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source: trunk/GSASIIIO.py @ 1962

Last change on this file since 1962 was 1962, checked in by vondreele, 8 years ago
made PackageVersions? a list so it comes out in same order as the other list slight reformatting so appearance is the same as well
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2015-08-26 15:00:44 +0000 (Wed, 26 Aug 2015) $
4	# $Author: vondreele $
5	# $Revision: 1962 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 1962 2015-08-26 15:00:44Z 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: 1962 $")
33	import GSASIIgrid as G2gd
34	import GSASIIspc as G2spc
35	import GSASIIlattice as G2lat
36	import GSASIIpwdGUI as G2pdG
37	import GSASIIimage as G2img
38	import GSASIIElem as G2el
39	import GSASIIstrIO as G2stIO
40	import GSASIImapvars as G2mv
41	import GSASIIctrls as G2G
42	import os
43	import os.path as ospath
44
45	DEBUG = False #=True for various prints
46	TRANSP = False #=true to transpose images for testing
47	npsind = lambda x: np.sin(x*np.pi/180.)
48
49	def sfloat(S):
50	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
51	if S.strip():
52	try:
53	return float(S)
54	except ValueError:
55	pass
56	return 0.0
57
58	def sint(S):
59	'Convert a string to int. An empty field is treated as zero'
60	if S.strip():
61	return int(S)
62	else:
63	return 0
64
65	def trim(val):
66	'''Simplify a string containing leading and trailing spaces
67	as well as newlines, tabs, repeated spaces etc. into a shorter and
68	more simple string, by replacing all ranges of whitespace
69	characters with a single space.
70
71	:param str val: the string to be simplified
72
73	:returns: the (usually) shortened version of the string
74	'''
75	return re.sub('\s+', ' ', val).strip()
76
77	def makeInstDict(names,data,codes):
78	inst = dict(zip(names,zip(data,data,codes)))
79	for item in inst:
80	inst[item] = list(inst[item])
81	return inst
82
83	def FileDlgFixExt(dlg,file):
84	'this is needed to fix a problem in linux wx.FileDialog'
85	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
86	if ext not in file:
87	file += ext
88	return file
89
90	def GetPowderPeaks(fileName):
91	'Read powder peaks from a file'
92	sind = lambda x: math.sin(x*math.pi/180.)
93	asind = lambda x: 180.*math.asin(x)/math.pi
94	Cuka = 1.54052
95	File = open(fileName,'Ur')
96	Comments = []
97	peaks = []
98	S = File.readline()
99	while S:
100	if S[:1] == '#':
101	Comments.append(S[:-1])
102	else:
103	item = S.split()
104	if len(item) == 1:
105	peaks.append([float(item[0]),1.0])
106	elif len(item) > 1:
107	peaks.append([float(item[0]),float(item[0])])
108	S = File.readline()
109	File.close()
110	if Comments:
111	print 'Comments on file:'
112	for Comment in Comments: print Comment
113	Peaks = []
114	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
115	for peak in peaks:
116	dsp = peak[0]
117	sth = Cuka/(2.0*dsp)
118	if sth < 1.0:
119	tth = 2.0*asind(sth)
120	else:
121	break
122	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
123	else: #2-thetas - assume Cuka (for now)
124	for peak in peaks:
125	tth = peak[0]
126	dsp = Cuka/(2.0*sind(tth/2.0))
127	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
128	return Comments,Peaks
129
130	def CheckImageFile(G2frame,imagefile):
131	'''Get an new image file name if the specified one does not
132	exist
133
134	:param wx.Frame G2frame: main GSAS-II Frame and data object
135
136	:param str imagefile: name of image file
137
138	:returns: imagefile, if it exists, or the name of a file
139	that does exist or False if the user presses Cancel
140
141	'''
142	if not os.path.exists(imagefile):
143	print 'Image file '+imagefile+' not found'
144	fil = imagefile.replace('\\','/') # windows?!
145	# see if we can find a file with same name or in a similarly named sub-dir
146	pth,fil = os.path.split(fil)
147	prevpth = None
148	while pth and pth != prevpth:
149	prevpth = pth
150	if os.path.exists(os.path.join(G2frame.dirname,fil)):
151	print 'found image file '+os.path.join(G2frame.dirname,fil)
152	return os.path.join(G2frame.dirname,fil)
153	pth,enddir = os.path.split(pth)
154	fil = os.path.join(enddir,fil)
155	# not found as a subdirectory, drop common parts of path for last saved & image file names
156	# if image was .../A/B/C/imgs/ima.ge
157	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
158	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
159	Controls = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
160	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
161	imgPath = imagefile.replace('\\','/').split('/')
162	for p1,p2 in zip(gpxPath,imgPath):
163	if p1 == p2:
164	gpxPath.pop(0),imgPath.pop(0)
165	else:
166	break
167	fil = os.path.join(*imgPath) # file with non-common prefix elements
168	prevpth = None
169	pth = os.path.abspath(G2frame.dirname)
170	while pth and pth != prevpth:
171	prevpth = pth
172	if os.path.exists(os.path.join(pth,fil)):
173	print 'found image file '+os.path.join(pth,fil)
174	return os.path.join(pth,fil)
175	pth,enddir = os.path.split(pth)
176	#GSASIIpath.IPyBreak()
177
178	if not os.path.exists(imagefile):
179	dlg = wx.FileDialog(G2frame, 'Previous image file not found; open here', '.', '',\
180	'Any image file (.edf;.tif;.tiff;.mar;.ge;.avg;.sum;.img;.cor;.stl)\
181	\|.edf;.tif;.tiff;.mar;.ge;.avg;.sum;.img;.cor;.stl\|\
182	European detector file (.edf)\|.edf\|\
183	Any detector tif (.tif;.tiff)\|.tif;.tiff\|\
184	MAR file (.mar)\|.mar\|\
185	GE Image (.ge;.avg;.sum;.cor)\|.ge;.avg;.sum;.cor\|\
186	ADSC Image (.img)\|.img\|\
187	Rigaku-Axis4 (.stl)\|.stl\|\
188	All files (.)\|.',wx.OPEN\|wx.CHANGE_DIR)
189	try:
190	dlg.SetFilename(''+ospath.split(imagefile)[1])
191	if dlg.ShowModal() == wx.ID_OK:
192	imagefile = dlg.GetPath()
193	else:
194	imagefile = False
195	finally:
196	dlg.Destroy()
197	return imagefile
198
199	def EditImageParms(parent,Data,Comments,Image,filename):
200	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
201	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
202	def onClose(event):
203	dlg.EndModal(wx.ID_OK)
204	mainsizer = wx.BoxSizer(wx.VERTICAL)
205	h,w = Image.shape[:2]
206	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,
207	'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
208	0,wx.ALIGN_LEFT\|wx.ALL, 2)
209
210	vsizer = wx.BoxSizer(wx.HORIZONTAL)
211	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
212	0,wx.ALIGN_LEFT\|wx.ALL, 2)
213	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
214	vsizer.Add(wdgt)
215	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
216
217	vsizer = wx.BoxSizer(wx.HORIZONTAL)
218	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
219	0,wx.ALIGN_LEFT\|wx.ALL, 2)
220	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
221	size=(50,-1))
222	vsizer.Add(wdgt)
223	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),
224	wx.ALIGN_LEFT\|wx.ALL, 2)
225	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,
226	size=(50,-1))
227	vsizer.Add(wdgt)
228	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
229
230	vsizer = wx.BoxSizer(wx.HORIZONTAL)
231	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
232	0,wx.ALIGN_LEFT\|wx.ALL, 2)
233	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
234	vsizer.Add(wdgt)
235	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
236
237	vsizer = wx.BoxSizer(wx.HORIZONTAL)
238	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
239	0,wx.ALIGN_LEFT\|wx.ALL, 2)
240	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,
241	size=(75,-1))
242	vsizer.Add(wdgt)
243	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),
244	wx.ALIGN_LEFT\|wx.ALL, 2)
245	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,
246	size=(75,-1))
247	vsizer.Add(wdgt)
248	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
249
250	vsizer = wx.BoxSizer(wx.HORIZONTAL)
251	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
252	0,wx.ALIGN_LEFT\|wx.ALL, 2)
253	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
254	vsizer.Add(wdgt)
255	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
256
257	btnsizer = wx.StdDialogButtonSizer()
258	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
259	OKbtn.SetDefault()
260	OKbtn.Bind(wx.EVT_BUTTON,onClose)
261	btnsizer.AddButton(OKbtn) # not sure why this is needed
262	btnsizer.Realize()
263	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
264	dlg.SetSizer(mainsizer)
265	dlg.CenterOnParent()
266	dlg.ShowModal()
267
268	def GetImageData(G2frame,imagefile,imageOnly=False):
269	'''Read an image with the file reader keyed by the
270	file extension
271
272	:param wx.Frame G2frame: main GSAS-II Frame and data object.
273
274	:param str imagefile: name of image file
275
276	:param bool imageOnly: If True return only the image,
277	otherwise (default) return more (see below)
278
279	:returns: an image as a numpy array or a list of four items:
280	Comments, Data, Npix and the Image, as selected by imageOnly
281
282	'''
283	ext = ospath.splitext(imagefile)[1]
284	Comments = []
285	Image = None
286	if ext == '.tif' or ext == '.tiff':
287	Comments,Data,Npix,Image = GetTifData(imagefile)
288	if Npix == 0:
289	print("GetTifData failed to read "+str(imagefile)+" Trying PIL")
290	import scipy.misc
291	Image = scipy.misc.imread(imagefile,flatten=True)
292	Npix = Image.size
293	Comments = ['no metadata']
294	Data = {'wavelength': 0.1, 'pixelSize': [200, 200], 'distance': 100.0}
295	Data['size'] = list(Image.shape)
296	Data['center'] = [int(i/2) for i in Image.shape]
297	if not imageOnly:
298	EditImageParms(G2frame,Data,Comments,Image,imagefile)
299	elif ext == '.edf':
300	Comments,Data,Npix,Image = GetEdfData(imagefile)
301	elif ext == '.img':
302	Comments,Data,Npix,Image = GetImgData(imagefile)
303	Image[0][0] = 0
304	elif ext in ['.mar3450','.mar2300','.mar2560']:
305	Comments,Data,Npix,Image = GetMAR345Data(imagefile)
306	elif ext in ['.sum','.avg','.cor'] or 'ge' in ext:
307	Comments,Data,Npix,Image = GetGEsumData(imagefile)
308	elif ext == '.G2img':
309	Comments,Data,Npix,Image = GetG2Image(imagefile)
310	elif ext == '.png':
311	Comments,Data,Npix,Image = GetPNGData(imagefile)
312	if not imageOnly:
313	EditImageParms(G2frame,Data,Comments,Image,imagefile)
314	elif ext == '.stl':
315	Comments,Data,Npix,Image = GetRigaku(imagefile)
316	# if not imageOnly:
317	# EditImageParms(G2frame,Data,Comments,Image,imagefile)
318	else:
319	print 'Extension for file '+imagefile+' not recognized'
320	if Image is None:
321	raise Exception('No image read')
322	if imageOnly:
323	if TRANSP:
324	return Image.T
325	else:
326	return Image
327	else:
328	if TRANSP:
329	return Comments,Data,Npix,Image.T
330	else:
331	return Comments,Data,Npix,Image
332
333	def PutG2Image(filename,Comments,Data,Npix,image):
334	'Write an image as a python pickle - might be better as an .edf file?'
335	File = open(filename,'wb')
336	cPickle.dump([Comments,Data,Npix,image],File,1)
337	File.close()
338	return
339
340	def GetG2Image(filename):
341	'Read an image as a python pickle'
342	File = open(filename,'rb')
343	Comments,Data,Npix,image = cPickle.load(File)
344	File.close()
345	return Comments,Data,Npix,image
346
347	def GetEdfData(filename,imageOnly=False):
348	'Read European detector data edf file'
349	import struct as st
350	import array as ar
351	if not imageOnly:
352	print 'Read European detector data edf file: ',filename
353	File = open(filename,'rb')
354	fileSize = os.stat(filename).st_size
355	head = File.read(3072)
356	lines = head.split('\n')
357	sizexy = [0,0]
358	pixSize = [154,154] #Pixium4700?
359	cent = [0,0]
360	wave = 1.54187 #default <CuKa>
361	dist = 1000.
362	head = ['European detector data',]
363	for line in lines:
364	line = line.replace(';',' ').strip()
365	fields = line.split()
366	if 'Dim_1' in line:
367	sizexy[0] = int(fields[2])
368	elif 'Dim_2' in line:
369	sizexy[1] = int(fields[2])
370	elif 'DataType' in line:
371	dType = fields[2]
372	elif 'wavelength' in line:
373	wave = float(fields[2])
374	elif 'Size' in line:
375	imSize = int(fields[2])
376	# elif 'DataType' in lines:
377	# dType = fields[2]
378	elif 'pixel_size_x' in line:
379	pixSize[0] = float(fields[2])
380	elif 'pixel_size_y' in line:
381	pixSize[1] = float(fields[2])
382	elif 'beam_center_x' in line:
383	cent[0] = float(fields[2])
384	elif 'beam_center_y' in line:
385	cent[1] = float(fields[2])
386	elif 'refined_distance' in line:
387	dist = float(fields[2])
388	if line:
389	head.append(line)
390	else: #blank line at end of header
391	break
392	File.seek(fileSize-imSize)
393	if dType == 'UnsignedShort':
394	image = np.array(ar.array('H',File.read(imSize)),dtype=np.int32)
395	elif dType == 'UnsignedInt':
396	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
397	elif dType == 'UnsignedLong':
398	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
399	elif dType == 'SignedInteger':
400	image = np.array(ar.array('l',File.read(imSize)),dtype=np.int32)
401	image = np.reshape(image,(sizexy[1],sizexy[0]))
402	data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'size':sizexy}
403	Npix = sizexy[0]*sizexy[1]
404	File.close()
405	if imageOnly:
406	return image
407	else:
408	return head,data,Npix,image
409
410	def GetRigaku(filename,imageOnly=False):
411	'Read Rigaku R-Axis IV image file'
412	import struct as st
413	import array as ar
414	if not imageOnly:
415	print 'Read Rigaku R-Axis IV file: ',filename
416	File = open(filename,'rb')
417	fileSize = os.stat(filename).st_size
418	Npix = (fileSize-6000)/2
419	Head = File.read(6000)
420	head = ['Rigaku R-Axis IV detector data',]
421	image = np.array(ar.array('H',File.read(fileSize-6000)),dtype=np.int32)
422	print fileSize,image.shape
423	print head
424	if Npix == 9000000:
425	sizexy = [3000,3000]
426	pixSize = [100.,100.]
427	elif Npix == 2250000:
428	sizexy = [1500,1500]
429	pixSize = [200.,200.]
430	else:
431	sizexy = [6000,6000]
432	pixSize = [50.,50.]
433	image = np.reshape(image,(sizexy[1],sizexy[0]))
434	data = {'pixelSize':pixSize,'wavelength':1.5428,'distance':250.0,'center':[150.,150.],'size':sizexy}
435	File.close()
436	if imageOnly:
437	return image
438	else:
439	return head,data,Npix,image
440
441
442	def GetGEsumData(filename,imageOnly=False):
443	'Read SUM file as produced at 1-ID from G.E. images'
444	import struct as st
445	import array as ar
446	if not imageOnly:
447	print 'Read GE sum file: ',filename
448	File = open(filename,'rb')
449	if '.sum' in filename or '.cor' in filename:
450	head = ['GE detector sum or cor data from APS 1-ID',]
451	sizexy = [2048,2048]
452	elif '.avg' in filename or '.ge' in filename:
453	head = ['GE detector avg or ge* data from APS 1-ID',]
454	sizexy = [2048,2048]
455	else:
456	head = ['GE detector raw data from APS 1-ID',]
457	File.seek(18)
458	size,nframes = st.unpack('<ih',File.read(6))
459	sizexy = [2048,2048]
460	pos = 8192
461	File.seek(pos)
462	Npix = sizexy[0]*sizexy[1]
463	if '.sum' in filename or '.cor' in filename:
464	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.int32)
465	elif '.avg' in filename or '.ge' in filename:
466	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
467	else:
468	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
469	while nframes > 1:
470	image += np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
471	nframes -= 1
472	image = np.reshape(image,(sizexy[1],sizexy[0]))
473	data = {'pixelSize':[200,200],'wavelength':0.15,'distance':250.0,'center':[204.8,204.8],'size':sizexy}
474	File.close()
475	if imageOnly:
476	return image
477	else:
478	return head,data,Npix,image
479
480	def GetImgData(filename,imageOnly=False):
481	'Read an ADSC image file'
482	import struct as st
483	import array as ar
484	if not imageOnly:
485	print 'Read ADSC img file: ',filename
486	File = open(filename,'rb')
487	head = File.read(511)
488	lines = head.split('\n')
489	head = []
490	center = [0,0]
491	for line in lines[1:-2]:
492	line = line.strip()[:-1]
493	if line:
494	if 'SIZE1' in line:
495	size = int(line.split('=')[1])
496	Npix = size*size
497	elif 'WAVELENGTH' in line:
498	wave = float(line.split('=')[1])
499	elif 'BIN' in line:
500	if line.split('=')[1] == '2x2':
501	pixel=(102,102)
502	else:
503	pixel = (51,51)
504	elif 'DISTANCE' in line:
505	distance = float(line.split('=')[1])
506	elif 'CENTER_X' in line:
507	center[0] = float(line.split('=')[1])
508	elif 'CENTER_Y' in line:
509	center[1] = float(line.split('=')[1])
510	head.append(line)
511	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center,'size':[size,size]}
512	image = []
513	row = 0
514	pos = 512
515	File.seek(pos)
516	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
517	image = np.reshape(image,(sizexy[1],sizexy[0]))
518	# image = np.zeros(shape=(size,size),dtype=np.int32)
519	# while row < size:
520	# File.seek(pos)
521	# line = ar.array('H',File.read(2*size))
522	# image[row] = np.asarray(line)
523	# row += 1
524	# pos += 2*size
525	File.close()
526	if imageOnly:
527	return image
528	else:
529	return lines[1:-2],data,Npix,image
530
531	def GetMAR345Data(filename,imageOnly=False):
532	'Read a MAR-345 image plate image'
533	import array as ar
534	import struct as st
535	try:
536	import pack_f as pf
537	except:
538	msg = wx.MessageDialog(None, message="Unable to load the GSAS MAR image decompression, pack_f",
539	caption="Import Error",
540	style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
541	msg.ShowModal()
542	return None,None,None,None
543
544	if not imageOnly:
545	print 'Read Mar345 file: ',filename
546	File = open(filename,'rb')
547	head = File.read(4095)
548	numbers = st.unpack('<iiiiiiiiii',head[:40])
549	lines = head[128:].split('\n')
550	head = []
551	for line in lines:
552	line = line.strip()
553	if 'PIXEL' in line:
554	values = line.split()
555	pixel = (int(values[2]),int(values[4])) #in microns
556	elif 'WAVELENGTH' in line:
557	wave = float(line.split()[1])
558	elif 'DISTANCE' in line:
559	distance = float(line.split()[1]) #in mm
560	elif 'CENTER' in line:
561	values = line.split()
562	center = [float(values[2])/10.,float(values[4])/10.] #make in mm from pixels
563	if line:
564	head.append(line)
565	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center}
566	for line in head:
567	if 'FORMAT' in line[0:6]:
568	items = line.split()
569	sizex = int(items[1])
570	Npix = int(items[3])
571	sizey = int(Npix/sizex)
572	pos = 4096
573	data['size'] = [sizex,sizey]
574	File.seek(pos)
575	line = File.read(8)
576	while 'CCP4' not in line: #get past overflow list for now
577	line = File.read(8)
578	pos += 8
579	pos += 37
580	File.seek(pos)
581	raw = File.read()
582	File.close()
583	image = np.zeros(shape=(sizex,sizey),dtype=np.int32)
584
585	image = np.flipud(pf.pack_f(len(raw),raw,sizex,sizey,image).T) #transpose to get it right way around & flip
586	if imageOnly:
587	return image
588	else:
589	return head,data,Npix,image
590
591	def GetPNGData(filename,imageOnly=False):
592	'''Read an image in a png format, assumes image is converted from CheMin tif file
593	so default parameters are that machine.
594	'''
595	import scipy.misc
596	Image = scipy.misc.imread(filename,flatten=True)
597	Npix = Image.size
598	Comments = ['no metadata']
599	pixy = list(Image.shape)
600	sizexy = [40,40]
601	Data = {'wavelength': 1.78892, 'pixelSize': sizexy, 'distance': 18.0,'size':pixy}
602	Data['center'] = [pixy[0]sizexy[0]/1000,pixy[1]sizexy[1]/2000]
603	if imageOnly:
604	return Image.T
605	else:
606	return Comments,Data,Npix,Image.T
607
608	def GetTifData(filename,imageOnly=False):
609	'''Read an image in a pseudo-tif format,
610	as produced by a wide variety of software, almost always
611	incorrectly in some way.
612	'''
613	import struct as st
614	try:
615	import Image as Im
616	except ImportError:
617	try:
618	from PIL import Image as Im
619	except ImportError:
620	print "PIL/pillow Image module not present. TIFs cannot be read without this"
621	raise Exception("PIL/pillow Image module not found")
622	import array as ar
623	import ReadMarCCDFrame as rmf
624	File = open(filename,'rb')
625	dataType = 5
626	center = [None,None]
627	wavelength = None
628	distance = None
629	try:
630	Meta = open(filename+'.metadata','Ur')
631	head = Meta.readlines()
632	for line in head:
633	line = line.strip()
634	if 'dataType=' in line:
635	dataType = int(line.split('=')[1])
636	Meta.close()
637	except IOError:
638	print 'no metadata file found - will try to read file anyway'
639	head = ['no metadata file found',]
640
641	tag = File.read(2)
642	byteOrd = '<'
643	if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
644	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
645	elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
646	byteOrd = '>'
647	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
648	else:
649	lines = ['not a detector tiff file',]
650	return lines,0,0,0
651	File.seek(IFD) #get number of directory entries
652	NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
653	IFD = {}
654	nSlice = 1
655	for ied in range(NED):
656	Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
657	nVal = st.unpack(byteOrd+'i',File.read(4))[0]
658	if DEBUG: print 'Try:',Tag,Type,nVal
659	if Type == 1:
660	Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
661	elif Type == 2:
662	Value = st.unpack(byteOrd+'i',File.read(4))
663	elif Type == 3:
664	Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
665	x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
666	elif Type == 4:
667	if Tag in [273,279]:
668	nSlice = nVal
669	nVal = 1
670	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
671	elif Type == 5:
672	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
673	elif Type == 11:
674	Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
675	IFD[Tag] = [Type,nVal,Value]
676	if DEBUG: print Tag,IFD[Tag]
677	sizexy = [IFD[256][2][0],IFD[257][2][0]]
678	[nx,ny] = sizexy
679	Npix = nx*ny
680	if 34710 in IFD:
681	if not imageOnly:
682	print 'Read MAR CCD tiff file: ',filename
683	marFrame = rmf.marFrame(File,byteOrd,IFD)
684	image = np.flipud(np.array(np.asarray(marFrame.image),dtype=np.int32))
685	tifType = marFrame.filetitle
686	pixy = [marFrame.pixelsizeX/1000.0,marFrame.pixelsizeY/1000.0]
687	head = marFrame.outputHead()
688	# extract resonable wavelength from header
689	wavelength = marFrame.sourceWavelength*1e-5
690	wavelength = (marFrame.opticsWavelength > 0) and marFrame.opticsWavelength*1e-5 or wavelength
691	wavelength = (wavelength <= 0) and None or wavelength
692	# extract resonable distance from header
693	distance = (marFrame.startXtalToDetector+marFrame.endXtalToDetector)*5e-4
694	distance = (distance <= 0) and marFrame.xtalToDetector*1e-3 or distance
695	distance = (distance <= 0) and None or distance
696	# extract resonable center from header
697	center = [marFrame.beamXmarFrame.pixelsizeX1e-9,marFrame.beamYmarFrame.pixelsizeY1e-9]
698	center = (center[0] != 0 and center[1] != 0) and center or [None,None]
699	#print head,tifType,pixy
700	elif nSlice > 1: #CheMin multislice tif file!
701	tifType = 'CheMin'
702	pixy = [40,40]
703	image = np.flipud(np.array(Im.open(filename)))*10.
704	distance = 18.0
705	center = [pixy[0]*sizexy[0]/2000,0] #the CheMin beam stop is here
706	wavelength = 1.78892
707	elif 272 in IFD:
708	ifd = IFD[272]
709	File.seek(ifd[2][0])
710	S = File.read(ifd[1])
711	if 'PILATUS' in S:
712	tifType = 'Pilatus'
713	dataType = 0
714	pixy = [172,172]
715	File.seek(4096)
716	if not imageOnly:
717	print 'Read Pilatus tiff file: ',filename
718	image = ar.array('L',File.read(4*Npix))
719	image = np.array(np.asarray(image),dtype=np.int32)
720	else:
721	if IFD[258][2][0] == 16:
722	tifType = 'GE'
723	pixy = [200,200]
724	File.seek(8)
725	if not imageOnly:
726	print 'Read GE-detector tiff file: ',filename
727	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
728	elif IFD[258][2][0] == 32:
729	tifType = 'CHESS'
730	pixy = [200,200]
731	File.seek(8)
732	if not imageOnly:
733	print 'Read CHESS-detector tiff file: ',filename
734	image = np.array(ar.array('L',File.read(4*Npix)),dtype=np.int32)
735
736	elif 262 in IFD and IFD[262][2][0] > 4:
737	tifType = 'DND'
738	pixy = [158,158]
739	File.seek(512)
740	if not imageOnly:
741	print 'Read DND SAX/WAX-detector tiff file: ',filename
742	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
743	elif sizexy == [1536,1536]:
744	tifType = 'APS Gold'
745	pixy = [150,150]
746	File.seek(64)
747	if not imageOnly:
748	print 'Read Gold tiff file:',filename
749	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
750	elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
751	if IFD[273][2][0] == 8:
752	if IFD[258][2][0] == 32:
753	tifType = 'PE'
754	pixy = [200,200]
755	File.seek(8)
756	if not imageOnly:
757	print 'Read APS PE-detector tiff file: ',filename
758	if dataType == 5:
759	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
760	else:
761	image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
762	elif IFD[258][2][0] == 16:
763	tifType = 'MedOptics D1'
764	pixy = [46.9,46.9]
765	File.seek(8)
766	if not imageOnly:
767	print 'Read MedOptics D1 tiff file: ',filename
768	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
769
770	elif IFD[273][2][0] == 4096:
771	if sizexy[0] == 3072:
772	pixy = [73,73]
773	tifType = 'MAR225'
774	else:
775	pixy = [158,158]
776	tifType = 'MAR325'
777	File.seek(4096)
778	if not imageOnly:
779	print 'Read MAR CCD tiff file: ',filename
780	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
781	elif IFD[273][2][0] == 512:
782	tiftype = '11-ID-C'
783	pixy = [200,200]
784	File.seek(512)
785	if not imageOnly:
786	print 'Read 11-ID-C tiff file: ',filename
787	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
788	elif sizexy == [4096,4096]:
789	if IFD[273][2][0] == 8:
790	if IFD[258][2][0] == 16:
791	tifType = 'scanCCD'
792	pixy = [9,9]
793	File.seek(8)
794	if not imageOnly:
795	print 'Read APS scanCCD tiff file: ',filename
796	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
797	elif IFD[273][2][0] == 4096:
798	tifType = 'Rayonix'
799	pixy = [73.242,73.242]
800	File.seek(4096)
801	if not imageOnly:
802	print 'Read Rayonix MX300HE tiff file: ',filename
803	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
804	# elif sizexy == [960,960]:
805	# tiftype = 'PE-BE'
806	# pixy = (200,200)
807	# File.seek(8)
808	# if not imageOnly:
809	# print 'Read Gold tiff file:',filename
810	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
811
812	else:
813	lines = ['not a known detector tiff file',]
814	return lines,0,0,0
815
816	image = np.reshape(image,(sizexy[1],sizexy[0]))
817	center = (not center[0]) and [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000] or center
818	wavelength = (not wavelength) and 0.10 or wavelength
819	distance = (not distance) and 100.0 or distance
820	data = {'pixelSize':pixy,'wavelength':wavelength,'distance':distance,'center':center,'size':sizexy}
821	File.close()
822	if imageOnly:
823	return image
824	else:
825	return head,data,Npix,image
826
827	#def GetTifData(filename,imageOnly=False):
828	# import struct as st
829	# import array as ar
830	# File = open(filename,'rb')
831	# dataType = 5
832	# try:
833	# Meta = open(filename+'.metadata','Ur')
834	# head = Meta.readlines()
835	# for line in head:
836	# line = line.strip()
837	# if 'dataType=' in line:
838	# dataType = int(line.split('=')[1])
839	# Meta.close()
840	# except IOError:
841	# print 'no metadata file found - will try to read file anyway'
842	# head = ['no metadata file found',]
843	#
844	# tag = File.read(2)
845	# byteOrd = '<'
846	# if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
847	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
848	# elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
849	# byteOrd = '>'
850	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
851	# else:
852	# lines = ['not a detector tiff file',]
853	# return lines,0,0,0
854	# File.seek(IFD) #get number of directory entries
855	# NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
856	# IFD = {}
857	# for ied in range(NED):
858	# Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
859	# nVal = st.unpack(byteOrd+'i',File.read(4))[0]
860	# if Type == 1:
861	# Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
862	# elif Type == 2:
863	# Value = st.unpack(byteOrd+'i',File.read(4))
864	# elif Type == 3:
865	# Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
866	# x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
867	# elif Type == 4:
868	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
869	# elif Type == 5:
870	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
871	# elif Type == 11:
872	# Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
873	# IFD[Tag] = [Type,nVal,Value]
874	## print Tag,IFD[Tag]
875	# sizexy = [IFD[256][2][0],IFD[257][2][0]]
876	# [nx,ny] = sizexy
877	# Npix = nx*ny
878	# if 272 in IFD:
879	# ifd = IFD[272]
880	# File.seek(ifd[2][0])
881	# S = File.read(ifd[1])
882	# if 'PILATUS' in S:
883	# tifType = 'Pilatus'
884	# dataType = 0
885	# pixy = (172,172)
886	# File.seek(4096)
887	# if not imageOnly:
888	# print 'Read Pilatus tiff file: ',filename
889	# image = ar.array('L',File.read(4*Npix))
890	# image = np.array(np.asarray(image),dtype=np.int32)
891	# elif 262 in IFD and IFD[262][2][0] > 4:
892	# tifType = 'DND'
893	# pixy = (158,158)
894	# File.seek(512)
895	# if not imageOnly:
896	# print 'Read DND SAX/WAX-detector tiff file: ',filename
897	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
898	# elif sizexy == [1536,1536]:
899	# tifType = 'APS Gold'
900	# pixy = (150,150)
901	# File.seek(64)
902	# if not imageOnly:
903	# print 'Read Gold tiff file:',filename
904	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
905	# elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
906	# if IFD[273][2][0] == 8:
907	# if IFD[258][2][0] == 32:
908	# tifType = 'PE'
909	# pixy = (200,200)
910	# File.seek(8)
911	# if not imageOnly:
912	# print 'Read APS PE-detector tiff file: ',filename
913	# if dataType == 5:
914	# image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
915	# else:
916	# image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
917	# elif IFD[273][2][0] == 4096:
918	# if sizexy[0] == 3072:
919	# pixy = (73,73)
920	# tifType = 'MAR225'
921	# else:
922	# pixy = (158,158)
923	# tifType = 'MAR325'
924	# File.seek(4096)
925	# if not imageOnly:
926	# print 'Read MAR CCD tiff file: ',filename
927	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
928	# elif IFD[273][2][0] == 512:
929	# tiftype = '11-ID-C'
930	# pixy = [200,200]
931	# File.seek(512)
932	# if not imageOnly:
933	# print 'Read 11-ID-C tiff file: ',filename
934	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
935	# elif sizexy == [4096,4096]:
936	# if IFD[273][2][0] == 8:
937	# if IFD[258][2][0] == 16:
938	# tifType = 'scanCCD'
939	# pixy = (9,9)
940	# File.seek(8)
941	# if not imageOnly:
942	# print 'Read APS scanCCD tiff file: ',filename
943	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
944	# elif IFD[273][2][0] == 4096:
945	# tifType = 'Rayonix'
946	# pixy = (73.242,73.242)
947	# File.seek(4096)
948	# if not imageOnly:
949	# print 'Read Rayonix MX300HE tiff file: ',filename
950	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
951	## elif sizexy == [960,960]:
952	## tiftype = 'PE-BE'
953	## pixy = (200,200)
954	## File.seek(8)
955	## if not imageOnly:
956	## print 'Read Gold tiff file:',filename
957	## image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
958	#
959	# else:
960	# lines = ['not a known detector tiff file',]
961	# return lines,0,0,0
962	#
963	# image = np.reshape(image,(sizexy[1],sizexy[0]))
964	# center = [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000]
965	# data = {'pixelSize':pixy,'wavelength':0.10,'distance':100.0,'center':center,'size':sizexy}
966	# File.close()
967	# if imageOnly:
968	# return image
969	# else:
970	# return head,data,Npix,image
971	#
972	def ProjFileOpen(G2frame):
973	'Read a GSAS-II project file and load into the G2 data tree'
974	if not os.path.exists(G2frame.GSASprojectfile):
975	print ('\n*** Error attempt to open project file that does not exist:\n '+
976	str(G2frame.GSASprojectfile))
977	return
978	LastSavedUsing = None
979	file = open(G2frame.GSASprojectfile,'rb')
980	print 'load from file: ',G2frame.GSASprojectfile
981	G2frame.SetTitle("GSAS-II data tree: "+
982	os.path.split(G2frame.GSASprojectfile)[1])
983	wx.BeginBusyCursor()
984	try:
985	while True:
986	try:
987	data = cPickle.load(file)
988	except EOFError:
989	break
990	datum = data[0]
991
992	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=datum[0])
993	if 'PWDR' in datum[0]:
994	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
995	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
996	G2frame.PatternTree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
997	elif datum[0].startswith('HKLF'):
998	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
999	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
1000	G2frame.PatternTree.SetItemPyData(Id,datum[1])
1001	else:
1002	G2frame.PatternTree.SetItemPyData(Id,datum[1])
1003	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
1004	LastSavedUsing = datum[1]['LastSavedUsing']
1005	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug'):
1006	print('Packages used to create .GPX file:')
1007	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
1008	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
1009	print("{:>14s}: {:s}".format(p[0],p[1]))
1010	else:
1011	for p in datum[1]['PythonVersions']:
1012	print("{:<12s} {:s}".format(p[0]+':',p[1]))
1013	for datus in data[1:]:
1014	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
1015	#patch
1016	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
1017	if 'PWDR' in datum[0]:
1018	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
1019	else:
1020	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
1021	for item in datus[1][0]: #zip makes tuples - now make lists!
1022	datus[1][0][item] = list(datus[1][0][item])
1023	#end patch
1024	G2frame.PatternTree.SetItemPyData(sub,datus[1])
1025	if 'IMG' in datum[0]: #retrieve image default flag & data if set
1026	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
1027	if Data['setDefault']:
1028	G2frame.imageDefault = Data
1029	file.close()
1030	if LastSavedUsing:
1031	print('GPX load successful. Last saved with GSAS-II version '+LastSavedUsing)
1032	else:
1033	print('project load successful')
1034	G2frame.NewPlot = True
1035	except:
1036	msg = wx.MessageDialog(G2frame,message="Error reading file "+
1037	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
1038	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
1039	msg.ShowModal()
1040	finally:
1041	wx.EndBusyCursor()
1042	G2frame.Status.SetStatusText('To reorder tree items, use mouse RB to drag/drop them')
1043
1044	def ProjFileSave(G2frame):
1045	'Save a GSAS-II project file'
1046	if not G2frame.PatternTree.IsEmpty():
1047	file = open(G2frame.GSASprojectfile,'wb')
1048	print 'save to file: ',G2frame.GSASprojectfile
1049	# stick the file name into the tree and version info into tree so they are saved.
1050	# (Controls should always be created at this point)
1051	try:
1052	Controls = G2frame.PatternTree.GetItemPyData(
1053	G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
1054	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
1055	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
1056	Controls['PythonVersions'] = G2frame.PackageVersions
1057	except:
1058	pass
1059	wx.BeginBusyCursor()
1060	try:
1061	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
1062	while item:
1063	data = []
1064	name = G2frame.PatternTree.GetItemText(item)
1065	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
1066	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
1067	while item2:
1068	name = G2frame.PatternTree.GetItemText(item2)
1069	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
1070	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
1071	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1072	cPickle.dump(data,file,1)
1073	file.close()
1074	finally:
1075	wx.EndBusyCursor()
1076	print('project save successful')
1077
1078	def SaveIntegration(G2frame,PickId,data):
1079	'Save image integration results as powder pattern(s)'
1080	azms = G2frame.Integrate[1]
1081	X = G2frame.Integrate[2][:-1]
1082	N = len(X)
1083	Id = G2frame.PatternTree.GetItemParent(PickId)
1084	name = G2frame.PatternTree.GetItemText(Id)
1085	name = name.replace('IMG ',data['type']+' ')
1086	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
1087	if 'PWDR' in name:
1088	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
1089	codes = [0 for i in range(11)]
1090	elif 'SASD' in name:
1091	names = ['Type','Lam','Zero','Azimuth']
1092	codes = [0 for i in range(4)]
1093	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
1094	Xminmax = [X[0],X[-1]]
1095	LRazm = data['LRazimuth']
1096	Azms = []
1097	dazm = 0.
1098	if data['fullIntegrate'] and data['outAzimuths'] == 1:
1099	Azms = [45.0,] #a poor man's average?
1100	else:
1101	for i,azm in enumerate(azms[:-1]):
1102	if azm > 360. and azms[i+1] > 360.:
1103	Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
1104	else:
1105	Azms.append(G2img.meanAzm(azm,azms[i+1]))
1106	dazm = np.min(np.abs(np.diff(azms)))/2.
1107	for i,azm in enumerate(azms[:-1]):
1108	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
1109	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
1110	nOcc = 0
1111	while item:
1112	Name = G2frame.PatternTree.GetItemText(item)
1113	if Aname in Name:
1114	nOcc += 1
1115	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1116	if nOcc:
1117	Aname += '(%d)'%(nOcc)
1118	Sample = G2pdG.SetDefaultSample()
1119	Sample['Gonio. radius'] = data['distance']
1120	Sample['Omega'] = data['GonioAngles'][0]
1121	Sample['Chi'] = data['GonioAngles'][1]
1122	Sample['Phi'] = data['GonioAngles'][2]
1123	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
1124	if 'PWDR' in Aname:
1125	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!
1126	elif 'SASD' in Aname:
1127	Sample['Trans'] = data['SampleAbs'][0]
1128	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
1129	Y = G2frame.Integrate[0][i]
1130	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
1131	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=Aname)
1132	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
1133	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
1134	if 'PWDR' in Aname:
1135	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
1136	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
1137	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
1138	for item in inst[0]:
1139	inst[0][item] = list(inst[0][item])
1140	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
1141	if 'PWDR' in Aname:
1142	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1143	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
1144	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[[],[]])
1145	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
1146	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
1147	elif 'SASD' in Aname:
1148	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
1149	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1150	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
1151	valuesdict = {
1152	'wtFactor':1.0,
1153	'Dummy':False,
1154	'ranId':ran.randint(0,sys.maxint),
1155	'Offset':[0.0,0.0],'delOffset':0.02,'refOffset':-1.0,'refDelt':0.01,
1156	'qPlot':False,'dPlot':False,'sqrtPlot':False
1157	}
1158	G2frame.PatternTree.SetItemPyData(
1159	Id,[valuesdict,
1160	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
1161	return Id #last powder pattern generated
1162
1163	# def powderFxyeSave(G2frame,exports,powderfile):
1164	# 'Save a powder histogram as a GSAS FXYE file'
1165	# head,tail = ospath.split(powderfile)
1166	# name,ext = tail.split('.')
1167	# for i,export in enumerate(exports):
1168	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1169	# prmname = filename.strip(ext)+'prm'
1170	# prm = open(prmname,'w') #old style GSAS parm file
1171	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1172	# Inst = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, \
1173	# PickId, 'Instrument Parameters'))[0]
1174	# prm.write( ' 123456789012345678901234567890123456789012345678901234567890 '+'\n')
1175	# prm.write( 'INS BANK 1 '+'\n')
1176	# prm.write(('INS HTYPE %sR '+'\n')%(Inst['Type'][0]))
1177	# if 'Lam1' in Inst: #Ka1 & Ka2
1178	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam1'][0],Inst['Lam2'][0]))
1179	# elif 'Lam' in Inst: #single wavelength
1180	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam'][1],0.0))
1181	# prm.write( 'INS 1 IRAD 0 '+'\n')
1182	# prm.write( 'INS 1I HEAD '+'\n')
1183	# prm.write( 'INS 1I ITYP 0 0.0000 180.0000 1 '+'\n')
1184	# prm.write(('INS 1DETAZM%10.3f '+'\n')%(Inst['Azimuth'][0]))
1185	# prm.write( 'INS 1PRCF1 3 8 0.00100 '+'\n')
1186	# prm.write(('INS 1PRCF11 %15.6g%15.6g%15.6g%15.6g '+'\n')%(Inst['U'][1],Inst['V'][1],Inst['W'][1],0.0))
1187	# 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.))
1188	# prm.close()
1189	# file = open(filename,'w')
1190	# print 'save powder pattern to file: ',filename
1191	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1192	# file.write(powderfile+'\n')
1193	# file.write('Instrument parameter file:'+ospath.split(prmname)[1]+'\n')
1194	# file.write('BANK 1 %d %d CONS %.2f %.2f 0 0 FXYE\n'%(len(x),len(x),\
1195	# 100.x[0],100.(x[1]-x[0])))
1196	# s = list(np.sqrt(1./np.array(w)))
1197	# XYW = zip(x,y,s)
1198	# for X,Y,S in XYW:
1199	# file.write("%15.6g %15.6g %15.6g\n" % (100.*X,Y,max(S,1.0)))
1200	# file.close()
1201	# print 'powder pattern file '+filename+' written'
1202
1203	# def powderXyeSave(G2frame,exports,powderfile):
1204	# 'Save a powder histogram as a Topas XYE file'
1205	# head,tail = ospath.split(powderfile)
1206	# name,ext = tail.split('.')
1207	# for i,export in enumerate(exports):
1208	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1209	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1210	# file = open(filename,'w')
1211	# file.write('#%s\n'%(export))
1212	# print 'save powder pattern to file: ',filename
1213	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1214	# s = list(np.sqrt(1./np.array(w)))
1215	# XYW = zip(x,y,s)
1216	# for X,Y,W in XYW:
1217	# file.write("%15.6g %15.6g %15.6g\n" % (X,Y,W))
1218	# file.close()
1219	# print 'powder pattern file '+filename+' written'
1220
1221	def PDFSave(G2frame,exports):
1222	'Save a PDF G(r) and S(Q) in column formats'
1223	for export in exports:
1224	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1225	SQname = 'S(Q)'+export[4:]
1226	GRname = 'G(R)'+export[4:]
1227	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
1228	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
1229	sqId = G2gd.GetPatternTreeItemId(G2frame, PickId, SQname)
1230	grId = G2gd.GetPatternTreeItemId(G2frame, PickId, GRname)
1231	sqdata = np.array(G2frame.PatternTree.GetItemPyData(sqId)[1][:2]).T
1232	grdata = np.array(G2frame.PatternTree.GetItemPyData(grId)[1][:2]).T
1233	sqfile = open(sqfilename,'w')
1234	grfile = open(grfilename,'w')
1235	sqfile.write('#T S(Q) %s\n'%(export))
1236	grfile.write('#T G(R) %s\n'%(export))
1237	sqfile.write('#L Q S(Q)\n')
1238	grfile.write('#L R G(R)\n')
1239	for q,sq in sqdata:
1240	sqfile.write("%15.6g %15.6g\n" % (q,sq))
1241	sqfile.close()
1242	for r,gr in grdata:
1243	grfile.write("%15.6g %15.6g\n" % (r,gr))
1244	grfile.close()
1245
1246	def PeakListSave(G2frame,file,peaks):
1247	'Save powder peaks to a data file'
1248	print 'save peak list to file: ',G2frame.peaklistfile
1249	if not peaks:
1250	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1251	try:
1252	result = dlg.ShowModal()
1253	finally:
1254	dlg.Destroy()
1255	return
1256	for peak in peaks:
1257	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1258	(peak[0],peak[2],peak[4],peak[6]))
1259	print 'peak list saved'
1260
1261	def IndexPeakListSave(G2frame,peaks):
1262	'Save powder peaks from the indexing list'
1263	file = open(G2frame.peaklistfile,'wa')
1264	print 'save index peak list to file: ',G2frame.peaklistfile
1265	wx.BeginBusyCursor()
1266	try:
1267	if not peaks:
1268	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1269	try:
1270	result = dlg.ShowModal()
1271	finally:
1272	dlg.Destroy()
1273	return
1274	for peak in peaks:
1275	file.write("%12.6f\n" % (peak[7]))
1276	file.close()
1277	finally:
1278	wx.EndBusyCursor()
1279	print 'index peak list saved'
1280
1281	def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1282	'''Create a new phase dict with default values for various parameters
1283
1284	:param str Name: Name for new Phase
1285
1286	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1287	defaults to data for P 1
1288
1289	:param list cell: unit cell parameter list; defaults to
1290	[1.0,1.0,1.0,90.,90,90.,1.]
1291
1292	'''
1293	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1294	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1295	phaseData = {
1296	'ranId':ran.randint(0,sys.maxint),
1297	'General':{
1298	'Name':Name,
1299	'Type':'nuclear',
1300	'AtomPtrs':[3,1,7,9],
1301	'SGData':SGData,
1302	'Cell':[False,]+cell,
1303	'Pawley dmin':1.0,
1304	'Data plot type':'None',
1305	'SH Texture':{
1306	'Order':0,
1307	'Model':'cylindrical',
1308	'Sample omega':[False,0.0],
1309	'Sample chi':[False,0.0],
1310	'Sample phi':[False,0.0],
1311	'SH Coeff':[False,{}],
1312	'SHShow':False,
1313	'PFhkl':[0,0,1],
1314	'PFxyz':[0,0,1],
1315	'PlotType':'Pole figure',
1316	'Penalty':[['',],0.1,False,1.0]}},
1317	'Atoms':[],
1318	'Drawing':{},
1319	'Histograms':{},
1320	'Pawley ref':[],
1321	'RBModels':{},
1322	}
1323	if Super and Super.get('Use',False):
1324	phaseData['General'].update({'Type':'modulated','Super':True,'SuperSg':Super['ssSymb']})
1325	phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])
1326	phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1327
1328	return phaseData
1329
1330	class MultipleChoicesDialog(wx.Dialog):
1331	'''A dialog that offers a series of choices, each with a
1332	title and a wx.Choice widget. Intended to be used Modally.
1333	typical input:
1334
1335	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1336	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1337
1338	selections are placed in self.chosen when OK is pressed
1339	'''
1340	def __init__(self,choicelist,headinglist,
1341	head='Select options',
1342	title='Please select from options below',
1343	parent=None):
1344	self.chosen = []
1345	wx.Dialog.__init__(
1346	self,parent,wx.ID_ANY,head,
1347	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1348	panel = wx.Panel(self)
1349	mainSizer = wx.BoxSizer(wx.VERTICAL)
1350	mainSizer.Add((10,10),1)
1351	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1352	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1353	self.ChItems = []
1354	for choice,lbl in zip(choicelist,headinglist):
1355	mainSizer.Add((10,10),1)
1356	self.chosen.append(0)
1357	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1358	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1359	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1360	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1361
1362	OkBtn = wx.Button(panel,-1,"Ok")
1363	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1364	cancelBtn = wx.Button(panel,-1,"Cancel")
1365	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1366	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1367	btnSizer.Add((20,20),1)
1368	btnSizer.Add(OkBtn)
1369	btnSizer.Add((20,20),1)
1370	btnSizer.Add(cancelBtn)
1371	btnSizer.Add((20,20),1)
1372	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1373	panel.SetSizer(mainSizer)
1374	panel.Fit()
1375	self.Fit()
1376
1377	def OnOk(self,event):
1378	parent = self.GetParent()
1379	if parent is not None: parent.Raise()
1380	# save the results from the choice widgets
1381	self.chosen = []
1382	for w in self.ChItems:
1383	self.chosen.append(w.GetSelection())
1384	self.EndModal(wx.ID_OK)
1385
1386	def OnCancel(self,event):
1387	parent = self.GetParent()
1388	if parent is not None: parent.Raise()
1389	self.chosen = []
1390	self.EndModal(wx.ID_CANCEL)
1391
1392	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1393	confirmoverwrite=True, parent=None,
1394	multipleselect=False):
1395	'''If the filename is a zip file, extract a file from that
1396	archive.
1397
1398	:param list Selection: used to predefine the name of the file
1399	to be extracted. Filename case and zip directory name are
1400	ignored in selection; the first matching file is used.
1401
1402	:param bool confirmread: if True asks the user to confirm before expanding
1403	the only file in a zip
1404
1405	:param bool confirmoverwrite: if True asks the user to confirm
1406	before overwriting if the extracted file already exists
1407
1408	:param bool multipleselect: if True allows more than one zip
1409	file to be extracted, a list of file(s) is returned.
1410	If only one file is present, do not ask which one, otherwise
1411	offer a list of choices (unless selection is used).
1412
1413	:returns: the name of the file that has been created or a
1414	list of files (see multipleselect)
1415
1416	If the file is not a zipfile, return the name of the input file.
1417	If the zipfile is empty or no file has been selected, return None
1418	'''
1419	import zipfile # do this now, since we can save startup time by doing this only on need
1420	import shutil
1421	zloc = os.path.split(filename)[0]
1422	if not zipfile.is_zipfile(filename):
1423	#print("not zip")
1424	return filename
1425
1426	z = zipfile.ZipFile(filename,'r')
1427	zinfo = z.infolist()
1428
1429	if len(zinfo) == 0:
1430	#print('Zip has no files!')
1431	zlist = [-1]
1432	if selection:
1433	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1434	if selection.lower() in choices:
1435	zlist = [choices.index(selection.lower())]
1436	else:
1437	print('debug: file '+str(selection)+' was not found in '+str(filename))
1438	zlist = [-1]
1439	elif len(zinfo) == 1 and confirmread:
1440	result = wx.ID_NO
1441	dlg = wx.MessageDialog(
1442	parent,
1443	'Is file '+str(zinfo[0].filename)+
1444	' what you want to extract from '+
1445	str(os.path.split(filename)[1])+'?',
1446	'Confirm file',
1447	wx.YES_NO \| wx.ICON_QUESTION)
1448	try:
1449	result = dlg.ShowModal()
1450	finally:
1451	dlg.Destroy()
1452	if result == wx.ID_NO:
1453	zlist = [-1]
1454	else:
1455	zlist = [0]
1456	elif len(zinfo) == 1:
1457	zlist = [0]
1458	elif multipleselect:
1459	# select one or more from a from list
1460	choices = [i.filename for i in zinfo]
1461	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1462	'Choose file(s)',choices)
1463	if dlg.ShowModal() == wx.ID_OK:
1464	zlist = dlg.GetSelections()
1465	else:
1466	zlist = []
1467	dlg.Destroy()
1468	else:
1469	# select one from a from list
1470	choices = [i.filename for i in zinfo]
1471	dlg = wx.SingleChoiceDialog(parent,
1472	'Select file to extract from zip file'+str(filename),'Choose file',
1473	choices,)
1474	if dlg.ShowModal() == wx.ID_OK:
1475	zlist = [dlg.GetSelection()]
1476	else:
1477	zlist = [-1]
1478	dlg.Destroy()
1479
1480	outlist = []
1481	for zindex in zlist:
1482	if zindex >= 0:
1483	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1484	if os.path.exists(efil) and confirmoverwrite:
1485	result = wx.ID_NO
1486	dlg = wx.MessageDialog(parent,
1487	'File '+str(efil)+' already exists. OK to overwrite it?',
1488	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1489	try:
1490	result = dlg.ShowModal()
1491	finally:
1492	dlg.Destroy()
1493	if result == wx.ID_NO:
1494	zindex = -1
1495	if zindex >= 0:
1496	# extract the file to the current directory, regardless of it's original path
1497	#z.extract(zinfo[zindex],zloc)
1498	eloc,efil = os.path.split(zinfo[zindex].filename)
1499	outfile = os.path.join(zloc, efil)
1500	fpin = z.open(zinfo[zindex])
1501	fpout = file(outfile, "wb")
1502	shutil.copyfileobj(fpin, fpout)
1503	fpin.close()
1504	fpout.close()
1505	outlist.append(outfile)
1506	z.close()
1507	if multipleselect and len(outlist) >= 1:
1508	return outlist
1509	elif len(outlist) == 1:
1510	return outlist[0]
1511	else:
1512	return None
1513
1514	######################################################################
1515	# base classes for reading various types of data files
1516	# not used directly, only by subclassing
1517	######################################################################
1518	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1519	P1SGData = SGData
1520	class ImportBaseclass(object):
1521	'''Defines a base class for the reading of input files (diffraction
1522	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1523	for an explanation on how to use a subclass of this class.
1524	'''
1525	class ImportException(Exception):
1526	'''Defines an Exception that is used when an import routine hits an expected error,
1527	usually in .Reader.
1528
1529	Good practice is that the Reader should define a value in self.errors that
1530	tells the user some information about what is wrong with their file.
1531	'''
1532	pass
1533
1534	def __init__(self,
1535	formatName,
1536	longFormatName=None,
1537	extensionlist=[],
1538	strictExtension=False,
1539	):
1540	self.formatName = formatName # short string naming file type
1541	if longFormatName: # longer string naming file type
1542	self.longFormatName = longFormatName
1543	else:
1544	self.longFormatName = formatName
1545	# define extensions that are allowed for the file type
1546	# for windows, remove any extensions that are duplicate, as case is ignored
1547	if sys.platform == 'windows' and extensionlist:
1548	extensionlist = list(set([s.lower() for s in extensionlist]))
1549	self.extensionlist = extensionlist
1550	# If strictExtension is True, the file will not be read, unless
1551	# the extension matches one in the extensionlist
1552	self.strictExtension = strictExtension
1553	self.errors = ''
1554	self.warnings = ''
1555	# used for readers that will use multiple passes to read
1556	# more than one data block
1557	self.repeat = False
1558	self.selections = []
1559	self.repeatcount = 0
1560	self.readfilename = '?'
1561	#print 'created',self.__class__
1562
1563	def ReInitialize(self):
1564	'Reinitialize the Reader to initial settings'
1565	self.errors = ''
1566	self.warnings = ''
1567	self.repeat = False
1568	self.repeatcount = 0
1569	self.readfilename = '?'
1570
1571	def BlockSelector(self, ChoiceList, ParentFrame=None,
1572	title='Select a block',
1573	size=None, header='Block Selector',
1574	useCancel=True):
1575	''' Provide a wx dialog to select a block if the file contains more
1576	than one set of data and one must be selected
1577	'''
1578	if useCancel:
1579	dlg = wx.SingleChoiceDialog(
1580	ParentFrame,title, header,ChoiceList)
1581	else:
1582	dlg = wx.SingleChoiceDialog(
1583	ParentFrame,title, header,ChoiceList,
1584	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1585	if size: dlg.SetSize(size)
1586	dlg.CenterOnParent()
1587	if dlg.ShowModal() == wx.ID_OK:
1588	sel = dlg.GetSelection()
1589	return sel
1590	else:
1591	return None
1592	dlg.Destroy()
1593
1594	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1595	title='Select a block',size=None, header='Block Selector'):
1596	'''Provide a wx dialog to select a block of data if the
1597	file contains more than one set of data and one must be
1598	selected.
1599
1600	:returns: a list of the selected blocks
1601	'''
1602	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1603	wx.CHOICEDLG_STYLE)
1604	dlg.CenterOnParent()
1605	if size: dlg.SetSize(size)
1606	if dlg.ShowModal() == wx.ID_OK:
1607	sel = dlg.GetSelections()
1608	else:
1609	return []
1610	dlg.Destroy()
1611	selected = []
1612	if len(ChoiceList) in sel:
1613	return range(len(ChoiceList))
1614	else:
1615	return sel
1616	return selected
1617
1618	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1619	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1620	widget. Typical input:
1621
1622	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1623
1624	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1625
1626	optional keyword parameters are: head (window title) and title
1627	returns a list of selected indicies for each choice (or None)
1628	'''
1629	result = None
1630	dlg = MultipleChoicesDialog(choicelist,headinglist,
1631	parent=ParentFrame, **kwargs)
1632	dlg.CenterOnParent()
1633	if dlg.ShowModal() == wx.ID_OK:
1634	result = dlg.chosen
1635	dlg.Destroy()
1636	return result
1637
1638	def ShowBusy(self):
1639	wx.BeginBusyCursor()
1640	# wx.Yield() # make it happen now!
1641
1642	def DoneBusy(self):
1643	wx.EndBusyCursor()
1644	wx.Yield() # make it happen now!
1645
1646	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1647	# '''This method must be supplied in the child class to read the file.
1648	# if the read fails either return False or raise an Exception
1649	# preferably of type ImportException.
1650	# '''
1651	# #start reading
1652	# raise ImportException("Error occurred while...")
1653	# self.errors += "Hint for user on why the error occur
1654	# return False # if an error occurs
1655	# return True # if read OK
1656
1657	def ExtensionValidator(self, filename):
1658	'''This methods checks if the file has the correct extension
1659	Return False if this filename will not be supported by this reader
1660	Return True if the extension matches the list supplied by the reader
1661	Return None if the reader allows un-registered extensions
1662	'''
1663	if filename:
1664	ext = os.path.splitext(filename)[1]
1665	if sys.platform == 'windows': ext = ext.lower()
1666	if ext in self.extensionlist: return True
1667	if self.strictExtension: return False
1668	return None
1669
1670	def ContentsValidator(self, filepointer):
1671	'''This routine will attempt to determine if the file can be read
1672	with the current format.
1673	This will typically be overridden with a method that
1674	takes a quick scan of [some of]
1675	the file contents to do a "sanity" check if the file
1676	appears to match the selected format.
1677	Expected to be called via self.Validator()
1678	'''
1679	#filepointer.seek(0) # rewind the file pointer
1680	return True
1681
1682	def CIFValidator(self, filepointer):
1683	'''A :meth:`ContentsValidator` for use to validate CIF files.
1684	'''
1685	for i,l in enumerate(filepointer):
1686	if i >= 1000: return True
1687	'''Encountered only blank lines or comments in first 1000
1688	lines. This is unlikely, but assume it is CIF anyway, since we are
1689	even less likely to find a file with nothing but hashes and
1690	blank lines'''
1691	line = l.strip()
1692	if len(line) == 0: # ignore blank lines
1693	continue
1694	elif line.startswith('#'): # ignore comments
1695	continue
1696	elif line.startswith('data_'): # on the right track, accept this file
1697	return True
1698	else: # found something invalid
1699	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1700	self.errors += ' '+str(l)
1701	self.errors += ' Note: a CIF should only have blank lines or comments before'
1702	self.errors += ' a data_ statement begins a block.'
1703	return False
1704
1705	class ImportPhase(ImportBaseclass):
1706	'''Defines a base class for the reading of files with coordinates
1707
1708	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1709	in :meth:`GSASII.GSASII.OnImportPhase`.
1710	See :ref:`Writing a Import Routine<Import_Routines>`
1711	for an explanation on how to use this class.
1712
1713	'''
1714	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1715	strictExtension=False,):
1716	# call parent __init__
1717	ImportBaseclass.__init__(self,formatName,longFormatName,
1718	extensionlist,strictExtension)
1719	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1720	self.Constraints = None
1721
1722	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1723	title='Select a phase', size=None,header='Phase Selector'):
1724	''' Provide a wx dialog to select a phase if the file contains more
1725	than one phase
1726	'''
1727	return self.BlockSelector(ChoiceList,ParentFrame,title,
1728	size,header)
1729
1730	class ImportStructFactor(ImportBaseclass):
1731	'''Defines a base class for the reading of files with tables
1732	of structure factors.
1733
1734	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1735	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1736	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1737	:meth:`Reader`.
1738
1739	See :ref:`Writing a Import Routine<Import_Routines>`
1740	for an explanation on how to use import classes in general. The specifics
1741	for reading a structure factor histogram require that
1742	the ``Reader()`` routine in the import
1743	class need to do only a few things: It
1744	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1745	and set :attr:`Parameters` with the instrument parameters
1746	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1747	'''
1748	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1749	strictExtension=False,):
1750	ImportBaseclass.__init__(self,formatName,longFormatName,
1751	extensionlist,strictExtension)
1752
1753	# define contents of Structure Factor entry
1754	self.Parameters = []
1755	'self.Parameters is a list with two dicts for data parameter settings'
1756	self.InitParameters()
1757	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1758	self.Banks = [] #for multi bank data (usually TOF)
1759	'''self.RefDict is a dict containing the reflection information, as read from the file.
1760	Item 'RefList' contains the reflection information. See the
1761	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1762	for the contents of each row. Dict element 'FF'
1763	contains the form factor values for each element type; if this entry
1764	is left as initialized (an empty list) it will be initialized as needed later.
1765	'''
1766	def ReInitialize(self):
1767	'Reinitialize the Reader to initial settings'
1768	ImportBaseclass.ReInitialize(self)
1769	self.InitParameters()
1770	self.Banks = [] #for multi bank data (usually TOF)
1771	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1772
1773	def InitParameters(self):
1774	'initialize the instrument parameters structure'
1775	Lambda = 0.70926
1776	HistType = 'SXC'
1777	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1778	'Lam':[Lambda,Lambda]
1779	}, {}]
1780	'Parameters is a list with two dicts for data parameter settings'
1781
1782	def UpdateParameters(self,Type=None,Wave=None):
1783	'Revise the instrument parameters'
1784	if Type is not None:
1785	self.Parameters[0]['Type'] = [Type,Type]
1786	if Wave is not None:
1787	self.Parameters[0]['Lam'] = [Wave,Wave]
1788
1789	######################################################################
1790	class ImportPowderData(ImportBaseclass):
1791	'''Defines a base class for the reading of files with powder data.
1792
1793	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1794	in :meth:`GSASII.GSASII.OnImportPowder`.
1795	See :ref:`Writing a Import Routine<Import_Routines>`
1796	for an explanation on how to use this class.
1797	'''
1798	def __init__(self,
1799	formatName,
1800	longFormatName=None,
1801	extensionlist=[],
1802	strictExtension=False,
1803	):
1804	ImportBaseclass.__init__(self,formatName,
1805	longFormatName,
1806	extensionlist,
1807	strictExtension)
1808	self.clockWd = None # used in TOF
1809	self.ReInitialize()
1810
1811	def ReInitialize(self):
1812	'Reinitialize the Reader to initial settings'
1813	ImportBaseclass.ReInitialize(self)
1814	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1815	self.powderdata = [] # Powder dataset
1816	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1817	np.array(x), # x-axis values
1818	np.array(y), # powder pattern intensities
1819	np.array(w), # 1/sig(intensity)^2 values (weights)
1820	np.array(yc), # calc. intensities (zero)
1821	np.array(yb), # calc. background (zero)
1822	np.array(yd), # obs-calc profiles
1823	'''
1824	self.comments = []
1825	self.idstring = ''
1826	self.Sample = G2pdG.SetDefaultSample() # default sample parameters
1827	self.Controls = {} # items to be placed in top-level Controls
1828	self.GSAS = None # used in TOF
1829	self.repeat_instparm = True # Should a parm file be
1830	# used for multiple histograms?
1831	self.instparm = None # name hint from file of instparm to use
1832	self.instfile = '' # full path name to instrument parameter file
1833	self.instbank = '' # inst parm bank number
1834	self.instmsg = '' # a label that gets printed to show
1835	# where instrument parameters are from
1836	self.numbanks = 1
1837	self.instdict = {} # place items here that will be transferred to the instrument parameters
1838	self.pwdparms = {} # place parameters that are transferred directly to the tree
1839	# here (typically from an existing GPX file)
1840	######################################################################
1841	class ImportSmallAngleData(ImportBaseclass):
1842	'''Defines a base class for the reading of files with small angle data.
1843	See :ref:`Writing a Import Routine<Import_Routines>`
1844	for an explanation on how to use this class.
1845	'''
1846	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1847	strictExtension=False,):
1848
1849	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1850	strictExtension)
1851	self.ReInitialize()
1852
1853	def ReInitialize(self):
1854	'Reinitialize the Reader to initial settings'
1855	ImportBaseclass.ReInitialize(self)
1856	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1857	self.smallangledata = [] # SASD dataset
1858	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1859	np.array(x), # x-axis values
1860	np.array(y), # powder pattern intensities
1861	np.array(w), # 1/sig(intensity)^2 values (weights)
1862	np.array(yc), # calc. intensities (zero)
1863	np.array(yd), # obs-calc profiles
1864	np.array(yb), # preset bkg
1865	'''
1866	self.comments = []
1867	self.idstring = ''
1868	self.Sample = G2pdG.SetDefaultSample()
1869	self.GSAS = None # used in TOF
1870	self.clockWd = None # used in TOF
1871	self.numbanks = 1
1872	self.instdict = {} # place items here that will be transferred to the instrument parameters
1873	######################################################################
1874	class ExportBaseclass(object):
1875	'''Defines a base class for the exporting of GSAS-II results.
1876
1877	This class is subclassed in the various exports/G2export_*.py files. Those files
1878	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
1879	appropriate menu items for each one and the .Exporter method is called
1880	directly from the menu item.
1881
1882	'''
1883	def __init__(self,
1884	G2frame,
1885	formatName,
1886	extension,
1887	longFormatName=None,
1888	):
1889	self.G2frame = G2frame
1890	self.formatName = formatName # short string naming file type
1891	self.extension = extension
1892	if longFormatName: # longer string naming file type
1893	self.longFormatName = longFormatName
1894	else:
1895	self.longFormatName = formatName
1896	self.OverallParms = {}
1897	self.Phases = {}
1898	self.Histograms = {}
1899	self.powderDict = {}
1900	self.xtalDict = {}
1901	self.parmDict = {}
1902	self.sigDict = {}
1903	# updated in InitExport:
1904	self.currentExportType = None # type of export that has been requested
1905	# updated in ExportSelect (when used):
1906	self.phasenam = None # a list of selected phases
1907	self.histnam = None # a list of selected histograms
1908	self.filename = None # name of file to be written (single export) or template (multiple files)
1909	self.dirname = '' # name of directory where file(s) will be written
1910	self.fullpath = '' # name of file being written -- full path
1911
1912	# items that should be defined in a subclass of this class
1913	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1914	# The following types are defined: 'project', "phase", "powder", "single"
1915	self.multiple = False # set as True if the class can export multiple phases or histograms
1916	# self.multiple is ignored for "project" exports
1917
1918	def InitExport(self,event):
1919	'''Determines the type of menu that called the Exporter and
1920	misc initialization.
1921	'''
1922	self.filename = None # name of file to be written (single export)
1923	self.dirname = '' # name of file to be written (multiple export)
1924	if event:
1925	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1926
1927	def MakePWDRfilename(self,hist):
1928	'''Make a filename root (no extension) from a PWDR histogram name
1929
1930	:param str hist: the histogram name in data tree (starts with "PWDR ")
1931	'''
1932	file0 = ''
1933	file1 = hist[5:]
1934	# replace repeated blanks
1935	while file1 != file0:
1936	file0 = file1
1937	file1 = file0.replace(' ',' ').strip()
1938	file0 = file1.replace('Azm= ','A')
1939	# if angle has unneeded decimal places on aziumuth, remove them
1940	if file0[-3:] == '.00': file0 = file0[:-3]
1941	file0 = file0.replace('.','_')
1942	file0 = file0.replace(' ','_')
1943	return file0
1944
1945	def ExportSelect(self,AskFile='ask'):
1946	'''Selects histograms or phases when needed. Sets a default file name when
1947	requested in self.filename; always sets a default directory in self.dirname.
1948
1949	:param bool AskFile: Determines how this routine processes getting a
1950	location to store the current export(s).
1951
1952	* if AskFile is 'ask' (default option), get the name of the file to be written;
1953	self.filename and self.dirname are always set. In the case where
1954	multiple files must be generated, the export routine should do this
1955	based on self.filename as a template.
1956	* if AskFile is 'dir', get the name of the directory to be used;
1957	self.filename is not used, but self.dirname is always set. The export routine
1958	will always generate the file name.
1959	* if AskFile is 'single', get only the name of the directory to be used when
1960	multiple items will be written (as multiple files) are used
1961	or a complete file name is requested when a single file
1962	name is selected. self.dirname is always set and self.filename used
1963	only when a single file is selected.
1964	* if AskFile is 'default', creates a name of the file to be used from
1965	the name of the project (.gpx) file. If the project has not been saved,
1966	then the name of file is requested.
1967	self.filename and self.dirname are always set. In the case where
1968	multiple file names must be generated, the export routine should do this
1969	based on self.filename.
1970	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1971	file. If the project has not been saved, then a directory is requested.
1972	self.filename is not used.
1973
1974	:returns: True in case of an error
1975	'''
1976
1977	numselected = 1
1978	if self.currentExportType == 'phase':
1979	if len(self.Phases) == 0:
1980	self.G2frame.ErrorDialog(
1981	'Empty project',
1982	'Project does not contain any phases.')
1983	return True
1984	elif len(self.Phases) == 1:
1985	self.phasenam = self.Phases.keys()
1986	elif self.multiple:
1987	choices = sorted(self.Phases.keys())
1988	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1989	if phasenum is None: return True
1990	self.phasenam = [choices[i] for i in phasenum]
1991	if not self.phasenam: return True
1992	numselected = len(self.phasenam)
1993	else:
1994	choices = sorted(self.Phases.keys())
1995	phasenum = G2G.ItemSelector(choices,self.G2frame)
1996	if phasenum is None: return True
1997	self.phasenam = [choices[phasenum]]
1998	numselected = len(self.phasenam)
1999	elif self.currentExportType == 'single':
2000	if len(self.xtalDict) == 0:
2001	self.G2frame.ErrorDialog(
2002	'Empty project',
2003	'Project does not contain any single crystal data.')
2004	return True
2005	elif len(self.xtalDict) == 1:
2006	self.histnam = self.xtalDict.values()
2007	elif self.multiple:
2008	choices = sorted(self.xtalDict.values())
2009	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
2010	if not hnum: return True
2011	self.histnam = [choices[i] for i in hnum]
2012	numselected = len(self.histnam)
2013	else:
2014	choices = sorted(self.xtalDict.values())
2015	hnum = G2G.ItemSelector(choices,self.G2frame)
2016	if hnum is None: return True
2017	self.histnam = [choices[hnum]]
2018	numselected = len(self.histnam)
2019	elif self.currentExportType == 'powder':
2020	if len(self.powderDict) == 0:
2021	self.G2frame.ErrorDialog(
2022	'Empty project',
2023	'Project does not contain any powder data.')
2024	return True
2025	elif len(self.powderDict) == 1:
2026	self.histnam = self.powderDict.values()
2027	elif self.multiple:
2028	choices = sorted(self.powderDict.values())
2029	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
2030	if not hnum: return True
2031	self.histnam = [choices[i] for i in hnum]
2032	numselected = len(self.histnam)
2033	else:
2034	choices = sorted(self.powderDict.values())
2035	hnum = G2G.ItemSelector(choices,self.G2frame)
2036	if hnum is None: return True
2037	self.histnam = [choices[hnum]]
2038	numselected = len(self.histnam)
2039	elif self.currentExportType == 'image':
2040	if len(self.Histograms) == 0:
2041	self.G2frame.ErrorDialog(
2042	'Empty project',
2043	'Project does not contain any images.')
2044	return True
2045	elif len(self.Histograms) == 1:
2046	self.histnam = self.Histograms.keys()
2047	else:
2048	choices = sorted(self.Histograms.keys())
2049	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
2050	if self.multiple:
2051	if not hnum: return True
2052	self.histnam = [choices[i] for i in hnum]
2053	else:
2054	if hnum is None: return True
2055	self.histnam = [choices[hnum]]
2056	numselected = len(self.histnam)
2057	if self.currentExportType == 'map':
2058	# search for phases with maps
2059	mapPhases = []
2060	choices = []
2061	for phasenam in sorted(self.Phases):
2062	phasedict = self.Phases[phasenam] # pointer to current phase info
2063	if len(phasedict['General']['Map'].get('rho',[])):
2064	mapPhases.append(phasenam)
2065	if phasedict['General']['Map'].get('Flip'):
2066	choices.append('Charge flip map: '+str(phasenam))
2067	elif phasedict['General']['Map'].get('MapType'):
2068	choices.append(
2069	str(phasedict['General']['Map'].get('MapType'))
2070	+ ' map: ' + str(phasenam))
2071	else:
2072	choices.append('unknown map: '+str(phasenam))
2073	# select a map if needed
2074	if len(mapPhases) == 0:
2075	self.G2frame.ErrorDialog(
2076	'Empty project',
2077	'Project does not contain any maps.')
2078	return True
2079	elif len(mapPhases) == 1:
2080	self.phasenam = mapPhases
2081	else:
2082	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
2083	if self.multiple:
2084	if not phasenum: return True
2085	self.phasenam = [mapPhases[i] for i in phasenum]
2086	else:
2087	if phasenum is None: return True
2088	self.phasenam = [mapPhases[phasenum]]
2089	numselected = len(self.phasenam)
2090
2091	# items selected, now set self.dirname and usually self.filename
2092	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
2093	AskFile == 'default' and not self.G2frame.GSASprojectfile
2094	):
2095	filename = self.askSaveFile()
2096	if not filename: return True
2097	self.dirname,self.filename = os.path.split(filename)
2098	elif AskFile == 'dir' or AskFile == 'single' or (
2099	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
2100	):
2101	self.dirname = self.askSaveDirectory()
2102	if not self.dirname: return True
2103	elif AskFile == 'default-dir' or AskFile == 'default':
2104	self.dirname,self.filename = os.path.split(
2105	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
2106	)
2107	else:
2108	raise Exception('This should not happen!')
2109
2110	def loadParmDict(self):
2111	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
2112	refined values to those from the last cycle and set the uncertainties for the
2113	refined parameters in another dict (self.sigDict).
2114
2115	Expands the parm & sig dicts to include values derived from constraints.
2116	'''
2117	self.parmDict = {}
2118	self.sigDict = {}
2119	rigidbodyDict = {}
2120	covDict = {}
2121	consDict = {}
2122	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2123	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2124	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2125	while item:
2126	name = self.G2frame.PatternTree.GetItemText(item)
2127	if name == 'Rigid bodies':
2128	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
2129	elif name == 'Covariance':
2130	covDict = self.G2frame.PatternTree.GetItemPyData(item)
2131	elif name == 'Constraints':
2132	consDict = self.G2frame.PatternTree.GetItemPyData(item)
2133	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2134	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
2135	self.parmDict.update(rbDict)
2136	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
2137	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,maxSSwave = G2stIO.GetPhaseData(
2138	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
2139	self.parmDict.update(phaseDict)
2140	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
2141	Phases,Histograms,Print=False,resetRefList=False)
2142	self.parmDict.update(hapDict)
2143	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
2144	self.parmDict.update(histDict)
2145	self.parmDict.update(zip(
2146	covDict.get('varyList',[]),
2147	covDict.get('variables',[])))
2148	self.sigDict = dict(zip(
2149	covDict.get('varyList',[]),
2150	covDict.get('sig',[])))
2151	# expand to include constraints: first compile a list of constraints
2152	constList = []
2153	for item in consDict:
2154	if item.startswith('_'): continue
2155	constList += consDict[item]
2156	# now process the constraints
2157	G2mv.InitVars()
2158	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
2159	varyList = covDict.get('varyListStart')
2160	if varyList is None and len(constDict) == 0:
2161	# no constraints can use varyList
2162	varyList = covDict.get('varyList')
2163	elif varyList is None:
2164	# old GPX file from before pre-constraint varyList is saved
2165	print ' * Old refinement: Please use Calculate/Refine to redo *'
2166	raise Exception(' * Export aborted *')
2167	else:
2168	varyList = list(varyList)
2169	try:
2170	groups,parmlist = G2mv.GroupConstraints(constDict)
2171	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
2172	except:
2173	# this really should not happen
2174	print ' * ERROR - constraints are internally inconsistent *'
2175	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
2176	print 'Errors',errmsg
2177	if warnmsg: print 'Warnings',warnmsg
2178	raise Exception(' * CIF creation aborted *')
2179	# add the constrained values to the parameter dictionary
2180	G2mv.Dict2Map(self.parmDict,varyList)
2181	# and add their uncertainties into the esd dictionary (sigDict)
2182	if covDict.get('covMatrix') is not None:
2183	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
2184
2185	def loadTree(self):
2186	'''Load the contents of the data tree into a set of dicts
2187	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2188	& self.xtalDict)
2189
2190	* The childrenless data tree items are overall parameters/controls for the
2191	entire project and are placed in self.OverallParms
2192	* Phase items are placed in self.Phases
2193	* Data items are placed in self.Histogram. The key for these data items
2194	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2195	'''
2196	self.OverallParms = {}
2197	self.powderDict = {}
2198	self.xtalDict = {}
2199	self.Phases = {}
2200	self.Histograms = {}
2201	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2202	histType = None
2203	if self.currentExportType == 'phase':
2204	# if exporting phases load them here
2205	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2206	if not sub:
2207	print 'no phases found'
2208	return True
2209	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2210	while item:
2211	phaseName = self.G2frame.PatternTree.GetItemText(item)
2212	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2213	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2214	return
2215	elif self.currentExportType == 'single':
2216	histType = 'HKLF'
2217	elif self.currentExportType == 'powder':
2218	histType = 'PWDR'
2219	elif self.currentExportType == 'image':
2220	histType = 'IMG'
2221
2222	if histType: # Loading just one kind of tree entry
2223	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2224	while item:
2225	name = self.G2frame.PatternTree.GetItemText(item)
2226	if name.startswith(histType):
2227	if self.Histograms.get(name): # there is already an item with this name
2228	print('Histogram name '+str(name)+' is repeated. Renaming')
2229	if name[-1] == '9':
2230	name = name[:-1] + '10'
2231	elif name[-1] in '012345678':
2232	name = name[:-1] + str(int(name[-1])+1)
2233	else:
2234	name += '-1'
2235	self.Histograms[name] = {}
2236	# the main info goes into Data, but the 0th
2237	# element contains refinement results, carry
2238	# that over too now.
2239	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2240	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2241	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2242	while item2:
2243	child = self.G2frame.PatternTree.GetItemText(item2)
2244	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2245	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2246	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2247	# index powder and single crystal histograms by number
2248	for hist in self.Histograms:
2249	if hist.startswith("PWDR"):
2250	d = self.powderDict
2251	elif hist.startswith("HKLF"):
2252	d = self.xtalDict
2253	else:
2254	return
2255	i = self.Histograms[hist].get('hId')
2256	if i is None and not d.keys():
2257	i = 0
2258	elif i is None or i in d.keys():
2259	i = max(d.keys())+1
2260	d[i] = hist
2261	return
2262	# else standard load: using all interlinked phases and histograms
2263	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2264	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2265	while item:
2266	name = self.G2frame.PatternTree.GetItemText(item)
2267	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2268	if not item2:
2269	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2270	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2271	# index powder and single crystal histograms
2272	for hist in self.Histograms:
2273	i = self.Histograms[hist]['hId']
2274	if hist.startswith("PWDR"):
2275	self.powderDict[i] = hist
2276	elif hist.startswith("HKLF"):
2277	self.xtalDict[i] = hist
2278
2279	def dumpTree(self,mode='type'):
2280	'''Print out information on the data tree dicts loaded in loadTree
2281	'''
2282	print '\nOverall'
2283	if mode == 'type':
2284	def Show(arg): return type(arg)
2285	else:
2286	def Show(arg): return arg
2287	for key in self.OverallParms:
2288	print ' ',key,Show(self.OverallParms[key])
2289	print 'Phases'
2290	for key1 in self.Phases:
2291	print ' ',key1,Show(self.Phases[key1])
2292	print 'Histogram'
2293	for key1 in self.Histograms:
2294	print ' ',key1,Show(self.Histograms[key1])
2295	for key2 in self.Histograms[key1]:
2296	print ' ',key2,Show(self.Histograms[key1][key2])
2297
2298	def defaultSaveFile(self):
2299	return os.path.abspath(
2300	os.path.splitext(self.G2frame.GSASprojectfile
2301	)[0]+self.extension)
2302
2303	def askSaveFile(self):
2304	'''Ask the user to supply a file name
2305
2306	:returns: a file name (str) or None if Cancel is pressed
2307	'''
2308	defnam = os.path.splitext(
2309	os.path.split(self.G2frame.GSASprojectfile)[1]
2310	)[0]+self.extension
2311	dlg = wx.FileDialog(
2312	self.G2frame, 'Input name for file to write', '.', defnam,
2313	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2314	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2315	dlg.CenterOnParent()
2316	try:
2317	if dlg.ShowModal() == wx.ID_OK:
2318	filename = dlg.GetPath()
2319	# make sure extension is correct
2320	filename = os.path.splitext(filename)[0]+self.extension
2321	else:
2322	filename = None
2323	finally:
2324	dlg.Destroy()
2325	return filename
2326
2327	def askSaveDirectory(self):
2328	'''Ask the user to supply a directory name. Path name is used as the
2329	starting point for the next export path search.
2330
2331	:returns: a directory name (str) or None if Cancel is pressed
2332	'''
2333	if self.G2frame.exportDir:
2334	startdir = self.G2frame.exportDir
2335	elif self.G2frame.GSASprojectfile:
2336	startdir = os.path.split(self.G2frame.GSASprojectfile)[0]
2337	elif self.G2frame.dirname:
2338	startdir = self.G2frame.dirname
2339	else:
2340	startdir = ''
2341	dlg = wx.DirDialog(
2342	self.G2frame, 'Input directory where file(s) will be written', startdir,
2343	wx.DD_DEFAULT_STYLE)
2344	dlg.CenterOnParent()
2345	try:
2346	if dlg.ShowModal() == wx.ID_OK:
2347	filename = dlg.GetPath()
2348	self.G2frame.exportDir = filename
2349	else:
2350	filename = None
2351	finally:
2352	dlg.Destroy()
2353	return filename
2354
2355	# Tools for file writing.
2356	def OpenFile(self,fil=None,mode='w'):
2357	'''Open the output file
2358
2359	:param str fil: The name of the file to open. If None (default)
2360	the name defaults to self.dirname + self.filename.
2361	If an extension is supplied, it is not overridded,
2362	but if not, the default extension is used.
2363	:returns: the file object opened by the routine which is also
2364	saved as self.fp
2365	'''
2366	if not fil:
2367	if not os.path.splitext(self.filename)[1]:
2368	self.filename += self.extension
2369	fil = os.path.join(self.dirname,self.filename)
2370	self.fullpath = fil
2371	self.fp = open(fil,mode)
2372	return self.fp
2373
2374	def Write(self,line):
2375	'''write a line of output, attaching a line-end character
2376
2377	:param str line: the text to be written.
2378	'''
2379	self.fp.write(line+'\n')
2380	def CloseFile(self,fp=None):
2381	'''Close a file opened in OpenFile
2382
2383	:param file fp: the file object to be closed. If None (default)
2384	file object self.fp is closed.
2385	'''
2386	if fp is None:
2387	fp = self.fp
2388	self.fp = None
2389	fp.close()
2390	# Tools to pull information out of the data arrays
2391	def GetCell(self,phasenam):
2392	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2393
2394	:param str phasenam: the name for the selected phase
2395	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2396	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2397	cell values and `cellSig` has their uncertainties.
2398	"""
2399	phasedict = self.Phases[phasenam] # pointer to current phase info
2400	try:
2401	pfx = str(phasedict['pId'])+'::'
2402	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2403	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
2404	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2405	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2406	return cellList,cellSig
2407	except KeyError:
2408	cell = phasedict['General']['Cell'][1:]
2409	return cell,7*[0]
2410
2411	def GetAtoms(self,phasenam):
2412	"""Gets the atoms associated with a phase. Can be used with standard
2413	or macromolecular phases
2414
2415	:param str phasenam: the name for the selected phase
2416	:returns: a list of items for eac atom where each item is a list containing:
2417	label, typ, mult, xyz, and td, where
2418
2419	* label and typ are the atom label and the scattering factor type (str)
2420	* mult is the site multiplicity (int)
2421	* xyz is contains a list with four pairs of numbers:
2422	x, y, z and fractional occupancy and
2423	their standard uncertainty (or a negative value)
2424	* td is contains a list with either one or six pairs of numbers:
2425	if one number it is U\ :sub:`iso` and with six numbers it is
2426	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2427	paired with their standard uncertainty (or a negative value)
2428	"""
2429	phasedict = self.Phases[phasenam] # pointer to current phase info
2430	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2431	cfrac = cx+3
2432	fpfx = str(phasedict['pId'])+'::Afrac:'
2433	atomslist = []
2434	for i,at in enumerate(phasedict['Atoms']):
2435	if phasedict['General']['Type'] == 'macromolecular':
2436	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2437	else:
2438	label = at[ct-1]
2439	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2440	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2441	mult = at[cs+1]
2442	typ = at[ct]
2443	xyz = []
2444	for j,v in enumerate(('x','y','z')):
2445	val = at[cx+j]
2446	pfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2447	sig = self.sigDict.get(pfx,-0.000009)
2448	xyz.append((val,sig))
2449	xyz.append((fval,fsig))
2450	td = []
2451	if at[cia] == 'I':
2452	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2453	val = self.parmDict.get(pfx,at[cia+1])
2454	sig = self.sigDict.get(pfx,-0.0009)
2455	td.append((val,sig))
2456	else:
2457	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2458	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2459	val = self.parmDict.get(pfx,at[cia+2+i])
2460	sig = self.sigDict.get(pfx,-0.0009)
2461	td.append((val,sig))
2462	atomslist.append((label,typ,mult,xyz,td))
2463	return atomslist
2464	######################################################################
2465
2466	def ReadCIF(URLorFile):
2467	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2468	(from James Hester).
2469	The open routine gets confused with DOS names that begin with a letter and colon
2470	"C:\dir\" so this routine will try to open the passed name as a file and if that
2471	fails, try it as a URL
2472
2473	:param str URLorFile: string containing a URL or a file name. Code will try first
2474	to open it as a file and then as a URL.
2475
2476	:returns: a PyCifRW CIF object.
2477	'''
2478	import CifFile as cif # PyCifRW from James Hester
2479
2480	# alternate approach:
2481	#import urllib
2482	#ciffile = 'file:'+urllib.pathname2url(filename)
2483
2484	try:
2485	fp = open(URLorFile,'r')
2486	cf = cif.ReadCif(fp)
2487	fp.close()
2488	return cf
2489	except IOError:
2490	return cif.ReadCif(URLorFile)
2491
2492	if __name__ == '__main__':
2493	app = wx.PySimpleApp()
2494	frm = wx.Frame(None) # create a frame
2495	frm.Show(True)
2496	filename = '/tmp/notzip.zip'
2497	filename = '/tmp/all.zip'
2498	#filename = '/tmp/11bmb_7652.zip'
2499
2500	#selection=None, confirmoverwrite=True, parent=None
2501	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2502	print ExtractFileFromZip(filename,multipleselect=True)
2503	#confirmread=False, confirmoverwrite=False)
2504
2505	# choicelist=[ ('a','b','c'),
2506	# ('test1','test2'),('no choice',)]
2507	# titles = [ 'a, b or c', 'tests', 'No option here']
2508	# dlg = MultipleChoicesDialog(
2509	# choicelist,titles,
2510	# parent=frm)
2511	# if dlg.ShowModal() == wx.ID_OK:
2512	# print 'Got OK'

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