenam: return True
1858	numselected = len(self.phasenam)
1859	else:
1860	choices = sorted(self.Phases.keys())
1861	phasenum = G2gd.ItemSelector(choices,self.G2frame)
1862	if phasenum is None: return True
1863	self.phasenam = [choices[phasenum]]
1864	numselected = len(self.phasenam)
1865	elif self.currentExportType == 'single':
1866	if len(self.xtalDict) == 0:
1867	self.G2frame.ErrorDialog(
1868	'Empty project',
1869	'Project does not contain any single crystal data.')
1870	return True
1871	elif len(self.xtalDict) == 1:
1872	self.histnam = self.xtalDict.values()
1873	elif self.multiple:
1874	choices = sorted(self.xtalDict.values())
1875	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1876	if not hnum: return True
1877	self.histnam = [choices[i] for i in hnum]
1878	numselected = len(self.histnam)
1879	else:
1880	choices = sorted(self.xtalDict.values())
1881	hnum = G2gd.ItemSelector(choices,self.G2frame)
1882	if hnum is None: return True
1883	self.histnam = [choices[hnum]]
1884	numselected = len(self.histnam)
1885	elif self.currentExportType == 'powder':
1886	if len(self.powderDict) == 0:
1887	self.G2frame.ErrorDialog(
1888	'Empty project',
1889	'Project does not contain any powder data.')
1890	return True
1891	elif len(self.powderDict) == 1:
1892	self.histnam = self.powderDict.values()
1893	elif self.multiple:
1894	choices = sorted(self.powderDict.values())
1895	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1896	if not hnum: return True
1897	self.histnam = [choices[i] for i in hnum]
1898	numselected = len(self.histnam)
1899	else:
1900	choices = sorted(self.powderDict.values())
1901	hnum = G2gd.ItemSelector(choices,self.G2frame)
1902	if hnum is None: return True
1903	self.histnam = [choices[hnum]]
1904	numselected = len(self.histnam)
1905	elif self.currentExportType == 'image':
1906	if len(self.Histograms) == 0:
1907	self.G2frame.ErrorDialog(
1908	'Empty project',
1909	'Project does not contain any images.')
1910	return True
1911	elif len(self.Histograms) == 1:
1912	self.histnam = self.Histograms.keys()
1913	else:
1914	choices = sorted(self.Histograms.keys())
1915	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1916	if self.multiple:
1917	if not hnum: return True
1918	self.histnam = [choices[i] for i in hnum]
1919	else:
1920	if hnum is None: return True
1921	self.histnam = [choices[hnum]]
1922	numselected = len(self.histnam)
1923	if self.currentExportType == 'map':
1924	# search for phases with maps
1925	mapPhases = []
1926	choices = []
1927	for phasenam in sorted(self.Phases):
1928	phasedict = self.Phases[phasenam] # pointer to current phase info
1929	if len(phasedict['General']['Map'].get('rho',[])):
1930	mapPhases.append(phasenam)
1931	if phasedict['General']['Map'].get('Flip'):
1932	choices.append('Charge flip map: '+str(phasenam))
1933	elif phasedict['General']['Map'].get('MapType'):
1934	choices.append(
1935	str(phasedict['General']['Map'].get('MapType'))
1936	+ ' map: ' + str(phasenam))
1937	else:
1938	choices.append('unknown map: '+str(phasenam))
1939	# select a map if needed
1940	if len(mapPhases) == 0:
1941	self.G2frame.ErrorDialog(
1942	'Empty project',
1943	'Project does not contain any maps.')
1944	return True
1945	elif len(mapPhases) == 1:
1946	self.phasenam = mapPhases
1947	else:
1948	phasenum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1949	if self.multiple:
1950	if not phasenum: return True
1951	self.phasenam = [mapPhases[i] for i in phasenum]
1952	else:
1953	if phasenum is None: return True
1954	self.phasenam = [mapPhases[phasenum]]
1955	numselected = len(self.phasenam)
1956
1957	# items selected, now set self.dirname and usually self.filename
1958	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1959	AskFile == 'default' and not self.G2frame.GSASprojectfile
1960	):
1961	filename = self.askSaveFile()
1962	if not filename: return True
1963	self.dirname,self.filename = os.path.split(filename)
1964	elif AskFile == 'dir' or AskFile == 'single' or (
1965	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1966	):
1967	self.dirname = self.askSaveDirectory()
1968	if not self.dirname: return True
1969	elif AskFile == 'default-dir' or AskFile == 'default':
1970	self.dirname,self.filename = os.path.split(
1971	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1972	)
1973	else:
1974	raise Exception('This should not happen!')
1975
1976	def loadParmDict(self):
1977	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1978	refined values to those from the last cycle and set the uncertainties for the
1979	refined parameters in another dict (self.sigDict).
1980
1981	Expands the parm & sig dicts to include values derived from constraints.
1982	'''
1983	self.parmDict = {}
1984	self.sigDict = {}
1985	rigidbodyDict = {}
1986	covDict = {}
1987	consDict = {}
1988	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1989	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
1990	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
1991	while item:
1992	name = self.G2frame.PatternTree.GetItemText(item)
1993	if name == 'Rigid bodies':
1994	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
1995	elif name == 'Covariance':
1996	covDict = self.G2frame.PatternTree.GetItemPyData(item)
1997	elif name == 'Constraints':
1998	consDict = self.G2frame.PatternTree.GetItemPyData(item)
1999	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2000	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
2001	self.parmDict.update(rbDict)
2002	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
2003	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables = G2stIO.GetPhaseData(
2004	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
2005	self.parmDict.update(phaseDict)
2006	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
2007	Phases,Histograms,Print=False,resetRefList=False)
2008	self.parmDict.update(hapDict)
2009	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
2010	self.parmDict.update(histDict)
2011	self.parmDict.update(zip(
2012	covDict.get('varyList',[]),
2013	covDict.get('variables',[])))
2014	self.sigDict = dict(zip(
2015	covDict.get('varyList',[]),
2016	covDict.get('sig',[])))
2017	# expand to include constraints: first compile a list of constraints
2018	constList = []
2019	for item in consDict:
2020	if item.startswith('_'): continue
2021	constList += consDict[item]
2022	# now process the constraints
2023	G2mv.InitVars()
2024	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
2025	varyList = covDict.get('varyListStart')
2026	if varyList is None and len(constDict) == 0:
2027	# no constraints can use varyList
2028	varyList = covDict.get('varyList')
2029	elif varyList is None:
2030	# old GPX file from before pre-constraint varyList is saved
2031	print ' * Old refinement: Please use Calculate/Refine to redo *'
2032	raise Exception(' * Export aborted *')
2033	else:
2034	varyList = list(varyList)
2035	try:
2036	groups,parmlist = G2mv.GroupConstraints(constDict)
2037	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
2038	except:
2039	# this really should not happen
2040	print ' * ERROR - constraints are internally inconsistent *'
2041	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
2042	print 'Errors',errmsg
2043	if warnmsg: print 'Warnings',warnmsg
2044	raise Exception(' * CIF creation aborted *')
2045	# add the constrained values to the parameter dictionary
2046	G2mv.Dict2Map(self.parmDict,varyList)
2047	# and add their uncertainties into the esd dictionary (sigDict)
2048	if covDict.get('covMatrix') is not None:
2049	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
2050
2051	def loadTree(self):
2052	'''Load the contents of the data tree into a set of dicts
2053	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2054	& self.xtalDict)
2055
2056	* The childrenless data tree items are overall parameters/controls for the
2057	entire project and are placed in self.OverallParms
2058	* Phase items are placed in self.Phases
2059	* Data items are placed in self.Histogram. The key for these data items
2060	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2061	'''
2062	self.OverallParms = {}
2063	self.powderDict = {}
2064	self.xtalDict = {}
2065	self.Phases = {}
2066	self.Histograms = {}
2067	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2068	histType = None
2069	if self.currentExportType == 'phase':
2070	# if exporting phases load them here
2071	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2072	if not sub:
2073	print 'no phases found'
2074	return True
2075	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2076	while item:
2077	phaseName = self.G2frame.PatternTree.GetItemText(item)
2078	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2079	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2080	return
2081	elif self.currentExportType == 'single':
2082	histType = 'HKLF'
2083	elif self.currentExportType == 'powder':
2084	histType = 'PWDR'
2085	elif self.currentExportType == 'image':
2086	histType = 'IMG'
2087
2088	if histType: # Loading just one kind of tree entry
2089	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2090	while item:
2091	name = self.G2frame.PatternTree.GetItemText(item)
2092	if name.startswith(histType):
2093	if self.Histograms.get(name): # there is already an item with this name
2094	print('Histogram name '+str(name)+' is repeated. Renaming')
2095	if name[-1] == '9':
2096	name = name[:-1] + '10'
2097	elif name[-1] in '012345678':
2098	name = name[:-1] + str(int(name[-1])+1)
2099	else:
2100	name += '-1'
2101	self.Histograms[name] = {}
2102	# the main info goes into Data, but the 0th
2103	# element contains refinement results, carry
2104	# that over too now.
2105	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2106	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2107	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2108	while item2:
2109	child = self.G2frame.PatternTree.GetItemText(item2)
2110	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2111	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2112	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2113	# index powder and single crystal histograms by number
2114	for hist in self.Histograms:
2115	if hist.startswith("PWDR"):
2116	d = self.powderDict
2117	elif hist.startswith("HKLF"):
2118	d = self.xtalDict
2119	else:
2120	return
2121	i = self.Histograms[hist].get('hId')
2122	if i is None and not d.keys():
2123	i = 0
2124	elif i is None or i in d.keys():
2125	i = max(d.keys())+1
2126	d[i] = hist
2127	return
2128	# else standard load: using all interlinked phases and histograms
2129	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2130	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2131	while item:
2132	name = self.G2frame.PatternTree.GetItemText(item)
2133	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2134	if not item2:
2135	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2136	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2137	# index powder and single crystal histograms
2138	for hist in self.Histograms:
2139	i = self.Histograms[hist]['hId']
2140	if hist.startswith("PWDR"):
2141	self.powderDict[i] = hist
2142	elif hist.startswith("HKLF"):
2143	self.xtalDict[i] = hist
2144
2145	def dumpTree(self,mode='type'):
2146	'''Print out information on the data tree dicts loaded in loadTree
2147	'''
2148	print '\nOverall'
2149	if mode == 'type':
2150	def Show(arg): return type(arg)
2151	else:
2152	def Show(arg): return arg
2153	for key in self.OverallParms:
2154	print ' ',key,Show(self.OverallParms[key])
2155	print 'Phases'
2156	for key1 in self.Phases:
2157	print ' ',key1,Show(self.Phases[key1])
2158	print 'Histogram'
2159	for key1 in self.Histograms:
2160	print ' ',key1,Show(self.Histograms[key1])
2161	for key2 in self.Histograms[key1]:
2162	print ' ',key2,Show(self.Histograms[key1][key2])
2163
2164	def defaultSaveFile(self):
2165	return os.path.abspath(
2166	os.path.splitext(self.G2frame.GSASprojectfile
2167	)[0]+self.extension)
2168
2169	def askSaveFile(self):
2170	'''Ask the user to supply a file name
2171
2172	:returns: a file name (str) or None if Cancel is pressed
2173	'''
2174	defnam = os.path.splitext(
2175	os.path.split(self.G2frame.GSASprojectfile)[1]
2176	)[0]+self.extension
2177	dlg = wx.FileDialog(
2178	self.G2frame, 'Input name for file to write', '.', defnam,
2179	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2180	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2181	dlg.CenterOnParent()
2182	try:
2183	if dlg.ShowModal() == wx.ID_OK:
2184	filename = dlg.GetPath()
2185	# make sure extension is correct
2186	filename = os.path.splitext(filename)[0]+self.extension
2187	else:
2188	filename = None
2189	finally:
2190	dlg.Destroy()
2191	return filename
2192
2193	def askSaveDirectory(self):
2194	'''Ask the user to supply a directory name. Path name is used as the
2195	starting point for the next export path search.
2196
2197	:returns: a directory name (str) or None if Cancel is pressed
2198	'''
2199	if self.G2frame.exportDir:
2200	startdir = self.G2frame.exportDir
2201	elif self.G2frame.GSASprojectfile:
2202	startdir = os.path.split(self.G2frame.GSASprojectfile)[0]
2203	elif self.G2frame.dirname:
2204	startdir = self.G2frame.dirname
2205	else:
2206	startdir = ''
2207	dlg = wx.DirDialog(
2208	self.G2frame, 'Input directory where file(s) will be written', startdir,
2209	wx.DD_DEFAULT_STYLE)
2210	dlg.CenterOnParent()
2211	try:
2212	if dlg.ShowModal() == wx.ID_OK:
2213	filename = dlg.GetPath()
2214	self.G2frame.exportDir = filename
2215	else:
2216	filename = None
2217	finally:
2218	dlg.Destroy()
2219	return filename
2220
2221	# Tools for file writing.
2222	def OpenFile(self,fil=None,mode='w'):
2223	'''Open the output file
2224
2225	:param str fil: The name of the file to open. If None (default)
2226	the name defaults to self.dirname + self.filename.
2227	If an extension is supplied, it is not overridded,
2228	but if not, the default extension is used.
2229	:returns: the file object opened by the routine which is also
2230	saved as self.fp
2231	'''
2232	if not fil:
2233	if not os.path.splitext(self.filename)[1]:
2234	self.filename += self.extension
2235	fil = os.path.join(self.dirname,self.filename)
2236	self.fullpath = fil
2237	self.fp = open(fil,mode)
2238	return self.fp
2239
2240	def Write(self,line):
2241	'''write a line of output, attaching a line-end character
2242
2243	:param str line: the text to be written.
2244	'''
2245	self.fp.write(line+'\n')
2246	def CloseFile(self,fp=None):
2247	'''Close a file opened in OpenFile
2248
2249	:param file fp: the file object to be closed. If None (default)
2250	file object self.fp is closed.
2251	'''
2252	if fp is None:
2253	fp = self.fp
2254	self.fp = None
2255	fp.close()
2256	# Tools to pull information out of the data arrays
2257	def GetCell(self,phasenam):
2258	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2259
2260	:param str phasenam: the name for the selected phase
2261	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2262	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2263	cell values and `cellSig` has their uncertainties.
2264	"""
2265	phasedict = self.Phases[phasenam] # pointer to current phase info
2266	try:
2267	pfx = str(phasedict['pId'])+'::'
2268	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2269	cellSig = G2stIO.getCellEsd(pfx,
2270	phasedict['General']['SGData'],A,
2271	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2272	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2273	return cellList,cellSig
2274	except KeyError:
2275	cell = phasedict['General']['Cell'][1:]
2276	return cell,7*[0]
2277
2278	def GetAtoms(self,phasenam):
2279	"""Gets the atoms associated with a phase. Can be used with standard
2280	or macromolecular phases
2281
2282	:param str phasenam: the name for the selected phase
2283	:returns: a list of items for eac atom where each item is a list containing:
2284	label, typ, mult, xyz, and td, where
2285
2286	* label and typ are the atom label and the scattering factor type (str)
2287	* mult is the site multiplicity (int)
2288	* xyz is contains a list with four pairs of numbers:
2289	x, y, z and fractional occupancy and
2290	their standard uncertainty (or a negative value)
2291	* td is contains a list with either one or six pairs of numbers:
2292	if one number it is U\ :sub:`iso` and with six numbers it is
2293	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2294	paired with their standard uncertainty (or a negative value)
2295	"""
2296	phasedict = self.Phases[phasenam] # pointer to current phase info
2297	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2298	cfrac = cx+3
2299	fpfx = str(phasedict['pId'])+'::Afrac:'
2300	atomslist = []
2301	for i,at in enumerate(phasedict['Atoms']):
2302	if phasedict['General']['Type'] == 'macromolecular':
2303	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2304	else:
2305	label = at[ct-1]
2306	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2307	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2308	mult = at[cs+1]
2309	typ = at[ct]
2310	xyz = []
2311	for j,v in enumerate(('x','y','z')):
2312	val = at[cx+j]
2313	pfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2314	sig = self.sigDict.get(pfx,-0.000009)
2315	xyz.append((val,sig))
2316	xyz.append((fval,fsig))
2317	td = []
2318	if at[cia] == 'I':
2319	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2320	val = self.parmDict.get(pfx,at[cia+1])
2321	sig = self.sigDict.get(pfx,-0.0009)
2322	td.append((val,sig))
2323	else:
2324	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2325	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2326	val = self.parmDict.get(pfx,at[cia+2+i])
2327	sig = self.sigDict.get(pfx,-0.0009)
2328	td.append((val,sig))
2329	atomslist.append((label,typ,mult,xyz,td))
2330	return atomslist
2331	######################################################################
2332
2333	def ReadCIF(URLorFile):
2334	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2335	(from James Hester).
2336	The open routine gets confused with DOS names that begin with a letter and colon
2337	"C:\dir\" so this routine will try to open the passed name as a file and if that
2338	fails, try it as a URL
2339
2340	:param str URLorFile: string containing a URL or a file name. Code will try first
2341	to open it as a file and then as a URL.
2342
2343	:returns: a PyCifRW CIF object.
2344	'''
2345	import CifFile as cif # PyCifRW from James Hester
2346
2347	# alternate approach:
2348	#import urllib
2349	#ciffile = 'file:'+urllib.pathname2url(filename)
2350
2351	try:
2352	fp = open(URLorFile,'r')
2353	cf = cif.ReadCif(fp)
2354	fp.close()
2355	return cf
2356	except IOError:
2357	return cif.ReadCif(URLorFile)
2358
2359	if __name__ == '__main__':
2360	app = wx.PySimpleApp()
2361	frm = wx.Frame(None) # create a frame
2362	frm.Show(True)
2363	filename = '/tmp/notzip.zip'
2364	filename = '/tmp/all.zip'
2365	#filename = '/tmp/11bmb_7652.zip'
2366
2367	#selection=None, confirmoverwrite=True, parent=None
2368	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2369	print ExtractFileFromZip(filename,multipleselect=True)
2370	#confirmread=False, confirmoverwrite=False)
2371
2372	# choicelist=[ ('a','b','c'),
2373	# ('test1','test2'),('no choice',)]
2374	# titles = [ 'a, b or c', 'tests', 'No option here']
2375	# dlg = MultipleChoicesDialog(
2376	# choicelist,titles,
2377	# parent=frm)
2378	# if dlg.ShowModal() == wx.ID_OK:
2379	# print 'Got OK'

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