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source: trunk/GSASIIIO.py @ 1603

Last change on this file since 1603 was 1603, checked in by vondreele, 9 years ago
fix typo
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2014-12-10 16:57:50 +0000 (Wed, 10 Dec 2014) $
4	# $Author: vondreele $
5	# $Revision: 1603 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 1603 2014-12-10 16:57:50Z 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: 1603 $")
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 os.path.exists(imagefile):
139	print 'Image file '+imagefile+' not found'
140	fil = imagefile.replace('\\','/') # windows?!
141	# see if we can find a file with same name or in a similarly named sub-dir
142	pth,fil = os.path.split(fil)
143	prevpth = None
144	while pth and pth != prevpth:
145	prevpth = pth
146	if os.path.exists(os.path.join(G2frame.dirname,fil)):
147	print 'found image file '+os.path.join(G2frame.dirname,fil)
148	return os.path.join(G2frame.dirname,fil)
149	pth,enddir = os.path.split(pth)
150	fil = os.path.join(enddir,fil)
151	# not found as a subdirectory, drop common parts of path for last saved & image file names
152	# if image was .../A/B/C/imgs/ima.ge
153	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
154	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
155	Controls = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
156	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
157	imgPath = imagefile.replace('\\','/').split('/')
158	for p1,p2 in zip(gpxPath,imgPath):
159	if p1 == p2:
160	gpxPath.pop(0),imgPath.pop(0)
161	else:
162	break
163	fil = os.path.join(*imgPath) # file with non-common prefix elements
164	prevpth = None
165	pth = os.path.abspath(G2frame.dirname)
166	while pth and pth != prevpth:
167	prevpth = pth
168	if os.path.exists(os.path.join(pth,fil)):
169	print 'found image file '+os.path.join(pth,fil)
170	return os.path.join(pth,fil)
171	pth,enddir = os.path.split(pth)
172	GSASIIpath.IPyBreak()
173
174	if not os.path.exists(imagefile):
175	dlg = wx.FileDialog(G2frame, 'Previous image file not found; open here', '.', '',\
176	'Any image file (.edf;.tif;.tiff;.mar;.ge;.avg;.sum;.img)\
177	\|.edf;.tif;.tiff;.mar;.ge;.avg;.sum;.img\|\
178	European detector file (.edf)\|.edf\|\
179	Any detector tif (.tif;.tiff)\|.tif;.tiff\|\
180	MAR file (.mar)\|.mar\|\
181	GE Image (.ge;.avg;.sum)\|.ge;.avg;.sum\|\
182	ADSC Image (.img)\|.img\|\
183	All files (.)\|.',wx.OPEN\|wx.CHANGE_DIR)
184	try:
185	dlg.SetFilename(''+ospath.split(imagefile)[1])
186	if dlg.ShowModal() == wx.ID_OK:
187	imagefile = dlg.GetPath()
188	else:
189	imagefile = False
190	finally:
191	dlg.Destroy()
192	return imagefile
193
194	def EditImageParms(parent,Data,Comments,Image,filename):
195	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
196	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
197	def onClose(event):
198	dlg.EndModal(wx.ID_OK)
199	mainsizer = wx.BoxSizer(wx.VERTICAL)
200	h,w = Image.shape[:2]
201	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,
202	'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
203	0,wx.ALIGN_LEFT\|wx.ALL, 2)
204
205	vsizer = wx.BoxSizer(wx.HORIZONTAL)
206	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
207	0,wx.ALIGN_LEFT\|wx.ALL, 2)
208	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data,'wavelength')
209	vsizer.Add(wdgt)
210	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
211
212	vsizer = wx.BoxSizer(wx.HORIZONTAL)
213	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
214	0,wx.ALIGN_LEFT\|wx.ALL, 2)
215	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
216	size=(50,-1))
217	vsizer.Add(wdgt)
218	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),
219	wx.ALIGN_LEFT\|wx.ALL, 2)
220	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,
221	size=(50,-1))
222	vsizer.Add(wdgt)
223	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
224
225	vsizer = wx.BoxSizer(wx.HORIZONTAL)
226	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
227	0,wx.ALIGN_LEFT\|wx.ALL, 2)
228	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data,'distance')
229	vsizer.Add(wdgt)
230	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
231
232	vsizer = wx.BoxSizer(wx.HORIZONTAL)
233	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
234	0,wx.ALIGN_LEFT\|wx.ALL, 2)
235	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data['center'],0,
236	size=(75,-1))
237	vsizer.Add(wdgt)
238	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),
239	wx.ALIGN_LEFT\|wx.ALL, 2)
240	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data['center'],1,
241	size=(75,-1))
242	vsizer.Add(wdgt)
243	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
244
245	vsizer = wx.BoxSizer(wx.HORIZONTAL)
246	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
247	0,wx.ALIGN_LEFT\|wx.ALL, 2)
248	wdgt = G2gd.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
249	vsizer.Add(wdgt)
250	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
251
252	btnsizer = wx.StdDialogButtonSizer()
253	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
254	OKbtn.SetDefault()
255	OKbtn.Bind(wx.EVT_BUTTON,onClose)
256	btnsizer.AddButton(OKbtn) # not sure why this is needed
257	btnsizer.Realize()
258	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
259	dlg.SetSizer(mainsizer)
260	dlg.CenterOnParent()
261	dlg.ShowModal()
262
263	def GetImageData(G2frame,imagefile,imageOnly=False):
264	'''Read an image with the file reader keyed by the
265	file extension
266
267	:param wx.Frame G2frame: main GSAS-II Frame and data object.
268
269	:param str imagefile: name of image file
270
271	:param bool imageOnly: If True return only the image,
272	otherwise (default) return more (see below)
273
274	:returns: an image as a numpy array or a list of four items:
275	Comments, Data, Npix and the Image, as selected by imageOnly
276
277	'''
278	ext = ospath.splitext(imagefile)[1]
279	Comments = []
280	Image = None
281	if ext == '.tif' or ext == '.tiff':
282	Comments,Data,Npix,Image = GetTifData(imagefile)
283	if Npix == 0:
284	print("GetTifData failed to read "+str(filename)+" Trying PIL")
285	import scipy.misc
286	Image = scipy.misc.imread(imagefile,flatten=True)
287	Npix = Image.size
288	Comments = ['no metadata']
289	Data = {'wavelength': 0.1, 'pixelSize': [200, 200], 'distance': 100.0}
290	Data['size'] = list(Image.shape)
291	Data['center'] = [int(i/2) for i in Image.shape]
292	if not imageOnly:
293	EditImageParms(G2frame,Data,Comments,Image,imagefile)
294	elif ext == '.edf':
295	Comments,Data,Npix,Image = GetEdfData(imagefile)
296	elif ext == '.img':
297	Comments,Data,Npix,Image = GetImgData(imagefile)
298	Image[0][0] = 0
299	elif ext == '.mar3450' or ext == '.mar2300':
300	Comments,Data,Npix,Image = GetMAR345Data(imagefile)
301	elif ext in ['.sum','.avg'] or 'ge' in ext:
302	Comments,Data,Npix,Image = GetGEsumData(imagefile)
303	elif ext == '.G2img':
304	Comments,Data,Npix,Image = GetG2Image(imagefile)
305	elif ext == '.png':
306	Comments,Data,Npix,Image = GetPNGData(imagefile)
307	if not imageOnly:
308	EditImageParms(G2frame,Data,Comments,Image,imagefile)
309	else:
310	print 'Extension for file '+imagefile+' not recognized'
311	if Image is None:
312	raise Exception('No image read')
313	if imageOnly:
314	if TRANSP:
315	return Image.T
316	else:
317	return Image
318	else:
319	if TRANSP:
320	return Comments,Data,Npix,Image.T
321	else:
322	return Comments,Data,Npix,Image
323
324	def PutG2Image(filename,Comments,Data,Npix,image):
325	'Write an image as a python pickle - might be better as an .edf file?'
326	File = open(filename,'wb')
327	cPickle.dump([Comments,Data,Npix,image],File,1)
328	File.close()
329	return
330
331	def GetG2Image(filename):
332	'Read an image as a python pickle'
333	File = open(filename,'rb')
334	Comments,Data,Npix,image = cPickle.load(File)
335	File.close()
336	return Comments,Data,Npix,image
337
338	def GetEdfData(filename,imageOnly=False):
339	'Read European detector data edf file'
340	import struct as st
341	import array as ar
342	if not imageOnly:
343	print 'Read European detector data edf file: ',filename
344	File = open(filename,'rb')
345	fileSize = os.stat(filename).st_size
346	head = File.read(3072)
347	lines = head.split('\n')
348	sizexy = [0,0]
349	pixSize = [154,154] #Pixium4700?
350	cent = [0,0]
351	wave = 1.54187 #default <CuKa>
352	dist = 1000.
353	head = ['European detector data',]
354	for line in lines:
355	line = line.replace(';',' ').strip()
356	fields = line.split()
357	if 'Dim_1' in line:
358	sizexy[0] = int(fields[2])
359	elif 'Dim_2' in line:
360	sizexy[1] = int(fields[2])
361	elif 'DataType' in line:
362	dType = fields[2]
363	elif 'wavelength' in line:
364	wave = float(fields[2])
365	elif 'Size' in line:
366	imSize = int(fields[2])
367	elif 'DataType' in lines:
368	dType = fields[2]
369	elif 'pixel_size_x' in line:
370	pixSize[0] = float(fields[2])
371	elif 'pixel_size_y' in line:
372	pixSize[1] = float(fields[2])
373	elif 'beam_center_x' in line:
374	cent[0] = float(fields[2])
375	elif 'beam_center_y' in line:
376	cent[1] = float(fields[2])
377	elif 'refined_distance' in line:
378	dist = float(fields[2])
379	if line:
380	head.append(line)
381	else: #blank line at end of header
382	break
383	File.seek(fileSize-imSize)
384	if dType == 'UnsignedShort':
385	image = np.array(ar.array('H',File.read(imSize)),dtype=np.int32)
386	elif dType == 'UnsignedInt':
387	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
388	elif dType == 'UnsignedLong':
389	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
390	image = np.reshape(image,(sizexy[1],sizexy[0]))
391	data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'size':sizexy}
392	Npix = sizexy[0]*sizexy[1]
393	File.close()
394	if imageOnly:
395	return image
396	else:
397	return head,data,Npix,image
398
399	def GetGEsumData(filename,imageOnly=False):
400	'Read SUM file as produced at 1-ID from G.E. images'
401	import struct as st
402	import array as ar
403	if not imageOnly:
404	print 'Read GE sum file: ',filename
405	File = open(filename,'rb')
406	if '.sum' in filename:
407	head = ['GE detector sum data from APS 1-ID',]
408	sizexy = [2048,2048]
409	elif '.avg' in filename or '.ge' in filename:
410	head = ['GE detector avg or ge* data from APS 1-ID',]
411	sizexy = [2048,2048]
412	else:
413	head = ['GE detector raw data from APS 1-ID',]
414	File.seek(18)
415	size,nframes = st.unpack('<ih',File.read(6))
416	sizexy = [2048,2048]
417	pos = 8192
418	File.seek(pos)
419	Npix = sizexy[0]*sizexy[1]
420	if '.sum' in filename:
421	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.int32)
422	elif '.avg' in filename or '.ge' in filename:
423	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
424	else:
425	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
426	while nframes > 1:
427	image += np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
428	nframes -= 1
429	image = np.reshape(image,(sizexy[1],sizexy[0]))
430	data = {'pixelSize':[200,200],'wavelength':0.15,'distance':250.0,'center':[204.8,204.8],'size':sizexy}
431	File.close()
432	if imageOnly:
433	return image
434	else:
435	return head,data,Npix,image
436
437	def GetImgData(filename,imageOnly=False):
438	'Read an ADSC image file'
439	import struct as st
440	import array as ar
441	if not imageOnly:
442	print 'Read ADSC img file: ',filename
443	File = open(filename,'rb')
444	head = File.read(511)
445	lines = head.split('\n')
446	head = []
447	center = [0,0]
448	for line in lines[1:-2]:
449	line = line.strip()[:-1]
450	if line:
451	if 'SIZE1' in line:
452	size = int(line.split('=')[1])
453	Npix = size*size
454	elif 'WAVELENGTH' in line:
455	wave = float(line.split('=')[1])
456	elif 'BIN' in line:
457	if line.split('=')[1] == '2x2':
458	pixel=(102,102)
459	else:
460	pixel = (51,51)
461	elif 'DISTANCE' in line:
462	distance = float(line.split('=')[1])
463	elif 'CENTER_X' in line:
464	center[0] = float(line.split('=')[1])
465	elif 'CENTER_Y' in line:
466	center[1] = float(line.split('=')[1])
467	head.append(line)
468	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center,'size':[size,size]}
469	image = []
470	row = 0
471	pos = 512
472	File.seek(pos)
473	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
474	image = np.reshape(image,(sizexy[1],sizexy[0]))
475	# image = np.zeros(shape=(size,size),dtype=np.int32)
476	# while row < size:
477	# File.seek(pos)
478	# line = ar.array('H',File.read(2*size))
479	# image[row] = np.asarray(line)
480	# row += 1
481	# pos += 2*size
482	File.close()
483	if imageOnly:
484	return image
485	else:
486	return lines[1:-2],data,Npix,image
487
488	def GetMAR345Data(filename,imageOnly=False):
489	'Read a MAR-345 image plate image'
490	import array as ar
491	import struct as st
492	try:
493	import pack_f as pf
494	except:
495	msg = wx.MessageDialog(None, message="Unable to load the GSAS MAR image decompression, pack_f",
496	caption="Import Error",
497	style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
498	msg.ShowModal()
499	return None,None,None,None
500
501	if not imageOnly:
502	print 'Read Mar345 file: ',filename
503	File = open(filename,'rb')
504	head = File.read(4095)
505	numbers = st.unpack('<iiiiiiiiii',head[:40])
506	lines = head[128:].split('\n')
507	head = []
508	for line in lines:
509	line = line.strip()
510	if 'PIXEL' in line:
511	values = line.split()
512	pixel = (int(values[2]),int(values[4])) #in microns
513	elif 'WAVELENGTH' in line:
514	wave = float(line.split()[1])
515	elif 'DISTANCE' in line:
516	distance = float(line.split()[1]) #in mm
517	elif 'CENTER' in line:
518	values = line.split()
519	center = [float(values[2])/10.,float(values[4])/10.] #make in mm from pixels
520	if line:
521	head.append(line)
522	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center}
523	for line in head:
524	if 'FORMAT' in line[0:6]:
525	items = line.split()
526	size = int(items[1])
527	Npix = size*size
528	pos = 4096
529	data['size'] = [size,size]
530	File.seek(pos)
531	line = File.read(8)
532	while 'CCP4' not in line: #get past overflow list for now
533	line = File.read(8)
534	pos += 8
535	pos += 37
536	File.seek(pos)
537	raw = File.read()
538	File.close()
539	image = np.zeros(shape=(size,size),dtype=np.int32)
540	image = np.flipud(pf.pack_f(len(raw),raw,size,image).T) #transpose to get it right way around & flip
541	if imageOnly:
542	return image
543	else:
544	return head,data,Npix,image
545
546	def GetPNGData(filename,imageOnly=False):
547	'''Read an image in a png format, assumes image is converted from CheMin tif file
548	so default parameters are that machine.
549	'''
550	import scipy.misc
551	Image = scipy.misc.imread(filename,flatten=True)
552	Npix = Image.size
553	Comments = ['no metadata']
554	pixy = list(Image.shape)
555	sizexy = [40,40]
556	Data = {'wavelength': 1.78892, 'pixelSize': sizexy, 'distance': 18.0,'size':pixy}
557	Data['center'] = [pixy[0]sizexy[0]/1000,pixy[1]sizexy[1]/2000]
558	if imageOnly:
559	return Image.T
560	else:
561	return Comments,Data,Npix,Image.T
562
563	def GetTifData(filename,imageOnly=False):
564	'''Read an image in a pseudo-tif format,
565	as produced by a wide variety of software, almost always
566	incorrectly in some way.
567	'''
568	import struct as st
569	try:
570	import Image as Im
571	except ImportError:
572	try:
573	from PIL import Image as Im
574	except ImportError:
575	print "PIL/pillow Image module not present. TIFs cannot be read without this"
576	raise Exception("PIL/pillow Image module not found")
577	import array as ar
578	import ReadMarCCDFrame as rmf
579	File = open(filename,'rb')
580	dataType = 5
581	center = [None,None]
582	wavelength = None
583	distance = None
584	try:
585	Meta = open(filename+'.metadata','Ur')
586	head = Meta.readlines()
587	for line in head:
588	line = line.strip()
589	if 'dataType=' in line:
590	dataType = int(line.split('=')[1])
591	Meta.close()
592	except IOError:
593	print 'no metadata file found - will try to read file anyway'
594	head = ['no metadata file found',]
595
596	tag = File.read(2)
597	byteOrd = '<'
598	if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
599	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
600	elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
601	byteOrd = '>'
602	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
603	else:
604	lines = ['not a detector tiff file',]
605	return lines,0,0,0
606	File.seek(IFD) #get number of directory entries
607	NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
608	IFD = {}
609	nSlice = 1
610	for ied in range(NED):
611	Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
612	nVal = st.unpack(byteOrd+'i',File.read(4))[0]
613	if DEBUG: print 'Try:',Tag,Type,nVal
614	if Type == 1:
615	Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
616	elif Type == 2:
617	Value = st.unpack(byteOrd+'i',File.read(4))
618	elif Type == 3:
619	Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
620	x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
621	elif Type == 4:
622	if Tag in [273,279]:
623	nSlice = nVal
624	nVal = 1
625	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
626	elif Type == 5:
627	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
628	elif Type == 11:
629	Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
630	IFD[Tag] = [Type,nVal,Value]
631	if DEBUG: print Tag,IFD[Tag]
632	sizexy = [IFD[256][2][0],IFD[257][2][0]]
633	[nx,ny] = sizexy
634	Npix = nx*ny
635	if 34710 in IFD:
636	if not imageOnly:
637	print 'Read MAR CCD tiff file: ',filename
638	marFrame = rmf.marFrame(File,byteOrd,IFD)
639	image = np.flipud(np.array(np.asarray(marFrame.image),dtype=np.int32))
640	tifType = marFrame.filetitle
641	pixy = [marFrame.pixelsizeX/1000.0,marFrame.pixelsizeY/1000.0]
642	head = marFrame.outputHead()
643	# extract resonable wavelength from header
644	wavelength = marFrame.sourceWavelength*1e-5
645	wavelength = (marFrame.opticsWavelength > 0) and marFrame.opticsWavelength*1e-5 or wavelength
646	wavelength = (wavelength <= 0) and None or wavelength
647	# extract resonable distance from header
648	distance = (marFrame.startXtalToDetector+marFrame.endXtalToDetector)*5e-4
649	distance = (distance <= 0) and marFrame.xtalToDetector*1e-3 or distance
650	distance = (distance <= 0) and None or distance
651	# extract resonable center from header
652	center = [marFrame.beamXmarFrame.pixelsizeX1e-9,marFrame.beamYmarFrame.pixelsizeY1e-9]
653	center = (center[0] != 0 and center[1] != 0) and center or [None,None]
654	#print head,tifType,pixy
655	elif nSlice > 1: #CheMin multislice tif file!
656	tifType = 'CheMin'
657	pixy = [40,40]
658	image = np.flipud(np.array(Im.open(filename)))*10.
659	distance = 18.0
660	center = [pixy[0]*sizexy[0]/2000,0] #the CheMin beam stop is here
661	wavelength = 1.78892
662	elif 272 in IFD:
663	ifd = IFD[272]
664	File.seek(ifd[2][0])
665	S = File.read(ifd[1])
666	if 'PILATUS' in S:
667	tifType = 'Pilatus'
668	dataType = 0
669	pixy = [172,172]
670	File.seek(4096)
671	if not imageOnly:
672	print 'Read Pilatus tiff file: ',filename
673	image = ar.array('L',File.read(4*Npix))
674	image = np.array(np.asarray(image),dtype=np.int32)
675	else:
676	if IFD[258][2][0] == 16:
677	tifType = 'GE'
678	pixy = [200,200]
679	File.seek(8)
680	if not imageOnly:
681	print 'Read GE-detector tiff file: ',filename
682	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
683	elif IFD[258][2][0] == 32:
684	tifType = 'CHESS'
685	pixy = [200,200]
686	File.seek(8)
687	if not imageOnly:
688	print 'Read CHESS-detector tiff file: ',filename
689	image = np.array(ar.array('L',File.read(4*Npix)),dtype=np.int32)
690
691	elif 262 in IFD and IFD[262][2][0] > 4:
692	tifType = 'DND'
693	pixy = [158,158]
694	File.seek(512)
695	if not imageOnly:
696	print 'Read DND SAX/WAX-detector tiff file: ',filename
697	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
698	elif sizexy == [1536,1536]:
699	tifType = 'APS Gold'
700	pixy = [150,150]
701	File.seek(64)
702	if not imageOnly:
703	print 'Read Gold tiff file:',filename
704	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
705	elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
706	if IFD[273][2][0] == 8:
707	if IFD[258][2][0] == 32:
708	tifType = 'PE'
709	pixy = [200,200]
710	File.seek(8)
711	if not imageOnly:
712	print 'Read APS PE-detector tiff file: ',filename
713	if dataType == 5:
714	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
715	else:
716	image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
717
718	elif IFD[273][2][0] == 4096:
719	if sizexy[0] == 3072:
720	pixy = [73,73]
721	tifType = 'MAR225'
722	else:
723	pixy = [158,158]
724	tifType = 'MAR325'
725	File.seek(4096)
726	if not imageOnly:
727	print 'Read MAR CCD tiff file: ',filename
728	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
729	elif IFD[273][2][0] == 512:
730	tiftype = '11-ID-C'
731	pixy = [200,200]
732	File.seek(512)
733	if not imageOnly:
734	print 'Read 11-ID-C tiff file: ',filename
735	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
736	elif sizexy == [4096,4096]:
737	if IFD[273][2][0] == 8:
738	if IFD[258][2][0] == 16:
739	tifType = 'scanCCD'
740	pixy = [9,9]
741	File.seek(8)
742	if not imageOnly:
743	print 'Read APS scanCCD tiff file: ',filename
744	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
745	elif IFD[273][2][0] == 4096:
746	tifType = 'Rayonix'
747	pixy = [73.242,73.242]
748	File.seek(4096)
749	if not imageOnly:
750	print 'Read Rayonix MX300HE tiff file: ',filename
751	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
752	# elif sizexy == [960,960]:
753	# tiftype = 'PE-BE'
754	# pixy = (200,200)
755	# File.seek(8)
756	# if not imageOnly:
757	# print 'Read Gold tiff file:',filename
758	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
759
760	else:
761	lines = ['not a known detector tiff file',]
762	return lines,0,0,0
763
764	image = np.reshape(image,(sizexy[1],sizexy[0]))
765	center = (not center[0]) and [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000] or center
766	wavelength = (not wavelength) and 0.10 or wavelength
767	distance = (not distance) and 100.0 or distance
768	data = {'pixelSize':pixy,'wavelength':wavelength,'distance':distance,'center':center,'size':sizexy}
769	File.close()
770	if imageOnly:
771	return image
772	else:
773	return head,data,Npix,image
774
775	#def GetTifData(filename,imageOnly=False):
776	# import struct as st
777	# import array as ar
778	# File = open(filename,'rb')
779	# dataType = 5
780	# try:
781	# Meta = open(filename+'.metadata','Ur')
782	# head = Meta.readlines()
783	# for line in head:
784	# line = line.strip()
785	# if 'dataType=' in line:
786	# dataType = int(line.split('=')[1])
787	# Meta.close()
788	# except IOError:
789	# print 'no metadata file found - will try to read file anyway'
790	# head = ['no metadata file found',]
791	#
792	# tag = File.read(2)
793	# byteOrd = '<'
794	# if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
795	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
796	# elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
797	# byteOrd = '>'
798	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
799	# else:
800	# lines = ['not a detector tiff file',]
801	# return lines,0,0,0
802	# File.seek(IFD) #get number of directory entries
803	# NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
804	# IFD = {}
805	# for ied in range(NED):
806	# Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
807	# nVal = st.unpack(byteOrd+'i',File.read(4))[0]
808	# if Type == 1:
809	# Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
810	# elif Type == 2:
811	# Value = st.unpack(byteOrd+'i',File.read(4))
812	# elif Type == 3:
813	# Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
814	# x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
815	# elif Type == 4:
816	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
817	# elif Type == 5:
818	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
819	# elif Type == 11:
820	# Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
821	# IFD[Tag] = [Type,nVal,Value]
822	## print Tag,IFD[Tag]
823	# sizexy = [IFD[256][2][0],IFD[257][2][0]]
824	# [nx,ny] = sizexy
825	# Npix = nx*ny
826	# if 272 in IFD:
827	# ifd = IFD[272]
828	# File.seek(ifd[2][0])
829	# S = File.read(ifd[1])
830	# if 'PILATUS' in S:
831	# tifType = 'Pilatus'
832	# dataType = 0
833	# pixy = (172,172)
834	# File.seek(4096)
835	# if not imageOnly:
836	# print 'Read Pilatus tiff file: ',filename
837	# image = ar.array('L',File.read(4*Npix))
838	# image = np.array(np.asarray(image),dtype=np.int32)
839	# elif 262 in IFD and IFD[262][2][0] > 4:
840	# tifType = 'DND'
841	# pixy = (158,158)
842	# File.seek(512)
843	# if not imageOnly:
844	# print 'Read DND SAX/WAX-detector tiff file: ',filename
845	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
846	# elif sizexy == [1536,1536]:
847	# tifType = 'APS Gold'
848	# pixy = (150,150)
849	# File.seek(64)
850	# if not imageOnly:
851	# print 'Read Gold tiff file:',filename
852	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
853	# elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
854	# if IFD[273][2][0] == 8:
855	# if IFD[258][2][0] == 32:
856	# tifType = 'PE'
857	# pixy = (200,200)
858	# File.seek(8)
859	# if not imageOnly:
860	# print 'Read APS PE-detector tiff file: ',filename
861	# if dataType == 5:
862	# image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
863	# else:
864	# image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
865	# elif IFD[273][2][0] == 4096:
866	# if sizexy[0] == 3072:
867	# pixy = (73,73)
868	# tifType = 'MAR225'
869	# else:
870	# pixy = (158,158)
871	# tifType = 'MAR325'
872	# File.seek(4096)
873	# if not imageOnly:
874	# print 'Read MAR CCD tiff file: ',filename
875	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
876	# elif IFD[273][2][0] == 512:
877	# tiftype = '11-ID-C'
878	# pixy = [200,200]
879	# File.seek(512)
880	# if not imageOnly:
881	# print 'Read 11-ID-C tiff file: ',filename
882	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
883	# elif sizexy == [4096,4096]:
884	# if IFD[273][2][0] == 8:
885	# if IFD[258][2][0] == 16:
886	# tifType = 'scanCCD'
887	# pixy = (9,9)
888	# File.seek(8)
889	# if not imageOnly:
890	# print 'Read APS scanCCD tiff file: ',filename
891	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
892	# elif IFD[273][2][0] == 4096:
893	# tifType = 'Rayonix'
894	# pixy = (73.242,73.242)
895	# File.seek(4096)
896	# if not imageOnly:
897	# print 'Read Rayonix MX300HE tiff file: ',filename
898	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
899	## elif sizexy == [960,960]:
900	## tiftype = 'PE-BE'
901	## pixy = (200,200)
902	## File.seek(8)
903	## if not imageOnly:
904	## print 'Read Gold tiff file:',filename
905	## image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
906	#
907	# else:
908	# lines = ['not a known detector tiff file',]
909	# return lines,0,0,0
910	#
911	# image = np.reshape(image,(sizexy[1],sizexy[0]))
912	# center = [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000]
913	# data = {'pixelSize':pixy,'wavelength':0.10,'distance':100.0,'center':center,'size':sizexy}
914	# File.close()
915	# if imageOnly:
916	# return image
917	# else:
918	# return head,data,Npix,image
919	#
920	def ProjFileOpen(G2frame):
921	'Read a GSAS-II project file and load into the G2 data tree'
922	if not os.path.exists(G2frame.GSASprojectfile):
923	print ('\n*** Error attempt to open project file that does not exist:\n '+
924	str(G2frame.GSASprojectfile))
925	return
926	file = open(G2frame.GSASprojectfile,'rb')
927	print 'load from file: ',G2frame.GSASprojectfile
928	G2frame.SetTitle("GSAS-II data tree: "+
929	os.path.split(G2frame.GSASprojectfile)[1])
930	wx.BeginBusyCursor()
931	try:
932	while True:
933	try:
934	data = cPickle.load(file)
935	except EOFError:
936	break
937	datum = data[0]
938
939	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=datum[0])
940	if 'PWDR' in datum[0]:
941	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
942	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
943	G2frame.PatternTree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
944	elif datum[0].startswith('HKLF'):
945	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
946	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
947	G2frame.PatternTree.SetItemPyData(Id,datum[1])
948	else:
949	G2frame.PatternTree.SetItemPyData(Id,datum[1])
950	for datus in data[1:]:
951	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
952	#patch
953	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
954	if 'PWDR' in datum[0]:
955	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
956	else:
957	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
958	for item in datus[1][0]: #zip makes tuples - now make lists!
959	datus[1][0][item] = list(datus[1][0][item])
960	#end patch
961	G2frame.PatternTree.SetItemPyData(sub,datus[1])
962	if 'IMG' in datum[0]: #retrieve image default flag & data if set
963	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
964	if Data['setDefault']:
965	G2frame.imageDefault = Data
966	file.close()
967	print('project load successful')
968	G2frame.NewPlot = True
969	except:
970	msg = wx.MessageDialog(G2frame,message="Error reading file "+
971	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
972	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
973	msg.ShowModal()
974	finally:
975	wx.EndBusyCursor()
976	G2frame.Status.SetStatusText('To reorder tree items, use mouse RB to drag/drop them')
977
978	def ProjFileSave(G2frame):
979	'Save a GSAS-II project file'
980	if not G2frame.PatternTree.IsEmpty():
981	file = open(G2frame.GSASprojectfile,'wb')
982	print 'save to file: ',G2frame.GSASprojectfile
983	# stick the file name into the tree, if possible
984	try:
985	Controls = G2frame.PatternTree.GetItemPyData(
986	G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
987	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
988	except:
989	pass
990	wx.BeginBusyCursor()
991	try:
992	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
993	while item:
994	data = []
995	name = G2frame.PatternTree.GetItemText(item)
996	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
997	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
998	while item2:
999	name = G2frame.PatternTree.GetItemText(item2)
1000	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
1001	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
1002	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1003	cPickle.dump(data,file,1)
1004	file.close()
1005	finally:
1006	wx.EndBusyCursor()
1007	print('project save successful')
1008
1009	def SaveIntegration(G2frame,PickId,data):
1010	'Save image integration results as powder pattern(s)'
1011	azms = G2frame.Integrate[1]
1012	X = G2frame.Integrate[2][:-1]
1013	N = len(X)
1014	Id = G2frame.PatternTree.GetItemParent(PickId)
1015	name = G2frame.PatternTree.GetItemText(Id)
1016	name = name.replace('IMG ',data['type']+' ')
1017	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
1018	if 'PWDR' in name:
1019	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
1020	codes = [0 for i in range(11)]
1021	elif 'SASD' in name:
1022	names = ['Type','Lam','Zero','Azimuth']
1023	codes = [0 for i in range(4)]
1024	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
1025	Xminmax = [X[0],X[-1]]
1026	LRazm = data['LRazimuth']
1027	Azms = []
1028	if data['fullIntegrate'] and data['outAzimuths'] == 1:
1029	Azms = [45.0,] #a poor man's average?
1030	else:
1031	for i,azm in enumerate(azms[:-1]):
1032	Azms.append((azms[i+1]+azm)/2.)
1033	for i,azm in enumerate(azms[:-1]):
1034	Aname = name+" Azm= %.2f"%(Azms[i])
1035	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
1036	nOcc = 0
1037	while item:
1038	Name = G2frame.PatternTree.GetItemText(item)
1039	if Aname in Name:
1040	nOcc += 1
1041	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1042	if nOcc:
1043	Aname += '(%d)'%(nOcc)
1044	Sample = G2pdG.SetDefaultSample()
1045	Sample['Gonio. radius'] = data['distance']
1046	Sample['Omega'] = data['GonioAngles'][0]
1047	Sample['Chi'] = data['GonioAngles'][1]
1048	Sample['Phi'] = data['GonioAngles'][2]
1049	if 'PWDR' in Aname:
1050	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!
1051	elif 'SASD' in Aname:
1052	Sample['Trans'] = data['SampleAbs'][0]
1053	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
1054	Y = G2frame.Integrate[0][i]
1055	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
1056	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=Aname)
1057	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
1058	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
1059	if 'PWDR' in Aname:
1060	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
1061	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
1062	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
1063	for item in inst[0]:
1064	inst[0][item] = list(inst[0][item])
1065	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
1066	if 'PWDR' in Aname:
1067	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1068	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
1069	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[[],[]])
1070	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
1071	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
1072	elif 'SASD' in Aname:
1073	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
1074	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1075	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
1076	valuesdict = {
1077	'wtFactor':1.0,
1078	'Dummy':False,
1079	'ranId':ran.randint(0,sys.maxint),
1080	}
1081	G2frame.PatternTree.SetItemPyData(
1082	Id,[valuesdict,
1083	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
1084	return Id #last powder pattern generated
1085
1086	# def powderFxyeSave(G2frame,exports,powderfile):
1087	# 'Save a powder histogram as a GSAS FXYE file'
1088	# head,tail = ospath.split(powderfile)
1089	# name,ext = tail.split('.')
1090	# for i,export in enumerate(exports):
1091	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1092	# prmname = filename.strip(ext)+'prm'
1093	# prm = open(prmname,'w') #old style GSAS parm file
1094	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1095	# Inst = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, \
1096	# PickId, 'Instrument Parameters'))[0]
1097	# prm.write( ' 123456789012345678901234567890123456789012345678901234567890 '+'\n')
1098	# prm.write( 'INS BANK 1 '+'\n')
1099	# prm.write(('INS HTYPE %sR '+'\n')%(Inst['Type'][0]))
1100	# if 'Lam1' in Inst: #Ka1 & Ka2
1101	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam1'][0],Inst['Lam2'][0]))
1102	# elif 'Lam' in Inst: #single wavelength
1103	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam'][1],0.0))
1104	# prm.write( 'INS 1 IRAD 0 '+'\n')
1105	# prm.write( 'INS 1I HEAD '+'\n')
1106	# prm.write( 'INS 1I ITYP 0 0.0000 180.0000 1 '+'\n')
1107	# prm.write(('INS 1DETAZM%10.3f '+'\n')%(Inst['Azimuth'][0]))
1108	# prm.write( 'INS 1PRCF1 3 8 0.00100 '+'\n')
1109	# prm.write(('INS 1PRCF11 %15.6g%15.6g%15.6g%15.6g '+'\n')%(Inst['U'][1],Inst['V'][1],Inst['W'][1],0.0))
1110	# 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.))
1111	# prm.close()
1112	# file = open(filename,'w')
1113	# print 'save powder pattern to file: ',filename
1114	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1115	# file.write(powderfile+'\n')
1116	# file.write('Instrument parameter file:'+ospath.split(prmname)[1]+'\n')
1117	# file.write('BANK 1 %d %d CONS %.2f %.2f 0 0 FXYE\n'%(len(x),len(x),\
1118	# 100.x[0],100.(x[1]-x[0])))
1119	# s = list(np.sqrt(1./np.array(w)))
1120	# XYW = zip(x,y,s)
1121	# for X,Y,S in XYW:
1122	# file.write("%15.6g %15.6g %15.6g\n" % (100.*X,Y,max(S,1.0)))
1123	# file.close()
1124	# print 'powder pattern file '+filename+' written'
1125
1126	# def powderXyeSave(G2frame,exports,powderfile):
1127	# 'Save a powder histogram as a Topas XYE file'
1128	# head,tail = ospath.split(powderfile)
1129	# name,ext = tail.split('.')
1130	# for i,export in enumerate(exports):
1131	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1132	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1133	# file = open(filename,'w')
1134	# file.write('#%s\n'%(export))
1135	# print 'save powder pattern to file: ',filename
1136	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1137	# s = list(np.sqrt(1./np.array(w)))
1138	# XYW = zip(x,y,s)
1139	# for X,Y,W in XYW:
1140	# file.write("%15.6g %15.6g %15.6g\n" % (X,Y,W))
1141	# file.close()
1142	# print 'powder pattern file '+filename+' written'
1143
1144	def PDFSave(G2frame,exports):
1145	'Save a PDF G(r) and S(Q) in column formats'
1146	for export in exports:
1147	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1148	SQname = 'S(Q)'+export[4:]
1149	GRname = 'G(R)'+export[4:]
1150	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
1151	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
1152	sqId = G2gd.GetPatternTreeItemId(G2frame, PickId, SQname)
1153	grId = G2gd.GetPatternTreeItemId(G2frame, PickId, GRname)
1154	sqdata = np.array(G2frame.PatternTree.GetItemPyData(sqId)[1][:2]).T
1155	grdata = np.array(G2frame.PatternTree.GetItemPyData(grId)[1][:2]).T
1156	sqfile = open(sqfilename,'w')
1157	grfile = open(grfilename,'w')
1158	sqfile.write('#T S(Q) %s\n'%(export))
1159	grfile.write('#T G(R) %s\n'%(export))
1160	sqfile.write('#L Q S(Q)\n')
1161	grfile.write('#L R G(R)\n')
1162	for q,sq in sqdata:
1163	sqfile.write("%15.6g %15.6g\n" % (q,sq))
1164	sqfile.close()
1165	for r,gr in grdata:
1166	grfile.write("%15.6g %15.6g\n" % (r,gr))
1167	grfile.close()
1168
1169	def PeakListSave(G2frame,file,peaks):
1170	'Save powder peaks to a data file'
1171	print 'save peak list to file: ',G2frame.peaklistfile
1172	if not peaks:
1173	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1174	try:
1175	result = dlg.ShowModal()
1176	finally:
1177	dlg.Destroy()
1178	return
1179	for peak in peaks:
1180	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1181	(peak[0],peak[2],peak[4],peak[6]))
1182	print 'peak list saved'
1183
1184	def IndexPeakListSave(G2frame,peaks):
1185	'Save powder peaks from the indexing list'
1186	file = open(G2frame.peaklistfile,'wa')
1187	print 'save index peak list to file: ',G2frame.peaklistfile
1188	wx.BeginBusyCursor()
1189	try:
1190	if not peaks:
1191	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1192	try:
1193	result = dlg.ShowModal()
1194	finally:
1195	dlg.Destroy()
1196	return
1197	for peak in peaks:
1198	file.write("%12.6f\n" % (peak[7]))
1199	file.close()
1200	finally:
1201	wx.EndBusyCursor()
1202	print 'index peak list saved'
1203
1204	def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1205	'''Create a new phase dict with default values for various parameters
1206
1207	:param str Name: Name for new Phase
1208
1209	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1210	defaults to data for P 1
1211
1212	:param list cell: unit cell parameter list; defaults to
1213	[1.0,1.0,1.0,90.,90,90.,1.]
1214
1215	'''
1216	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1217	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1218	phaseData = {
1219	'ranId':ran.randint(0,sys.maxint),
1220	'General':{
1221	'Name':Name,
1222	'Type':'nuclear',
1223	'AtomPtrs':[3,1,7,9],
1224	'SGData':SGData,
1225	'Cell':[False,]+cell,
1226	'Pawley dmin':1.0,
1227	'Data plot type':'None',
1228	'SH Texture':{
1229	'Order':0,
1230	'Model':'cylindrical',
1231	'Sample omega':[False,0.0],
1232	'Sample chi':[False,0.0],
1233	'Sample phi':[False,0.0],
1234	'SH Coeff':[False,{}],
1235	'SHShow':False,
1236	'PFhkl':[0,0,1],
1237	'PFxyz':[0,0,1],
1238	'PlotType':'Pole figure'}},
1239	'Atoms':[],
1240	'Drawing':{},
1241	'Histograms':{},
1242	'Pawley ref':[],
1243	'RBModels':{},
1244	}
1245	if Super and Super.get('Use',False):
1246	phaseData['General'].update({'Type':'modulated','Super':True,'SuperSg':Super['ssSymb']})
1247	phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])
1248	phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1249
1250	return phaseData
1251
1252	class MultipleChoicesDialog(wx.Dialog):
1253	'''A dialog that offers a series of choices, each with a
1254	title and a wx.Choice widget. Intended to be used Modally.
1255	typical input:
1256
1257	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1258	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1259
1260	selections are placed in self.chosen when OK is pressed
1261	'''
1262	def __init__(self,choicelist,headinglist,
1263	head='Select options',
1264	title='Please select from options below',
1265	parent=None):
1266	self.chosen = []
1267	wx.Dialog.__init__(
1268	self,parent,wx.ID_ANY,head,
1269	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1270	panel = wx.Panel(self)
1271	mainSizer = wx.BoxSizer(wx.VERTICAL)
1272	mainSizer.Add((10,10),1)
1273	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1274	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1275	self.ChItems = []
1276	for choice,lbl in zip(choicelist,headinglist):
1277	mainSizer.Add((10,10),1)
1278	self.chosen.append(0)
1279	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1280	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1281	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1282	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1283
1284	OkBtn = wx.Button(panel,-1,"Ok")
1285	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1286	cancelBtn = wx.Button(panel,-1,"Cancel")
1287	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1288	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1289	btnSizer.Add((20,20),1)
1290	btnSizer.Add(OkBtn)
1291	btnSizer.Add((20,20),1)
1292	btnSizer.Add(cancelBtn)
1293	btnSizer.Add((20,20),1)
1294	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1295	panel.SetSizer(mainSizer)
1296	panel.Fit()
1297	self.Fit()
1298
1299	def OnOk(self,event):
1300	parent = self.GetParent()
1301	if parent is not None: parent.Raise()
1302	# save the results from the choice widgets
1303	self.chosen = []
1304	for w in self.ChItems:
1305	self.chosen.append(w.GetSelection())
1306	self.EndModal(wx.ID_OK)
1307
1308	def OnCancel(self,event):
1309	parent = self.GetParent()
1310	if parent is not None: parent.Raise()
1311	self.chosen = []
1312	self.EndModal(wx.ID_CANCEL)
1313
1314	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1315	confirmoverwrite=True, parent=None,
1316	multipleselect=False):
1317	'''If the filename is a zip file, extract a file from that
1318	archive.
1319
1320	:param list Selection: used to predefine the name of the file
1321	to be extracted. Filename case and zip directory name are
1322	ignored in selection; the first matching file is used.
1323
1324	:param bool confirmread: if True asks the user to confirm before expanding
1325	the only file in a zip
1326
1327	:param bool confirmoverwrite: if True asks the user to confirm
1328	before overwriting if the extracted file already exists
1329
1330	:param bool multipleselect: if True allows more than one zip
1331	file to be extracted, a list of file(s) is returned.
1332	If only one file is present, do not ask which one, otherwise
1333	offer a list of choices (unless selection is used).
1334
1335	:returns: the name of the file that has been created or a
1336	list of files (see multipleselect)
1337
1338	If the file is not a zipfile, return the name of the input file.
1339	If the zipfile is empty or no file has been selected, return None
1340	'''
1341	import zipfile # do this now, since we can save startup time by doing this only on need
1342	import shutil
1343	zloc = os.path.split(filename)[0]
1344	if not zipfile.is_zipfile(filename):
1345	#print("not zip")
1346	return filename
1347
1348	z = zipfile.ZipFile(filename,'r')
1349	zinfo = z.infolist()
1350
1351	if len(zinfo) == 0:
1352	#print('Zip has no files!')
1353	zlist = [-1]
1354	if selection:
1355	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1356	if selection.lower() in choices:
1357	zlist = [choices.index(selection.lower())]
1358	else:
1359	print('debug: file '+str(selection)+' was not found in '+str(filename))
1360	zlist = [-1]
1361	elif len(zinfo) == 1 and confirmread:
1362	result = wx.ID_NO
1363	dlg = wx.MessageDialog(
1364	parent,
1365	'Is file '+str(zinfo[0].filename)+
1366	' what you want to extract from '+
1367	str(os.path.split(filename)[1])+'?',
1368	'Confirm file',
1369	wx.YES_NO \| wx.ICON_QUESTION)
1370	try:
1371	result = dlg.ShowModal()
1372	finally:
1373	dlg.Destroy()
1374	if result == wx.ID_NO:
1375	zlist = [-1]
1376	else:
1377	zlist = [0]
1378	elif len(zinfo) == 1:
1379	zlist = [0]
1380	elif multipleselect:
1381	# select one or more from a from list
1382	choices = [i.filename for i in zinfo]
1383	dlg = G2gd.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1384	'Choose file(s)',choices)
1385	if dlg.ShowModal() == wx.ID_OK:
1386	zlist = dlg.GetSelections()
1387	else:
1388	zlist = []
1389	dlg.Destroy()
1390	else:
1391	# select one from a from list
1392	choices = [i.filename for i in zinfo]
1393	dlg = wx.SingleChoiceDialog(parent,
1394	'Select file to extract from zip file'+str(filename),'Choose file',
1395	choices,)
1396	if dlg.ShowModal() == wx.ID_OK:
1397	zlist = [dlg.GetSelection()]
1398	else:
1399	zlist = [-1]
1400	dlg.Destroy()
1401
1402	outlist = []
1403	for zindex in zlist:
1404	if zindex >= 0:
1405	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1406	if os.path.exists(efil) and confirmoverwrite:
1407	result = wx.ID_NO
1408	dlg = wx.MessageDialog(parent,
1409	'File '+str(efil)+' already exists. OK to overwrite it?',
1410	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1411	try:
1412	result = dlg.ShowModal()
1413	finally:
1414	dlg.Destroy()
1415	if result == wx.ID_NO:
1416	zindex = -1
1417	if zindex >= 0:
1418	# extract the file to the current directory, regardless of it's original path
1419	#z.extract(zinfo[zindex],zloc)
1420	eloc,efil = os.path.split(zinfo[zindex].filename)
1421	outfile = os.path.join(zloc, efil)
1422	fpin = z.open(zinfo[zindex])
1423	fpout = file(outfile, "wb")
1424	shutil.copyfileobj(fpin, fpout)
1425	fpin.close()
1426	fpout.close()
1427	outlist.append(outfile)
1428	z.close()
1429	if multipleselect and len(outlist) >= 1:
1430	return outlist
1431	elif len(outlist) == 1:
1432	return outlist[0]
1433	else:
1434	return None
1435
1436	######################################################################
1437	# base classes for reading various types of data files
1438	# not used directly, only by subclassing
1439	######################################################################
1440	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1441	P1SGData = SGData
1442	class ImportBaseclass(object):
1443	'''Defines a base class for the reading of input files (diffraction
1444	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1445	for an explanation on how to use a subclass of this class.
1446	'''
1447	class ImportException(Exception):
1448	'''Defines an Exception that is used when an import routine hits an expected error,
1449	usually in .Reader.
1450
1451	Good practice is that the Reader should define a value in self.errors that
1452	tells the user some information about what is wrong with their file.
1453	'''
1454	pass
1455
1456	def __init__(self,
1457	formatName,
1458	longFormatName=None,
1459	extensionlist=[],
1460	strictExtension=False,
1461	):
1462	self.formatName = formatName # short string naming file type
1463	if longFormatName: # longer string naming file type
1464	self.longFormatName = longFormatName
1465	else:
1466	self.longFormatName = formatName
1467	# define extensions that are allowed for the file type
1468	# for windows, remove any extensions that are duplicate, as case is ignored
1469	if sys.platform == 'windows' and extensionlist:
1470	extensionlist = list(set([s.lower() for s in extensionlist]))
1471	self.extensionlist = extensionlist
1472	# If strictExtension is True, the file will not be read, unless
1473	# the extension matches one in the extensionlist
1474	self.strictExtension = strictExtension
1475	self.errors = ''
1476	self.warnings = ''
1477	# used for readers that will use multiple passes to read
1478	# more than one data block
1479	self.repeat = False
1480	self.selections = []
1481	self.repeatcount = 0
1482	self.readfilename = '?'
1483	#print 'created',self.__class__
1484
1485	def ReInitialize(self):
1486	'Reinitialize the Reader to initial settings'
1487	self.errors = ''
1488	self.warnings = ''
1489	self.repeat = False
1490	self.repeatcount = 0
1491	self.readfilename = '?'
1492
1493	def BlockSelector(self, ChoiceList, ParentFrame=None,
1494	title='Select a block',
1495	size=None, header='Block Selector',
1496	useCancel=True):
1497	''' Provide a wx dialog to select a block if the file contains more
1498	than one set of data and one must be selected
1499	'''
1500	if useCancel:
1501	dlg = wx.SingleChoiceDialog(
1502	ParentFrame,title, header,ChoiceList)
1503	else:
1504	dlg = wx.SingleChoiceDialog(
1505	ParentFrame,title, header,ChoiceList,
1506	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1507	if size: dlg.SetSize(size)
1508	dlg.CenterOnParent()
1509	if dlg.ShowModal() == wx.ID_OK:
1510	sel = dlg.GetSelection()
1511	return sel
1512	else:
1513	return None
1514	dlg.Destroy()
1515
1516	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1517	title='Select a block',size=None, header='Block Selector'):
1518	'''Provide a wx dialog to select a block of data if the
1519	file contains more than one set of data and one must be
1520	selected.
1521
1522	:returns: a list of the selected blocks
1523	'''
1524	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1525	wx.CHOICEDLG_STYLE)
1526	dlg.CenterOnParent()
1527	if size: dlg.SetSize(size)
1528	if dlg.ShowModal() == wx.ID_OK:
1529	sel = dlg.GetSelections()
1530	else:
1531	return []
1532	dlg.Destroy()
1533	selected = []
1534	if len(ChoiceList) in sel:
1535	return range(len(ChoiceList))
1536	else:
1537	return sel
1538	return selected
1539
1540	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1541	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1542	widget. Typical input:
1543
1544	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1545
1546	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1547
1548	optional keyword parameters are: head (window title) and title
1549	returns a list of selected indicies for each choice (or None)
1550	'''
1551	result = None
1552	dlg = MultipleChoicesDialog(choicelist,headinglist,
1553	parent=ParentFrame, **kwargs)
1554	dlg.CenterOnParent()
1555	if dlg.ShowModal() == wx.ID_OK:
1556	result = dlg.chosen
1557	dlg.Destroy()
1558	return result
1559
1560	def ShowBusy(self):
1561	wx.BeginBusyCursor()
1562	wx.Yield() # make it happen now!
1563
1564	def DoneBusy(self):
1565	wx.EndBusyCursor()
1566	wx.Yield() # make it happen now!
1567
1568	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1569	# '''This method must be supplied in the child class to read the file.
1570	# if the read fails either return False or raise an Exception
1571	# preferably of type ImportException.
1572	# '''
1573	# #start reading
1574	# raise ImportException("Error occurred while...")
1575	# self.errors += "Hint for user on why the error occur
1576	# return False # if an error occurs
1577	# return True # if read OK
1578
1579	def ExtensionValidator(self, filename):
1580	'''This methods checks if the file has the correct extension
1581	Return False if this filename will not be supported by this reader
1582	Return True if the extension matches the list supplied by the reader
1583	Return None if the reader allows un-registered extensions
1584	'''
1585	if filename:
1586	ext = os.path.splitext(filename)[1]
1587	if sys.platform == 'windows': ext = ext.lower()
1588	if ext in self.extensionlist: return True
1589	if self.strictExtension: return False
1590	return None
1591
1592	def ContentsValidator(self, filepointer):
1593	'''This routine will attempt to determine if the file can be read
1594	with the current format.
1595	This will typically be overridden with a method that
1596	takes a quick scan of [some of]
1597	the file contents to do a "sanity" check if the file
1598	appears to match the selected format.
1599	Expected to be called via self.Validator()
1600	'''
1601	#filepointer.seek(0) # rewind the file pointer
1602	return True
1603
1604	def CIFValidator(self, filepointer):
1605	'''A :meth:`ContentsValidator` for use to validate CIF files.
1606	'''
1607	for i,l in enumerate(filepointer):
1608	if i >= 1000: return True
1609	'''Encountered only blank lines or comments in first 1000
1610	lines. This is unlikely, but assume it is CIF anyway, since we are
1611	even less likely to find a file with nothing but hashes and
1612	blank lines'''
1613	line = l.strip()
1614	if len(line) == 0: # ignore blank lines
1615	continue
1616	elif line.startswith('#'): # ignore comments
1617	continue
1618	elif line.startswith('data_'): # on the right track, accept this file
1619	return True
1620	else: # found something invalid
1621	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1622	self.errors += ' '+str(l)
1623	self.errors += ' Note: a CIF should only have blank lines or comments before'
1624	self.errors += ' a data_ statement begins a block.'
1625	return False
1626
1627	class ImportPhase(ImportBaseclass):
1628	'''Defines a base class for the reading of files with coordinates
1629
1630	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1631	in :meth:`GSASII.GSASII.OnImportPhase`.
1632	See :ref:`Writing a Import Routine<Import_Routines>`
1633	for an explanation on how to use this class.
1634
1635	'''
1636	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1637	strictExtension=False,):
1638	# call parent __init__
1639	ImportBaseclass.__init__(self,formatName,longFormatName,
1640	extensionlist,strictExtension)
1641	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1642	self.Constraints = None
1643
1644	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1645	title='Select a phase', size=None,header='Phase Selector'):
1646	''' Provide a wx dialog to select a phase if the file contains more
1647	than one phase
1648	'''
1649	return self.BlockSelector(ChoiceList,ParentFrame,title,
1650	size,header)
1651
1652	class ImportStructFactor(ImportBaseclass):
1653	'''Defines a base class for the reading of files with tables
1654	of structure factors.
1655
1656	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1657	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1658	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1659	:meth:`Reader`.
1660
1661	See :ref:`Writing a Import Routine<Import_Routines>`
1662	for an explanation on how to use import classes in general. The specifics
1663	for reading a structure factor histogram require that
1664	the ``Reader()`` routine in the import
1665	class need to do only a few things: It
1666	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1667	and set :attr:`Parameters` with the instrument parameters
1668	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1669	'''
1670	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1671	strictExtension=False,):
1672	ImportBaseclass.__init__(self,formatName,longFormatName,
1673	extensionlist,strictExtension)
1674
1675	# define contents of Structure Factor entry
1676	self.Parameters = []
1677	'self.Parameters is a list with two dicts for data parameter settings'
1678	self.InitParameters()
1679	self.RefDict = {'RefList':[],'FF':[],'Super':0}
1680	self.Banks = [] #for multi bank data (usually TOF)
1681	'''self.RefDict is a dict containing the reflection information, as read from the file.
1682	Item 'RefList' contains the reflection information. See the
1683	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1684	for the contents of each row. Dict element 'FF'
1685	contains the form factor values for each element type; if this entry
1686	is left as initialized (an empty list) it will be initialized as needed later.
1687	'''
1688	def ReInitialize(self):
1689	'Reinitialize the Reader to initial settings'
1690	ImportBaseclass.ReInitialize(self)
1691	self.InitParameters()
1692	self.Banks = [] #for multi bank data (usually TOF)
1693	self.RefDict = {'RefList':[],'FF':[],'Super':0}
1694
1695	def InitParameters(self):
1696	'initialize the instrument parameters structure'
1697	Lambda = 0.70926
1698	HistType = 'SXC'
1699	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1700	'Lam':[Lambda,Lambda]
1701	}, {}]
1702	'Parameters is a list with two dicts for data parameter settings'
1703
1704	def UpdateParameters(self,Type=None,Wave=None):
1705	'Revise the instrument parameters'
1706	if Type is not None:
1707	self.Parameters[0]['Type'] = [Type,Type]
1708	if Wave is not None:
1709	self.Parameters[0]['Lam'] = [Wave,Wave]
1710
1711	######################################################################
1712	class ImportPowderData(ImportBaseclass):
1713	'''Defines a base class for the reading of files with powder data.
1714
1715	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1716	in :meth:`GSASII.GSASII.OnImportPowder`.
1717	See :ref:`Writing a Import Routine<Import_Routines>`
1718	for an explanation on how to use this class.
1719	'''
1720	def __init__(self,
1721	formatName,
1722	longFormatName=None,
1723	extensionlist=[],
1724	strictExtension=False,
1725	):
1726	ImportBaseclass.__init__(self,formatName,
1727	longFormatName,
1728	extensionlist,
1729	strictExtension)
1730	self.clockWd = None # used in TOF
1731	self.ReInitialize()
1732
1733	def ReInitialize(self):
1734	'Reinitialize the Reader to initial settings'
1735	ImportBaseclass.ReInitialize(self)
1736	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1737	self.powderdata = [] # Powder dataset
1738	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1739	np.array(x), # x-axis values
1740	np.array(y), # powder pattern intensities
1741	np.array(w), # 1/sig(intensity)^2 values (weights)
1742	np.array(yc), # calc. intensities (zero)
1743	np.array(yb), # calc. background (zero)
1744	np.array(yd), # obs-calc profiles
1745	'''
1746	self.comments = []
1747	self.idstring = ''
1748	self.Sample = G2pdG.SetDefaultSample()
1749	self.GSAS = None # used in TOF
1750	self.repeat_instparm = True # Should a parm file be
1751	# used for multiple histograms?
1752	self.instparm = None # name hint from file of instparm to use
1753	self.instfile = '' # full path name to instrument parameter file
1754	self.instbank = '' # inst parm bank number
1755	self.instmsg = '' # a label that gets printed to show
1756	# where instrument parameters are from
1757	self.numbanks = 1
1758	self.instdict = {} # place items here that will be transferred to the instrument parameters
1759	self.pwdparms = {} # place parameters that are transferred directly to the tree
1760	# here (typically from an existing GPX file)
1761	######################################################################
1762	class ImportSmallAngleData(ImportBaseclass):
1763	'''Defines a base class for the reading of files with small angle data.
1764	See :ref:`Writing a Import Routine<Import_Routines>`
1765	for an explanation on how to use this class.
1766	'''
1767	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1768	strictExtension=False,):
1769
1770	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1771	strictExtension)
1772	self.ReInitialize()
1773
1774	def ReInitialize(self):
1775	'Reinitialize the Reader to initial settings'
1776	ImportBaseclass.ReInitialize(self)
1777	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1778	self.smallangledata = [] # SASD dataset
1779	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1780	np.array(x), # x-axis values
1781	np.array(y), # powder pattern intensities
1782	np.array(w), # 1/sig(intensity)^2 values (weights)
1783	np.array(yc), # calc. intensities (zero)
1784	np.array(yd), # obs-calc profiles
1785	np.array(yb), # preset bkg
1786	'''
1787	self.comments = []
1788	self.idstring = ''
1789	self.Sample = G2pdG.SetDefaultSample()
1790	self.GSAS = None # used in TOF
1791	self.clockWd = None # used in TOF
1792	self.numbanks = 1
1793	self.instdict = {} # place items here that will be transferred to the instrument parameters
1794	######################################################################
1795	class ExportBaseclass(object):
1796	'''Defines a base class for the exporting of GSAS-II results.
1797
1798	This class is subclassed in the various exports/G2export_*.py files. Those files
1799	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
1800	appropriate menu items for each one and the .Exporter method is called
1801	directly from the menu item.
1802
1803	'''
1804	def __init__(self,
1805	G2frame,
1806	formatName,
1807	extension,
1808	longFormatName=None,
1809	):
1810	self.G2frame = G2frame
1811	self.formatName = formatName # short string naming file type
1812	self.extension = extension
1813	if longFormatName: # longer string naming file type
1814	self.longFormatName = longFormatName
1815	else:
1816	self.longFormatName = formatName
1817	self.OverallParms = {}
1818	self.Phases = {}
1819	self.Histograms = {}
1820	self.powderDict = {}
1821	self.xtalDict = {}
1822	self.parmDict = {}
1823	self.sigDict = {}
1824	# updated in InitExport:
1825	self.currentExportType = None # type of export that has been requested
1826	# updated in ExportSelect (when used):
1827	self.phasenam = None # a list of selected phases
1828	self.histnam = None # a list of selected histograms
1829	self.filename = None # name of file to be written (single export) or template (multiple files)
1830	self.dirname = '' # name of directory where file(s) will be written
1831	self.fullpath = '' # name of file being written -- full path
1832
1833	# items that should be defined in a subclass of this class
1834	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1835	# The following types are defined: 'project', "phase", "powder", "single"
1836	self.multiple = False # set as True if the class can export multiple phases or histograms
1837	# self.multiple is ignored for "project" exports
1838
1839	def InitExport(self,event):
1840	'''Determines the type of menu that called the Exporter and
1841	misc initialization.
1842	'''
1843	self.filename = None # name of file to be written (single export)
1844	self.dirname = '' # name of file to be written (multiple export)
1845	if event:
1846	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1847
1848	def MakePWDRfilename(self,hist):
1849	'''Make a filename root (no extension) from a PWDR histogram name
1850
1851	:param str hist: the histogram name in data tree (starts with "PWDR ")
1852	'''
1853	file0 = ''
1854	file1 = hist[5:]
1855	# replace repeated blanks
1856	while file1 != file0:
1857	file0 = file1
1858	file1 = file0.replace(' ',' ').strip()
1859	file0 = file1.replace('Azm= ','A')
1860	# if angle has unneeded decimal places on aziumuth, remove them
1861	if file0[-3:] == '.00': file0 = file0[:-3]
1862	file0 = file0.replace('.','_')
1863	file0 = file0.replace(' ','_')
1864	return file0
1865
1866	def ExportSelect(self,AskFile='ask'):
1867	'''Selects histograms or phases when needed. Sets a default file name when
1868	requested in self.filename; always sets a default directory in self.dirname.
1869
1870	:param bool AskFile: Determines how this routine processes getting a
1871	location to store the current export(s).
1872
1873	* if AskFile is 'ask' (default option), get the name of the file to be written;
1874	self.filename and self.dirname are always set. In the case where
1875	multiple files must be generated, the export routine should do this
1876	based on self.filename as a template.
1877	* if AskFile is 'dir', get the name of the directory to be used;
1878	self.filename is not used, but self.dirname is always set. The export routine
1879	will always generate the file name.
1880	* if AskFile is 'single', get only the name of the directory to be used when
1881	multiple items will be written (as multiple files) are used
1882	or a complete file name is requested when a single file
1883	name is selected. self.dirname is always set and self.filename used
1884	only when a single file is selected.
1885	* if AskFile is 'default', creates a name of the file to be used from
1886	the name of the project (.gpx) file. If the project has not been saved,
1887	then the name of file is requested.
1888	self.filename and self.dirname are always set. In the case where
1889	multiple file names must be generated, the export routine should do this
1890	based on self.filename.
1891	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1892	file. If the project has not been saved, then a directory is requested.
1893	self.filename is not used.
1894
1895	:returns: True in case of an error
1896	'''
1897
1898	numselected = 1
1899	if self.currentExportType == 'phase':
1900	if len(self.Phases) == 0:
1901	self.G2frame.ErrorDialog(
1902	'Empty project',
1903	'Project does not contain any phases.')
1904	return True
1905	elif len(self.Phases) == 1:
1906	self.phasenam = self.Phases.keys()
1907	elif self.multiple:
1908	choices = sorted(self.Phases.keys())
1909	phasenum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1910	if phasenum is None: return True
1911	self.phasenam = [choices[i] for i in phasenum]
1912	if not self.phasenam: return True
1913	numselected = len(self.phasenam)
1914	else:
1915	choices = sorted(self.Phases.keys())
1916	phasenum = G2gd.ItemSelector(choices,self.G2frame)
1917	if phasenum is None: return True
1918	self.phasenam = [choices[phasenum]]
1919	numselected = len(self.phasenam)
1920	elif self.currentExportType == 'single':
1921	if len(self.xtalDict) == 0:
1922	self.G2frame.ErrorDialog(
1923	'Empty project',
1924	'Project does not contain any single crystal data.')
1925	return True
1926	elif len(self.xtalDict) == 1:
1927	self.histnam = self.xtalDict.values()
1928	elif self.multiple:
1929	choices = sorted(self.xtalDict.values())
1930	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1931	if not hnum: return True
1932	self.histnam = [choices[i] for i in hnum]
1933	numselected = len(self.histnam)
1934	else:
1935	choices = sorted(self.xtalDict.values())
1936	hnum = G2gd.ItemSelector(choices,self.G2frame)
1937	if hnum is None: return True
1938	self.histnam = [choices[hnum]]
1939	numselected = len(self.histnam)
1940	elif self.currentExportType == 'powder':
1941	if len(self.powderDict) == 0:
1942	self.G2frame.ErrorDialog(
1943	'Empty project',
1944	'Project does not contain any powder data.')
1945	return True
1946	elif len(self.powderDict) == 1:
1947	self.histnam = self.powderDict.values()
1948	elif self.multiple:
1949	choices = sorted(self.powderDict.values())
1950	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1951	if not hnum: return True
1952	self.histnam = [choices[i] for i in hnum]
1953	numselected = len(self.histnam)
1954	else:
1955	choices = sorted(self.powderDict.values())
1956	hnum = G2gd.ItemSelector(choices,self.G2frame)
1957	if hnum is None: return True
1958	self.histnam = [choices[hnum]]
1959	numselected = len(self.histnam)
1960	elif self.currentExportType == 'image':
1961	if len(self.Histograms) == 0:
1962	self.G2frame.ErrorDialog(
1963	'Empty project',
1964	'Project does not contain any images.')
1965	return True
1966	elif len(self.Histograms) == 1:
1967	self.histnam = self.Histograms.keys()
1968	else:
1969	choices = sorted(self.Histograms.keys())
1970	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1971	if self.multiple:
1972	if not hnum: return True
1973	self.histnam = [choices[i] for i in hnum]
1974	else:
1975	if hnum is None: return True
1976	self.histnam = [choices[hnum]]
1977	numselected = len(self.histnam)
1978	if self.currentExportType == 'map':
1979	# search for phases with maps
1980	mapPhases = []
1981	choices = []
1982	for phasenam in sorted(self.Phases):
1983	phasedict = self.Phases[phasenam] # pointer to current phase info
1984	if len(phasedict['General']['Map'].get('rho',[])):
1985	mapPhases.append(phasenam)
1986	if phasedict['General']['Map'].get('Flip'):
1987	choices.append('Charge flip map: '+str(phasenam))
1988	elif phasedict['General']['Map'].get('MapType'):
1989	choices.append(
1990	str(phasedict['General']['Map'].get('MapType'))
1991	+ ' map: ' + str(phasenam))
1992	else:
1993	choices.append('unknown map: '+str(phasenam))
1994	# select a map if needed
1995	if len(mapPhases) == 0:
1996	self.G2frame.ErrorDialog(
1997	'Empty project',
1998	'Project does not contain any maps.')
1999	return True
2000	elif len(mapPhases) == 1:
2001	self.phasenam = mapPhases
2002	else:
2003	phasenum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
2004	if self.multiple:
2005	if not phasenum: return True
2006	self.phasenam = [mapPhases[i] for i in phasenum]
2007	else:
2008	if phasenum is None: return True
2009	self.phasenam = [mapPhases[phasenum]]
2010	numselected = len(self.phasenam)
2011
2012	# items selected, now set self.dirname and usually self.filename
2013	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
2014	AskFile == 'default' and not self.G2frame.GSASprojectfile
2015	):
2016	filename = self.askSaveFile()
2017	if not filename: return True
2018	self.dirname,self.filename = os.path.split(filename)
2019	elif AskFile == 'dir' or AskFile == 'single' or (
2020	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
2021	):
2022	self.dirname = self.askSaveDirectory()
2023	if not self.dirname: return True
2024	elif AskFile == 'default-dir' or AskFile == 'default':
2025	self.dirname,self.filename = os.path.split(
2026	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
2027	)
2028	else:
2029	raise Exception('This should not happen!')
2030
2031	def loadParmDict(self):
2032	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
2033	refined values to those from the last cycle and set the uncertainties for the
2034	refined parameters in another dict (self.sigDict).
2035
2036	Expands the parm & sig dicts to include values derived from constraints.
2037	'''
2038	self.parmDict = {}
2039	self.sigDict = {}
2040	rigidbodyDict = {}
2041	covDict = {}
2042	consDict = {}
2043	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2044	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2045	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2046	while item:
2047	name = self.G2frame.PatternTree.GetItemText(item)
2048	if name == 'Rigid bodies':
2049	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
2050	elif name == 'Covariance':
2051	covDict = self.G2frame.PatternTree.GetItemPyData(item)
2052	elif name == 'Constraints':
2053	consDict = self.G2frame.PatternTree.GetItemPyData(item)
2054	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2055	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
2056	self.parmDict.update(rbDict)
2057	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
2058	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables = G2stIO.GetPhaseData(
2059	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
2060	self.parmDict.update(phaseDict)
2061	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
2062	Phases,Histograms,Print=False,resetRefList=False)
2063	self.parmDict.update(hapDict)
2064	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
2065	self.parmDict.update(histDict)
2066	self.parmDict.update(zip(
2067	covDict.get('varyList',[]),
2068	covDict.get('variables',[])))
2069	self.sigDict = dict(zip(
2070	covDict.get('varyList',[]),
2071	covDict.get('sig',[])))
2072	# expand to include constraints: first compile a list of constraints
2073	constList = []
2074	for item in consDict:
2075	if item.startswith('_'): continue
2076	constList += consDict[item]
2077	# now process the constraints
2078	G2mv.InitVars()
2079	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
2080	varyList = covDict.get('varyListStart')
2081	if varyList is None and len(constDict) == 0:
2082	# no constraints can use varyList
2083	varyList = covDict.get('varyList')
2084	elif varyList is None:
2085	# old GPX file from before pre-constraint varyList is saved
2086	print ' * Old refinement: Please use Calculate/Refine to redo *'
2087	raise Exception(' * Export aborted *')
2088	else:
2089	varyList = list(varyList)
2090	try:
2091	groups,parmlist = G2mv.GroupConstraints(constDict)
2092	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
2093	except:
2094	# this really should not happen
2095	print ' * ERROR - constraints are internally inconsistent *'
2096	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
2097	print 'Errors',errmsg
2098	if warnmsg: print 'Warnings',warnmsg
2099	raise Exception(' * CIF creation aborted *')
2100	# add the constrained values to the parameter dictionary
2101	G2mv.Dict2Map(self.parmDict,varyList)
2102	# and add their uncertainties into the esd dictionary (sigDict)
2103	if covDict.get('covMatrix') is not None:
2104	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
2105
2106	def loadTree(self):
2107	'''Load the contents of the data tree into a set of dicts
2108	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2109	& self.xtalDict)
2110
2111	* The childrenless data tree items are overall parameters/controls for the
2112	entire project and are placed in self.OverallParms
2113	* Phase items are placed in self.Phases
2114	* Data items are placed in self.Histogram. The key for these data items
2115	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2116	'''
2117	self.OverallParms = {}
2118	self.powderDict = {}
2119	self.xtalDict = {}
2120	self.Phases = {}
2121	self.Histograms = {}
2122	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2123	histType = None
2124	if self.currentExportType == 'phase':
2125	# if exporting phases load them here
2126	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2127	if not sub:
2128	print 'no phases found'
2129	return True
2130	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2131	while item:
2132	phaseName = self.G2frame.PatternTree.GetItemText(item)
2133	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2134	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2135	return
2136	elif self.currentExportType == 'single':
2137	histType = 'HKLF'
2138	elif self.currentExportType == 'powder':
2139	histType = 'PWDR'
2140	elif self.currentExportType == 'image':
2141	histType = 'IMG'
2142
2143	if histType: # Loading just one kind of tree entry
2144	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2145	while item:
2146	name = self.G2frame.PatternTree.GetItemText(item)
2147	if name.startswith(histType):
2148	if self.Histograms.get(name): # there is already an item with this name
2149	print('Histogram name '+str(name)+' is repeated. Renaming')
2150	if name[-1] == '9':
2151	name = name[:-1] + '10'
2152	elif name[-1] in '012345678':
2153	name = name[:-1] + str(int(name[-1])+1)
2154	else:
2155	name += '-1'
2156	self.Histograms[name] = {}
2157	# the main info goes into Data, but the 0th
2158	# element contains refinement results, carry
2159	# that over too now.
2160	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2161	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2162	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2163	while item2:
2164	child = self.G2frame.PatternTree.GetItemText(item2)
2165	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2166	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2167	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2168	# index powder and single crystal histograms by number
2169	for hist in self.Histograms:
2170	if hist.startswith("PWDR"):
2171	d = self.powderDict
2172	elif hist.startswith("HKLF"):
2173	d = self.xtalDict
2174	else:
2175	return
2176	i = self.Histograms[hist].get('hId')
2177	if i is None and not d.keys():
2178	i = 0
2179	elif i is None or i in d.keys():
2180	i = max(d.keys())+1
2181	d[i] = hist
2182	return
2183	# else standard load: using all interlinked phases and histograms
2184	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2185	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2186	while item:
2187	name = self.G2frame.PatternTree.GetItemText(item)
2188	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2189	if not item2:
2190	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2191	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2192	# index powder and single crystal histograms
2193	for hist in self.Histograms:
2194	i = self.Histograms[hist]['hId']
2195	if hist.startswith("PWDR"):
2196	self.powderDict[i] = hist
2197	elif hist.startswith("HKLF"):
2198	self.xtalDict[i] = hist
2199
2200	def dumpTree(self,mode='type'):
2201	'''Print out information on the data tree dicts loaded in loadTree
2202	'''
2203	print '\nOverall'
2204	if mode == 'type':
2205	def Show(arg): return type(arg)
2206	else:
2207	def Show(arg): return arg
2208	for key in self.OverallParms:
2209	print ' ',key,Show(self.OverallParms[key])
2210	print 'Phases'
2211	for key1 in self.Phases:
2212	print ' ',key1,Show(self.Phases[key1])
2213	print 'Histogram'
2214	for key1 in self.Histograms:
2215	print ' ',key1,Show(self.Histograms[key1])
2216	for key2 in self.Histograms[key1]:
2217	print ' ',key2,Show(self.Histograms[key1][key2])
2218
2219	def defaultSaveFile(self):
2220	return os.path.abspath(
2221	os.path.splitext(self.G2frame.GSASprojectfile
2222	)[0]+self.extension)
2223
2224	def askSaveFile(self):
2225	'''Ask the user to supply a file name
2226
2227	:returns: a file name (str) or None if Cancel is pressed
2228	'''
2229	defnam = os.path.splitext(
2230	os.path.split(self.G2frame.GSASprojectfile)[1]
2231	)[0]+self.extension
2232	dlg = wx.FileDialog(
2233	self.G2frame, 'Input name for file to write', '.', defnam,
2234	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2235	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2236	dlg.CenterOnParent()
2237	try:
2238	if dlg.ShowModal() == wx.ID_OK:
2239	filename = dlg.GetPath()
2240	# make sure extension is correct
2241	filename = os.path.splitext(filename)[0]+self.extension
2242	else:
2243	filename = None
2244	finally:
2245	dlg.Destroy()
2246	return filename
2247
2248	def askSaveDirectory(self):
2249	'''Ask the user to supply a directory name. Path name is used as the
2250	starting point for the next export path search.
2251
2252	:returns: a directory name (str) or None if Cancel is pressed
2253	'''
2254	if self.G2frame.exportDir:
2255	startdir = self.G2frame.exportDir
2256	elif self.G2frame.GSASprojectfile:
2257	startdir = os.path.split(self.G2frame.GSASprojectfile)[0]
2258	elif self.G2frame.dirname:
2259	startdir = self.G2frame.dirname
2260	else:
2261	startdir = ''
2262	dlg = wx.DirDialog(
2263	self.G2frame, 'Input directory where file(s) will be written', startdir,
2264	wx.DD_DEFAULT_STYLE)
2265	dlg.CenterOnParent()
2266	try:
2267	if dlg.ShowModal() == wx.ID_OK:
2268	filename = dlg.GetPath()
2269	self.G2frame.exportDir = filename
2270	else:
2271	filename = None
2272	finally:
2273	dlg.Destroy()
2274	return filename
2275
2276	# Tools for file writing.
2277	def OpenFile(self,fil=None,mode='w'):
2278	'''Open the output file
2279
2280	:param str fil: The name of the file to open. If None (default)
2281	the name defaults to self.dirname + self.filename.
2282	If an extension is supplied, it is not overridded,
2283	but if not, the default extension is used.
2284	:returns: the file object opened by the routine which is also
2285	saved as self.fp
2286	'''
2287	if not fil:
2288	if not os.path.splitext(self.filename)[1]:
2289	self.filename += self.extension
2290	fil = os.path.join(self.dirname,self.filename)
2291	self.fullpath = fil
2292	self.fp = open(fil,mode)
2293	return self.fp
2294
2295	def Write(self,line):
2296	'''write a line of output, attaching a line-end character
2297
2298	:param str line: the text to be written.
2299	'''
2300	self.fp.write(line+'\n')
2301	def CloseFile(self,fp=None):
2302	'''Close a file opened in OpenFile
2303
2304	:param file fp: the file object to be closed. If None (default)
2305	file object self.fp is closed.
2306	'''
2307	if fp is None:
2308	fp = self.fp
2309	self.fp = None
2310	fp.close()
2311	# Tools to pull information out of the data arrays
2312	def GetCell(self,phasenam):
2313	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2314
2315	:param str phasenam: the name for the selected phase
2316	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2317	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2318	cell values and `cellSig` has their uncertainties.
2319	"""
2320	phasedict = self.Phases[phasenam] # pointer to current phase info
2321	try:
2322	pfx = str(phasedict['pId'])+'::'
2323	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2324	cellSig = G2stIO.getCellEsd(pfx,
2325	phasedict['General']['SGData'],A,
2326	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2327	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2328	return cellList,cellSig
2329	except KeyError:
2330	cell = phasedict['General']['Cell'][1:]
2331	return cell,7*[0]
2332
2333	def GetAtoms(self,phasenam):
2334	"""Gets the atoms associated with a phase. Can be used with standard
2335	or macromolecular phases
2336
2337	:param str phasenam: the name for the selected phase
2338	:returns: a list of items for eac atom where each item is a list containing:
2339	label, typ, mult, xyz, and td, where
2340
2341	* label and typ are the atom label and the scattering factor type (str)
2342	* mult is the site multiplicity (int)
2343	* xyz is contains a list with four pairs of numbers:
2344	x, y, z and fractional occupancy and
2345	their standard uncertainty (or a negative value)
2346	* td is contains a list with either one or six pairs of numbers:
2347	if one number it is U\ :sub:`iso` and with six numbers it is
2348	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2349	paired with their standard uncertainty (or a negative value)
2350	"""
2351	phasedict = self.Phases[phasenam] # pointer to current phase info
2352	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2353	cfrac = cx+3
2354	fpfx = str(phasedict['pId'])+'::Afrac:'
2355	atomslist = []
2356	for i,at in enumerate(phasedict['Atoms']):
2357	if phasedict['General']['Type'] == 'macromolecular':
2358	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2359	else:
2360	label = at[ct-1]
2361	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2362	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2363	mult = at[cs+1]
2364	typ = at[ct]
2365	xyz = []
2366	for j,v in enumerate(('x','y','z')):
2367	val = at[cx+j]
2368	pfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2369	sig = self.sigDict.get(pfx,-0.000009)
2370	xyz.append((val,sig))
2371	xyz.append((fval,fsig))
2372	td = []
2373	if at[cia] == 'I':
2374	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2375	val = self.parmDict.get(pfx,at[cia+1])
2376	sig = self.sigDict.get(pfx,-0.0009)
2377	td.append((val,sig))
2378	else:
2379	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2380	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2381	val = self.parmDict.get(pfx,at[cia+2+i])
2382	sig = self.sigDict.get(pfx,-0.0009)
2383	td.append((val,sig))
2384	atomslist.append((label,typ,mult,xyz,td))
2385	return atomslist
2386	######################################################################
2387
2388	def ReadCIF(URLorFile):
2389	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2390	(from James Hester).
2391	The open routine gets confused with DOS names that begin with a letter and colon
2392	"C:\dir\" so this routine will try to open the passed name as a file and if that
2393	fails, try it as a URL
2394
2395	:param str URLorFile: string containing a URL or a file name. Code will try first
2396	to open it as a file and then as a URL.
2397
2398	:returns: a PyCifRW CIF object.
2399	'''
2400	import CifFile as cif # PyCifRW from James Hester
2401
2402	# alternate approach:
2403	#import urllib
2404	#ciffile = 'file:'+urllib.pathname2url(filename)
2405
2406	try:
2407	fp = open(URLorFile,'r')
2408	cf = cif.ReadCif(fp)
2409	fp.close()
2410	return cf
2411	except IOError:
2412	return cif.ReadCif(URLorFile)
2413
2414	if __name__ == '__main__':
2415	app = wx.PySimpleApp()
2416	frm = wx.Frame(None) # create a frame
2417	frm.Show(True)
2418	filename = '/tmp/notzip.zip'
2419	filename = '/tmp/all.zip'
2420	#filename = '/tmp/11bmb_7652.zip'
2421
2422	#selection=None, confirmoverwrite=True, parent=None
2423	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2424	print ExtractFileFromZip(filename,multipleselect=True)
2425	#confirmread=False, confirmoverwrite=False)
2426
2427	# choicelist=[ ('a','b','c'),
2428	# ('test1','test2'),('no choice',)]
2429	# titles = [ 'a, b or c', 'tests', 'No option here']
2430	# dlg = MultipleChoicesDialog(
2431	# choicelist,titles,
2432	# parent=frm)
2433	# if dlg.ShowModal() == wx.ID_OK:
2434	# print 'Got OK'

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