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source: trunk/GSASIIIO.py @ 1619

Last change on this file since 1619 was 1619, checked in by toby, 9 years ago
add columnsorter for hetrogeneous seq ref; reorg to start moving widgets out of g2grid
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2014-12-27 03:58:22 +0000 (Sat, 27 Dec 2014) $
4	# $Author: toby $
5	# $Revision: 1619 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 1619 2014-12-27 03:58:22Z toby $
8	########### SVN repository information ###################
9	'''
10	GSASIIIO: Misc I/O routines
11	=============================
12
13	Module with miscellaneous routines for input and output. Many
14	are GUI routines to interact with user.
15
16	Includes support for image reading.
17
18	Also includes base classes for data import routines.
19
20	'''
21	"""GSASIIIO: functions for IO of data
22	Copyright: 2008, Robert B. Von Dreele (Argonne National Laboratory)
23	"""
24	import wx
25	import math
26	import numpy as np
27	import cPickle
28	import sys
29	import re
30	import random as ran
31	import GSASIIpath
32	GSASIIpath.SetVersionNumber("$Revision: 1619 $")
33	import GSASIIgrid as G2gd
34	import GSASIIspc as G2spc
35	import GSASIIlattice as G2lat
36	import GSASIIpwdGUI as G2pdG
37	import GSASIIElem as G2el
38	import GSASIIstrIO as G2stIO
39	import GSASIImapvars as G2mv
40	import GSASIIctrls as G2G
41	import os
42	import os.path as ospath
43
44	DEBUG = False #=True for various prints
45	TRANSP = False #=true to transpose images for testing
46	npsind = lambda x: np.sin(x*np.pi/180.)
47
48	def sfloat(S):
49	'Convert a string to float. An empty field is treated as zero'
50	if S.strip():
51	return float(S)
52	else:
53	return 0.0
54
55	def sint(S):
56	'Convert a string to int. An empty field is treated as zero'
57	if S.strip():
58	return int(S)
59	else:
60	return 0
61
62	def trim(val):
63	'''Simplify a string containing leading and trailing spaces
64	as well as newlines, tabs, repeated spaces etc. into a shorter and
65	more simple string, by replacing all ranges of whitespace
66	characters with a single space.
67
68	:param str val: the string to be simplified
69
70	:returns: the (usually) shortened version of the string
71	'''
72	return re.sub('\s+', ' ', val).strip()
73
74	def makeInstDict(names,data,codes):
75	inst = dict(zip(names,zip(data,data,codes)))
76	for item in inst:
77	inst[item] = list(inst[item])
78	return inst
79
80	def FileDlgFixExt(dlg,file):
81	'this is needed to fix a problem in linux wx.FileDialog'
82	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
83	if ext not in file:
84	file += ext
85	return file
86
87	def GetPowderPeaks(fileName):
88	'Read powder peaks from a file'
89	sind = lambda x: math.sin(x*math.pi/180.)
90	asind = lambda x: 180.*math.asin(x)/math.pi
91	Cuka = 1.54052
92	File = open(fileName,'Ur')
93	Comments = []
94	peaks = []
95	S = File.readline()
96	while S:
97	if S[:1] == '#':
98	Comments.append(S[:-1])
99	else:
100	item = S.split()
101	if len(item) == 1:
102	peaks.append([float(item[0]),1.0])
103	elif len(item) > 1:
104	peaks.append([float(item[0]),float(item[0])])
105	S = File.readline()
106	File.close()
107	if Comments:
108	print 'Comments on file:'
109	for Comment in Comments: print Comment
110	Peaks = []
111	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
112	for peak in peaks:
113	dsp = peak[0]
114	sth = Cuka/(2.0*dsp)
115	if sth < 1.0:
116	tth = 2.0*asind(sth)
117	else:
118	break
119	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
120	else: #2-thetas - assume Cuka (for now)
121	for peak in peaks:
122	tth = peak[0]
123	dsp = Cuka/(2.0*sind(tth/2.0))
124	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
125	return Comments,Peaks
126
127	def CheckImageFile(G2frame,imagefile):
128	'''Get an new image file name if the specified one does not
129	exist
130
131	:param wx.Frame G2frame: main GSAS-II Frame and data object
132
133	:param str imagefile: name of image file
134
135	:returns: imagefile, if it exists, or the name of a file
136	that does exist or False if the user presses Cancel
137
138	'''
139	if not os.path.exists(imagefile):
140	print 'Image file '+imagefile+' not found'
141	fil = imagefile.replace('\\','/') # windows?!
142	# see if we can find a file with same name or in a similarly named sub-dir
143	pth,fil = os.path.split(fil)
144	prevpth = None
145	while pth and pth != prevpth:
146	prevpth = pth
147	if os.path.exists(os.path.join(G2frame.dirname,fil)):
148	print 'found image file '+os.path.join(G2frame.dirname,fil)
149	return os.path.join(G2frame.dirname,fil)
150	pth,enddir = os.path.split(pth)
151	fil = os.path.join(enddir,fil)
152	# not found as a subdirectory, drop common parts of path for last saved & image file names
153	# if image was .../A/B/C/imgs/ima.ge
154	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
155	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
156	Controls = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
157	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
158	imgPath = imagefile.replace('\\','/').split('/')
159	for p1,p2 in zip(gpxPath,imgPath):
160	if p1 == p2:
161	gpxPath.pop(0),imgPath.pop(0)
162	else:
163	break
164	fil = os.path.join(*imgPath) # file with non-common prefix elements
165	prevpth = None
166	pth = os.path.abspath(G2frame.dirname)
167	while pth and pth != prevpth:
168	prevpth = pth
169	if os.path.exists(os.path.join(pth,fil)):
170	print 'found image file '+os.path.join(pth,fil)
171	return os.path.join(pth,fil)
172	pth,enddir = os.path.split(pth)
173	GSASIIpath.IPyBreak()
174
175	if not os.path.exists(imagefile):
176	dlg = wx.FileDialog(G2frame, 'Previous image file not found; open here', '.', '',\
177	'Any image file (.edf;.tif;.tiff;.mar;.ge;.avg;.sum;.img)\
178	\|.edf;.tif;.tiff;.mar;.ge;.avg;.sum;.img\|\
179	European detector file (.edf)\|.edf\|\
180	Any detector tif (.tif;.tiff)\|.tif;.tiff\|\
181	MAR file (.mar)\|.mar\|\
182	GE Image (.ge;.avg;.sum)\|.ge;.avg;.sum\|\
183	ADSC Image (.img)\|.img\|\
184	All files (.)\|.',wx.OPEN\|wx.CHANGE_DIR)
185	try:
186	dlg.SetFilename(''+ospath.split(imagefile)[1])
187	if dlg.ShowModal() == wx.ID_OK:
188	imagefile = dlg.GetPath()
189	else:
190	imagefile = False
191	finally:
192	dlg.Destroy()
193	return imagefile
194
195	def EditImageParms(parent,Data,Comments,Image,filename):
196	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
197	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
198	def onClose(event):
199	dlg.EndModal(wx.ID_OK)
200	mainsizer = wx.BoxSizer(wx.VERTICAL)
201	h,w = Image.shape[:2]
202	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,
203	'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
204	0,wx.ALIGN_LEFT\|wx.ALL, 2)
205
206	vsizer = wx.BoxSizer(wx.HORIZONTAL)
207	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
208	0,wx.ALIGN_LEFT\|wx.ALL, 2)
209	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
210	vsizer.Add(wdgt)
211	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
212
213	vsizer = wx.BoxSizer(wx.HORIZONTAL)
214	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
215	0,wx.ALIGN_LEFT\|wx.ALL, 2)
216	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
217	size=(50,-1))
218	vsizer.Add(wdgt)
219	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),
220	wx.ALIGN_LEFT\|wx.ALL, 2)
221	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,
222	size=(50,-1))
223	vsizer.Add(wdgt)
224	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
225
226	vsizer = wx.BoxSizer(wx.HORIZONTAL)
227	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
228	0,wx.ALIGN_LEFT\|wx.ALL, 2)
229	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
230	vsizer.Add(wdgt)
231	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
232
233	vsizer = wx.BoxSizer(wx.HORIZONTAL)
234	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
235	0,wx.ALIGN_LEFT\|wx.ALL, 2)
236	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,
237	size=(75,-1))
238	vsizer.Add(wdgt)
239	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),
240	wx.ALIGN_LEFT\|wx.ALL, 2)
241	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,
242	size=(75,-1))
243	vsizer.Add(wdgt)
244	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
245
246	vsizer = wx.BoxSizer(wx.HORIZONTAL)
247	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
248	0,wx.ALIGN_LEFT\|wx.ALL, 2)
249	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
250	vsizer.Add(wdgt)
251	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
252
253	btnsizer = wx.StdDialogButtonSizer()
254	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
255	OKbtn.SetDefault()
256	OKbtn.Bind(wx.EVT_BUTTON,onClose)
257	btnsizer.AddButton(OKbtn) # not sure why this is needed
258	btnsizer.Realize()
259	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
260	dlg.SetSizer(mainsizer)
261	dlg.CenterOnParent()
262	dlg.ShowModal()
263
264	def GetImageData(G2frame,imagefile,imageOnly=False):
265	'''Read an image with the file reader keyed by the
266	file extension
267
268	:param wx.Frame G2frame: main GSAS-II Frame and data object.
269
270	:param str imagefile: name of image file
271
272	:param bool imageOnly: If True return only the image,
273	otherwise (default) return more (see below)
274
275	:returns: an image as a numpy array or a list of four items:
276	Comments, Data, Npix and the Image, as selected by imageOnly
277
278	'''
279	ext = ospath.splitext(imagefile)[1]
280	Comments = []
281	Image = None
282	if ext == '.tif' or ext == '.tiff':
283	Comments,Data,Npix,Image = GetTifData(imagefile)
284	if Npix == 0:
285	print("GetTifData failed to read "+str(filename)+" Trying PIL")
286	import scipy.misc
287	Image = scipy.misc.imread(imagefile,flatten=True)
288	Npix = Image.size
289	Comments = ['no metadata']
290	Data = {'wavelength': 0.1, 'pixelSize': [200, 200], 'distance': 100.0}
291	Data['size'] = list(Image.shape)
292	Data['center'] = [int(i/2) for i in Image.shape]
293	if not imageOnly:
294	EditImageParms(G2frame,Data,Comments,Image,imagefile)
295	elif ext == '.edf':
296	Comments,Data,Npix,Image = GetEdfData(imagefile)
297	elif ext == '.img':
298	Comments,Data,Npix,Image = GetImgData(imagefile)
299	Image[0][0] = 0
300	elif ext == '.mar3450' or ext == '.mar2300':
301	Comments,Data,Npix,Image = GetMAR345Data(imagefile)
302	elif ext in ['.sum','.avg'] or 'ge' in ext:
303	Comments,Data,Npix,Image = GetGEsumData(imagefile)
304	elif ext == '.G2img':
305	Comments,Data,Npix,Image = GetG2Image(imagefile)
306	elif ext == '.png':
307	Comments,Data,Npix,Image = GetPNGData(imagefile)
308	if not imageOnly:
309	EditImageParms(G2frame,Data,Comments,Image,imagefile)
310	else:
311	print 'Extension for file '+imagefile+' not recognized'
312	if Image is None:
313	raise Exception('No image read')
314	if imageOnly:
315	if TRANSP:
316	return Image.T
317	else:
318	return Image
319	else:
320	if TRANSP:
321	return Comments,Data,Npix,Image.T
322	else:
323	return Comments,Data,Npix,Image
324
325	def PutG2Image(filename,Comments,Data,Npix,image):
326	'Write an image as a python pickle - might be better as an .edf file?'
327	File = open(filename,'wb')
328	cPickle.dump([Comments,Data,Npix,image],File,1)
329	File.close()
330	return
331
332	def GetG2Image(filename):
333	'Read an image as a python pickle'
334	File = open(filename,'rb')
335	Comments,Data,Npix,image = cPickle.load(File)
336	File.close()
337	return Comments,Data,Npix,image
338
339	def GetEdfData(filename,imageOnly=False):
340	'Read European detector data edf file'
341	import struct as st
342	import array as ar
343	if not imageOnly:
344	print 'Read European detector data edf file: ',filename
345	File = open(filename,'rb')
346	fileSize = os.stat(filename).st_size
347	head = File.read(3072)
348	lines = head.split('\n')
349	sizexy = [0,0]
350	pixSize = [154,154] #Pixium4700?
351	cent = [0,0]
352	wave = 1.54187 #default <CuKa>
353	dist = 1000.
354	head = ['European detector data',]
355	for line in lines:
356	line = line.replace(';',' ').strip()
357	fields = line.split()
358	if 'Dim_1' in line:
359	sizexy[0] = int(fields[2])
360	elif 'Dim_2' in line:
361	sizexy[1] = int(fields[2])
362	elif 'DataType' in line:
363	dType = fields[2]
364	elif 'wavelength' in line:
365	wave = float(fields[2])
366	elif 'Size' in line:
367	imSize = int(fields[2])
368	elif 'DataType' in lines:
369	dType = fields[2]
370	elif 'pixel_size_x' in line:
371	pixSize[0] = float(fields[2])
372	elif 'pixel_size_y' in line:
373	pixSize[1] = float(fields[2])
374	elif 'beam_center_x' in line:
375	cent[0] = float(fields[2])
376	elif 'beam_center_y' in line:
377	cent[1] = float(fields[2])
378	elif 'refined_distance' in line:
379	dist = float(fields[2])
380	if line:
381	head.append(line)
382	else: #blank line at end of header
383	break
384	File.seek(fileSize-imSize)
385	if dType == 'UnsignedShort':
386	image = np.array(ar.array('H',File.read(imSize)),dtype=np.int32)
387	elif dType == 'UnsignedInt':
388	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
389	elif dType == 'UnsignedLong':
390	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
391	image = np.reshape(image,(sizexy[1],sizexy[0]))
392	data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'size':sizexy}
393	Npix = sizexy[0]*sizexy[1]
394	File.close()
395	if imageOnly:
396	return image
397	else:
398	return head,data,Npix,image
399
400	def GetGEsumData(filename,imageOnly=False):
401	'Read SUM file as produced at 1-ID from G.E. images'
402	import struct as st
403	import array as ar
404	if not imageOnly:
405	print 'Read GE sum file: ',filename
406	File = open(filename,'rb')
407	if '.sum' in filename:
408	head = ['GE detector sum data from APS 1-ID',]
409	sizexy = [2048,2048]
410	elif '.avg' in filename or '.ge' in filename:
411	head = ['GE detector avg or ge* data from APS 1-ID',]
412	sizexy = [2048,2048]
413	else:
414	head = ['GE detector raw data from APS 1-ID',]
415	File.seek(18)
416	size,nframes = st.unpack('<ih',File.read(6))
417	sizexy = [2048,2048]
418	pos = 8192
419	File.seek(pos)
420	Npix = sizexy[0]*sizexy[1]
421	if '.sum' in filename:
422	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.int32)
423	elif '.avg' in filename or '.ge' in filename:
424	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
425	else:
426	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
427	while nframes > 1:
428	image += np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
429	nframes -= 1
430	image = np.reshape(image,(sizexy[1],sizexy[0]))
431	data = {'pixelSize':[200,200],'wavelength':0.15,'distance':250.0,'center':[204.8,204.8],'size':sizexy}
432	File.close()
433	if imageOnly:
434	return image
435	else:
436	return head,data,Npix,image
437
438	def GetImgData(filename,imageOnly=False):
439	'Read an ADSC image file'
440	import struct as st
441	import array as ar
442	if not imageOnly:
443	print 'Read ADSC img file: ',filename
444	File = open(filename,'rb')
445	head = File.read(511)
446	lines = head.split('\n')
447	head = []
448	center = [0,0]
449	for line in lines[1:-2]:
450	line = line.strip()[:-1]
451	if line:
452	if 'SIZE1' in line:
453	size = int(line.split('=')[1])
454	Npix = size*size
455	elif 'WAVELENGTH' in line:
456	wave = float(line.split('=')[1])
457	elif 'BIN' in line:
458	if line.split('=')[1] == '2x2':
459	pixel=(102,102)
460	else:
461	pixel = (51,51)
462	elif 'DISTANCE' in line:
463	distance = float(line.split('=')[1])
464	elif 'CENTER_X' in line:
465	center[0] = float(line.split('=')[1])
466	elif 'CENTER_Y' in line:
467	center[1] = float(line.split('=')[1])
468	head.append(line)
469	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center,'size':[size,size]}
470	image = []
471	row = 0
472	pos = 512
473	File.seek(pos)
474	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
475	image = np.reshape(image,(sizexy[1],sizexy[0]))
476	# image = np.zeros(shape=(size,size),dtype=np.int32)
477	# while row < size:
478	# File.seek(pos)
479	# line = ar.array('H',File.read(2*size))
480	# image[row] = np.asarray(line)
481	# row += 1
482	# pos += 2*size
483	File.close()
484	if imageOnly:
485	return image
486	else:
487	return lines[1:-2],data,Npix,image
488
489	def GetMAR345Data(filename,imageOnly=False):
490	'Read a MAR-345 image plate image'
491	import array as ar
492	import struct as st
493	try:
494	import pack_f as pf
495	except:
496	msg = wx.MessageDialog(None, message="Unable to load the GSAS MAR image decompression, pack_f",
497	caption="Import Error",
498	style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
499	msg.ShowModal()
500	return None,None,None,None
501
502	if not imageOnly:
503	print 'Read Mar345 file: ',filename
504	File = open(filename,'rb')
505	head = File.read(4095)
506	numbers = st.unpack('<iiiiiiiiii',head[:40])
507	lines = head[128:].split('\n')
508	head = []
509	for line in lines:
510	line = line.strip()
511	if 'PIXEL' in line:
512	values = line.split()
513	pixel = (int(values[2]),int(values[4])) #in microns
514	elif 'WAVELENGTH' in line:
515	wave = float(line.split()[1])
516	elif 'DISTANCE' in line:
517	distance = float(line.split()[1]) #in mm
518	elif 'CENTER' in line:
519	values = line.split()
520	center = [float(values[2])/10.,float(values[4])/10.] #make in mm from pixels
521	if line:
522	head.append(line)
523	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center}
524	for line in head:
525	if 'FORMAT' in line[0:6]:
526	items = line.split()
527	size = int(items[1])
528	Npix = size*size
529	pos = 4096
530	data['size'] = [size,size]
531	File.seek(pos)
532	line = File.read(8)
533	while 'CCP4' not in line: #get past overflow list for now
534	line = File.read(8)
535	pos += 8
536	pos += 37
537	File.seek(pos)
538	raw = File.read()
539	File.close()
540	image = np.zeros(shape=(size,size),dtype=np.int32)
541	image = np.flipud(pf.pack_f(len(raw),raw,size,image).T) #transpose to get it right way around & flip
542	if imageOnly:
543	return image
544	else:
545	return head,data,Npix,image
546
547	def GetPNGData(filename,imageOnly=False):
548	'''Read an image in a png format, assumes image is converted from CheMin tif file
549	so default parameters are that machine.
550	'''
551	import scipy.misc
552	Image = scipy.misc.imread(filename,flatten=True)
553	Npix = Image.size
554	Comments = ['no metadata']
555	pixy = list(Image.shape)
556	sizexy = [40,40]
557	Data = {'wavelength': 1.78892, 'pixelSize': sizexy, 'distance': 18.0,'size':pixy}
558	Data['center'] = [pixy[0]sizexy[0]/1000,pixy[1]sizexy[1]/2000]
559	if imageOnly:
560	return Image.T
561	else:
562	return Comments,Data,Npix,Image.T
563
564	def GetTifData(filename,imageOnly=False):
565	'''Read an image in a pseudo-tif format,
566	as produced by a wide variety of software, almost always
567	incorrectly in some way.
568	'''
569	import struct as st
570	try:
571	import Image as Im
572	except ImportError:
573	try:
574	from PIL import Image as Im
575	except ImportError:
576	print "PIL/pillow Image module not present. TIFs cannot be read without this"
577	raise Exception("PIL/pillow Image module not found")
578	import array as ar
579	import ReadMarCCDFrame as rmf
580	File = open(filename,'rb')
581	dataType = 5
582	center = [None,None]
583	wavelength = None
584	distance = None
585	try:
586	Meta = open(filename+'.metadata','Ur')
587	head = Meta.readlines()
588	for line in head:
589	line = line.strip()
590	if 'dataType=' in line:
591	dataType = int(line.split('=')[1])
592	Meta.close()
593	except IOError:
594	print 'no metadata file found - will try to read file anyway'
595	head = ['no metadata file found',]
596
597	tag = File.read(2)
598	byteOrd = '<'
599	if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
600	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
601	elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
602	byteOrd = '>'
603	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
604	else:
605	lines = ['not a detector tiff file',]
606	return lines,0,0,0
607	File.seek(IFD) #get number of directory entries
608	NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
609	IFD = {}
610	nSlice = 1
611	for ied in range(NED):
612	Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
613	nVal = st.unpack(byteOrd+'i',File.read(4))[0]
614	if DEBUG: print 'Try:',Tag,Type,nVal
615	if Type == 1:
616	Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
617	elif Type == 2:
618	Value = st.unpack(byteOrd+'i',File.read(4))
619	elif Type == 3:
620	Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
621	x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
622	elif Type == 4:
623	if Tag in [273,279]:
624	nSlice = nVal
625	nVal = 1
626	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
627	elif Type == 5:
628	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
629	elif Type == 11:
630	Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
631	IFD[Tag] = [Type,nVal,Value]
632	if DEBUG: print Tag,IFD[Tag]
633	sizexy = [IFD[256][2][0],IFD[257][2][0]]
634	[nx,ny] = sizexy
635	Npix = nx*ny
636	if 34710 in IFD:
637	if not imageOnly:
638	print 'Read MAR CCD tiff file: ',filename
639	marFrame = rmf.marFrame(File,byteOrd,IFD)
640	image = np.flipud(np.array(np.asarray(marFrame.image),dtype=np.int32))
641	tifType = marFrame.filetitle
642	pixy = [marFrame.pixelsizeX/1000.0,marFrame.pixelsizeY/1000.0]
643	head = marFrame.outputHead()
644	# extract resonable wavelength from header
645	wavelength = marFrame.sourceWavelength*1e-5
646	wavelength = (marFrame.opticsWavelength > 0) and marFrame.opticsWavelength*1e-5 or wavelength
647	wavelength = (wavelength <= 0) and None or wavelength
648	# extract resonable distance from header
649	distance = (marFrame.startXtalToDetector+marFrame.endXtalToDetector)*5e-4
650	distance = (distance <= 0) and marFrame.xtalToDetector*1e-3 or distance
651	distance = (distance <= 0) and None or distance
652	# extract resonable center from header
653	center = [marFrame.beamXmarFrame.pixelsizeX1e-9,marFrame.beamYmarFrame.pixelsizeY1e-9]
654	center = (center[0] != 0 and center[1] != 0) and center or [None,None]
655	#print head,tifType,pixy
656	elif nSlice > 1: #CheMin multislice tif file!
657	tifType = 'CheMin'
658	pixy = [40,40]
659	image = np.flipud(np.array(Im.open(filename)))*10.
660	distance = 18.0
661	center = [pixy[0]*sizexy[0]/2000,0] #the CheMin beam stop is here
662	wavelength = 1.78892
663	elif 272 in IFD:
664	ifd = IFD[272]
665	File.seek(ifd[2][0])
666	S = File.read(ifd[1])
667	if 'PILATUS' in S:
668	tifType = 'Pilatus'
669	dataType = 0
670	pixy = [172,172]
671	File.seek(4096)
672	if not imageOnly:
673	print 'Read Pilatus tiff file: ',filename
674	image = ar.array('L',File.read(4*Npix))
675	image = np.array(np.asarray(image),dtype=np.int32)
676	else:
677	if IFD[258][2][0] == 16:
678	tifType = 'GE'
679	pixy = [200,200]
680	File.seek(8)
681	if not imageOnly:
682	print 'Read GE-detector tiff file: ',filename
683	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
684	elif IFD[258][2][0] == 32:
685	tifType = 'CHESS'
686	pixy = [200,200]
687	File.seek(8)
688	if not imageOnly:
689	print 'Read CHESS-detector tiff file: ',filename
690	image = np.array(ar.array('L',File.read(4*Npix)),dtype=np.int32)
691
692	elif 262 in IFD and IFD[262][2][0] > 4:
693	tifType = 'DND'
694	pixy = [158,158]
695	File.seek(512)
696	if not imageOnly:
697	print 'Read DND SAX/WAX-detector tiff file: ',filename
698	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
699	elif sizexy == [1536,1536]:
700	tifType = 'APS Gold'
701	pixy = [150,150]
702	File.seek(64)
703	if not imageOnly:
704	print 'Read Gold tiff file:',filename
705	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
706	elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
707	if IFD[273][2][0] == 8:
708	if IFD[258][2][0] == 32:
709	tifType = 'PE'
710	pixy = [200,200]
711	File.seek(8)
712	if not imageOnly:
713	print 'Read APS PE-detector tiff file: ',filename
714	if dataType == 5:
715	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
716	else:
717	image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
718
719	elif IFD[273][2][0] == 4096:
720	if sizexy[0] == 3072:
721	pixy = [73,73]
722	tifType = 'MAR225'
723	else:
724	pixy = [158,158]
725	tifType = 'MAR325'
726	File.seek(4096)
727	if not imageOnly:
728	print 'Read MAR CCD tiff file: ',filename
729	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
730	elif IFD[273][2][0] == 512:
731	tiftype = '11-ID-C'
732	pixy = [200,200]
733	File.seek(512)
734	if not imageOnly:
735	print 'Read 11-ID-C tiff file: ',filename
736	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
737	elif sizexy == [4096,4096]:
738	if IFD[273][2][0] == 8:
739	if IFD[258][2][0] == 16:
740	tifType = 'scanCCD'
741	pixy = [9,9]
742	File.seek(8)
743	if not imageOnly:
744	print 'Read APS scanCCD tiff file: ',filename
745	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
746	elif IFD[273][2][0] == 4096:
747	tifType = 'Rayonix'
748	pixy = [73.242,73.242]
749	File.seek(4096)
750	if not imageOnly:
751	print 'Read Rayonix MX300HE tiff file: ',filename
752	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
753	# elif sizexy == [960,960]:
754	# tiftype = 'PE-BE'
755	# pixy = (200,200)
756	# File.seek(8)
757	# if not imageOnly:
758	# print 'Read Gold tiff file:',filename
759	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
760
761	else:
762	lines = ['not a known detector tiff file',]
763	return lines,0,0,0
764
765	image = np.reshape(image,(sizexy[1],sizexy[0]))
766	center = (not center[0]) and [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000] or center
767	wavelength = (not wavelength) and 0.10 or wavelength
768	distance = (not distance) and 100.0 or distance
769	data = {'pixelSize':pixy,'wavelength':wavelength,'distance':distance,'center':center,'size':sizexy}
770	File.close()
771	if imageOnly:
772	return image
773	else:
774	return head,data,Npix,image
775
776	#def GetTifData(filename,imageOnly=False):
777	# import struct as st
778	# import array as ar
779	# File = open(filename,'rb')
780	# dataType = 5
781	# try:
782	# Meta = open(filename+'.metadata','Ur')
783	# head = Meta.readlines()
784	# for line in head:
785	# line = line.strip()
786	# if 'dataType=' in line:
787	# dataType = int(line.split('=')[1])
788	# Meta.close()
789	# except IOError:
790	# print 'no metadata file found - will try to read file anyway'
791	# head = ['no metadata file found',]
792	#
793	# tag = File.read(2)
794	# byteOrd = '<'
795	# if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
796	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
797	# elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
798	# byteOrd = '>'
799	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
800	# else:
801	# lines = ['not a detector tiff file',]
802	# return lines,0,0,0
803	# File.seek(IFD) #get number of directory entries
804	# NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
805	# IFD = {}
806	# for ied in range(NED):
807	# Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
808	# nVal = st.unpack(byteOrd+'i',File.read(4))[0]
809	# if Type == 1:
810	# Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
811	# elif Type == 2:
812	# Value = st.unpack(byteOrd+'i',File.read(4))
813	# elif Type == 3:
814	# Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
815	# x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
816	# elif Type == 4:
817	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
818	# elif Type == 5:
819	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
820	# elif Type == 11:
821	# Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
822	# IFD[Tag] = [Type,nVal,Value]
823	## print Tag,IFD[Tag]
824	# sizexy = [IFD[256][2][0],IFD[257][2][0]]
825	# [nx,ny] = sizexy
826	# Npix = nx*ny
827	# if 272 in IFD:
828	# ifd = IFD[272]
829	# File.seek(ifd[2][0])
830	# S = File.read(ifd[1])
831	# if 'PILATUS' in S:
832	# tifType = 'Pilatus'
833	# dataType = 0
834	# pixy = (172,172)
835	# File.seek(4096)
836	# if not imageOnly:
837	# print 'Read Pilatus tiff file: ',filename
838	# image = ar.array('L',File.read(4*Npix))
839	# image = np.array(np.asarray(image),dtype=np.int32)
840	# elif 262 in IFD and IFD[262][2][0] > 4:
841	# tifType = 'DND'
842	# pixy = (158,158)
843	# File.seek(512)
844	# if not imageOnly:
845	# print 'Read DND SAX/WAX-detector tiff file: ',filename
846	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
847	# elif sizexy == [1536,1536]:
848	# tifType = 'APS Gold'
849	# pixy = (150,150)
850	# File.seek(64)
851	# if not imageOnly:
852	# print 'Read Gold tiff file:',filename
853	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
854	# elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
855	# if IFD[273][2][0] == 8:
856	# if IFD[258][2][0] == 32:
857	# tifType = 'PE'
858	# pixy = (200,200)
859	# File.seek(8)
860	# if not imageOnly:
861	# print 'Read APS PE-detector tiff file: ',filename
862	# if dataType == 5:
863	# image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
864	# else:
865	# image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
866	# elif IFD[273][2][0] == 4096:
867	# if sizexy[0] == 3072:
868	# pixy = (73,73)
869	# tifType = 'MAR225'
870	# else:
871	# pixy = (158,158)
872	# tifType = 'MAR325'
873	# File.seek(4096)
874	# if not imageOnly:
875	# print 'Read MAR CCD tiff file: ',filename
876	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
877	# elif IFD[273][2][0] == 512:
878	# tiftype = '11-ID-C'
879	# pixy = [200,200]
880	# File.seek(512)
881	# if not imageOnly:
882	# print 'Read 11-ID-C tiff file: ',filename
883	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
884	# elif sizexy == [4096,4096]:
885	# if IFD[273][2][0] == 8:
886	# if IFD[258][2][0] == 16:
887	# tifType = 'scanCCD'
888	# pixy = (9,9)
889	# File.seek(8)
890	# if not imageOnly:
891	# print 'Read APS scanCCD tiff file: ',filename
892	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
893	# elif IFD[273][2][0] == 4096:
894	# tifType = 'Rayonix'
895	# pixy = (73.242,73.242)
896	# File.seek(4096)
897	# if not imageOnly:
898	# print 'Read Rayonix MX300HE tiff file: ',filename
899	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
900	## elif sizexy == [960,960]:
901	## tiftype = 'PE-BE'
902	## pixy = (200,200)
903	## File.seek(8)
904	## if not imageOnly:
905	## print 'Read Gold tiff file:',filename
906	## image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
907	#
908	# else:
909	# lines = ['not a known detector tiff file',]
910	# return lines,0,0,0
911	#
912	# image = np.reshape(image,(sizexy[1],sizexy[0]))
913	# center = [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000]
914	# data = {'pixelSize':pixy,'wavelength':0.10,'distance':100.0,'center':center,'size':sizexy}
915	# File.close()
916	# if imageOnly:
917	# return image
918	# else:
919	# return head,data,Npix,image
920	#
921	def ProjFileOpen(G2frame):
922	'Read a GSAS-II project file and load into the G2 data tree'
923	if not os.path.exists(G2frame.GSASprojectfile):
924	print ('\n*** Error attempt to open project file that does not exist:\n '+
925	str(G2frame.GSASprojectfile))
926	return
927	file = open(G2frame.GSASprojectfile,'rb')
928	print 'load from file: ',G2frame.GSASprojectfile
929	G2frame.SetTitle("GSAS-II data tree: "+
930	os.path.split(G2frame.GSASprojectfile)[1])
931	wx.BeginBusyCursor()
932	try:
933	while True:
934	try:
935	data = cPickle.load(file)
936	except EOFError:
937	break
938	datum = data[0]
939
940	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=datum[0])
941	if 'PWDR' in datum[0]:
942	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
943	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
944	G2frame.PatternTree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
945	elif datum[0].startswith('HKLF'):
946	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
947	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
948	G2frame.PatternTree.SetItemPyData(Id,datum[1])
949	else:
950	G2frame.PatternTree.SetItemPyData(Id,datum[1])
951	for datus in data[1:]:
952	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
953	#patch
954	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
955	if 'PWDR' in datum[0]:
956	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
957	else:
958	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
959	for item in datus[1][0]: #zip makes tuples - now make lists!
960	datus[1][0][item] = list(datus[1][0][item])
961	#end patch
962	G2frame.PatternTree.SetItemPyData(sub,datus[1])
963	if 'IMG' in datum[0]: #retrieve image default flag & data if set
964	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
965	if Data['setDefault']:
966	G2frame.imageDefault = Data
967	file.close()
968	print('project load successful')
969	G2frame.NewPlot = True
970	except:
971	msg = wx.MessageDialog(G2frame,message="Error reading file "+
972	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
973	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
974	msg.ShowModal()
975	finally:
976	wx.EndBusyCursor()
977	G2frame.Status.SetStatusText('To reorder tree items, use mouse RB to drag/drop them')
978
979	def ProjFileSave(G2frame):
980	'Save a GSAS-II project file'
981	if not G2frame.PatternTree.IsEmpty():
982	file = open(G2frame.GSASprojectfile,'wb')
983	print 'save to file: ',G2frame.GSASprojectfile
984	# stick the file name into the tree, if possible
985	try:
986	Controls = G2frame.PatternTree.GetItemPyData(
987	G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
988	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
989	except:
990	pass
991	wx.BeginBusyCursor()
992	try:
993	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
994	while item:
995	data = []
996	name = G2frame.PatternTree.GetItemText(item)
997	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
998	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
999	while item2:
1000	name = G2frame.PatternTree.GetItemText(item2)
1001	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
1002	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
1003	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1004	cPickle.dump(data,file,1)
1005	file.close()
1006	finally:
1007	wx.EndBusyCursor()
1008	print('project save successful')
1009
1010	def SaveIntegration(G2frame,PickId,data):
1011	'Save image integration results as powder pattern(s)'
1012	azms = G2frame.Integrate[1]
1013	X = G2frame.Integrate[2][:-1]
1014	N = len(X)
1015	Id = G2frame.PatternTree.GetItemParent(PickId)
1016	name = G2frame.PatternTree.GetItemText(Id)
1017	name = name.replace('IMG ',data['type']+' ')
1018	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
1019	if 'PWDR' in name:
1020	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
1021	codes = [0 for i in range(11)]
1022	elif 'SASD' in name:
1023	names = ['Type','Lam','Zero','Azimuth']
1024	codes = [0 for i in range(4)]
1025	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
1026	Xminmax = [X[0],X[-1]]
1027	LRazm = data['LRazimuth']
1028	Azms = []
1029	if data['fullIntegrate'] and data['outAzimuths'] == 1:
1030	Azms = [45.0,] #a poor man's average?
1031	else:
1032	for i,azm in enumerate(azms[:-1]):
1033	Azms.append((azms[i+1]+azm)/2.)
1034	for i,azm in enumerate(azms[:-1]):
1035	Aname = name+" Azm= %.2f"%(Azms[i])
1036	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
1037	nOcc = 0
1038	while item:
1039	Name = G2frame.PatternTree.GetItemText(item)
1040	if Aname in Name:
1041	nOcc += 1
1042	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1043	if nOcc:
1044	Aname += '(%d)'%(nOcc)
1045	Sample = G2pdG.SetDefaultSample()
1046	Sample['Gonio. radius'] = data['distance']
1047	Sample['Omega'] = data['GonioAngles'][0]
1048	Sample['Chi'] = data['GonioAngles'][1]
1049	Sample['Phi'] = data['GonioAngles'][2]
1050	if 'PWDR' in Aname:
1051	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!
1052	elif 'SASD' in Aname:
1053	Sample['Trans'] = data['SampleAbs'][0]
1054	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
1055	Y = G2frame.Integrate[0][i]
1056	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
1057	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=Aname)
1058	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
1059	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
1060	if 'PWDR' in Aname:
1061	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
1062	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
1063	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
1064	for item in inst[0]:
1065	inst[0][item] = list(inst[0][item])
1066	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
1067	if 'PWDR' in Aname:
1068	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1069	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
1070	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[[],[]])
1071	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
1072	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
1073	elif 'SASD' in Aname:
1074	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
1075	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1076	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
1077	valuesdict = {
1078	'wtFactor':1.0,
1079	'Dummy':False,
1080	'ranId':ran.randint(0,sys.maxint),
1081	}
1082	G2frame.PatternTree.SetItemPyData(
1083	Id,[valuesdict,
1084	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
1085	return Id #last powder pattern generated
1086
1087	# def powderFxyeSave(G2frame,exports,powderfile):
1088	# 'Save a powder histogram as a GSAS FXYE file'
1089	# head,tail = ospath.split(powderfile)
1090	# name,ext = tail.split('.')
1091	# for i,export in enumerate(exports):
1092	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1093	# prmname = filename.strip(ext)+'prm'
1094	# prm = open(prmname,'w') #old style GSAS parm file
1095	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1096	# Inst = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, \
1097	# PickId, 'Instrument Parameters'))[0]
1098	# prm.write( ' 123456789012345678901234567890123456789012345678901234567890 '+'\n')
1099	# prm.write( 'INS BANK 1 '+'\n')
1100	# prm.write(('INS HTYPE %sR '+'\n')%(Inst['Type'][0]))
1101	# if 'Lam1' in Inst: #Ka1 & Ka2
1102	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam1'][0],Inst['Lam2'][0]))
1103	# elif 'Lam' in Inst: #single wavelength
1104	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam'][1],0.0))
1105	# prm.write( 'INS 1 IRAD 0 '+'\n')
1106	# prm.write( 'INS 1I HEAD '+'\n')
1107	# prm.write( 'INS 1I ITYP 0 0.0000 180.0000 1 '+'\n')
1108	# prm.write(('INS 1DETAZM%10.3f '+'\n')%(Inst['Azimuth'][0]))
1109	# prm.write( 'INS 1PRCF1 3 8 0.00100 '+'\n')
1110	# prm.write(('INS 1PRCF11 %15.6g%15.6g%15.6g%15.6g '+'\n')%(Inst['U'][1],Inst['V'][1],Inst['W'][1],0.0))
1111	# 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.))
1112	# prm.close()
1113	# file = open(filename,'w')
1114	# print 'save powder pattern to file: ',filename
1115	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1116	# file.write(powderfile+'\n')
1117	# file.write('Instrument parameter file:'+ospath.split(prmname)[1]+'\n')
1118	# file.write('BANK 1 %d %d CONS %.2f %.2f 0 0 FXYE\n'%(len(x),len(x),\
1119	# 100.x[0],100.(x[1]-x[0])))
1120	# s = list(np.sqrt(1./np.array(w)))
1121	# XYW = zip(x,y,s)
1122	# for X,Y,S in XYW:
1123	# file.write("%15.6g %15.6g %15.6g\n" % (100.*X,Y,max(S,1.0)))
1124	# file.close()
1125	# print 'powder pattern file '+filename+' written'
1126
1127	# def powderXyeSave(G2frame,exports,powderfile):
1128	# 'Save a powder histogram as a Topas XYE file'
1129	# head,tail = ospath.split(powderfile)
1130	# name,ext = tail.split('.')
1131	# for i,export in enumerate(exports):
1132	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1133	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1134	# file = open(filename,'w')
1135	# file.write('#%s\n'%(export))
1136	# print 'save powder pattern to file: ',filename
1137	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1138	# s = list(np.sqrt(1./np.array(w)))
1139	# XYW = zip(x,y,s)
1140	# for X,Y,W in XYW:
1141	# file.write("%15.6g %15.6g %15.6g\n" % (X,Y,W))
1142	# file.close()
1143	# print 'powder pattern file '+filename+' written'
1144
1145	def PDFSave(G2frame,exports):
1146	'Save a PDF G(r) and S(Q) in column formats'
1147	for export in exports:
1148	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1149	SQname = 'S(Q)'+export[4:]
1150	GRname = 'G(R)'+export[4:]
1151	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
1152	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
1153	sqId = G2gd.GetPatternTreeItemId(G2frame, PickId, SQname)
1154	grId = G2gd.GetPatternTreeItemId(G2frame, PickId, GRname)
1155	sqdata = np.array(G2frame.PatternTree.GetItemPyData(sqId)[1][:2]).T
1156	grdata = np.array(G2frame.PatternTree.GetItemPyData(grId)[1][:2]).T
1157	sqfile = open(sqfilename,'w')
1158	grfile = open(grfilename,'w')
1159	sqfile.write('#T S(Q) %s\n'%(export))
1160	grfile.write('#T G(R) %s\n'%(export))
1161	sqfile.write('#L Q S(Q)\n')
1162	grfile.write('#L R G(R)\n')
1163	for q,sq in sqdata:
1164	sqfile.write("%15.6g %15.6g\n" % (q,sq))
1165	sqfile.close()
1166	for r,gr in grdata:
1167	grfile.write("%15.6g %15.6g\n" % (r,gr))
1168	grfile.close()
1169
1170	def PeakListSave(G2frame,file,peaks):
1171	'Save powder peaks to a data file'
1172	print 'save peak list to file: ',G2frame.peaklistfile
1173	if not peaks:
1174	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1175	try:
1176	result = dlg.ShowModal()
1177	finally:
1178	dlg.Destroy()
1179	return
1180	for peak in peaks:
1181	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1182	(peak[0],peak[2],peak[4],peak[6]))
1183	print 'peak list saved'
1184
1185	def IndexPeakListSave(G2frame,peaks):
1186	'Save powder peaks from the indexing list'
1187	file = open(G2frame.peaklistfile,'wa')
1188	print 'save index peak list to file: ',G2frame.peaklistfile
1189	wx.BeginBusyCursor()
1190	try:
1191	if not peaks:
1192	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1193	try:
1194	result = dlg.ShowModal()
1195	finally:
1196	dlg.Destroy()
1197	return
1198	for peak in peaks:
1199	file.write("%12.6f\n" % (peak[7]))
1200	file.close()
1201	finally:
1202	wx.EndBusyCursor()
1203	print 'index peak list saved'
1204
1205	def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1206	'''Create a new phase dict with default values for various parameters
1207
1208	:param str Name: Name for new Phase
1209
1210	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1211	defaults to data for P 1
1212
1213	:param list cell: unit cell parameter list; defaults to
1214	[1.0,1.0,1.0,90.,90,90.,1.]
1215
1216	'''
1217	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1218	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1219	phaseData = {
1220	'ranId':ran.randint(0,sys.maxint),
1221	'General':{
1222	'Name':Name,
1223	'Type':'nuclear',
1224	'AtomPtrs':[3,1,7,9],
1225	'SGData':SGData,
1226	'Cell':[False,]+cell,
1227	'Pawley dmin':1.0,
1228	'Data plot type':'None',
1229	'SH Texture':{
1230	'Order':0,
1231	'Model':'cylindrical',
1232	'Sample omega':[False,0.0],
1233	'Sample chi':[False,0.0],
1234	'Sample phi':[False,0.0],
1235	'SH Coeff':[False,{}],
1236	'SHShow':False,
1237	'PFhkl':[0,0,1],
1238	'PFxyz':[0,0,1],
1239	'PlotType':'Pole figure'}},
1240	'Atoms':[],
1241	'Drawing':{},
1242	'Histograms':{},
1243	'Pawley ref':[],
1244	'RBModels':{},
1245	}
1246	if Super and Super.get('Use',False):
1247	phaseData['General'].update({'Type':'modulated','Super':True,'SuperSg':Super['ssSymb']})
1248	phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])
1249	phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1250
1251	return phaseData
1252
1253	class MultipleChoicesDialog(wx.Dialog):
1254	'''A dialog that offers a series of choices, each with a
1255	title and a wx.Choice widget. Intended to be used Modally.
1256	typical input:
1257
1258	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1259	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1260
1261	selections are placed in self.chosen when OK is pressed
1262	'''
1263	def __init__(self,choicelist,headinglist,
1264	head='Select options',
1265	title='Please select from options below',
1266	parent=None):
1267	self.chosen = []
1268	wx.Dialog.__init__(
1269	self,parent,wx.ID_ANY,head,
1270	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1271	panel = wx.Panel(self)
1272	mainSizer = wx.BoxSizer(wx.VERTICAL)
1273	mainSizer.Add((10,10),1)
1274	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1275	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1276	self.ChItems = []
1277	for choice,lbl in zip(choicelist,headinglist):
1278	mainSizer.Add((10,10),1)
1279	self.chosen.append(0)
1280	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1281	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1282	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1283	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1284
1285	OkBtn = wx.Button(panel,-1,"Ok")
1286	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1287	cancelBtn = wx.Button(panel,-1,"Cancel")
1288	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1289	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1290	btnSizer.Add((20,20),1)
1291	btnSizer.Add(OkBtn)
1292	btnSizer.Add((20,20),1)
1293	btnSizer.Add(cancelBtn)
1294	btnSizer.Add((20,20),1)
1295	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1296	panel.SetSizer(mainSizer)
1297	panel.Fit()
1298	self.Fit()
1299
1300	def OnOk(self,event):
1301	parent = self.GetParent()
1302	if parent is not None: parent.Raise()
1303	# save the results from the choice widgets
1304	self.chosen = []
1305	for w in self.ChItems:
1306	self.chosen.append(w.GetSelection())
1307	self.EndModal(wx.ID_OK)
1308
1309	def OnCancel(self,event):
1310	parent = self.GetParent()
1311	if parent is not None: parent.Raise()
1312	self.chosen = []
1313	self.EndModal(wx.ID_CANCEL)
1314
1315	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1316	confirmoverwrite=True, parent=None,
1317	multipleselect=False):
1318	'''If the filename is a zip file, extract a file from that
1319	archive.
1320
1321	:param list Selection: used to predefine the name of the file
1322	to be extracted. Filename case and zip directory name are
1323	ignored in selection; the first matching file is used.
1324
1325	:param bool confirmread: if True asks the user to confirm before expanding
1326	the only file in a zip
1327
1328	:param bool confirmoverwrite: if True asks the user to confirm
1329	before overwriting if the extracted file already exists
1330
1331	:param bool multipleselect: if True allows more than one zip
1332	file to be extracted, a list of file(s) is returned.
1333	If only one file is present, do not ask which one, otherwise
1334	offer a list of choices (unless selection is used).
1335
1336	:returns: the name of the file that has been created or a
1337	list of files (see multipleselect)
1338
1339	If the file is not a zipfile, return the name of the input file.
1340	If the zipfile is empty or no file has been selected, return None
1341	'''
1342	import zipfile # do this now, since we can save startup time by doing this only on need
1343	import shutil
1344	zloc = os.path.split(filename)[0]
1345	if not zipfile.is_zipfile(filename):
1346	#print("not zip")
1347	return filename
1348
1349	z = zipfile.ZipFile(filename,'r')
1350	zinfo = z.infolist()
1351
1352	if len(zinfo) == 0:
1353	#print('Zip has no files!')
1354	zlist = [-1]
1355	if selection:
1356	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1357	if selection.lower() in choices:
1358	zlist = [choices.index(selection.lower())]
1359	else:
1360	print('debug: file '+str(selection)+' was not found in '+str(filename))
1361	zlist = [-1]
1362	elif len(zinfo) == 1 and confirmread:
1363	result = wx.ID_NO
1364	dlg = wx.MessageDialog(
1365	parent,
1366	'Is file '+str(zinfo[0].filename)+
1367	' what you want to extract from '+
1368	str(os.path.split(filename)[1])+'?',
1369	'Confirm file',
1370	wx.YES_NO \| wx.ICON_QUESTION)
1371	try:
1372	result = dlg.ShowModal()
1373	finally:
1374	dlg.Destroy()
1375	if result == wx.ID_NO:
1376	zlist = [-1]
1377	else:
1378	zlist = [0]
1379	elif len(zinfo) == 1:
1380	zlist = [0]
1381	elif multipleselect:
1382	# select one or more from a from list
1383	choices = [i.filename for i in zinfo]
1384	dlg = G2gd.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1385	'Choose file(s)',choices)
1386	if dlg.ShowModal() == wx.ID_OK:
1387	zlist = dlg.GetSelections()
1388	else:
1389	zlist = []
1390	dlg.Destroy()
1391	else:
1392	# select one from a from list
1393	choices = [i.filename for i in zinfo]
1394	dlg = wx.SingleChoiceDialog(parent,
1395	'Select file to extract from zip file'+str(filename),'Choose file',
1396	choices,)
1397	if dlg.ShowModal() == wx.ID_OK:
1398	zlist = [dlg.GetSelection()]
1399	else:
1400	zlist = [-1]
1401	dlg.Destroy()
1402
1403	outlist = []
1404	for zindex in zlist:
1405	if zindex >= 0:
1406	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1407	if os.path.exists(efil) and confirmoverwrite:
1408	result = wx.ID_NO
1409	dlg = wx.MessageDialog(parent,
1410	'File '+str(efil)+' already exists. OK to overwrite it?',
1411	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1412	try:
1413	result = dlg.ShowModal()
1414	finally:
1415	dlg.Destroy()
1416	if result == wx.ID_NO:
1417	zindex = -1
1418	if zindex >= 0:
1419	# extract the file to the current directory, regardless of it's original path
1420	#z.extract(zinfo[zindex],zloc)
1421	eloc,efil = os.path.split(zinfo[zindex].filename)
1422	outfile = os.path.join(zloc, efil)
1423	fpin = z.open(zinfo[zindex])
1424	fpout = file(outfile, "wb")
1425	shutil.copyfileobj(fpin, fpout)
1426	fpin.close()
1427	fpout.close()
1428	outlist.append(outfile)
1429	z.close()
1430	if multipleselect and len(outlist) >= 1:
1431	return outlist
1432	elif len(outlist) == 1:
1433	return outlist[0]
1434	else:
1435	return None
1436
1437	######################################################################
1438	# base classes for reading various types of data files
1439	# not used directly, only by subclassing
1440	######################################################################
1441	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1442	P1SGData = SGData
1443	class ImportBaseclass(object):
1444	'''Defines a base class for the reading of input files (diffraction
1445	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1446	for an explanation on how to use a subclass of this class.
1447	'''
1448	class ImportException(Exception):
1449	'''Defines an Exception that is used when an import routine hits an expected error,
1450	usually in .Reader.
1451
1452	Good practice is that the Reader should define a value in self.errors that
1453	tells the user some information about what is wrong with their file.
1454	'''
1455	pass
1456
1457	def __init__(self,
1458	formatName,
1459	longFormatName=None,
1460	extensionlist=[],
1461	strictExtension=False,
1462	):
1463	self.formatName = formatName # short string naming file type
1464	if longFormatName: # longer string naming file type
1465	self.longFormatName = longFormatName
1466	else:
1467	self.longFormatName = formatName
1468	# define extensions that are allowed for the file type
1469	# for windows, remove any extensions that are duplicate, as case is ignored
1470	if sys.platform == 'windows' and extensionlist:
1471	extensionlist = list(set([s.lower() for s in extensionlist]))
1472	self.extensionlist = extensionlist
1473	# If strictExtension is True, the file will not be read, unless
1474	# the extension matches one in the extensionlist
1475	self.strictExtension = strictExtension
1476	self.errors = ''
1477	self.warnings = ''
1478	# used for readers that will use multiple passes to read
1479	# more than one data block
1480	self.repeat = False
1481	self.selections = []
1482	self.repeatcount = 0
1483	self.readfilename = '?'
1484	#print 'created',self.__class__
1485
1486	def ReInitialize(self):
1487	'Reinitialize the Reader to initial settings'
1488	self.errors = ''
1489	self.warnings = ''
1490	self.repeat = False
1491	self.repeatcount = 0
1492	self.readfilename = '?'
1493
1494	def BlockSelector(self, ChoiceList, ParentFrame=None,
1495	title='Select a block',
1496	size=None, header='Block Selector',
1497	useCancel=True):
1498	''' Provide a wx dialog to select a block if the file contains more
1499	than one set of data and one must be selected
1500	'''
1501	if useCancel:
1502	dlg = wx.SingleChoiceDialog(
1503	ParentFrame,title, header,ChoiceList)
1504	else:
1505	dlg = wx.SingleChoiceDialog(
1506	ParentFrame,title, header,ChoiceList,
1507	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1508	if size: dlg.SetSize(size)
1509	dlg.CenterOnParent()
1510	if dlg.ShowModal() == wx.ID_OK:
1511	sel = dlg.GetSelection()
1512	return sel
1513	else:
1514	return None
1515	dlg.Destroy()
1516
1517	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1518	title='Select a block',size=None, header='Block Selector'):
1519	'''Provide a wx dialog to select a block of data if the
1520	file contains more than one set of data and one must be
1521	selected.
1522
1523	:returns: a list of the selected blocks
1524	'''
1525	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1526	wx.CHOICEDLG_STYLE)
1527	dlg.CenterOnParent()
1528	if size: dlg.SetSize(size)
1529	if dlg.ShowModal() == wx.ID_OK:
1530	sel = dlg.GetSelections()
1531	else:
1532	return []
1533	dlg.Destroy()
1534	selected = []
1535	if len(ChoiceList) in sel:
1536	return range(len(ChoiceList))
1537	else:
1538	return sel
1539	return selected
1540
1541	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1542	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1543	widget. Typical input:
1544
1545	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1546
1547	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1548
1549	optional keyword parameters are: head (window title) and title
1550	returns a list of selected indicies for each choice (or None)
1551	'''
1552	result = None
1553	dlg = MultipleChoicesDialog(choicelist,headinglist,
1554	parent=ParentFrame, **kwargs)
1555	dlg.CenterOnParent()
1556	if dlg.ShowModal() == wx.ID_OK:
1557	result = dlg.chosen
1558	dlg.Destroy()
1559	return result
1560
1561	def ShowBusy(self):
1562	wx.BeginBusyCursor()
1563	wx.Yield() # make it happen now!
1564
1565	def DoneBusy(self):
1566	wx.EndBusyCursor()
1567	wx.Yield() # make it happen now!
1568
1569	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1570	# '''This method must be supplied in the child class to read the file.
1571	# if the read fails either return False or raise an Exception
1572	# preferably of type ImportException.
1573	# '''
1574	# #start reading
1575	# raise ImportException("Error occurred while...")
1576	# self.errors += "Hint for user on why the error occur
1577	# return False # if an error occurs
1578	# return True # if read OK
1579
1580	def ExtensionValidator(self, filename):
1581	'''This methods checks if the file has the correct extension
1582	Return False if this filename will not be supported by this reader
1583	Return True if the extension matches the list supplied by the reader
1584	Return None if the reader allows un-registered extensions
1585	'''
1586	if filename:
1587	ext = os.path.splitext(filename)[1]
1588	if sys.platform == 'windows': ext = ext.lower()
1589	if ext in self.extensionlist: return True
1590	if self.strictExtension: return False
1591	return None
1592
1593	def ContentsValidator(self, filepointer):
1594	'''This routine will attempt to determine if the file can be read
1595	with the current format.
1596	This will typically be overridden with a method that
1597	takes a quick scan of [some of]
1598	the file contents to do a "sanity" check if the file
1599	appears to match the selected format.
1600	Expected to be called via self.Validator()
1601	'''
1602	#filepointer.seek(0) # rewind the file pointer
1603	return True
1604
1605	def CIFValidator(self, filepointer):
1606	'''A :meth:`ContentsValidator` for use to validate CIF files.
1607	'''
1608	for i,l in enumerate(filepointer):
1609	if i >= 1000: return True
1610	'''Encountered only blank lines or comments in first 1000
1611	lines. This is unlikely, but assume it is CIF anyway, since we are
1612	even less likely to find a file with nothing but hashes and
1613	blank lines'''
1614	line = l.strip()
1615	if len(line) == 0: # ignore blank lines
1616	continue
1617	elif line.startswith('#'): # ignore comments
1618	continue
1619	elif line.startswith('data_'): # on the right track, accept this file
1620	return True
1621	else: # found something invalid
1622	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1623	self.errors += ' '+str(l)
1624	self.errors += ' Note: a CIF should only have blank lines or comments before'
1625	self.errors += ' a data_ statement begins a block.'
1626	return False
1627
1628	class ImportPhase(ImportBaseclass):
1629	'''Defines a base class for the reading of files with coordinates
1630
1631	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1632	in :meth:`GSASII.GSASII.OnImportPhase`.
1633	See :ref:`Writing a Import Routine<Import_Routines>`
1634	for an explanation on how to use this class.
1635
1636	'''
1637	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1638	strictExtension=False,):
1639	# call parent __init__
1640	ImportBaseclass.__init__(self,formatName,longFormatName,
1641	extensionlist,strictExtension)
1642	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1643	self.Constraints = None
1644
1645	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1646	title='Select a phase', size=None,header='Phase Selector'):
1647	''' Provide a wx dialog to select a phase if the file contains more
1648	than one phase
1649	'''
1650	return self.BlockSelector(ChoiceList,ParentFrame,title,
1651	size,header)
1652
1653	class ImportStructFactor(ImportBaseclass):
1654	'''Defines a base class for the reading of files with tables
1655	of structure factors.
1656
1657	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1658	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1659	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1660	:meth:`Reader`.
1661
1662	See :ref:`Writing a Import Routine<Import_Routines>`
1663	for an explanation on how to use import classes in general. The specifics
1664	for reading a structure factor histogram require that
1665	the ``Reader()`` routine in the import
1666	class need to do only a few things: It
1667	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1668	and set :attr:`Parameters` with the instrument parameters
1669	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1670	'''
1671	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1672	strictExtension=False,):
1673	ImportBaseclass.__init__(self,formatName,longFormatName,
1674	extensionlist,strictExtension)
1675
1676	# define contents of Structure Factor entry
1677	self.Parameters = []
1678	'self.Parameters is a list with two dicts for data parameter settings'
1679	self.InitParameters()
1680	self.RefDict = {'RefList':[],'FF':[],'Super':0}
1681	self.Banks = [] #for multi bank data (usually TOF)
1682	'''self.RefDict is a dict containing the reflection information, as read from the file.
1683	Item 'RefList' contains the reflection information. See the
1684	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1685	for the contents of each row. Dict element 'FF'
1686	contains the form factor values for each element type; if this entry
1687	is left as initialized (an empty list) it will be initialized as needed later.
1688	'''
1689	def ReInitialize(self):
1690	'Reinitialize the Reader to initial settings'
1691	ImportBaseclass.ReInitialize(self)
1692	self.InitParameters()
1693	self.Banks = [] #for multi bank data (usually TOF)
1694	self.RefDict = {'RefList':[],'FF':[],'Super':0}
1695
1696	def InitParameters(self):
1697	'initialize the instrument parameters structure'
1698	Lambda = 0.70926
1699	HistType = 'SXC'
1700	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1701	'Lam':[Lambda,Lambda]
1702	}, {}]
1703	'Parameters is a list with two dicts for data parameter settings'
1704
1705	def UpdateParameters(self,Type=None,Wave=None):
1706	'Revise the instrument parameters'
1707	if Type is not None:
1708	self.Parameters[0]['Type'] = [Type,Type]
1709	if Wave is not None:
1710	self.Parameters[0]['Lam'] = [Wave,Wave]
1711
1712	######################################################################
1713	class ImportPowderData(ImportBaseclass):
1714	'''Defines a base class for the reading of files with powder data.
1715
1716	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1717	in :meth:`GSASII.GSASII.OnImportPowder`.
1718	See :ref:`Writing a Import Routine<Import_Routines>`
1719	for an explanation on how to use this class.
1720	'''
1721	def __init__(self,
1722	formatName,
1723	longFormatName=None,
1724	extensionlist=[],
1725	strictExtension=False,
1726	):
1727	ImportBaseclass.__init__(self,formatName,
1728	longFormatName,
1729	extensionlist,
1730	strictExtension)
1731	self.clockWd = None # used in TOF
1732	self.ReInitialize()
1733
1734	def ReInitialize(self):
1735	'Reinitialize the Reader to initial settings'
1736	ImportBaseclass.ReInitialize(self)
1737	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1738	self.powderdata = [] # Powder dataset
1739	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1740	np.array(x), # x-axis values
1741	np.array(y), # powder pattern intensities
1742	np.array(w), # 1/sig(intensity)^2 values (weights)
1743	np.array(yc), # calc. intensities (zero)
1744	np.array(yb), # calc. background (zero)
1745	np.array(yd), # obs-calc profiles
1746	'''
1747	self.comments = []
1748	self.idstring = ''
1749	self.Sample = G2pdG.SetDefaultSample()
1750	self.GSAS = None # used in TOF
1751	self.repeat_instparm = True # Should a parm file be
1752	# used for multiple histograms?
1753	self.instparm = None # name hint from file of instparm to use
1754	self.instfile = '' # full path name to instrument parameter file
1755	self.instbank = '' # inst parm bank number
1756	self.instmsg = '' # a label that gets printed to show
1757	# where instrument parameters are from
1758	self.numbanks = 1
1759	self.instdict = {} # place items here that will be transferred to the instrument parameters
1760	self.pwdparms = {} # place parameters that are transferred directly to the tree
1761	# here (typically from an existing GPX file)
1762	######################################################################
1763	class ImportSmallAngleData(ImportBaseclass):
1764	'''Defines a base class for the reading of files with small angle data.
1765	See :ref:`Writing a Import Routine<Import_Routines>`
1766	for an explanation on how to use this class.
1767	'''
1768	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1769	strictExtension=False,):
1770
1771	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1772	strictExtension)
1773	self.ReInitialize()
1774
1775	def ReInitialize(self):
1776	'Reinitialize the Reader to initial settings'
1777	ImportBaseclass.ReInitialize(self)
1778	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1779	self.smallangledata = [] # SASD dataset
1780	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1781	np.array(x), # x-axis values
1782	np.array(y), # powder pattern intensities
1783	np.array(w), # 1/sig(intensity)^2 values (weights)
1784	np.array(yc), # calc. intensities (zero)
1785	np.array(yd), # obs-calc profiles
1786	np.array(yb), # preset bkg
1787	'''
1788	self.comments = []
1789	self.idstring = ''
1790	self.Sample = G2pdG.SetDefaultSample()
1791	self.GSAS = None # used in TOF
1792	self.clockWd = None # used in TOF
1793	self.numbanks = 1
1794	self.instdict = {} # place items here that will be transferred to the instrument parameters
1795	######################################################################
1796	class ExportBaseclass(object):
1797	'''Defines a base class for the exporting of GSAS-II results.
1798
1799	This class is subclassed in the various exports/G2export_*.py files. Those files
1800	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
1801	appropriate menu items for each one and the .Exporter method is called
1802	directly from the menu item.
1803
1804	'''
1805	def __init__(self,
1806	G2frame,
1807	formatName,
1808	extension,
1809	longFormatName=None,
1810	):
1811	self.G2frame = G2frame
1812	self.formatName = formatName # short string naming file type
1813	self.extension = extension
1814	if longFormatName: # longer string naming file type
1815	self.longFormatName = longFormatName
1816	else:
1817	self.longFormatName = formatName
1818	self.OverallParms = {}
1819	self.Phases = {}
1820	self.Histograms = {}
1821	self.powderDict = {}
1822	self.xtalDict = {}
1823	self.parmDict = {}
1824	self.sigDict = {}
1825	# updated in InitExport:
1826	self.currentExportType = None # type of export that has been requested
1827	# updated in ExportSelect (when used):
1828	self.phasenam = None # a list of selected phases
1829	self.histnam = None # a list of selected histograms
1830	self.filename = None # name of file to be written (single export) or template (multiple files)
1831	self.dirname = '' # name of directory where file(s) will be written
1832	self.fullpath = '' # name of file being written -- full path
1833
1834	# items that should be defined in a subclass of this class
1835	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1836	# The following types are defined: 'project', "phase", "powder", "single"
1837	self.multiple = False # set as True if the class can export multiple phases or histograms
1838	# self.multiple is ignored for "project" exports
1839
1840	def InitExport(self,event):
1841	'''Determines the type of menu that called the Exporter and
1842	misc initialization.
1843	'''
1844	self.filename = None # name of file to be written (single export)
1845	self.dirname = '' # name of file to be written (multiple export)
1846	if event:
1847	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1848
1849	def MakePWDRfilename(self,hist):
1850	'''Make a filename root (no extension) from a PWDR histogram name
1851
1852	:param str hist: the histogram name in data tree (starts with "PWDR ")
1853	'''
1854	file0 = ''
1855	file1 = hist[5:]
1856	# replace repeated blanks
1857	while file1 != file0:
1858	file0 = file1
1859	file1 = file0.replace(' ',' ').strip()
1860	file0 = file1.replace('Azm= ','A')
1861	# if angle has unneeded decimal places on aziumuth, remove them
1862	if file0[-3:] == '.00': file0 = file0[:-3]
1863	file0 = file0.replace('.','_')
1864	file0 = file0.replace(' ','_')
1865	return file0
1866
1867	def ExportSelect(self,AskFile='ask'):
1868	'''Selects histograms or phases when needed. Sets a default file name when
1869	requested in self.filename; always sets a default directory in self.dirname.
1870
1871	:param bool AskFile: Determines how this routine processes getting a
1872	location to store the current export(s).
1873
1874	* if AskFile is 'ask' (default option), get the name of the file to be written;
1875	self.filename and self.dirname are always set. In the case where
1876	multiple files must be generated, the export routine should do this
1877	based on self.filename as a template.
1878	* if AskFile is 'dir', get the name of the directory to be used;
1879	self.filename is not used, but self.dirname is always set. The export routine
1880	will always generate the file name.
1881	* if AskFile is 'single', get only the name of the directory to be used when
1882	multiple items will be written (as multiple files) are used
1883	or a complete file name is requested when a single file
1884	name is selected. self.dirname is always set and self.filename used
1885	only when a single file is selected.
1886	* if AskFile is 'default', creates a name of the file to be used from
1887	the name of the project (.gpx) file. If the project has not been saved,
1888	then the name of file is requested.
1889	self.filename and self.dirname are always set. In the case where
1890	multiple file names must be generated, the export routine should do this
1891	based on self.filename.
1892	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1893	file. If the project has not been saved, then a directory is requested.
1894	self.filename is not used.
1895
1896	:returns: True in case of an error
1897	'''
1898
1899	numselected = 1
1900	if self.currentExportType == 'phase':
1901	if len(self.Phases) == 0:
1902	self.G2frame.ErrorDialog(
1903	'Empty project',
1904	'Project does not contain any phases.')
1905	return True
1906	elif len(self.Phases) == 1:
1907	self.phasenam = self.Phases.keys()
1908	elif self.multiple:
1909	choices = sorted(self.Phases.keys())
1910	phasenum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1911	if phasenum is None: return True
1912	self.phasenam = [choices[i] for i in phasenum]
1913	if not self.phasenam: return True
1914	numselected = len(self.phasenam)
1915	else:
1916	choices = sorted(self.Phases.keys())
1917	phasenum = G2gd.ItemSelector(choices,self.G2frame)
1918	if phasenum is None: return True
1919	self.phasenam = [choices[phasenum]]
1920	numselected = len(self.phasenam)
1921	elif self.currentExportType == 'single':
1922	if len(self.xtalDict) == 0:
1923	self.G2frame.ErrorDialog(
1924	'Empty project',
1925	'Project does not contain any single crystal data.')
1926	return True
1927	elif len(self.xtalDict) == 1:
1928	self.histnam = self.xtalDict.values()
1929	elif self.multiple:
1930	choices = sorted(self.xtalDict.values())
1931	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1932	if not hnum: return True
1933	self.histnam = [choices[i] for i in hnum]
1934	numselected = len(self.histnam)
1935	else:
1936	choices = sorted(self.xtalDict.values())
1937	hnum = G2gd.ItemSelector(choices,self.G2frame)
1938	if hnum is None: return True
1939	self.histnam = [choices[hnum]]
1940	numselected = len(self.histnam)
1941	elif self.currentExportType == 'powder':
1942	if len(self.powderDict) == 0:
1943	self.G2frame.ErrorDialog(
1944	'Empty project',
1945	'Project does not contain any powder data.')
1946	return True
1947	elif len(self.powderDict) == 1:
1948	self.histnam = self.powderDict.values()
1949	elif self.multiple:
1950	choices = sorted(self.powderDict.values())
1951	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1952	if not hnum: return True
1953	self.histnam = [choices[i] for i in hnum]
1954	numselected = len(self.histnam)
1955	else:
1956	choices = sorted(self.powderDict.values())
1957	hnum = G2gd.ItemSelector(choices,self.G2frame)
1958	if hnum is None: return True
1959	self.histnam = [choices[hnum]]
1960	numselected = len(self.histnam)
1961	elif self.currentExportType == 'image':
1962	if len(self.Histograms) == 0:
1963	self.G2frame.ErrorDialog(
1964	'Empty project',
1965	'Project does not contain any images.')
1966	return True
1967	elif len(self.Histograms) == 1:
1968	self.histnam = self.Histograms.keys()
1969	else:
1970	choices = sorted(self.Histograms.keys())
1971	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1972	if self.multiple:
1973	if not hnum: return True
1974	self.histnam = [choices[i] for i in hnum]
1975	else:
1976	if hnum is None: return True
1977	self.histnam = [choices[hnum]]
1978	numselected = len(self.histnam)
1979	if self.currentExportType == 'map':
1980	# search for phases with maps
1981	mapPhases = []
1982	choices = []
1983	for phasenam in sorted(self.Phases):
1984	phasedict = self.Phases[phasenam] # pointer to current phase info
1985	if len(phasedict['General']['Map'].get('rho',[])):
1986	mapPhases.append(phasenam)
1987	if phasedict['General']['Map'].get('Flip'):
1988	choices.append('Charge flip map: '+str(phasenam))
1989	elif phasedict['General']['Map'].get('MapType'):
1990	choices.append(
1991	str(phasedict['General']['Map'].get('MapType'))
1992	+ ' map: ' + str(phasenam))
1993	else:
1994	choices.append('unknown map: '+str(phasenam))
1995	# select a map if needed
1996	if len(mapPhases) == 0:
1997	self.G2frame.ErrorDialog(
1998	'Empty project',
1999	'Project does not contain any maps.')
2000	return True
2001	elif len(mapPhases) == 1:
2002	self.phasenam = mapPhases
2003	else:
2004	phasenum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
2005	if self.multiple:
2006	if not phasenum: return True
2007	self.phasenam = [mapPhases[i] for i in phasenum]
2008	else:
2009	if phasenum is None: return True
2010	self.phasenam = [mapPhases[phasenum]]
2011	numselected = len(self.phasenam)
2012
2013	# items selected, now set self.dirname and usually self.filename
2014	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
2015	AskFile == 'default' and not self.G2frame.GSASprojectfile
2016	):
2017	filename = self.askSaveFile()
2018	if not filename: return True
2019	self.dirname,self.filename = os.path.split(filename)
2020	elif AskFile == 'dir' or AskFile == 'single' or (
2021	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
2022	):
2023	self.dirname = self.askSaveDirectory()
2024	if not self.dirname: return True
2025	elif AskFile == 'default-dir' or AskFile == 'default':
2026	self.dirname,self.filename = os.path.split(
2027	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
2028	)
2029	else:
2030	raise Exception('This should not happen!')
2031
2032	def loadParmDict(self):
2033	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
2034	refined values to those from the last cycle and set the uncertainties for the
2035	refined parameters in another dict (self.sigDict).
2036
2037	Expands the parm & sig dicts to include values derived from constraints.
2038	'''
2039	self.parmDict = {}
2040	self.sigDict = {}
2041	rigidbodyDict = {}
2042	covDict = {}
2043	consDict = {}
2044	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2045	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2046	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2047	while item:
2048	name = self.G2frame.PatternTree.GetItemText(item)
2049	if name == 'Rigid bodies':
2050	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
2051	elif name == 'Covariance':
2052	covDict = self.G2frame.PatternTree.GetItemPyData(item)
2053	elif name == 'Constraints':
2054	consDict = self.G2frame.PatternTree.GetItemPyData(item)
2055	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2056	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
2057	self.parmDict.update(rbDict)
2058	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
2059	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables = G2stIO.GetPhaseData(
2060	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
2061	self.parmDict.update(phaseDict)
2062	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
2063	Phases,Histograms,Print=False,resetRefList=False)
2064	self.parmDict.update(hapDict)
2065	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
2066	self.parmDict.update(histDict)
2067	self.parmDict.update(zip(
2068	covDict.get('varyList',[]),
2069	covDict.get('variables',[])))
2070	self.sigDict = dict(zip(
2071	covDict.get('varyList',[]),
2072	covDict.get('sig',[])))
2073	# expand to include constraints: first compile a list of constraints
2074	constList = []
2075	for item in consDict:
2076	if item.startswith('_'): continue
2077	constList += consDict[item]
2078	# now process the constraints
2079	G2mv.InitVars()
2080	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
2081	varyList = covDict.get('varyListStart')
2082	if varyList is None and len(constDict) == 0:
2083	# no constraints can use varyList
2084	varyList = covDict.get('varyList')
2085	elif varyList is None:
2086	# old GPX file from before pre-constraint varyList is saved
2087	print ' * Old refinement: Please use Calculate/Refine to redo *'
2088	raise Exception(' * Export aborted *')
2089	else:
2090	varyList = list(varyList)
2091	try:
2092	groups,parmlist = G2mv.GroupConstraints(constDict)
2093	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
2094	except:
2095	# this really should not happen
2096	print ' * ERROR - constraints are internally inconsistent *'
2097	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
2098	print 'Errors',errmsg
2099	if warnmsg: print 'Warnings',warnmsg
2100	raise Exception(' * CIF creation aborted *')
2101	# add the constrained values to the parameter dictionary
2102	G2mv.Dict2Map(self.parmDict,varyList)
2103	# and add their uncertainties into the esd dictionary (sigDict)
2104	if covDict.get('covMatrix') is not None:
2105	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
2106
2107	def loadTree(self):
2108	'''Load the contents of the data tree into a set of dicts
2109	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2110	& self.xtalDict)
2111
2112	* The childrenless data tree items are overall parameters/controls for the
2113	entire project and are placed in self.OverallParms
2114	* Phase items are placed in self.Phases
2115	* Data items are placed in self.Histogram. The key for these data items
2116	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2117	'''
2118	self.OverallParms = {}
2119	self.powderDict = {}
2120	self.xtalDict = {}
2121	self.Phases = {}
2122	self.Histograms = {}
2123	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2124	histType = None
2125	if self.currentExportType == 'phase':
2126	# if exporting phases load them here
2127	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2128	if not sub:
2129	print 'no phases found'
2130	return True
2131	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2132	while item:
2133	phaseName = self.G2frame.PatternTree.GetItemText(item)
2134	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2135	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2136	return
2137	elif self.currentExportType == 'single':
2138	histType = 'HKLF'
2139	elif self.currentExportType == 'powder':
2140	histType = 'PWDR'
2141	elif self.currentExportType == 'image':
2142	histType = 'IMG'
2143
2144	if histType: # Loading just one kind of tree entry
2145	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2146	while item:
2147	name = self.G2frame.PatternTree.GetItemText(item)
2148	if name.startswith(histType):
2149	if self.Histograms.get(name): # there is already an item with this name
2150	print('Histogram name '+str(name)+' is repeated. Renaming')
2151	if name[-1] == '9':
2152	name = name[:-1] + '10'
2153	elif name[-1] in '012345678':
2154	name = name[:-1] + str(int(name[-1])+1)
2155	else:
2156	name += '-1'
2157	self.Histograms[name] = {}
2158	# the main info goes into Data, but the 0th
2159	# element contains refinement results, carry
2160	# that over too now.
2161	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2162	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2163	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2164	while item2:
2165	child = self.G2frame.PatternTree.GetItemText(item2)
2166	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2167	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2168	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2169	# index powder and single crystal histograms by number
2170	for hist in self.Histograms:
2171	if hist.startswith("PWDR"):
2172	d = self.powderDict
2173	elif hist.startswith("HKLF"):
2174	d = self.xtalDict
2175	else:
2176	return
2177	i = self.Histograms[hist].get('hId')
2178	if i is None and not d.keys():
2179	i = 0
2180	elif i is None or i in d.keys():
2181	i = max(d.keys())+1
2182	d[i] = hist
2183	return
2184	# else standard load: using all interlinked phases and histograms
2185	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2186	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2187	while item:
2188	name = self.G2frame.PatternTree.GetItemText(item)
2189	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2190	if not item2:
2191	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2192	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2193	# index powder and single crystal histograms
2194	for hist in self.Histograms:
2195	i = self.Histograms[hist]['hId']
2196	if hist.startswith("PWDR"):
2197	self.powderDict[i] = hist
2198	elif hist.startswith("HKLF"):
2199	self.xtalDict[i] = hist
2200
2201	def dumpTree(self,mode='type'):
2202	'''Print out information on the data tree dicts loaded in loadTree
2203	'''
2204	print '\nOverall'
2205	if mode == 'type':
2206	def Show(arg): return type(arg)
2207	else:
2208	def Show(arg): return arg
2209	for key in self.OverallParms:
2210	print ' ',key,Show(self.OverallParms[key])
2211	print 'Phases'
2212	for key1 in self.Phases:
2213	print ' ',key1,Show(self.Phases[key1])
2214	print 'Histogram'
2215	for key1 in self.Histograms:
2216	print ' ',key1,Show(self.Histograms[key1])
2217	for key2 in self.Histograms[key1]:
2218	print ' ',key2,Show(self.Histograms[key1][key2])
2219
2220	def defaultSaveFile(self):
2221	return os.path.abspath(
2222	os.path.splitext(self.G2frame.GSASprojectfile
2223	)[0]+self.extension)
2224
2225	def askSaveFile(self):
2226	'''Ask the user to supply a file name
2227
2228	:returns: a file name (str) or None if Cancel is pressed
2229	'''
2230	defnam = os.path.splitext(
2231	os.path.split(self.G2frame.GSASprojectfile)[1]
2232	)[0]+self.extension
2233	dlg = wx.FileDialog(
2234	self.G2frame, 'Input name for file to write', '.', defnam,
2235	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2236	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2237	dlg.CenterOnParent()
2238	try:
2239	if dlg.ShowModal() == wx.ID_OK:
2240	filename = dlg.GetPath()
2241	# make sure extension is correct
2242	filename = os.path.splitext(filename)[0]+self.extension
2243	else:
2244	filename = None
2245	finally:
2246	dlg.Destroy()
2247	return filename
2248
2249	def askSaveDirectory(self):
2250	'''Ask the user to supply a directory name. Path name is used as the
2251	starting point for the next export path search.
2252
2253	:returns: a directory name (str) or None if Cancel is pressed
2254	'''
2255	if self.G2frame.exportDir:
2256	startdir = self.G2frame.exportDir
2257	elif self.G2frame.GSASprojectfile:
2258	startdir = os.path.split(self.G2frame.GSASprojectfile)[0]
2259	elif self.G2frame.dirname:
2260	startdir = self.G2frame.dirname
2261	else:
2262	startdir = ''
2263	dlg = wx.DirDialog(
2264	self.G2frame, 'Input directory where file(s) will be written', startdir,
2265	wx.DD_DEFAULT_STYLE)
2266	dlg.CenterOnParent()
2267	try:
2268	if dlg.ShowModal() == wx.ID_OK:
2269	filename = dlg.GetPath()
2270	self.G2frame.exportDir = filename
2271	else:
2272	filename = None
2273	finally:
2274	dlg.Destroy()
2275	return filename
2276
2277	# Tools for file writing.
2278	def OpenFile(self,fil=None,mode='w'):
2279	'''Open the output file
2280
2281	:param str fil: The name of the file to open. If None (default)
2282	the name defaults to self.dirname + self.filename.
2283	If an extension is supplied, it is not overridded,
2284	but if not, the default extension is used.
2285	:returns: the file object opened by the routine which is also
2286	saved as self.fp
2287	'''
2288	if not fil:
2289	if not os.path.splitext(self.filename)[1]:
2290	self.filename += self.extension
2291	fil = os.path.join(self.dirname,self.filename)
2292	self.fullpath = fil
2293	self.fp = open(fil,mode)
2294	return self.fp
2295
2296	def Write(self,line):
2297	'''write a line of output, attaching a line-end character
2298
2299	:param str line: the text to be written.
2300	'''
2301	self.fp.write(line+'\n')
2302	def CloseFile(self,fp=None):
2303	'''Close a file opened in OpenFile
2304
2305	:param file fp: the file object to be closed. If None (default)
2306	file object self.fp is closed.
2307	'''
2308	if fp is None:
2309	fp = self.fp
2310	self.fp = None
2311	fp.close()
2312	# Tools to pull information out of the data arrays
2313	def GetCell(self,phasenam):
2314	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2315
2316	:param str phasenam: the name for the selected phase
2317	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2318	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2319	cell values and `cellSig` has their uncertainties.
2320	"""
2321	phasedict = self.Phases[phasenam] # pointer to current phase info
2322	try:
2323	pfx = str(phasedict['pId'])+'::'
2324	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2325	cellSig = G2stIO.getCellEsd(pfx,
2326	phasedict['General']['SGData'],A,
2327	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2328	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2329	return cellList,cellSig
2330	except KeyError:
2331	cell = phasedict['General']['Cell'][1:]
2332	return cell,7*[0]
2333
2334	def GetAtoms(self,phasenam):
2335	"""Gets the atoms associated with a phase. Can be used with standard
2336	or macromolecular phases
2337
2338	:param str phasenam: the name for the selected phase
2339	:returns: a list of items for eac atom where each item is a list containing:
2340	label, typ, mult, xyz, and td, where
2341
2342	* label and typ are the atom label and the scattering factor type (str)
2343	* mult is the site multiplicity (int)
2344	* xyz is contains a list with four pairs of numbers:
2345	x, y, z and fractional occupancy and
2346	their standard uncertainty (or a negative value)
2347	* td is contains a list with either one or six pairs of numbers:
2348	if one number it is U\ :sub:`iso` and with six numbers it is
2349	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2350	paired with their standard uncertainty (or a negative value)
2351	"""
2352	phasedict = self.Phases[phasenam] # pointer to current phase info
2353	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2354	cfrac = cx+3
2355	fpfx = str(phasedict['pId'])+'::Afrac:'
2356	atomslist = []
2357	for i,at in enumerate(phasedict['Atoms']):
2358	if phasedict['General']['Type'] == 'macromolecular':
2359	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2360	else:
2361	label = at[ct-1]
2362	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2363	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2364	mult = at[cs+1]
2365	typ = at[ct]
2366	xyz = []
2367	for j,v in enumerate(('x','y','z')):
2368	val = at[cx+j]
2369	pfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2370	sig = self.sigDict.get(pfx,-0.000009)
2371	xyz.append((val,sig))
2372	xyz.append((fval,fsig))
2373	td = []
2374	if at[cia] == 'I':
2375	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2376	val = self.parmDict.get(pfx,at[cia+1])
2377	sig = self.sigDict.get(pfx,-0.0009)
2378	td.append((val,sig))
2379	else:
2380	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2381	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2382	val = self.parmDict.get(pfx,at[cia+2+i])
2383	sig = self.sigDict.get(pfx,-0.0009)
2384	td.append((val,sig))
2385	atomslist.append((label,typ,mult,xyz,td))
2386	return atomslist
2387	######################################################################
2388
2389	def ReadCIF(URLorFile):
2390	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2391	(from James Hester).
2392	The open routine gets confused with DOS names that begin with a letter and colon
2393	"C:\dir\" so this routine will try to open the passed name as a file and if that
2394	fails, try it as a URL
2395
2396	:param str URLorFile: string containing a URL or a file name. Code will try first
2397	to open it as a file and then as a URL.
2398
2399	:returns: a PyCifRW CIF object.
2400	'''
2401	import CifFile as cif # PyCifRW from James Hester
2402
2403	# alternate approach:
2404	#import urllib
2405	#ciffile = 'file:'+urllib.pathname2url(filename)
2406
2407	try:
2408	fp = open(URLorFile,'r')
2409	cf = cif.ReadCif(fp)
2410	fp.close()
2411	return cf
2412	except IOError:
2413	return cif.ReadCif(URLorFile)
2414
2415	if __name__ == '__main__':
2416	app = wx.PySimpleApp()
2417	frm = wx.Frame(None) # create a frame
2418	frm.Show(True)
2419	filename = '/tmp/notzip.zip'
2420	filename = '/tmp/all.zip'
2421	#filename = '/tmp/11bmb_7652.zip'
2422
2423	#selection=None, confirmoverwrite=True, parent=None
2424	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2425	print ExtractFileFromZip(filename,multipleselect=True)
2426	#confirmread=False, confirmoverwrite=False)
2427
2428	# choicelist=[ ('a','b','c'),
2429	# ('test1','test2'),('no choice',)]
2430	# titles = [ 'a, b or c', 'tests', 'No option here']
2431	# dlg = MultipleChoicesDialog(
2432	# choicelist,titles,
2433	# parent=frm)
2434	# if dlg.ShowModal() == wx.ID_OK:
2435	# print 'Got OK'

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