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source: trunk/GSASIIIO.py @ 1770

Last change on this file since 1770 was 1770, checked in by vondreele, 10 years ago
moved MultipleChoicesDialog? and SingleChoiceDialog? from G2grid to G2ctrls
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2015-03-30 18:39:46 +0000 (Mon, 30 Mar 2015) $
4	# $Author: vondreele $
5	# $Revision: 1770 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 1770 2015-03-30 18:39:46Z 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: 1770 $")
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 is treated as zero'
51	if S.strip():
52	return float(S)
53	else:
54	return 0.0
55
56	def sint(S):
57	'Convert a string to int. An empty field is treated as zero'
58	if S.strip():
59	return int(S)
60	else:
61	return 0
62
63	def trim(val):
64	'''Simplify a string containing leading and trailing spaces
65	as well as newlines, tabs, repeated spaces etc. into a shorter and
66	more simple string, by replacing all ranges of whitespace
67	characters with a single space.
68
69	:param str val: the string to be simplified
70
71	:returns: the (usually) shortened version of the string
72	'''
73	return re.sub('\s+', ' ', val).strip()
74
75	def makeInstDict(names,data,codes):
76	inst = dict(zip(names,zip(data,data,codes)))
77	for item in inst:
78	inst[item] = list(inst[item])
79	return inst
80
81	def FileDlgFixExt(dlg,file):
82	'this is needed to fix a problem in linux wx.FileDialog'
83	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
84	if ext not in file:
85	file += ext
86	return file
87
88	def GetPowderPeaks(fileName):
89	'Read powder peaks from a file'
90	sind = lambda x: math.sin(x*math.pi/180.)
91	asind = lambda x: 180.*math.asin(x)/math.pi
92	Cuka = 1.54052
93	File = open(fileName,'Ur')
94	Comments = []
95	peaks = []
96	S = File.readline()
97	while S:
98	if S[:1] == '#':
99	Comments.append(S[:-1])
100	else:
101	item = S.split()
102	if len(item) == 1:
103	peaks.append([float(item[0]),1.0])
104	elif len(item) > 1:
105	peaks.append([float(item[0]),float(item[0])])
106	S = File.readline()
107	File.close()
108	if Comments:
109	print 'Comments on file:'
110	for Comment in Comments: print Comment
111	Peaks = []
112	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
113	for peak in peaks:
114	dsp = peak[0]
115	sth = Cuka/(2.0*dsp)
116	if sth < 1.0:
117	tth = 2.0*asind(sth)
118	else:
119	break
120	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
121	else: #2-thetas - assume Cuka (for now)
122	for peak in peaks:
123	tth = peak[0]
124	dsp = Cuka/(2.0*sind(tth/2.0))
125	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
126	return Comments,Peaks
127
128	def CheckImageFile(G2frame,imagefile):
129	'''Get an new image file name if the specified one does not
130	exist
131
132	:param wx.Frame G2frame: main GSAS-II Frame and data object
133
134	:param str imagefile: name of image file
135
136	:returns: imagefile, if it exists, or the name of a file
137	that does exist or False if the user presses Cancel
138
139	'''
140	if not os.path.exists(imagefile):
141	print 'Image file '+imagefile+' not found'
142	fil = imagefile.replace('\\','/') # windows?!
143	# see if we can find a file with same name or in a similarly named sub-dir
144	pth,fil = os.path.split(fil)
145	prevpth = None
146	while pth and pth != prevpth:
147	prevpth = pth
148	if os.path.exists(os.path.join(G2frame.dirname,fil)):
149	print 'found image file '+os.path.join(G2frame.dirname,fil)
150	return os.path.join(G2frame.dirname,fil)
151	pth,enddir = os.path.split(pth)
152	fil = os.path.join(enddir,fil)
153	# not found as a subdirectory, drop common parts of path for last saved & image file names
154	# if image was .../A/B/C/imgs/ima.ge
155	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
156	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
157	Controls = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
158	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
159	imgPath = imagefile.replace('\\','/').split('/')
160	for p1,p2 in zip(gpxPath,imgPath):
161	if p1 == p2:
162	gpxPath.pop(0),imgPath.pop(0)
163	else:
164	break
165	fil = os.path.join(*imgPath) # file with non-common prefix elements
166	prevpth = None
167	pth = os.path.abspath(G2frame.dirname)
168	while pth and pth != prevpth:
169	prevpth = pth
170	if os.path.exists(os.path.join(pth,fil)):
171	print 'found image file '+os.path.join(pth,fil)
172	return os.path.join(pth,fil)
173	pth,enddir = os.path.split(pth)
174	GSASIIpath.IPyBreak()
175
176	if not os.path.exists(imagefile):
177	dlg = wx.FileDialog(G2frame, 'Previous image file not found; open here', '.', '',\
178	'Any image file (.edf;.tif;.tiff;.mar;.ge;.avg;.sum;.img)\
179	\|.edf;.tif;.tiff;.mar;.ge;.avg;.sum;.img\|\
180	European detector file (.edf)\|.edf\|\
181	Any detector tif (.tif;.tiff)\|.tif;.tiff\|\
182	MAR file (.mar)\|.mar\|\
183	GE Image (.ge;.avg;.sum)\|.ge;.avg;.sum\|\
184	ADSC Image (.img)\|.img\|\
185	All files (.)\|.',wx.OPEN\|wx.CHANGE_DIR)
186	try:
187	dlg.SetFilename(''+ospath.split(imagefile)[1])
188	if dlg.ShowModal() == wx.ID_OK:
189	imagefile = dlg.GetPath()
190	else:
191	imagefile = False
192	finally:
193	dlg.Destroy()
194	return imagefile
195
196	def EditImageParms(parent,Data,Comments,Image,filename):
197	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
198	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
199	def onClose(event):
200	dlg.EndModal(wx.ID_OK)
201	mainsizer = wx.BoxSizer(wx.VERTICAL)
202	h,w = Image.shape[:2]
203	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,
204	'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
205	0,wx.ALIGN_LEFT\|wx.ALL, 2)
206
207	vsizer = wx.BoxSizer(wx.HORIZONTAL)
208	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
209	0,wx.ALIGN_LEFT\|wx.ALL, 2)
210	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
211	vsizer.Add(wdgt)
212	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
213
214	vsizer = wx.BoxSizer(wx.HORIZONTAL)
215	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
216	0,wx.ALIGN_LEFT\|wx.ALL, 2)
217	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
218	size=(50,-1))
219	vsizer.Add(wdgt)
220	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),
221	wx.ALIGN_LEFT\|wx.ALL, 2)
222	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,
223	size=(50,-1))
224	vsizer.Add(wdgt)
225	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
226
227	vsizer = wx.BoxSizer(wx.HORIZONTAL)
228	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
229	0,wx.ALIGN_LEFT\|wx.ALL, 2)
230	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
231	vsizer.Add(wdgt)
232	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
233
234	vsizer = wx.BoxSizer(wx.HORIZONTAL)
235	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
236	0,wx.ALIGN_LEFT\|wx.ALL, 2)
237	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,
238	size=(75,-1))
239	vsizer.Add(wdgt)
240	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),
241	wx.ALIGN_LEFT\|wx.ALL, 2)
242	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,
243	size=(75,-1))
244	vsizer.Add(wdgt)
245	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
246
247	vsizer = wx.BoxSizer(wx.HORIZONTAL)
248	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
249	0,wx.ALIGN_LEFT\|wx.ALL, 2)
250	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
251	vsizer.Add(wdgt)
252	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
253
254	btnsizer = wx.StdDialogButtonSizer()
255	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
256	OKbtn.SetDefault()
257	OKbtn.Bind(wx.EVT_BUTTON,onClose)
258	btnsizer.AddButton(OKbtn) # not sure why this is needed
259	btnsizer.Realize()
260	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
261	dlg.SetSizer(mainsizer)
262	dlg.CenterOnParent()
263	dlg.ShowModal()
264
265	def GetImageData(G2frame,imagefile,imageOnly=False):
266	'''Read an image with the file reader keyed by the
267	file extension
268
269	:param wx.Frame G2frame: main GSAS-II Frame and data object.
270
271	:param str imagefile: name of image file
272
273	:param bool imageOnly: If True return only the image,
274	otherwise (default) return more (see below)
275
276	:returns: an image as a numpy array or a list of four items:
277	Comments, Data, Npix and the Image, as selected by imageOnly
278
279	'''
280	ext = ospath.splitext(imagefile)[1]
281	Comments = []
282	Image = None
283	if ext == '.tif' or ext == '.tiff':
284	Comments,Data,Npix,Image = GetTifData(imagefile)
285	if Npix == 0:
286	print("GetTifData failed to read "+str(filename)+" Trying PIL")
287	import scipy.misc
288	Image = scipy.misc.imread(imagefile,flatten=True)
289	Npix = Image.size
290	Comments = ['no metadata']
291	Data = {'wavelength': 0.1, 'pixelSize': [200, 200], 'distance': 100.0}
292	Data['size'] = list(Image.shape)
293	Data['center'] = [int(i/2) for i in Image.shape]
294	if not imageOnly:
295	EditImageParms(G2frame,Data,Comments,Image,imagefile)
296	elif ext == '.edf':
297	Comments,Data,Npix,Image = GetEdfData(imagefile)
298	elif ext == '.img':
299	Comments,Data,Npix,Image = GetImgData(imagefile)
300	Image[0][0] = 0
301	elif ext == '.mar3450' or ext == '.mar2300':
302	Comments,Data,Npix,Image = GetMAR345Data(imagefile)
303	elif ext in ['.sum','.avg'] or 'ge' in ext:
304	Comments,Data,Npix,Image = GetGEsumData(imagefile)
305	elif ext == '.G2img':
306	Comments,Data,Npix,Image = GetG2Image(imagefile)
307	elif ext == '.png':
308	Comments,Data,Npix,Image = GetPNGData(imagefile)
309	if not imageOnly:
310	EditImageParms(G2frame,Data,Comments,Image,imagefile)
311	else:
312	print 'Extension for file '+imagefile+' not recognized'
313	if Image is None:
314	raise Exception('No image read')
315	if imageOnly:
316	if TRANSP:
317	return Image.T
318	else:
319	return Image
320	else:
321	if TRANSP:
322	return Comments,Data,Npix,Image.T
323	else:
324	return Comments,Data,Npix,Image
325
326	def PutG2Image(filename,Comments,Data,Npix,image):
327	'Write an image as a python pickle - might be better as an .edf file?'
328	File = open(filename,'wb')
329	cPickle.dump([Comments,Data,Npix,image],File,1)
330	File.close()
331	return
332
333	def GetG2Image(filename):
334	'Read an image as a python pickle'
335	File = open(filename,'rb')
336	Comments,Data,Npix,image = cPickle.load(File)
337	File.close()
338	return Comments,Data,Npix,image
339
340	def GetEdfData(filename,imageOnly=False):
341	'Read European detector data edf file'
342	import struct as st
343	import array as ar
344	if not imageOnly:
345	print 'Read European detector data edf file: ',filename
346	File = open(filename,'rb')
347	fileSize = os.stat(filename).st_size
348	head = File.read(3072)
349	lines = head.split('\n')
350	sizexy = [0,0]
351	pixSize = [154,154] #Pixium4700?
352	cent = [0,0]
353	wave = 1.54187 #default <CuKa>
354	dist = 1000.
355	head = ['European detector data',]
356	for line in lines:
357	line = line.replace(';',' ').strip()
358	fields = line.split()
359	if 'Dim_1' in line:
360	sizexy[0] = int(fields[2])
361	elif 'Dim_2' in line:
362	sizexy[1] = int(fields[2])
363	elif 'DataType' in line:
364	dType = fields[2]
365	elif 'wavelength' in line:
366	wave = float(fields[2])
367	elif 'Size' in line:
368	imSize = int(fields[2])
369	elif 'DataType' in lines:
370	dType = fields[2]
371	elif 'pixel_size_x' in line:
372	pixSize[0] = float(fields[2])
373	elif 'pixel_size_y' in line:
374	pixSize[1] = float(fields[2])
375	elif 'beam_center_x' in line:
376	cent[0] = float(fields[2])
377	elif 'beam_center_y' in line:
378	cent[1] = float(fields[2])
379	elif 'refined_distance' in line:
380	dist = float(fields[2])
381	if line:
382	head.append(line)
383	else: #blank line at end of header
384	break
385	File.seek(fileSize-imSize)
386	if dType == 'UnsignedShort':
387	image = np.array(ar.array('H',File.read(imSize)),dtype=np.int32)
388	elif dType == 'UnsignedInt':
389	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
390	elif dType == 'UnsignedLong':
391	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
392	elif dType == 'SignedInteger':
393	image = np.array(ar.array('l',File.read(imSize)),dtype=np.int32)
394	image = np.reshape(image,(sizexy[1],sizexy[0]))
395	data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'size':sizexy}
396	Npix = sizexy[0]*sizexy[1]
397	File.close()
398	if imageOnly:
399	return image
400	else:
401	return head,data,Npix,image
402
403	def GetGEsumData(filename,imageOnly=False):
404	'Read SUM file as produced at 1-ID from G.E. images'
405	import struct as st
406	import array as ar
407	if not imageOnly:
408	print 'Read GE sum file: ',filename
409	File = open(filename,'rb')
410	if '.sum' in filename:
411	head = ['GE detector sum data from APS 1-ID',]
412	sizexy = [2048,2048]
413	elif '.avg' in filename or '.ge' in filename:
414	head = ['GE detector avg or ge* data from APS 1-ID',]
415	sizexy = [2048,2048]
416	else:
417	head = ['GE detector raw data from APS 1-ID',]
418	File.seek(18)
419	size,nframes = st.unpack('<ih',File.read(6))
420	sizexy = [2048,2048]
421	pos = 8192
422	File.seek(pos)
423	Npix = sizexy[0]*sizexy[1]
424	if '.sum' in filename:
425	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.int32)
426	elif '.avg' in filename or '.ge' in filename:
427	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
428	else:
429	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
430	while nframes > 1:
431	image += np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
432	nframes -= 1
433	image = np.reshape(image,(sizexy[1],sizexy[0]))
434	data = {'pixelSize':[200,200],'wavelength':0.15,'distance':250.0,'center':[204.8,204.8],'size':sizexy}
435	File.close()
436	if imageOnly:
437	return image
438	else:
439	return head,data,Npix,image
440
441	def GetImgData(filename,imageOnly=False):
442	'Read an ADSC image file'
443	import struct as st
444	import array as ar
445	if not imageOnly:
446	print 'Read ADSC img file: ',filename
447	File = open(filename,'rb')
448	head = File.read(511)
449	lines = head.split('\n')
450	head = []
451	center = [0,0]
452	for line in lines[1:-2]:
453	line = line.strip()[:-1]
454	if line:
455	if 'SIZE1' in line:
456	size = int(line.split('=')[1])
457	Npix = size*size
458	elif 'WAVELENGTH' in line:
459	wave = float(line.split('=')[1])
460	elif 'BIN' in line:
461	if line.split('=')[1] == '2x2':
462	pixel=(102,102)
463	else:
464	pixel = (51,51)
465	elif 'DISTANCE' in line:
466	distance = float(line.split('=')[1])
467	elif 'CENTER_X' in line:
468	center[0] = float(line.split('=')[1])
469	elif 'CENTER_Y' in line:
470	center[1] = float(line.split('=')[1])
471	head.append(line)
472	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center,'size':[size,size]}
473	image = []
474	row = 0
475	pos = 512
476	File.seek(pos)
477	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
478	image = np.reshape(image,(sizexy[1],sizexy[0]))
479	# image = np.zeros(shape=(size,size),dtype=np.int32)
480	# while row < size:
481	# File.seek(pos)
482	# line = ar.array('H',File.read(2*size))
483	# image[row] = np.asarray(line)
484	# row += 1
485	# pos += 2*size
486	File.close()
487	if imageOnly:
488	return image
489	else:
490	return lines[1:-2],data,Npix,image
491
492	def GetMAR345Data(filename,imageOnly=False):
493	'Read a MAR-345 image plate image'
494	import array as ar
495	import struct as st
496	try:
497	import pack_f as pf
498	except:
499	msg = wx.MessageDialog(None, message="Unable to load the GSAS MAR image decompression, pack_f",
500	caption="Import Error",
501	style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
502	msg.ShowModal()
503	return None,None,None,None
504
505	if not imageOnly:
506	print 'Read Mar345 file: ',filename
507	File = open(filename,'rb')
508	head = File.read(4095)
509	numbers = st.unpack('<iiiiiiiiii',head[:40])
510	lines = head[128:].split('\n')
511	head = []
512	for line in lines:
513	line = line.strip()
514	if 'PIXEL' in line:
515	values = line.split()
516	pixel = (int(values[2]),int(values[4])) #in microns
517	elif 'WAVELENGTH' in line:
518	wave = float(line.split()[1])
519	elif 'DISTANCE' in line:
520	distance = float(line.split()[1]) #in mm
521	elif 'CENTER' in line:
522	values = line.split()
523	center = [float(values[2])/10.,float(values[4])/10.] #make in mm from pixels
524	if line:
525	head.append(line)
526	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center}
527	for line in head:
528	if 'FORMAT' in line[0:6]:
529	items = line.split()
530	size = int(items[1])
531	Npix = size*size
532	pos = 4096
533	data['size'] = [size,size]
534	File.seek(pos)
535	line = File.read(8)
536	while 'CCP4' not in line: #get past overflow list for now
537	line = File.read(8)
538	pos += 8
539	pos += 37
540	File.seek(pos)
541	raw = File.read()
542	File.close()
543	image = np.zeros(shape=(size,size),dtype=np.int32)
544	image = np.flipud(pf.pack_f(len(raw),raw,size,image).T) #transpose to get it right way around & flip
545	if imageOnly:
546	return image
547	else:
548	return head,data,Npix,image
549
550	def GetPNGData(filename,imageOnly=False):
551	'''Read an image in a png format, assumes image is converted from CheMin tif file
552	so default parameters are that machine.
553	'''
554	import scipy.misc
555	Image = scipy.misc.imread(filename,flatten=True)
556	Npix = Image.size
557	Comments = ['no metadata']
558	pixy = list(Image.shape)
559	sizexy = [40,40]
560	Data = {'wavelength': 1.78892, 'pixelSize': sizexy, 'distance': 18.0,'size':pixy}
561	Data['center'] = [pixy[0]sizexy[0]/1000,pixy[1]sizexy[1]/2000]
562	if imageOnly:
563	return Image.T
564	else:
565	return Comments,Data,Npix,Image.T
566
567	def GetTifData(filename,imageOnly=False):
568	'''Read an image in a pseudo-tif format,
569	as produced by a wide variety of software, almost always
570	incorrectly in some way.
571	'''
572	import struct as st
573	try:
574	import Image as Im
575	except ImportError:
576	try:
577	from PIL import Image as Im
578	except ImportError:
579	print "PIL/pillow Image module not present. TIFs cannot be read without this"
580	raise Exception("PIL/pillow Image module not found")
581	import array as ar
582	import ReadMarCCDFrame as rmf
583	File = open(filename,'rb')
584	dataType = 5
585	center = [None,None]
586	wavelength = None
587	distance = None
588	try:
589	Meta = open(filename+'.metadata','Ur')
590	head = Meta.readlines()
591	for line in head:
592	line = line.strip()
593	if 'dataType=' in line:
594	dataType = int(line.split('=')[1])
595	Meta.close()
596	except IOError:
597	print 'no metadata file found - will try to read file anyway'
598	head = ['no metadata file found',]
599
600	tag = File.read(2)
601	byteOrd = '<'
602	if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
603	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
604	elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
605	byteOrd = '>'
606	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
607	else:
608	lines = ['not a detector tiff file',]
609	return lines,0,0,0
610	File.seek(IFD) #get number of directory entries
611	NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
612	IFD = {}
613	nSlice = 1
614	for ied in range(NED):
615	Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
616	nVal = st.unpack(byteOrd+'i',File.read(4))[0]
617	if DEBUG: print 'Try:',Tag,Type,nVal
618	if Type == 1:
619	Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
620	elif Type == 2:
621	Value = st.unpack(byteOrd+'i',File.read(4))
622	elif Type == 3:
623	Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
624	x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
625	elif Type == 4:
626	if Tag in [273,279]:
627	nSlice = nVal
628	nVal = 1
629	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
630	elif Type == 5:
631	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
632	elif Type == 11:
633	Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
634	IFD[Tag] = [Type,nVal,Value]
635	if DEBUG: print Tag,IFD[Tag]
636	sizexy = [IFD[256][2][0],IFD[257][2][0]]
637	[nx,ny] = sizexy
638	Npix = nx*ny
639	if 34710 in IFD:
640	if not imageOnly:
641	print 'Read MAR CCD tiff file: ',filename
642	marFrame = rmf.marFrame(File,byteOrd,IFD)
643	image = np.flipud(np.array(np.asarray(marFrame.image),dtype=np.int32))
644	tifType = marFrame.filetitle
645	pixy = [marFrame.pixelsizeX/1000.0,marFrame.pixelsizeY/1000.0]
646	head = marFrame.outputHead()
647	# extract resonable wavelength from header
648	wavelength = marFrame.sourceWavelength*1e-5
649	wavelength = (marFrame.opticsWavelength > 0) and marFrame.opticsWavelength*1e-5 or wavelength
650	wavelength = (wavelength <= 0) and None or wavelength
651	# extract resonable distance from header
652	distance = (marFrame.startXtalToDetector+marFrame.endXtalToDetector)*5e-4
653	distance = (distance <= 0) and marFrame.xtalToDetector*1e-3 or distance
654	distance = (distance <= 0) and None or distance
655	# extract resonable center from header
656	center = [marFrame.beamXmarFrame.pixelsizeX1e-9,marFrame.beamYmarFrame.pixelsizeY1e-9]
657	center = (center[0] != 0 and center[1] != 0) and center or [None,None]
658	#print head,tifType,pixy
659	elif nSlice > 1: #CheMin multislice tif file!
660	tifType = 'CheMin'
661	pixy = [40,40]
662	image = np.flipud(np.array(Im.open(filename)))*10.
663	distance = 18.0
664	center = [pixy[0]*sizexy[0]/2000,0] #the CheMin beam stop is here
665	wavelength = 1.78892
666	elif 272 in IFD:
667	ifd = IFD[272]
668	File.seek(ifd[2][0])
669	S = File.read(ifd[1])
670	if 'PILATUS' in S:
671	tifType = 'Pilatus'
672	dataType = 0
673	pixy = [172,172]
674	File.seek(4096)
675	if not imageOnly:
676	print 'Read Pilatus tiff file: ',filename
677	image = ar.array('L',File.read(4*Npix))
678	image = np.array(np.asarray(image),dtype=np.int32)
679	else:
680	if IFD[258][2][0] == 16:
681	tifType = 'GE'
682	pixy = [200,200]
683	File.seek(8)
684	if not imageOnly:
685	print 'Read GE-detector tiff file: ',filename
686	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
687	elif IFD[258][2][0] == 32:
688	tifType = 'CHESS'
689	pixy = [200,200]
690	File.seek(8)
691	if not imageOnly:
692	print 'Read CHESS-detector tiff file: ',filename
693	image = np.array(ar.array('L',File.read(4*Npix)),dtype=np.int32)
694
695	elif 262 in IFD and IFD[262][2][0] > 4:
696	tifType = 'DND'
697	pixy = [158,158]
698	File.seek(512)
699	if not imageOnly:
700	print 'Read DND SAX/WAX-detector tiff file: ',filename
701	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
702	elif sizexy == [1536,1536]:
703	tifType = 'APS Gold'
704	pixy = [150,150]
705	File.seek(64)
706	if not imageOnly:
707	print 'Read Gold tiff file:',filename
708	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
709	elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
710	if IFD[273][2][0] == 8:
711	if IFD[258][2][0] == 32:
712	tifType = 'PE'
713	pixy = [200,200]
714	File.seek(8)
715	if not imageOnly:
716	print 'Read APS PE-detector tiff file: ',filename
717	if dataType == 5:
718	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
719	else:
720	image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
721	elif IFD[258][2][0] == 16:
722	tifType = 'MedOptics D1'
723	pixy = [46.9,46.9]
724	File.seek(8)
725	if not imageOnly:
726	print 'Read MedOptics D1 tiff file: ',filename
727	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
728
729	elif IFD[273][2][0] == 4096:
730	if sizexy[0] == 3072:
731	pixy = [73,73]
732	tifType = 'MAR225'
733	else:
734	pixy = [158,158]
735	tifType = 'MAR325'
736	File.seek(4096)
737	if not imageOnly:
738	print 'Read MAR CCD tiff file: ',filename
739	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
740	elif IFD[273][2][0] == 512:
741	tiftype = '11-ID-C'
742	pixy = [200,200]
743	File.seek(512)
744	if not imageOnly:
745	print 'Read 11-ID-C tiff file: ',filename
746	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
747	elif sizexy == [4096,4096]:
748	if IFD[273][2][0] == 8:
749	if IFD[258][2][0] == 16:
750	tifType = 'scanCCD'
751	pixy = [9,9]
752	File.seek(8)
753	if not imageOnly:
754	print 'Read APS scanCCD tiff file: ',filename
755	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
756	elif IFD[273][2][0] == 4096:
757	tifType = 'Rayonix'
758	pixy = [73.242,73.242]
759	File.seek(4096)
760	if not imageOnly:
761	print 'Read Rayonix MX300HE tiff file: ',filename
762	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
763	# elif sizexy == [960,960]:
764	# tiftype = 'PE-BE'
765	# pixy = (200,200)
766	# File.seek(8)
767	# if not imageOnly:
768	# print 'Read Gold tiff file:',filename
769	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
770
771	else:
772	lines = ['not a known detector tiff file',]
773	return lines,0,0,0
774
775	image = np.reshape(image,(sizexy[1],sizexy[0]))
776	center = (not center[0]) and [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000] or center
777	wavelength = (not wavelength) and 0.10 or wavelength
778	distance = (not distance) and 100.0 or distance
779	data = {'pixelSize':pixy,'wavelength':wavelength,'distance':distance,'center':center,'size':sizexy}
780	File.close()
781	if imageOnly:
782	return image
783	else:
784	return head,data,Npix,image
785
786	#def GetTifData(filename,imageOnly=False):
787	# import struct as st
788	# import array as ar
789	# File = open(filename,'rb')
790	# dataType = 5
791	# try:
792	# Meta = open(filename+'.metadata','Ur')
793	# head = Meta.readlines()
794	# for line in head:
795	# line = line.strip()
796	# if 'dataType=' in line:
797	# dataType = int(line.split('=')[1])
798	# Meta.close()
799	# except IOError:
800	# print 'no metadata file found - will try to read file anyway'
801	# head = ['no metadata file found',]
802	#
803	# tag = File.read(2)
804	# byteOrd = '<'
805	# if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
806	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
807	# elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
808	# byteOrd = '>'
809	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
810	# else:
811	# lines = ['not a detector tiff file',]
812	# return lines,0,0,0
813	# File.seek(IFD) #get number of directory entries
814	# NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
815	# IFD = {}
816	# for ied in range(NED):
817	# Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
818	# nVal = st.unpack(byteOrd+'i',File.read(4))[0]
819	# if Type == 1:
820	# Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
821	# elif Type == 2:
822	# Value = st.unpack(byteOrd+'i',File.read(4))
823	# elif Type == 3:
824	# Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
825	# x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
826	# elif Type == 4:
827	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
828	# elif Type == 5:
829	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
830	# elif Type == 11:
831	# Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
832	# IFD[Tag] = [Type,nVal,Value]
833	## print Tag,IFD[Tag]
834	# sizexy = [IFD[256][2][0],IFD[257][2][0]]
835	# [nx,ny] = sizexy
836	# Npix = nx*ny
837	# if 272 in IFD:
838	# ifd = IFD[272]
839	# File.seek(ifd[2][0])
840	# S = File.read(ifd[1])
841	# if 'PILATUS' in S:
842	# tifType = 'Pilatus'
843	# dataType = 0
844	# pixy = (172,172)
845	# File.seek(4096)
846	# if not imageOnly:
847	# print 'Read Pilatus tiff file: ',filename
848	# image = ar.array('L',File.read(4*Npix))
849	# image = np.array(np.asarray(image),dtype=np.int32)
850	# elif 262 in IFD and IFD[262][2][0] > 4:
851	# tifType = 'DND'
852	# pixy = (158,158)
853	# File.seek(512)
854	# if not imageOnly:
855	# print 'Read DND SAX/WAX-detector tiff file: ',filename
856	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
857	# elif sizexy == [1536,1536]:
858	# tifType = 'APS Gold'
859	# pixy = (150,150)
860	# File.seek(64)
861	# if not imageOnly:
862	# print 'Read Gold tiff file:',filename
863	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
864	# elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
865	# if IFD[273][2][0] == 8:
866	# if IFD[258][2][0] == 32:
867	# tifType = 'PE'
868	# pixy = (200,200)
869	# File.seek(8)
870	# if not imageOnly:
871	# print 'Read APS PE-detector tiff file: ',filename
872	# if dataType == 5:
873	# image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
874	# else:
875	# image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
876	# elif IFD[273][2][0] == 4096:
877	# if sizexy[0] == 3072:
878	# pixy = (73,73)
879	# tifType = 'MAR225'
880	# else:
881	# pixy = (158,158)
882	# tifType = 'MAR325'
883	# File.seek(4096)
884	# if not imageOnly:
885	# print 'Read MAR CCD tiff file: ',filename
886	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
887	# elif IFD[273][2][0] == 512:
888	# tiftype = '11-ID-C'
889	# pixy = [200,200]
890	# File.seek(512)
891	# if not imageOnly:
892	# print 'Read 11-ID-C tiff file: ',filename
893	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
894	# elif sizexy == [4096,4096]:
895	# if IFD[273][2][0] == 8:
896	# if IFD[258][2][0] == 16:
897	# tifType = 'scanCCD'
898	# pixy = (9,9)
899	# File.seek(8)
900	# if not imageOnly:
901	# print 'Read APS scanCCD tiff file: ',filename
902	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
903	# elif IFD[273][2][0] == 4096:
904	# tifType = 'Rayonix'
905	# pixy = (73.242,73.242)
906	# File.seek(4096)
907	# if not imageOnly:
908	# print 'Read Rayonix MX300HE tiff file: ',filename
909	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
910	## elif sizexy == [960,960]:
911	## tiftype = 'PE-BE'
912	## pixy = (200,200)
913	## File.seek(8)
914	## if not imageOnly:
915	## print 'Read Gold tiff file:',filename
916	## image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
917	#
918	# else:
919	# lines = ['not a known detector tiff file',]
920	# return lines,0,0,0
921	#
922	# image = np.reshape(image,(sizexy[1],sizexy[0]))
923	# center = [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000]
924	# data = {'pixelSize':pixy,'wavelength':0.10,'distance':100.0,'center':center,'size':sizexy}
925	# File.close()
926	# if imageOnly:
927	# return image
928	# else:
929	# return head,data,Npix,image
930	#
931	def ProjFileOpen(G2frame):
932	'Read a GSAS-II project file and load into the G2 data tree'
933	if not os.path.exists(G2frame.GSASprojectfile):
934	print ('\n*** Error attempt to open project file that does not exist:\n '+
935	str(G2frame.GSASprojectfile))
936	return
937	file = open(G2frame.GSASprojectfile,'rb')
938	print 'load from file: ',G2frame.GSASprojectfile
939	G2frame.SetTitle("GSAS-II data tree: "+
940	os.path.split(G2frame.GSASprojectfile)[1])
941	wx.BeginBusyCursor()
942	try:
943	while True:
944	try:
945	data = cPickle.load(file)
946	except EOFError:
947	break
948	datum = data[0]
949
950	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=datum[0])
951	if 'PWDR' in datum[0]:
952	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
953	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
954	G2frame.PatternTree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
955	elif datum[0].startswith('HKLF'):
956	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
957	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
958	G2frame.PatternTree.SetItemPyData(Id,datum[1])
959	else:
960	G2frame.PatternTree.SetItemPyData(Id,datum[1])
961	for datus in data[1:]:
962	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
963	#patch
964	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
965	if 'PWDR' in datum[0]:
966	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
967	else:
968	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
969	for item in datus[1][0]: #zip makes tuples - now make lists!
970	datus[1][0][item] = list(datus[1][0][item])
971	#end patch
972	G2frame.PatternTree.SetItemPyData(sub,datus[1])
973	if 'IMG' in datum[0]: #retrieve image default flag & data if set
974	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
975	if Data['setDefault']:
976	G2frame.imageDefault = Data
977	file.close()
978	print('project load successful')
979	G2frame.NewPlot = True
980	except:
981	msg = wx.MessageDialog(G2frame,message="Error reading file "+
982	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
983	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
984	msg.ShowModal()
985	finally:
986	wx.EndBusyCursor()
987	G2frame.Status.SetStatusText('To reorder tree items, use mouse RB to drag/drop them')
988
989	def ProjFileSave(G2frame):
990	'Save a GSAS-II project file'
991	if not G2frame.PatternTree.IsEmpty():
992	file = open(G2frame.GSASprojectfile,'wb')
993	print 'save to file: ',G2frame.GSASprojectfile
994	# stick the file name into the tree, if possible
995	try:
996	Controls = G2frame.PatternTree.GetItemPyData(
997	G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
998	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
999	except:
1000	pass
1001	wx.BeginBusyCursor()
1002	try:
1003	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
1004	while item:
1005	data = []
1006	name = G2frame.PatternTree.GetItemText(item)
1007	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
1008	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
1009	while item2:
1010	name = G2frame.PatternTree.GetItemText(item2)
1011	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
1012	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
1013	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1014	cPickle.dump(data,file,1)
1015	file.close()
1016	finally:
1017	wx.EndBusyCursor()
1018	print('project save successful')
1019
1020	def SaveIntegration(G2frame,PickId,data):
1021	'Save image integration results as powder pattern(s)'
1022	azms = G2frame.Integrate[1]
1023	X = G2frame.Integrate[2][:-1]
1024	N = len(X)
1025	Id = G2frame.PatternTree.GetItemParent(PickId)
1026	name = G2frame.PatternTree.GetItemText(Id)
1027	name = name.replace('IMG ',data['type']+' ')
1028	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
1029	if 'PWDR' in name:
1030	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
1031	codes = [0 for i in range(11)]
1032	elif 'SASD' in name:
1033	names = ['Type','Lam','Zero','Azimuth']
1034	codes = [0 for i in range(4)]
1035	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
1036	Xminmax = [X[0],X[-1]]
1037	LRazm = data['LRazimuth']
1038	Azms = []
1039	if data['fullIntegrate'] and data['outAzimuths'] == 1:
1040	Azms = [45.0,] #a poor man's average?
1041	else:
1042	for i,azm in enumerate(azms[:-1]):
1043	Azms.append(G2img.meanAzm(azm,azms[i+1]))
1044	for i,azm in enumerate(azms[:-1]):
1045	Aname = name+" Azm= %.2f"%(Azms[i])
1046	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
1047	nOcc = 0
1048	while item:
1049	Name = G2frame.PatternTree.GetItemText(item)
1050	if Aname in Name:
1051	nOcc += 1
1052	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1053	if nOcc:
1054	Aname += '(%d)'%(nOcc)
1055	Sample = G2pdG.SetDefaultSample()
1056	Sample['Gonio. radius'] = data['distance']
1057	Sample['Omega'] = data['GonioAngles'][0]
1058	Sample['Chi'] = data['GonioAngles'][1]
1059	Sample['Phi'] = data['GonioAngles'][2]
1060	if 'PWDR' in Aname:
1061	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!
1062	elif 'SASD' in Aname:
1063	Sample['Trans'] = data['SampleAbs'][0]
1064	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
1065	Y = G2frame.Integrate[0][i]
1066	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
1067	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=Aname)
1068	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
1069	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
1070	if 'PWDR' in Aname:
1071	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
1072	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
1073	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
1074	for item in inst[0]:
1075	inst[0][item] = list(inst[0][item])
1076	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
1077	if 'PWDR' in Aname:
1078	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1079	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
1080	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[[],[]])
1081	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
1082	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
1083	elif 'SASD' in Aname:
1084	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
1085	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1086	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
1087	valuesdict = {
1088	'wtFactor':1.0,
1089	'Dummy':False,
1090	'ranId':ran.randint(0,sys.maxint),
1091	'Offset':[0.0,0.0],'delOffset':0.02,'refOffset':-1.0,'refDelt':0.01,
1092	'qPlot':False,'dPlot':False,'sqrtPlot':False
1093	}
1094	G2frame.PatternTree.SetItemPyData(
1095	Id,[valuesdict,
1096	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
1097	return Id #last powder pattern generated
1098
1099	# def powderFxyeSave(G2frame,exports,powderfile):
1100	# 'Save a powder histogram as a GSAS FXYE file'
1101	# head,tail = ospath.split(powderfile)
1102	# name,ext = tail.split('.')
1103	# for i,export in enumerate(exports):
1104	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1105	# prmname = filename.strip(ext)+'prm'
1106	# prm = open(prmname,'w') #old style GSAS parm file
1107	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1108	# Inst = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, \
1109	# PickId, 'Instrument Parameters'))[0]
1110	# prm.write( ' 123456789012345678901234567890123456789012345678901234567890 '+'\n')
1111	# prm.write( 'INS BANK 1 '+'\n')
1112	# prm.write(('INS HTYPE %sR '+'\n')%(Inst['Type'][0]))
1113	# if 'Lam1' in Inst: #Ka1 & Ka2
1114	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam1'][0],Inst['Lam2'][0]))
1115	# elif 'Lam' in Inst: #single wavelength
1116	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam'][1],0.0))
1117	# prm.write( 'INS 1 IRAD 0 '+'\n')
1118	# prm.write( 'INS 1I HEAD '+'\n')
1119	# prm.write( 'INS 1I ITYP 0 0.0000 180.0000 1 '+'\n')
1120	# prm.write(('INS 1DETAZM%10.3f '+'\n')%(Inst['Azimuth'][0]))
1121	# prm.write( 'INS 1PRCF1 3 8 0.00100 '+'\n')
1122	# prm.write(('INS 1PRCF11 %15.6g%15.6g%15.6g%15.6g '+'\n')%(Inst['U'][1],Inst['V'][1],Inst['W'][1],0.0))
1123	# 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.))
1124	# prm.close()
1125	# file = open(filename,'w')
1126	# print 'save powder pattern to file: ',filename
1127	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1128	# file.write(powderfile+'\n')
1129	# file.write('Instrument parameter file:'+ospath.split(prmname)[1]+'\n')
1130	# file.write('BANK 1 %d %d CONS %.2f %.2f 0 0 FXYE\n'%(len(x),len(x),\
1131	# 100.x[0],100.(x[1]-x[0])))
1132	# s = list(np.sqrt(1./np.array(w)))
1133	# XYW = zip(x,y,s)
1134	# for X,Y,S in XYW:
1135	# file.write("%15.6g %15.6g %15.6g\n" % (100.*X,Y,max(S,1.0)))
1136	# file.close()
1137	# print 'powder pattern file '+filename+' written'
1138
1139	# def powderXyeSave(G2frame,exports,powderfile):
1140	# 'Save a powder histogram as a Topas XYE file'
1141	# head,tail = ospath.split(powderfile)
1142	# name,ext = tail.split('.')
1143	# for i,export in enumerate(exports):
1144	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1145	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1146	# file = open(filename,'w')
1147	# file.write('#%s\n'%(export))
1148	# print 'save powder pattern to file: ',filename
1149	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1150	# s = list(np.sqrt(1./np.array(w)))
1151	# XYW = zip(x,y,s)
1152	# for X,Y,W in XYW:
1153	# file.write("%15.6g %15.6g %15.6g\n" % (X,Y,W))
1154	# file.close()
1155	# print 'powder pattern file '+filename+' written'
1156
1157	def PDFSave(G2frame,exports):
1158	'Save a PDF G(r) and S(Q) in column formats'
1159	for export in exports:
1160	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1161	SQname = 'S(Q)'+export[4:]
1162	GRname = 'G(R)'+export[4:]
1163	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
1164	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
1165	sqId = G2gd.GetPatternTreeItemId(G2frame, PickId, SQname)
1166	grId = G2gd.GetPatternTreeItemId(G2frame, PickId, GRname)
1167	sqdata = np.array(G2frame.PatternTree.GetItemPyData(sqId)[1][:2]).T
1168	grdata = np.array(G2frame.PatternTree.GetItemPyData(grId)[1][:2]).T
1169	sqfile = open(sqfilename,'w')
1170	grfile = open(grfilename,'w')
1171	sqfile.write('#T S(Q) %s\n'%(export))
1172	grfile.write('#T G(R) %s\n'%(export))
1173	sqfile.write('#L Q S(Q)\n')
1174	grfile.write('#L R G(R)\n')
1175	for q,sq in sqdata:
1176	sqfile.write("%15.6g %15.6g\n" % (q,sq))
1177	sqfile.close()
1178	for r,gr in grdata:
1179	grfile.write("%15.6g %15.6g\n" % (r,gr))
1180	grfile.close()
1181
1182	def PeakListSave(G2frame,file,peaks):
1183	'Save powder peaks to a data file'
1184	print 'save peak list to file: ',G2frame.peaklistfile
1185	if not peaks:
1186	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1187	try:
1188	result = dlg.ShowModal()
1189	finally:
1190	dlg.Destroy()
1191	return
1192	for peak in peaks:
1193	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1194	(peak[0],peak[2],peak[4],peak[6]))
1195	print 'peak list saved'
1196
1197	def IndexPeakListSave(G2frame,peaks):
1198	'Save powder peaks from the indexing list'
1199	file = open(G2frame.peaklistfile,'wa')
1200	print 'save index peak list to file: ',G2frame.peaklistfile
1201	wx.BeginBusyCursor()
1202	try:
1203	if not peaks:
1204	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1205	try:
1206	result = dlg.ShowModal()
1207	finally:
1208	dlg.Destroy()
1209	return
1210	for peak in peaks:
1211	file.write("%12.6f\n" % (peak[7]))
1212	file.close()
1213	finally:
1214	wx.EndBusyCursor()
1215	print 'index peak list saved'
1216
1217	def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1218	'''Create a new phase dict with default values for various parameters
1219
1220	:param str Name: Name for new Phase
1221
1222	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1223	defaults to data for P 1
1224
1225	:param list cell: unit cell parameter list; defaults to
1226	[1.0,1.0,1.0,90.,90,90.,1.]
1227
1228	'''
1229	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1230	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1231	phaseData = {
1232	'ranId':ran.randint(0,sys.maxint),
1233	'General':{
1234	'Name':Name,
1235	'Type':'nuclear',
1236	'AtomPtrs':[3,1,7,9],
1237	'SGData':SGData,
1238	'Cell':[False,]+cell,
1239	'Pawley dmin':1.0,
1240	'Data plot type':'None',
1241	'SH Texture':{
1242	'Order':0,
1243	'Model':'cylindrical',
1244	'Sample omega':[False,0.0],
1245	'Sample chi':[False,0.0],
1246	'Sample phi':[False,0.0],
1247	'SH Coeff':[False,{}],
1248	'SHShow':False,
1249	'PFhkl':[0,0,1],
1250	'PFxyz':[0,0,1],
1251	'PlotType':'Pole figure'}},
1252	'Atoms':[],
1253	'Drawing':{},
1254	'Histograms':{},
1255	'Pawley ref':[],
1256	'RBModels':{},
1257	}
1258	if Super and Super.get('Use',False):
1259	phaseData['General'].update({'Type':'modulated','Super':True,'SuperSg':Super['ssSymb']})
1260	phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])
1261	phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1262
1263	return phaseData
1264
1265	class MultipleChoicesDialog(wx.Dialog):
1266	'''A dialog that offers a series of choices, each with a
1267	title and a wx.Choice widget. Intended to be used Modally.
1268	typical input:
1269
1270	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1271	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1272
1273	selections are placed in self.chosen when OK is pressed
1274	'''
1275	def __init__(self,choicelist,headinglist,
1276	head='Select options',
1277	title='Please select from options below',
1278	parent=None):
1279	self.chosen = []
1280	wx.Dialog.__init__(
1281	self,parent,wx.ID_ANY,head,
1282	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1283	panel = wx.Panel(self)
1284	mainSizer = wx.BoxSizer(wx.VERTICAL)
1285	mainSizer.Add((10,10),1)
1286	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1287	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1288	self.ChItems = []
1289	for choice,lbl in zip(choicelist,headinglist):
1290	mainSizer.Add((10,10),1)
1291	self.chosen.append(0)
1292	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1293	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1294	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1295	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1296
1297	OkBtn = wx.Button(panel,-1,"Ok")
1298	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1299	cancelBtn = wx.Button(panel,-1,"Cancel")
1300	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1301	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1302	btnSizer.Add((20,20),1)
1303	btnSizer.Add(OkBtn)
1304	btnSizer.Add((20,20),1)
1305	btnSizer.Add(cancelBtn)
1306	btnSizer.Add((20,20),1)
1307	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1308	panel.SetSizer(mainSizer)
1309	panel.Fit()
1310	self.Fit()
1311
1312	def OnOk(self,event):
1313	parent = self.GetParent()
1314	if parent is not None: parent.Raise()
1315	# save the results from the choice widgets
1316	self.chosen = []
1317	for w in self.ChItems:
1318	self.chosen.append(w.GetSelection())
1319	self.EndModal(wx.ID_OK)
1320
1321	def OnCancel(self,event):
1322	parent = self.GetParent()
1323	if parent is not None: parent.Raise()
1324	self.chosen = []
1325	self.EndModal(wx.ID_CANCEL)
1326
1327	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1328	confirmoverwrite=True, parent=None,
1329	multipleselect=False):
1330	'''If the filename is a zip file, extract a file from that
1331	archive.
1332
1333	:param list Selection: used to predefine the name of the file
1334	to be extracted. Filename case and zip directory name are
1335	ignored in selection; the first matching file is used.
1336
1337	:param bool confirmread: if True asks the user to confirm before expanding
1338	the only file in a zip
1339
1340	:param bool confirmoverwrite: if True asks the user to confirm
1341	before overwriting if the extracted file already exists
1342
1343	:param bool multipleselect: if True allows more than one zip
1344	file to be extracted, a list of file(s) is returned.
1345	If only one file is present, do not ask which one, otherwise
1346	offer a list of choices (unless selection is used).
1347
1348	:returns: the name of the file that has been created or a
1349	list of files (see multipleselect)
1350
1351	If the file is not a zipfile, return the name of the input file.
1352	If the zipfile is empty or no file has been selected, return None
1353	'''
1354	import zipfile # do this now, since we can save startup time by doing this only on need
1355	import shutil
1356	zloc = os.path.split(filename)[0]
1357	if not zipfile.is_zipfile(filename):
1358	#print("not zip")
1359	return filename
1360
1361	z = zipfile.ZipFile(filename,'r')
1362	zinfo = z.infolist()
1363
1364	if len(zinfo) == 0:
1365	#print('Zip has no files!')
1366	zlist = [-1]
1367	if selection:
1368	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1369	if selection.lower() in choices:
1370	zlist = [choices.index(selection.lower())]
1371	else:
1372	print('debug: file '+str(selection)+' was not found in '+str(filename))
1373	zlist = [-1]
1374	elif len(zinfo) == 1 and confirmread:
1375	result = wx.ID_NO
1376	dlg = wx.MessageDialog(
1377	parent,
1378	'Is file '+str(zinfo[0].filename)+
1379	' what you want to extract from '+
1380	str(os.path.split(filename)[1])+'?',
1381	'Confirm file',
1382	wx.YES_NO \| wx.ICON_QUESTION)
1383	try:
1384	result = dlg.ShowModal()
1385	finally:
1386	dlg.Destroy()
1387	if result == wx.ID_NO:
1388	zlist = [-1]
1389	else:
1390	zlist = [0]
1391	elif len(zinfo) == 1:
1392	zlist = [0]
1393	elif multipleselect:
1394	# select one or more from a from list
1395	choices = [i.filename for i in zinfo]
1396	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1397	'Choose file(s)',choices)
1398	if dlg.ShowModal() == wx.ID_OK:
1399	zlist = dlg.GetSelections()
1400	else:
1401	zlist = []
1402	dlg.Destroy()
1403	else:
1404	# select one from a from list
1405	choices = [i.filename for i in zinfo]
1406	dlg = wx.SingleChoiceDialog(parent,
1407	'Select file to extract from zip file'+str(filename),'Choose file',
1408	choices,)
1409	if dlg.ShowModal() == wx.ID_OK:
1410	zlist = [dlg.GetSelection()]
1411	else:
1412	zlist = [-1]
1413	dlg.Destroy()
1414
1415	outlist = []
1416	for zindex in zlist:
1417	if zindex >= 0:
1418	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1419	if os.path.exists(efil) and confirmoverwrite:
1420	result = wx.ID_NO
1421	dlg = wx.MessageDialog(parent,
1422	'File '+str(efil)+' already exists. OK to overwrite it?',
1423	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1424	try:
1425	result = dlg.ShowModal()
1426	finally:
1427	dlg.Destroy()
1428	if result == wx.ID_NO:
1429	zindex = -1
1430	if zindex >= 0:
1431	# extract the file to the current directory, regardless of it's original path
1432	#z.extract(zinfo[zindex],zloc)
1433	eloc,efil = os.path.split(zinfo[zindex].filename)
1434	outfile = os.path.join(zloc, efil)
1435	fpin = z.open(zinfo[zindex])
1436	fpout = file(outfile, "wb")
1437	shutil.copyfileobj(fpin, fpout)
1438	fpin.close()
1439	fpout.close()
1440	outlist.append(outfile)
1441	z.close()
1442	if multipleselect and len(outlist) >= 1:
1443	return outlist
1444	elif len(outlist) == 1:
1445	return outlist[0]
1446	else:
1447	return None
1448
1449	######################################################################
1450	# base classes for reading various types of data files
1451	# not used directly, only by subclassing
1452	######################################################################
1453	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1454	P1SGData = SGData
1455	class ImportBaseclass(object):
1456	'''Defines a base class for the reading of input files (diffraction
1457	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1458	for an explanation on how to use a subclass of this class.
1459	'''
1460	class ImportException(Exception):
1461	'''Defines an Exception that is used when an import routine hits an expected error,
1462	usually in .Reader.
1463
1464	Good practice is that the Reader should define a value in self.errors that
1465	tells the user some information about what is wrong with their file.
1466	'''
1467	pass
1468
1469	def __init__(self,
1470	formatName,
1471	longFormatName=None,
1472	extensionlist=[],
1473	strictExtension=False,
1474	):
1475	self.formatName = formatName # short string naming file type
1476	if longFormatName: # longer string naming file type
1477	self.longFormatName = longFormatName
1478	else:
1479	self.longFormatName = formatName
1480	# define extensions that are allowed for the file type
1481	# for windows, remove any extensions that are duplicate, as case is ignored
1482	if sys.platform == 'windows' and extensionlist:
1483	extensionlist = list(set([s.lower() for s in extensionlist]))
1484	self.extensionlist = extensionlist
1485	# If strictExtension is True, the file will not be read, unless
1486	# the extension matches one in the extensionlist
1487	self.strictExtension = strictExtension
1488	self.errors = ''
1489	self.warnings = ''
1490	# used for readers that will use multiple passes to read
1491	# more than one data block
1492	self.repeat = False
1493	self.selections = []
1494	self.repeatcount = 0
1495	self.readfilename = '?'
1496	#print 'created',self.__class__
1497
1498	def ReInitialize(self):
1499	'Reinitialize the Reader to initial settings'
1500	self.errors = ''
1501	self.warnings = ''
1502	self.repeat = False
1503	self.repeatcount = 0
1504	self.readfilename = '?'
1505
1506	def BlockSelector(self, ChoiceList, ParentFrame=None,
1507	title='Select a block',
1508	size=None, header='Block Selector',
1509	useCancel=True):
1510	''' Provide a wx dialog to select a block if the file contains more
1511	than one set of data and one must be selected
1512	'''
1513	if useCancel:
1514	dlg = wx.SingleChoiceDialog(
1515	ParentFrame,title, header,ChoiceList)
1516	else:
1517	dlg = wx.SingleChoiceDialog(
1518	ParentFrame,title, header,ChoiceList,
1519	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1520	if size: dlg.SetSize(size)
1521	dlg.CenterOnParent()
1522	if dlg.ShowModal() == wx.ID_OK:
1523	sel = dlg.GetSelection()
1524	return sel
1525	else:
1526	return None
1527	dlg.Destroy()
1528
1529	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1530	title='Select a block',size=None, header='Block Selector'):
1531	'''Provide a wx dialog to select a block of data if the
1532	file contains more than one set of data and one must be
1533	selected.
1534
1535	:returns: a list of the selected blocks
1536	'''
1537	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1538	wx.CHOICEDLG_STYLE)
1539	dlg.CenterOnParent()
1540	if size: dlg.SetSize(size)
1541	if dlg.ShowModal() == wx.ID_OK:
1542	sel = dlg.GetSelections()
1543	else:
1544	return []
1545	dlg.Destroy()
1546	selected = []
1547	if len(ChoiceList) in sel:
1548	return range(len(ChoiceList))
1549	else:
1550	return sel
1551	return selected
1552
1553	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1554	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1555	widget. Typical input:
1556
1557	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1558
1559	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1560
1561	optional keyword parameters are: head (window title) and title
1562	returns a list of selected indicies for each choice (or None)
1563	'''
1564	result = None
1565	dlg = MultipleChoicesDialog(choicelist,headinglist,
1566	parent=ParentFrame, **kwargs)
1567	dlg.CenterOnParent()
1568	if dlg.ShowModal() == wx.ID_OK:
1569	result = dlg.chosen
1570	dlg.Destroy()
1571	return result
1572
1573	def ShowBusy(self):
1574	wx.BeginBusyCursor()
1575	# wx.Yield() # make it happen now!
1576
1577	def DoneBusy(self):
1578	wx.EndBusyCursor()
1579	wx.Yield() # make it happen now!
1580
1581	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1582	# '''This method must be supplied in the child class to read the file.
1583	# if the read fails either return False or raise an Exception
1584	# preferably of type ImportException.
1585	# '''
1586	# #start reading
1587	# raise ImportException("Error occurred while...")
1588	# self.errors += "Hint for user on why the error occur
1589	# return False # if an error occurs
1590	# return True # if read OK
1591
1592	def ExtensionValidator(self, filename):
1593	'''This methods checks if the file has the correct extension
1594	Return False if this filename will not be supported by this reader
1595	Return True if the extension matches the list supplied by the reader
1596	Return None if the reader allows un-registered extensions
1597	'''
1598	if filename:
1599	ext = os.path.splitext(filename)[1]
1600	if sys.platform == 'windows': ext = ext.lower()
1601	if ext in self.extensionlist: return True
1602	if self.strictExtension: return False
1603	return None
1604
1605	def ContentsValidator(self, filepointer):
1606	'''This routine will attempt to determine if the file can be read
1607	with the current format.
1608	This will typically be overridden with a method that
1609	takes a quick scan of [some of]
1610	the file contents to do a "sanity" check if the file
1611	appears to match the selected format.
1612	Expected to be called via self.Validator()
1613	'''
1614	#filepointer.seek(0) # rewind the file pointer
1615	return True
1616
1617	def CIFValidator(self, filepointer):
1618	'''A :meth:`ContentsValidator` for use to validate CIF files.
1619	'''
1620	for i,l in enumerate(filepointer):
1621	if i >= 1000: return True
1622	'''Encountered only blank lines or comments in first 1000
1623	lines. This is unlikely, but assume it is CIF anyway, since we are
1624	even less likely to find a file with nothing but hashes and
1625	blank lines'''
1626	line = l.strip()
1627	if len(line) == 0: # ignore blank lines
1628	continue
1629	elif line.startswith('#'): # ignore comments
1630	continue
1631	elif line.startswith('data_'): # on the right track, accept this file
1632	return True
1633	else: # found something invalid
1634	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1635	self.errors += ' '+str(l)
1636	self.errors += ' Note: a CIF should only have blank lines or comments before'
1637	self.errors += ' a data_ statement begins a block.'
1638	return False
1639
1640	class ImportPhase(ImportBaseclass):
1641	'''Defines a base class for the reading of files with coordinates
1642
1643	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1644	in :meth:`GSASII.GSASII.OnImportPhase`.
1645	See :ref:`Writing a Import Routine<Import_Routines>`
1646	for an explanation on how to use this class.
1647
1648	'''
1649	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1650	strictExtension=False,):
1651	# call parent __init__
1652	ImportBaseclass.__init__(self,formatName,longFormatName,
1653	extensionlist,strictExtension)
1654	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1655	self.Constraints = None
1656
1657	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1658	title='Select a phase', size=None,header='Phase Selector'):
1659	''' Provide a wx dialog to select a phase if the file contains more
1660	than one phase
1661	'''
1662	return self.BlockSelector(ChoiceList,ParentFrame,title,
1663	size,header)
1664
1665	class ImportStructFactor(ImportBaseclass):
1666	'''Defines a base class for the reading of files with tables
1667	of structure factors.
1668
1669	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1670	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1671	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1672	:meth:`Reader`.
1673
1674	See :ref:`Writing a Import Routine<Import_Routines>`
1675	for an explanation on how to use import classes in general. The specifics
1676	for reading a structure factor histogram require that
1677	the ``Reader()`` routine in the import
1678	class need to do only a few things: It
1679	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1680	and set :attr:`Parameters` with the instrument parameters
1681	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1682	'''
1683	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1684	strictExtension=False,):
1685	ImportBaseclass.__init__(self,formatName,longFormatName,
1686	extensionlist,strictExtension)
1687
1688	# define contents of Structure Factor entry
1689	self.Parameters = []
1690	'self.Parameters is a list with two dicts for data parameter settings'
1691	self.InitParameters()
1692	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1693	self.Banks = [] #for multi bank data (usually TOF)
1694	'''self.RefDict is a dict containing the reflection information, as read from the file.
1695	Item 'RefList' contains the reflection information. See the
1696	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1697	for the contents of each row. Dict element 'FF'
1698	contains the form factor values for each element type; if this entry
1699	is left as initialized (an empty list) it will be initialized as needed later.
1700	'''
1701	def ReInitialize(self):
1702	'Reinitialize the Reader to initial settings'
1703	ImportBaseclass.ReInitialize(self)
1704	self.InitParameters()
1705	self.Banks = [] #for multi bank data (usually TOF)
1706	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1707
1708	def InitParameters(self):
1709	'initialize the instrument parameters structure'
1710	Lambda = 0.70926
1711	HistType = 'SXC'
1712	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1713	'Lam':[Lambda,Lambda]
1714	}, {}]
1715	'Parameters is a list with two dicts for data parameter settings'
1716
1717	def UpdateParameters(self,Type=None,Wave=None):
1718	'Revise the instrument parameters'
1719	if Type is not None:
1720	self.Parameters[0]['Type'] = [Type,Type]
1721	if Wave is not None:
1722	self.Parameters[0]['Lam'] = [Wave,Wave]
1723
1724	######################################################################
1725	class ImportPowderData(ImportBaseclass):
1726	'''Defines a base class for the reading of files with powder data.
1727
1728	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1729	in :meth:`GSASII.GSASII.OnImportPowder`.
1730	See :ref:`Writing a Import Routine<Import_Routines>`
1731	for an explanation on how to use this class.
1732	'''
1733	def __init__(self,
1734	formatName,
1735	longFormatName=None,
1736	extensionlist=[],
1737	strictExtension=False,
1738	):
1739	ImportBaseclass.__init__(self,formatName,
1740	longFormatName,
1741	extensionlist,
1742	strictExtension)
1743	self.clockWd = None # used in TOF
1744	self.ReInitialize()
1745
1746	def ReInitialize(self):
1747	'Reinitialize the Reader to initial settings'
1748	ImportBaseclass.ReInitialize(self)
1749	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1750	self.powderdata = [] # Powder dataset
1751	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1752	np.array(x), # x-axis values
1753	np.array(y), # powder pattern intensities
1754	np.array(w), # 1/sig(intensity)^2 values (weights)
1755	np.array(yc), # calc. intensities (zero)
1756	np.array(yb), # calc. background (zero)
1757	np.array(yd), # obs-calc profiles
1758	'''
1759	self.comments = []
1760	self.idstring = ''
1761	self.Sample = G2pdG.SetDefaultSample() # default sample parameters
1762	self.Controls = {} # items to be placed in top-level Controls
1763	self.GSAS = None # used in TOF
1764	self.repeat_instparm = True # Should a parm file be
1765	# used for multiple histograms?
1766	self.instparm = None # name hint from file of instparm to use
1767	self.instfile = '' # full path name to instrument parameter file
1768	self.instbank = '' # inst parm bank number
1769	self.instmsg = '' # a label that gets printed to show
1770	# where instrument parameters are from
1771	self.numbanks = 1
1772	self.instdict = {} # place items here that will be transferred to the instrument parameters
1773	self.pwdparms = {} # place parameters that are transferred directly to the tree
1774	# here (typically from an existing GPX file)
1775	######################################################################
1776	class ImportSmallAngleData(ImportBaseclass):
1777	'''Defines a base class for the reading of files with small angle data.
1778	See :ref:`Writing a Import Routine<Import_Routines>`
1779	for an explanation on how to use this class.
1780	'''
1781	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1782	strictExtension=False,):
1783
1784	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1785	strictExtension)
1786	self.ReInitialize()
1787
1788	def ReInitialize(self):
1789	'Reinitialize the Reader to initial settings'
1790	ImportBaseclass.ReInitialize(self)
1791	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1792	self.smallangledata = [] # SASD dataset
1793	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1794	np.array(x), # x-axis values
1795	np.array(y), # powder pattern intensities
1796	np.array(w), # 1/sig(intensity)^2 values (weights)
1797	np.array(yc), # calc. intensities (zero)
1798	np.array(yd), # obs-calc profiles
1799	np.array(yb), # preset bkg
1800	'''
1801	self.comments = []
1802	self.idstring = ''
1803	self.Sample = G2pdG.SetDefaultSample()
1804	self.GSAS = None # used in TOF
1805	self.clockWd = None # used in TOF
1806	self.numbanks = 1
1807	self.instdict = {} # place items here that will be transferred to the instrument parameters
1808	######################################################################
1809	class ExportBaseclass(object):
1810	'''Defines a base class for the exporting of GSAS-II results.
1811
1812	This class is subclassed in the various exports/G2export_*.py files. Those files
1813	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
1814	appropriate menu items for each one and the .Exporter method is called
1815	directly from the menu item.
1816
1817	'''
1818	def __init__(self,
1819	G2frame,
1820	formatName,
1821	extension,
1822	longFormatName=None,
1823	):
1824	self.G2frame = G2frame
1825	self.formatName = formatName # short string naming file type
1826	self.extension = extension
1827	if longFormatName: # longer string naming file type
1828	self.longFormatName = longFormatName
1829	else:
1830	self.longFormatName = formatName
1831	self.OverallParms = {}
1832	self.Phases = {}
1833	self.Histograms = {}
1834	self.powderDict = {}
1835	self.xtalDict = {}
1836	self.parmDict = {}
1837	self.sigDict = {}
1838	# updated in InitExport:
1839	self.currentExportType = None # type of export that has been requested
1840	# updated in ExportSelect (when used):
1841	self.phasenam = None # a list of selected phases
1842	self.histnam = None # a list of selected histograms
1843	self.filename = None # name of file to be written (single export) or template (multiple files)
1844	self.dirname = '' # name of directory where file(s) will be written
1845	self.fullpath = '' # name of file being written -- full path
1846
1847	# items that should be defined in a subclass of this class
1848	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1849	# The following types are defined: 'project', "phase", "powder", "single"
1850	self.multiple = False # set as True if the class can export multiple phases or histograms
1851	# self.multiple is ignored for "project" exports
1852
1853	def InitExport(self,event):
1854	'''Determines the type of menu that called the Exporter and
1855	misc initialization.
1856	'''
1857	self.filename = None # name of file to be written (single export)
1858	self.dirname = '' # name of file to be written (multiple export)
1859	if event:
1860	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1861
1862	def MakePWDRfilename(self,hist):
1863	'''Make a filename root (no extension) from a PWDR histogram name
1864
1865	:param str hist: the histogram name in data tree (starts with "PWDR ")
1866	'''
1867	file0 = ''
1868	file1 = hist[5:]
1869	# replace repeated blanks
1870	while file1 != file0:
1871	file0 = file1
1872	file1 = file0.replace(' ',' ').strip()
1873	file0 = file1.replace('Azm= ','A')
1874	# if angle has unneeded decimal places on aziumuth, remove them
1875	if file0[-3:] == '.00': file0 = file0[:-3]
1876	file0 = file0.replace('.','_')
1877	file0 = file0.replace(' ','_')
1878	return file0
1879
1880	def ExportSelect(self,AskFile='ask'):
1881	'''Selects histograms or phases when needed. Sets a default file name when
1882	requested in self.filename; always sets a default directory in self.dirname.
1883
1884	:param bool AskFile: Determines how this routine processes getting a
1885	location to store the current export(s).
1886
1887	* if AskFile is 'ask' (default option), get the name of the file to be written;
1888	self.filename and self.dirname are always set. In the case where
1889	multiple files must be generated, the export routine should do this
1890	based on self.filename as a template.
1891	* if AskFile is 'dir', get the name of the directory to be used;
1892	self.filename is not used, but self.dirname is always set. The export routine
1893	will always generate the file name.
1894	* if AskFile is 'single', get only the name of the directory to be used when
1895	multiple items will be written (as multiple files) are used
1896	or a complete file name is requested when a single file
1897	name is selected. self.dirname is always set and self.filename used
1898	only when a single file is selected.
1899	* if AskFile is 'default', creates a name of the file to be used from
1900	the name of the project (.gpx) file. If the project has not been saved,
1901	then the name of file is requested.
1902	self.filename and self.dirname are always set. In the case where
1903	multiple file names must be generated, the export routine should do this
1904	based on self.filename.
1905	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1906	file. If the project has not been saved, then a directory is requested.
1907	self.filename is not used.
1908
1909	:returns: True in case of an error
1910	'''
1911
1912	numselected = 1
1913	if self.currentExportType == 'phase':
1914	if len(self.Phases) == 0:
1915	self.G2frame.ErrorDialog(
1916	'Empty project',
1917	'Project does not contain any phases.')
1918	return True
1919	elif len(self.Phases) == 1:
1920	self.phasenam = self.Phases.keys()
1921	elif self.multiple:
1922	choices = sorted(self.Phases.keys())
1923	phasenum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1924	if phasenum is None: return True
1925	self.phasenam = [choices[i] for i in phasenum]
1926	if not self.phasenam: return True
1927	numselected = len(self.phasenam)
1928	else:
1929	choices = sorted(self.Phases.keys())
1930	phasenum = G2gd.ItemSelector(choices,self.G2frame)
1931	if phasenum is None: return True
1932	self.phasenam = [choices[phasenum]]
1933	numselected = len(self.phasenam)
1934	elif self.currentExportType == 'single':
1935	if len(self.xtalDict) == 0:
1936	self.G2frame.ErrorDialog(
1937	'Empty project',
1938	'Project does not contain any single crystal data.')
1939	return True
1940	elif len(self.xtalDict) == 1:
1941	self.histnam = self.xtalDict.values()
1942	elif self.multiple:
1943	choices = sorted(self.xtalDict.values())
1944	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1945	if not hnum: return True
1946	self.histnam = [choices[i] for i in hnum]
1947	numselected = len(self.histnam)
1948	else:
1949	choices = sorted(self.xtalDict.values())
1950	hnum = G2gd.ItemSelector(choices,self.G2frame)
1951	if hnum is None: return True
1952	self.histnam = [choices[hnum]]
1953	numselected = len(self.histnam)
1954	elif self.currentExportType == 'powder':
1955	if len(self.powderDict) == 0:
1956	self.G2frame.ErrorDialog(
1957	'Empty project',
1958	'Project does not contain any powder data.')
1959	return True
1960	elif len(self.powderDict) == 1:
1961	self.histnam = self.powderDict.values()
1962	elif self.multiple:
1963	choices = sorted(self.powderDict.values())
1964	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1965	if not hnum: return True
1966	self.histnam = [choices[i] for i in hnum]
1967	numselected = len(self.histnam)
1968	else:
1969	choices = sorted(self.powderDict.values())
1970	hnum = G2gd.ItemSelector(choices,self.G2frame)
1971	if hnum is None: return True
1972	self.histnam = [choices[hnum]]
1973	numselected = len(self.histnam)
1974	elif self.currentExportType == 'image':
1975	if len(self.Histograms) == 0:
1976	self.G2frame.ErrorDialog(
1977	'Empty project',
1978	'Project does not contain any images.')
1979	return True
1980	elif len(self.Histograms) == 1:
1981	self.histnam = self.Histograms.keys()
1982	else:
1983	choices = sorted(self.Histograms.keys())
1984	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1985	if self.multiple:
1986	if not hnum: return True
1987	self.histnam = [choices[i] for i in hnum]
1988	else:
1989	if hnum is None: return True
1990	self.histnam = [choices[hnum]]
1991	numselected = len(self.histnam)
1992	if self.currentExportType == 'map':
1993	# search for phases with maps
1994	mapPhases = []
1995	choices = []
1996	for phasenam in sorted(self.Phases):
1997	phasedict = self.Phases[phasenam] # pointer to current phase info
1998	if len(phasedict['General']['Map'].get('rho',[])):
1999	mapPhases.append(phasenam)
2000	if phasedict['General']['Map'].get('Flip'):
2001	choices.append('Charge flip map: '+str(phasenam))
2002	elif phasedict['General']['Map'].get('MapType'):
2003	choices.append(
2004	str(phasedict['General']['Map'].get('MapType'))
2005	+ ' map: ' + str(phasenam))
2006	else:
2007	choices.append('unknown map: '+str(phasenam))
2008	# select a map if needed
2009	if len(mapPhases) == 0:
2010	self.G2frame.ErrorDialog(
2011	'Empty project',
2012	'Project does not contain any maps.')
2013	return True
2014	elif len(mapPhases) == 1:
2015	self.phasenam = mapPhases
2016	else:
2017	phasenum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
2018	if self.multiple:
2019	if not phasenum: return True
2020	self.phasenam = [mapPhases[i] for i in phasenum]
2021	else:
2022	if phasenum is None: return True
2023	self.phasenam = [mapPhases[phasenum]]
2024	numselected = len(self.phasenam)
2025
2026	# items selected, now set self.dirname and usually self.filename
2027	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
2028	AskFile == 'default' and not self.G2frame.GSASprojectfile
2029	):
2030	filename = self.askSaveFile()
2031	if not filename: return True
2032	self.dirname,self.filename = os.path.split(filename)
2033	elif AskFile == 'dir' or AskFile == 'single' or (
2034	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
2035	):
2036	self.dirname = self.askSaveDirectory()
2037	if not self.dirname: return True
2038	elif AskFile == 'default-dir' or AskFile == 'default':
2039	self.dirname,self.filename = os.path.split(
2040	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
2041	)
2042	else:
2043	raise Exception('This should not happen!')
2044
2045	def loadParmDict(self):
2046	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
2047	refined values to those from the last cycle and set the uncertainties for the
2048	refined parameters in another dict (self.sigDict).
2049
2050	Expands the parm & sig dicts to include values derived from constraints.
2051	'''
2052	self.parmDict = {}
2053	self.sigDict = {}
2054	rigidbodyDict = {}
2055	covDict = {}
2056	consDict = {}
2057	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2058	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2059	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2060	while item:
2061	name = self.G2frame.PatternTree.GetItemText(item)
2062	if name == 'Rigid bodies':
2063	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
2064	elif name == 'Covariance':
2065	covDict = self.G2frame.PatternTree.GetItemPyData(item)
2066	elif name == 'Constraints':
2067	consDict = self.G2frame.PatternTree.GetItemPyData(item)
2068	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2069	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
2070	self.parmDict.update(rbDict)
2071	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
2072	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,maxSSwave = G2stIO.GetPhaseData(
2073	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
2074	self.parmDict.update(phaseDict)
2075	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
2076	Phases,Histograms,Print=False,resetRefList=False)
2077	self.parmDict.update(hapDict)
2078	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
2079	self.parmDict.update(histDict)
2080	self.parmDict.update(zip(
2081	covDict.get('varyList',[]),
2082	covDict.get('variables',[])))
2083	self.sigDict = dict(zip(
2084	covDict.get('varyList',[]),
2085	covDict.get('sig',[])))
2086	# expand to include constraints: first compile a list of constraints
2087	constList = []
2088	for item in consDict:
2089	if item.startswith('_'): continue
2090	constList += consDict[item]
2091	# now process the constraints
2092	G2mv.InitVars()
2093	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
2094	varyList = covDict.get('varyListStart')
2095	if varyList is None and len(constDict) == 0:
2096	# no constraints can use varyList
2097	varyList = covDict.get('varyList')
2098	elif varyList is None:
2099	# old GPX file from before pre-constraint varyList is saved
2100	print ' * Old refinement: Please use Calculate/Refine to redo *'
2101	raise Exception(' * Export aborted *')
2102	else:
2103	varyList = list(varyList)
2104	try:
2105	groups,parmlist = G2mv.GroupConstraints(constDict)
2106	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
2107	except:
2108	# this really should not happen
2109	print ' * ERROR - constraints are internally inconsistent *'
2110	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
2111	print 'Errors',errmsg
2112	if warnmsg: print 'Warnings',warnmsg
2113	raise Exception(' * CIF creation aborted *')
2114	# add the constrained values to the parameter dictionary
2115	G2mv.Dict2Map(self.parmDict,varyList)
2116	# and add their uncertainties into the esd dictionary (sigDict)
2117	if covDict.get('covMatrix') is not None:
2118	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
2119
2120	def loadTree(self):
2121	'''Load the contents of the data tree into a set of dicts
2122	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2123	& self.xtalDict)
2124
2125	* The childrenless data tree items are overall parameters/controls for the
2126	entire project and are placed in self.OverallParms
2127	* Phase items are placed in self.Phases
2128	* Data items are placed in self.Histogram. The key for these data items
2129	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2130	'''
2131	self.OverallParms = {}
2132	self.powderDict = {}
2133	self.xtalDict = {}
2134	self.Phases = {}
2135	self.Histograms = {}
2136	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2137	histType = None
2138	if self.currentExportType == 'phase':
2139	# if exporting phases load them here
2140	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2141	if not sub:
2142	print 'no phases found'
2143	return True
2144	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2145	while item:
2146	phaseName = self.G2frame.PatternTree.GetItemText(item)
2147	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2148	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2149	return
2150	elif self.currentExportType == 'single':
2151	histType = 'HKLF'
2152	elif self.currentExportType == 'powder':
2153	histType = 'PWDR'
2154	elif self.currentExportType == 'image':
2155	histType = 'IMG'
2156
2157	if histType: # Loading just one kind of tree entry
2158	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2159	while item:
2160	name = self.G2frame.PatternTree.GetItemText(item)
2161	if name.startswith(histType):
2162	if self.Histograms.get(name): # there is already an item with this name
2163	print('Histogram name '+str(name)+' is repeated. Renaming')
2164	if name[-1] == '9':
2165	name = name[:-1] + '10'
2166	elif name[-1] in '012345678':
2167	name = name[:-1] + str(int(name[-1])+1)
2168	else:
2169	name += '-1'
2170	self.Histograms[name] = {}
2171	# the main info goes into Data, but the 0th
2172	# element contains refinement results, carry
2173	# that over too now.
2174	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2175	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2176	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2177	while item2:
2178	child = self.G2frame.PatternTree.GetItemText(item2)
2179	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2180	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2181	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2182	# index powder and single crystal histograms by number
2183	for hist in self.Histograms:
2184	if hist.startswith("PWDR"):
2185	d = self.powderDict
2186	elif hist.startswith("HKLF"):
2187	d = self.xtalDict
2188	else:
2189	return
2190	i = self.Histograms[hist].get('hId')
2191	if i is None and not d.keys():
2192	i = 0
2193	elif i is None or i in d.keys():
2194	i = max(d.keys())+1
2195	d[i] = hist
2196	return
2197	# else standard load: using all interlinked phases and histograms
2198	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2199	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2200	while item:
2201	name = self.G2frame.PatternTree.GetItemText(item)
2202	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2203	if not item2:
2204	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2205	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2206	# index powder and single crystal histograms
2207	for hist in self.Histograms:
2208	i = self.Histograms[hist]['hId']
2209	if hist.startswith("PWDR"):
2210	self.powderDict[i] = hist
2211	elif hist.startswith("HKLF"):
2212	self.xtalDict[i] = hist
2213
2214	def dumpTree(self,mode='type'):
2215	'''Print out information on the data tree dicts loaded in loadTree
2216	'''
2217	print '\nOverall'
2218	if mode == 'type':
2219	def Show(arg): return type(arg)
2220	else:
2221	def Show(arg): return arg
2222	for key in self.OverallParms:
2223	print ' ',key,Show(self.OverallParms[key])
2224	print 'Phases'
2225	for key1 in self.Phases:
2226	print ' ',key1,Show(self.Phases[key1])
2227	print 'Histogram'
2228	for key1 in self.Histograms:
2229	print ' ',key1,Show(self.Histograms[key1])
2230	for key2 in self.Histograms[key1]:
2231	print ' ',key2,Show(self.Histograms[key1][key2])
2232
2233	def defaultSaveFile(self):
2234	return os.path.abspath(
2235	os.path.splitext(self.G2frame.GSASprojectfile
2236	)[0]+self.extension)
2237
2238	def askSaveFile(self):
2239	'''Ask the user to supply a file name
2240
2241	:returns: a file name (str) or None if Cancel is pressed
2242	'''
2243	defnam = os.path.splitext(
2244	os.path.split(self.G2frame.GSASprojectfile)[1]
2245	)[0]+self.extension
2246	dlg = wx.FileDialog(
2247	self.G2frame, 'Input name for file to write', '.', defnam,
2248	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2249	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2250	dlg.CenterOnParent()
2251	try:
2252	if dlg.ShowModal() == wx.ID_OK:
2253	filename = dlg.GetPath()
2254	# make sure extension is correct
2255	filename = os.path.splitext(filename)[0]+self.extension
2256	else:
2257	filename = None
2258	finally:
2259	dlg.Destroy()
2260	return filename
2261
2262	def askSaveDirectory(self):
2263	'''Ask the user to supply a directory name. Path name is used as the
2264	starting point for the next export path search.
2265
2266	:returns: a directory name (str) or None if Cancel is pressed
2267	'''
2268	if self.G2frame.exportDir:
2269	startdir = self.G2frame.exportDir
2270	elif self.G2frame.GSASprojectfile:
2271	startdir = os.path.split(self.G2frame.GSASprojectfile)[0]
2272	elif self.G2frame.dirname:
2273	startdir = self.G2frame.dirname
2274	else:
2275	startdir = ''
2276	dlg = wx.DirDialog(
2277	self.G2frame, 'Input directory where file(s) will be written', startdir,
2278	wx.DD_DEFAULT_STYLE)
2279	dlg.CenterOnParent()
2280	try:
2281	if dlg.ShowModal() == wx.ID_OK:
2282	filename = dlg.GetPath()
2283	self.G2frame.exportDir = filename
2284	else:
2285	filename = None
2286	finally:
2287	dlg.Destroy()
2288	return filename
2289
2290	# Tools for file writing.
2291	def OpenFile(self,fil=None,mode='w'):
2292	'''Open the output file
2293
2294	:param str fil: The name of the file to open. If None (default)
2295	the name defaults to self.dirname + self.filename.
2296	If an extension is supplied, it is not overridded,
2297	but if not, the default extension is used.
2298	:returns: the file object opened by the routine which is also
2299	saved as self.fp
2300	'''
2301	if not fil:
2302	if not os.path.splitext(self.filename)[1]:
2303	self.filename += self.extension
2304	fil = os.path.join(self.dirname,self.filename)
2305	self.fullpath = fil
2306	self.fp = open(fil,mode)
2307	return self.fp
2308
2309	def Write(self,line):
2310	'''write a line of output, attaching a line-end character
2311
2312	:param str line: the text to be written.
2313	'''
2314	self.fp.write(line+'\n')
2315	def CloseFile(self,fp=None):
2316	'''Close a file opened in OpenFile
2317
2318	:param file fp: the file object to be closed. If None (default)
2319	file object self.fp is closed.
2320	'''
2321	if fp is None:
2322	fp = self.fp
2323	self.fp = None
2324	fp.close()
2325	# Tools to pull information out of the data arrays
2326	def GetCell(self,phasenam):
2327	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2328
2329	:param str phasenam: the name for the selected phase
2330	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2331	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2332	cell values and `cellSig` has their uncertainties.
2333	"""
2334	phasedict = self.Phases[phasenam] # pointer to current phase info
2335	try:
2336	pfx = str(phasedict['pId'])+'::'
2337	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2338	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
2339	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2340	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2341	return cellList,cellSig
2342	except KeyError:
2343	cell = phasedict['General']['Cell'][1:]
2344	return cell,7*[0]
2345
2346	def GetAtoms(self,phasenam):
2347	"""Gets the atoms associated with a phase. Can be used with standard
2348	or macromolecular phases
2349
2350	:param str phasenam: the name for the selected phase
2351	:returns: a list of items for eac atom where each item is a list containing:
2352	label, typ, mult, xyz, and td, where
2353
2354	* label and typ are the atom label and the scattering factor type (str)
2355	* mult is the site multiplicity (int)
2356	* xyz is contains a list with four pairs of numbers:
2357	x, y, z and fractional occupancy and
2358	their standard uncertainty (or a negative value)
2359	* td is contains a list with either one or six pairs of numbers:
2360	if one number it is U\ :sub:`iso` and with six numbers it is
2361	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2362	paired with their standard uncertainty (or a negative value)
2363	"""
2364	phasedict = self.Phases[phasenam] # pointer to current phase info
2365	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2366	cfrac = cx+3
2367	fpfx = str(phasedict['pId'])+'::Afrac:'
2368	atomslist = []
2369	for i,at in enumerate(phasedict['Atoms']):
2370	if phasedict['General']['Type'] == 'macromolecular':
2371	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2372	else:
2373	label = at[ct-1]
2374	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2375	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2376	mult = at[cs+1]
2377	typ = at[ct]
2378	xyz = []
2379	for j,v in enumerate(('x','y','z')):
2380	val = at[cx+j]
2381	pfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2382	sig = self.sigDict.get(pfx,-0.000009)
2383	xyz.append((val,sig))
2384	xyz.append((fval,fsig))
2385	td = []
2386	if at[cia] == 'I':
2387	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2388	val = self.parmDict.get(pfx,at[cia+1])
2389	sig = self.sigDict.get(pfx,-0.0009)
2390	td.append((val,sig))
2391	else:
2392	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2393	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2394	val = self.parmDict.get(pfx,at[cia+2+i])
2395	sig = self.sigDict.get(pfx,-0.0009)
2396	td.append((val,sig))
2397	atomslist.append((label,typ,mult,xyz,td))
2398	return atomslist
2399	######################################################################
2400
2401	def ReadCIF(URLorFile):
2402	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2403	(from James Hester).
2404	The open routine gets confused with DOS names that begin with a letter and colon
2405	"C:\dir\" so this routine will try to open the passed name as a file and if that
2406	fails, try it as a URL
2407
2408	:param str URLorFile: string containing a URL or a file name. Code will try first
2409	to open it as a file and then as a URL.
2410
2411	:returns: a PyCifRW CIF object.
2412	'''
2413	import CifFile as cif # PyCifRW from James Hester
2414
2415	# alternate approach:
2416	#import urllib
2417	#ciffile = 'file:'+urllib.pathname2url(filename)
2418
2419	try:
2420	fp = open(URLorFile,'r')
2421	cf = cif.ReadCif(fp)
2422	fp.close()
2423	return cf
2424	except IOError:
2425	return cif.ReadCif(URLorFile)
2426
2427	if __name__ == '__main__':
2428	app = wx.PySimpleApp()
2429	frm = wx.Frame(None) # create a frame
2430	frm.Show(True)
2431	filename = '/tmp/notzip.zip'
2432	filename = '/tmp/all.zip'
2433	#filename = '/tmp/11bmb_7652.zip'
2434
2435	#selection=None, confirmoverwrite=True, parent=None
2436	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2437	print ExtractFileFromZip(filename,multipleselect=True)
2438	#confirmread=False, confirmoverwrite=False)
2439
2440	# choicelist=[ ('a','b','c'),
2441	# ('test1','test2'),('no choice',)]
2442	# titles = [ 'a, b or c', 'tests', 'No option here']
2443	# dlg = MultipleChoicesDialog(
2444	# choicelist,titles,
2445	# parent=frm)
2446	# if dlg.ShowModal() == wx.ID_OK:
2447	# print 'Got OK'

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