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source: trunk/GSASIIIO.py @ 1814

Last change on this file since 1814 was 1814, checked in by toby, 9 years ago
save selected tree text name at time of selection (see G2frame.PickId?)
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2015-04-27 22:11:13 +0000 (Mon, 27 Apr 2015) $
4	# $Author: toby $
5	# $Revision: 1814 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 1814 2015-04-27 22:11:13Z toby $
8	########### SVN repository information ###################
9	'''
10	GSASIIIO: Misc I/O routines
11	=============================
12
13	Module with miscellaneous routines for input and output. Many
14	are GUI routines to interact with user.
15
16	Includes support for image reading.
17
18	Also includes base classes for data import routines.
19
20	'''
21	"""GSASIIIO: functions for IO of data
22	Copyright: 2008, Robert B. Von Dreele (Argonne National Laboratory)
23	"""
24	import wx
25	import math
26	import numpy as np
27	import cPickle
28	import sys
29	import re
30	import random as ran
31	import GSASIIpath
32	GSASIIpath.SetVersionNumber("$Revision: 1814 $")
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	if azm > 360. and azms[i+1] > 360.:
1044	Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
1045	else:
1046	Azms.append(G2img.meanAzm(azm,azms[i+1]))
1047	for i,azm in enumerate(azms[:-1]):
1048	Aname = name+" Azm= %.2f"%(Azms[i])
1049	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
1050	nOcc = 0
1051	while item:
1052	Name = G2frame.PatternTree.GetItemText(item)
1053	if Aname in Name:
1054	nOcc += 1
1055	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
1056	if nOcc:
1057	Aname += '(%d)'%(nOcc)
1058	Sample = G2pdG.SetDefaultSample()
1059	Sample['Gonio. radius'] = data['distance']
1060	Sample['Omega'] = data['GonioAngles'][0]
1061	Sample['Chi'] = data['GonioAngles'][1]
1062	Sample['Phi'] = data['GonioAngles'][2]
1063	Sample['Azimuth'] = Azms[i] #put here too
1064	if 'PWDR' in Aname:
1065	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!
1066	elif 'SASD' in Aname:
1067	Sample['Trans'] = data['SampleAbs'][0]
1068	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
1069	Y = G2frame.Integrate[0][i]
1070	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
1071	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=Aname)
1072	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
1073	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
1074	if 'PWDR' in Aname:
1075	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
1076	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
1077	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
1078	for item in inst[0]:
1079	inst[0][item] = list(inst[0][item])
1080	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
1081	if 'PWDR' in Aname:
1082	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1083	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
1084	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[[],[]])
1085	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
1086	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
1087	elif 'SASD' in Aname:
1088	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
1089	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1090	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
1091	valuesdict = {
1092	'wtFactor':1.0,
1093	'Dummy':False,
1094	'ranId':ran.randint(0,sys.maxint),
1095	'Offset':[0.0,0.0],'delOffset':0.02,'refOffset':-1.0,'refDelt':0.01,
1096	'qPlot':False,'dPlot':False,'sqrtPlot':False
1097	}
1098	G2frame.PatternTree.SetItemPyData(
1099	Id,[valuesdict,
1100	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
1101	return Id #last powder pattern generated
1102
1103	# def powderFxyeSave(G2frame,exports,powderfile):
1104	# 'Save a powder histogram as a GSAS FXYE file'
1105	# head,tail = ospath.split(powderfile)
1106	# name,ext = tail.split('.')
1107	# for i,export in enumerate(exports):
1108	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1109	# prmname = filename.strip(ext)+'prm'
1110	# prm = open(prmname,'w') #old style GSAS parm file
1111	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1112	# Inst = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, \
1113	# PickId, 'Instrument Parameters'))[0]
1114	# prm.write( ' 123456789012345678901234567890123456789012345678901234567890 '+'\n')
1115	# prm.write( 'INS BANK 1 '+'\n')
1116	# prm.write(('INS HTYPE %sR '+'\n')%(Inst['Type'][0]))
1117	# if 'Lam1' in Inst: #Ka1 & Ka2
1118	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam1'][0],Inst['Lam2'][0]))
1119	# elif 'Lam' in Inst: #single wavelength
1120	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam'][1],0.0))
1121	# prm.write( 'INS 1 IRAD 0 '+'\n')
1122	# prm.write( 'INS 1I HEAD '+'\n')
1123	# prm.write( 'INS 1I ITYP 0 0.0000 180.0000 1 '+'\n')
1124	# prm.write(('INS 1DETAZM%10.3f '+'\n')%(Inst['Azimuth'][0]))
1125	# prm.write( 'INS 1PRCF1 3 8 0.00100 '+'\n')
1126	# prm.write(('INS 1PRCF11 %15.6g%15.6g%15.6g%15.6g '+'\n')%(Inst['U'][1],Inst['V'][1],Inst['W'][1],0.0))
1127	# 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.))
1128	# prm.close()
1129	# file = open(filename,'w')
1130	# print 'save powder pattern to file: ',filename
1131	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1132	# file.write(powderfile+'\n')
1133	# file.write('Instrument parameter file:'+ospath.split(prmname)[1]+'\n')
1134	# file.write('BANK 1 %d %d CONS %.2f %.2f 0 0 FXYE\n'%(len(x),len(x),\
1135	# 100.x[0],100.(x[1]-x[0])))
1136	# s = list(np.sqrt(1./np.array(w)))
1137	# XYW = zip(x,y,s)
1138	# for X,Y,S in XYW:
1139	# file.write("%15.6g %15.6g %15.6g\n" % (100.*X,Y,max(S,1.0)))
1140	# file.close()
1141	# print 'powder pattern file '+filename+' written'
1142
1143	# def powderXyeSave(G2frame,exports,powderfile):
1144	# 'Save a powder histogram as a Topas XYE file'
1145	# head,tail = ospath.split(powderfile)
1146	# name,ext = tail.split('.')
1147	# for i,export in enumerate(exports):
1148	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1149	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1150	# file = open(filename,'w')
1151	# file.write('#%s\n'%(export))
1152	# print 'save powder pattern to file: ',filename
1153	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1154	# s = list(np.sqrt(1./np.array(w)))
1155	# XYW = zip(x,y,s)
1156	# for X,Y,W in XYW:
1157	# file.write("%15.6g %15.6g %15.6g\n" % (X,Y,W))
1158	# file.close()
1159	# print 'powder pattern file '+filename+' written'
1160
1161	def PDFSave(G2frame,exports):
1162	'Save a PDF G(r) and S(Q) in column formats'
1163	for export in exports:
1164	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1165	SQname = 'S(Q)'+export[4:]
1166	GRname = 'G(R)'+export[4:]
1167	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
1168	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
1169	sqId = G2gd.GetPatternTreeItemId(G2frame, PickId, SQname)
1170	grId = G2gd.GetPatternTreeItemId(G2frame, PickId, GRname)
1171	sqdata = np.array(G2frame.PatternTree.GetItemPyData(sqId)[1][:2]).T
1172	grdata = np.array(G2frame.PatternTree.GetItemPyData(grId)[1][:2]).T
1173	sqfile = open(sqfilename,'w')
1174	grfile = open(grfilename,'w')
1175	sqfile.write('#T S(Q) %s\n'%(export))
1176	grfile.write('#T G(R) %s\n'%(export))
1177	sqfile.write('#L Q S(Q)\n')
1178	grfile.write('#L R G(R)\n')
1179	for q,sq in sqdata:
1180	sqfile.write("%15.6g %15.6g\n" % (q,sq))
1181	sqfile.close()
1182	for r,gr in grdata:
1183	grfile.write("%15.6g %15.6g\n" % (r,gr))
1184	grfile.close()
1185
1186	def PeakListSave(G2frame,file,peaks):
1187	'Save powder peaks to a data file'
1188	print 'save peak list to file: ',G2frame.peaklistfile
1189	if not peaks:
1190	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1191	try:
1192	result = dlg.ShowModal()
1193	finally:
1194	dlg.Destroy()
1195	return
1196	for peak in peaks:
1197	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1198	(peak[0],peak[2],peak[4],peak[6]))
1199	print 'peak list saved'
1200
1201	def IndexPeakListSave(G2frame,peaks):
1202	'Save powder peaks from the indexing list'
1203	file = open(G2frame.peaklistfile,'wa')
1204	print 'save index peak list to file: ',G2frame.peaklistfile
1205	wx.BeginBusyCursor()
1206	try:
1207	if not peaks:
1208	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1209	try:
1210	result = dlg.ShowModal()
1211	finally:
1212	dlg.Destroy()
1213	return
1214	for peak in peaks:
1215	file.write("%12.6f\n" % (peak[7]))
1216	file.close()
1217	finally:
1218	wx.EndBusyCursor()
1219	print 'index peak list saved'
1220
1221	def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1222	'''Create a new phase dict with default values for various parameters
1223
1224	:param str Name: Name for new Phase
1225
1226	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1227	defaults to data for P 1
1228
1229	:param list cell: unit cell parameter list; defaults to
1230	[1.0,1.0,1.0,90.,90,90.,1.]
1231
1232	'''
1233	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1234	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1235	phaseData = {
1236	'ranId':ran.randint(0,sys.maxint),
1237	'General':{
1238	'Name':Name,
1239	'Type':'nuclear',
1240	'AtomPtrs':[3,1,7,9],
1241	'SGData':SGData,
1242	'Cell':[False,]+cell,
1243	'Pawley dmin':1.0,
1244	'Data plot type':'None',
1245	'SH Texture':{
1246	'Order':0,
1247	'Model':'cylindrical',
1248	'Sample omega':[False,0.0],
1249	'Sample chi':[False,0.0],
1250	'Sample phi':[False,0.0],
1251	'SH Coeff':[False,{}],
1252	'SHShow':False,
1253	'PFhkl':[0,0,1],
1254	'PFxyz':[0,0,1],
1255	'PlotType':'Pole figure'}},
1256	'Atoms':[],
1257	'Drawing':{},
1258	'Histograms':{},
1259	'Pawley ref':[],
1260	'RBModels':{},
1261	}
1262	if Super and Super.get('Use',False):
1263	phaseData['General'].update({'Type':'modulated','Super':True,'SuperSg':Super['ssSymb']})
1264	phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])
1265	phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1266
1267	return phaseData
1268
1269	class MultipleChoicesDialog(wx.Dialog):
1270	'''A dialog that offers a series of choices, each with a
1271	title and a wx.Choice widget. Intended to be used Modally.
1272	typical input:
1273
1274	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1275	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1276
1277	selections are placed in self.chosen when OK is pressed
1278	'''
1279	def __init__(self,choicelist,headinglist,
1280	head='Select options',
1281	title='Please select from options below',
1282	parent=None):
1283	self.chosen = []
1284	wx.Dialog.__init__(
1285	self,parent,wx.ID_ANY,head,
1286	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1287	panel = wx.Panel(self)
1288	mainSizer = wx.BoxSizer(wx.VERTICAL)
1289	mainSizer.Add((10,10),1)
1290	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1291	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1292	self.ChItems = []
1293	for choice,lbl in zip(choicelist,headinglist):
1294	mainSizer.Add((10,10),1)
1295	self.chosen.append(0)
1296	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1297	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1298	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1299	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1300
1301	OkBtn = wx.Button(panel,-1,"Ok")
1302	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1303	cancelBtn = wx.Button(panel,-1,"Cancel")
1304	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1305	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1306	btnSizer.Add((20,20),1)
1307	btnSizer.Add(OkBtn)
1308	btnSizer.Add((20,20),1)
1309	btnSizer.Add(cancelBtn)
1310	btnSizer.Add((20,20),1)
1311	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1312	panel.SetSizer(mainSizer)
1313	panel.Fit()
1314	self.Fit()
1315
1316	def OnOk(self,event):
1317	parent = self.GetParent()
1318	if parent is not None: parent.Raise()
1319	# save the results from the choice widgets
1320	self.chosen = []
1321	for w in self.ChItems:
1322	self.chosen.append(w.GetSelection())
1323	self.EndModal(wx.ID_OK)
1324
1325	def OnCancel(self,event):
1326	parent = self.GetParent()
1327	if parent is not None: parent.Raise()
1328	self.chosen = []
1329	self.EndModal(wx.ID_CANCEL)
1330
1331	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1332	confirmoverwrite=True, parent=None,
1333	multipleselect=False):
1334	'''If the filename is a zip file, extract a file from that
1335	archive.
1336
1337	:param list Selection: used to predefine the name of the file
1338	to be extracted. Filename case and zip directory name are
1339	ignored in selection; the first matching file is used.
1340
1341	:param bool confirmread: if True asks the user to confirm before expanding
1342	the only file in a zip
1343
1344	:param bool confirmoverwrite: if True asks the user to confirm
1345	before overwriting if the extracted file already exists
1346
1347	:param bool multipleselect: if True allows more than one zip
1348	file to be extracted, a list of file(s) is returned.
1349	If only one file is present, do not ask which one, otherwise
1350	offer a list of choices (unless selection is used).
1351
1352	:returns: the name of the file that has been created or a
1353	list of files (see multipleselect)
1354
1355	If the file is not a zipfile, return the name of the input file.
1356	If the zipfile is empty or no file has been selected, return None
1357	'''
1358	import zipfile # do this now, since we can save startup time by doing this only on need
1359	import shutil
1360	zloc = os.path.split(filename)[0]
1361	if not zipfile.is_zipfile(filename):
1362	#print("not zip")
1363	return filename
1364
1365	z = zipfile.ZipFile(filename,'r')
1366	zinfo = z.infolist()
1367
1368	if len(zinfo) == 0:
1369	#print('Zip has no files!')
1370	zlist = [-1]
1371	if selection:
1372	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1373	if selection.lower() in choices:
1374	zlist = [choices.index(selection.lower())]
1375	else:
1376	print('debug: file '+str(selection)+' was not found in '+str(filename))
1377	zlist = [-1]
1378	elif len(zinfo) == 1 and confirmread:
1379	result = wx.ID_NO
1380	dlg = wx.MessageDialog(
1381	parent,
1382	'Is file '+str(zinfo[0].filename)+
1383	' what you want to extract from '+
1384	str(os.path.split(filename)[1])+'?',
1385	'Confirm file',
1386	wx.YES_NO \| wx.ICON_QUESTION)
1387	try:
1388	result = dlg.ShowModal()
1389	finally:
1390	dlg.Destroy()
1391	if result == wx.ID_NO:
1392	zlist = [-1]
1393	else:
1394	zlist = [0]
1395	elif len(zinfo) == 1:
1396	zlist = [0]
1397	elif multipleselect:
1398	# select one or more from a from list
1399	choices = [i.filename for i in zinfo]
1400	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1401	'Choose file(s)',choices)
1402	if dlg.ShowModal() == wx.ID_OK:
1403	zlist = dlg.GetSelections()
1404	else:
1405	zlist = []
1406	dlg.Destroy()
1407	else:
1408	# select one from a from list
1409	choices = [i.filename for i in zinfo]
1410	dlg = wx.SingleChoiceDialog(parent,
1411	'Select file to extract from zip file'+str(filename),'Choose file',
1412	choices,)
1413	if dlg.ShowModal() == wx.ID_OK:
1414	zlist = [dlg.GetSelection()]
1415	else:
1416	zlist = [-1]
1417	dlg.Destroy()
1418
1419	outlist = []
1420	for zindex in zlist:
1421	if zindex >= 0:
1422	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1423	if os.path.exists(efil) and confirmoverwrite:
1424	result = wx.ID_NO
1425	dlg = wx.MessageDialog(parent,
1426	'File '+str(efil)+' already exists. OK to overwrite it?',
1427	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1428	try:
1429	result = dlg.ShowModal()
1430	finally:
1431	dlg.Destroy()
1432	if result == wx.ID_NO:
1433	zindex = -1
1434	if zindex >= 0:
1435	# extract the file to the current directory, regardless of it's original path
1436	#z.extract(zinfo[zindex],zloc)
1437	eloc,efil = os.path.split(zinfo[zindex].filename)
1438	outfile = os.path.join(zloc, efil)
1439	fpin = z.open(zinfo[zindex])
1440	fpout = file(outfile, "wb")
1441	shutil.copyfileobj(fpin, fpout)
1442	fpin.close()
1443	fpout.close()
1444	outlist.append(outfile)
1445	z.close()
1446	if multipleselect and len(outlist) >= 1:
1447	return outlist
1448	elif len(outlist) == 1:
1449	return outlist[0]
1450	else:
1451	return None
1452
1453	######################################################################
1454	# base classes for reading various types of data files
1455	# not used directly, only by subclassing
1456	######################################################################
1457	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1458	P1SGData = SGData
1459	class ImportBaseclass(object):
1460	'''Defines a base class for the reading of input files (diffraction
1461	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1462	for an explanation on how to use a subclass of this class.
1463	'''
1464	class ImportException(Exception):
1465	'''Defines an Exception that is used when an import routine hits an expected error,
1466	usually in .Reader.
1467
1468	Good practice is that the Reader should define a value in self.errors that
1469	tells the user some information about what is wrong with their file.
1470	'''
1471	pass
1472
1473	def __init__(self,
1474	formatName,
1475	longFormatName=None,
1476	extensionlist=[],
1477	strictExtension=False,
1478	):
1479	self.formatName = formatName # short string naming file type
1480	if longFormatName: # longer string naming file type
1481	self.longFormatName = longFormatName
1482	else:
1483	self.longFormatName = formatName
1484	# define extensions that are allowed for the file type
1485	# for windows, remove any extensions that are duplicate, as case is ignored
1486	if sys.platform == 'windows' and extensionlist:
1487	extensionlist = list(set([s.lower() for s in extensionlist]))
1488	self.extensionlist = extensionlist
1489	# If strictExtension is True, the file will not be read, unless
1490	# the extension matches one in the extensionlist
1491	self.strictExtension = strictExtension
1492	self.errors = ''
1493	self.warnings = ''
1494	# used for readers that will use multiple passes to read
1495	# more than one data block
1496	self.repeat = False
1497	self.selections = []
1498	self.repeatcount = 0
1499	self.readfilename = '?'
1500	#print 'created',self.__class__
1501
1502	def ReInitialize(self):
1503	'Reinitialize the Reader to initial settings'
1504	self.errors = ''
1505	self.warnings = ''
1506	self.repeat = False
1507	self.repeatcount = 0
1508	self.readfilename = '?'
1509
1510	def BlockSelector(self, ChoiceList, ParentFrame=None,
1511	title='Select a block',
1512	size=None, header='Block Selector',
1513	useCancel=True):
1514	''' Provide a wx dialog to select a block if the file contains more
1515	than one set of data and one must be selected
1516	'''
1517	if useCancel:
1518	dlg = wx.SingleChoiceDialog(
1519	ParentFrame,title, header,ChoiceList)
1520	else:
1521	dlg = wx.SingleChoiceDialog(
1522	ParentFrame,title, header,ChoiceList,
1523	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1524	if size: dlg.SetSize(size)
1525	dlg.CenterOnParent()
1526	if dlg.ShowModal() == wx.ID_OK:
1527	sel = dlg.GetSelection()
1528	return sel
1529	else:
1530	return None
1531	dlg.Destroy()
1532
1533	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1534	title='Select a block',size=None, header='Block Selector'):
1535	'''Provide a wx dialog to select a block of data if the
1536	file contains more than one set of data and one must be
1537	selected.
1538
1539	:returns: a list of the selected blocks
1540	'''
1541	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1542	wx.CHOICEDLG_STYLE)
1543	dlg.CenterOnParent()
1544	if size: dlg.SetSize(size)
1545	if dlg.ShowModal() == wx.ID_OK:
1546	sel = dlg.GetSelections()
1547	else:
1548	return []
1549	dlg.Destroy()
1550	selected = []
1551	if len(ChoiceList) in sel:
1552	return range(len(ChoiceList))
1553	else:
1554	return sel
1555	return selected
1556
1557	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1558	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1559	widget. Typical input:
1560
1561	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1562
1563	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1564
1565	optional keyword parameters are: head (window title) and title
1566	returns a list of selected indicies for each choice (or None)
1567	'''
1568	result = None
1569	dlg = MultipleChoicesDialog(choicelist,headinglist,
1570	parent=ParentFrame, **kwargs)
1571	dlg.CenterOnParent()
1572	if dlg.ShowModal() == wx.ID_OK:
1573	result = dlg.chosen
1574	dlg.Destroy()
1575	return result
1576
1577	def ShowBusy(self):
1578	wx.BeginBusyCursor()
1579	# wx.Yield() # make it happen now!
1580
1581	def DoneBusy(self):
1582	wx.EndBusyCursor()
1583	wx.Yield() # make it happen now!
1584
1585	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1586	# '''This method must be supplied in the child class to read the file.
1587	# if the read fails either return False or raise an Exception
1588	# preferably of type ImportException.
1589	# '''
1590	# #start reading
1591	# raise ImportException("Error occurred while...")
1592	# self.errors += "Hint for user on why the error occur
1593	# return False # if an error occurs
1594	# return True # if read OK
1595
1596	def ExtensionValidator(self, filename):
1597	'''This methods checks if the file has the correct extension
1598	Return False if this filename will not be supported by this reader
1599	Return True if the extension matches the list supplied by the reader
1600	Return None if the reader allows un-registered extensions
1601	'''
1602	if filename:
1603	ext = os.path.splitext(filename)[1]
1604	if sys.platform == 'windows': ext = ext.lower()
1605	if ext in self.extensionlist: return True
1606	if self.strictExtension: return False
1607	return None
1608
1609	def ContentsValidator(self, filepointer):
1610	'''This routine will attempt to determine if the file can be read
1611	with the current format.
1612	This will typically be overridden with a method that
1613	takes a quick scan of [some of]
1614	the file contents to do a "sanity" check if the file
1615	appears to match the selected format.
1616	Expected to be called via self.Validator()
1617	'''
1618	#filepointer.seek(0) # rewind the file pointer
1619	return True
1620
1621	def CIFValidator(self, filepointer):
1622	'''A :meth:`ContentsValidator` for use to validate CIF files.
1623	'''
1624	for i,l in enumerate(filepointer):
1625	if i >= 1000: return True
1626	'''Encountered only blank lines or comments in first 1000
1627	lines. This is unlikely, but assume it is CIF anyway, since we are
1628	even less likely to find a file with nothing but hashes and
1629	blank lines'''
1630	line = l.strip()
1631	if len(line) == 0: # ignore blank lines
1632	continue
1633	elif line.startswith('#'): # ignore comments
1634	continue
1635	elif line.startswith('data_'): # on the right track, accept this file
1636	return True
1637	else: # found something invalid
1638	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1639	self.errors += ' '+str(l)
1640	self.errors += ' Note: a CIF should only have blank lines or comments before'
1641	self.errors += ' a data_ statement begins a block.'
1642	return False
1643
1644	class ImportPhase(ImportBaseclass):
1645	'''Defines a base class for the reading of files with coordinates
1646
1647	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1648	in :meth:`GSASII.GSASII.OnImportPhase`.
1649	See :ref:`Writing a Import Routine<Import_Routines>`
1650	for an explanation on how to use this class.
1651
1652	'''
1653	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1654	strictExtension=False,):
1655	# call parent __init__
1656	ImportBaseclass.__init__(self,formatName,longFormatName,
1657	extensionlist,strictExtension)
1658	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1659	self.Constraints = None
1660
1661	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1662	title='Select a phase', size=None,header='Phase Selector'):
1663	''' Provide a wx dialog to select a phase if the file contains more
1664	than one phase
1665	'''
1666	return self.BlockSelector(ChoiceList,ParentFrame,title,
1667	size,header)
1668
1669	class ImportStructFactor(ImportBaseclass):
1670	'''Defines a base class for the reading of files with tables
1671	of structure factors.
1672
1673	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1674	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1675	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1676	:meth:`Reader`.
1677
1678	See :ref:`Writing a Import Routine<Import_Routines>`
1679	for an explanation on how to use import classes in general. The specifics
1680	for reading a structure factor histogram require that
1681	the ``Reader()`` routine in the import
1682	class need to do only a few things: It
1683	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1684	and set :attr:`Parameters` with the instrument parameters
1685	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1686	'''
1687	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1688	strictExtension=False,):
1689	ImportBaseclass.__init__(self,formatName,longFormatName,
1690	extensionlist,strictExtension)
1691
1692	# define contents of Structure Factor entry
1693	self.Parameters = []
1694	'self.Parameters is a list with two dicts for data parameter settings'
1695	self.InitParameters()
1696	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1697	self.Banks = [] #for multi bank data (usually TOF)
1698	'''self.RefDict is a dict containing the reflection information, as read from the file.
1699	Item 'RefList' contains the reflection information. See the
1700	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1701	for the contents of each row. Dict element 'FF'
1702	contains the form factor values for each element type; if this entry
1703	is left as initialized (an empty list) it will be initialized as needed later.
1704	'''
1705	def ReInitialize(self):
1706	'Reinitialize the Reader to initial settings'
1707	ImportBaseclass.ReInitialize(self)
1708	self.InitParameters()
1709	self.Banks = [] #for multi bank data (usually TOF)
1710	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1711
1712	def InitParameters(self):
1713	'initialize the instrument parameters structure'
1714	Lambda = 0.70926
1715	HistType = 'SXC'
1716	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1717	'Lam':[Lambda,Lambda]
1718	}, {}]
1719	'Parameters is a list with two dicts for data parameter settings'
1720
1721	def UpdateParameters(self,Type=None,Wave=None):
1722	'Revise the instrument parameters'
1723	if Type is not None:
1724	self.Parameters[0]['Type'] = [Type,Type]
1725	if Wave is not None:
1726	self.Parameters[0]['Lam'] = [Wave,Wave]
1727
1728	######################################################################
1729	class ImportPowderData(ImportBaseclass):
1730	'''Defines a base class for the reading of files with powder data.
1731
1732	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1733	in :meth:`GSASII.GSASII.OnImportPowder`.
1734	See :ref:`Writing a Import Routine<Import_Routines>`
1735	for an explanation on how to use this class.
1736	'''
1737	def __init__(self,
1738	formatName,
1739	longFormatName=None,
1740	extensionlist=[],
1741	strictExtension=False,
1742	):
1743	ImportBaseclass.__init__(self,formatName,
1744	longFormatName,
1745	extensionlist,
1746	strictExtension)
1747	self.clockWd = None # used in TOF
1748	self.ReInitialize()
1749
1750	def ReInitialize(self):
1751	'Reinitialize the Reader to initial settings'
1752	ImportBaseclass.ReInitialize(self)
1753	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1754	self.powderdata = [] # Powder dataset
1755	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1756	np.array(x), # x-axis values
1757	np.array(y), # powder pattern intensities
1758	np.array(w), # 1/sig(intensity)^2 values (weights)
1759	np.array(yc), # calc. intensities (zero)
1760	np.array(yb), # calc. background (zero)
1761	np.array(yd), # obs-calc profiles
1762	'''
1763	self.comments = []
1764	self.idstring = ''
1765	self.Sample = G2pdG.SetDefaultSample() # default sample parameters
1766	self.Controls = {} # items to be placed in top-level Controls
1767	self.GSAS = None # used in TOF
1768	self.repeat_instparm = True # Should a parm file be
1769	# used for multiple histograms?
1770	self.instparm = None # name hint from file of instparm to use
1771	self.instfile = '' # full path name to instrument parameter file
1772	self.instbank = '' # inst parm bank number
1773	self.instmsg = '' # a label that gets printed to show
1774	# where instrument parameters are from
1775	self.numbanks = 1
1776	self.instdict = {} # place items here that will be transferred to the instrument parameters
1777	self.pwdparms = {} # place parameters that are transferred directly to the tree
1778	# here (typically from an existing GPX file)
1779	######################################################################
1780	class ImportSmallAngleData(ImportBaseclass):
1781	'''Defines a base class for the reading of files with small angle data.
1782	See :ref:`Writing a Import Routine<Import_Routines>`
1783	for an explanation on how to use this class.
1784	'''
1785	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1786	strictExtension=False,):
1787
1788	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1789	strictExtension)
1790	self.ReInitialize()
1791
1792	def ReInitialize(self):
1793	'Reinitialize the Reader to initial settings'
1794	ImportBaseclass.ReInitialize(self)
1795	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1796	self.smallangledata = [] # SASD dataset
1797	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1798	np.array(x), # x-axis values
1799	np.array(y), # powder pattern intensities
1800	np.array(w), # 1/sig(intensity)^2 values (weights)
1801	np.array(yc), # calc. intensities (zero)
1802	np.array(yd), # obs-calc profiles
1803	np.array(yb), # preset bkg
1804	'''
1805	self.comments = []
1806	self.idstring = ''
1807	self.Sample = G2pdG.SetDefaultSample()
1808	self.GSAS = None # used in TOF
1809	self.clockWd = None # used in TOF
1810	self.numbanks = 1
1811	self.instdict = {} # place items here that will be transferred to the instrument parameters
1812	######################################################################
1813	class ExportBaseclass(object):
1814	'''Defines a base class for the exporting of GSAS-II results.
1815
1816	This class is subclassed in the various exports/G2export_*.py files. Those files
1817	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
1818	appropriate menu items for each one and the .Exporter method is called
1819	directly from the menu item.
1820
1821	'''
1822	def __init__(self,
1823	G2frame,
1824	formatName,
1825	extension,
1826	longFormatName=None,
1827	):
1828	self.G2frame = G2frame
1829	self.formatName = formatName # short string naming file type
1830	self.extension = extension
1831	if longFormatName: # longer string naming file type
1832	self.longFormatName = longFormatName
1833	else:
1834	self.longFormatName = formatName
1835	self.OverallParms = {}
1836	self.Phases = {}
1837	self.Histograms = {}
1838	self.powderDict = {}
1839	self.xtalDict = {}
1840	self.parmDict = {}
1841	self.sigDict = {}
1842	# updated in InitExport:
1843	self.currentExportType = None # type of export that has been requested
1844	# updated in ExportSelect (when used):
1845	self.phasenam = None # a list of selected phases
1846	self.histnam = None # a list of selected histograms
1847	self.filename = None # name of file to be written (single export) or template (multiple files)
1848	self.dirname = '' # name of directory where file(s) will be written
1849	self.fullpath = '' # name of file being written -- full path
1850
1851	# items that should be defined in a subclass of this class
1852	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1853	# The following types are defined: 'project', "phase", "powder", "single"
1854	self.multiple = False # set as True if the class can export multiple phases or histograms
1855	# self.multiple is ignored for "project" exports
1856
1857	def InitExport(self,event):
1858	'''Determines the type of menu that called the Exporter and
1859	misc initialization.
1860	'''
1861	self.filename = None # name of file to be written (single export)
1862	self.dirname = '' # name of file to be written (multiple export)
1863	if event:
1864	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1865
1866	def MakePWDRfilename(self,hist):
1867	'''Make a filename root (no extension) from a PWDR histogram name
1868
1869	:param str hist: the histogram name in data tree (starts with "PWDR ")
1870	'''
1871	file0 = ''
1872	file1 = hist[5:]
1873	# replace repeated blanks
1874	while file1 != file0:
1875	file0 = file1
1876	file1 = file0.replace(' ',' ').strip()
1877	file0 = file1.replace('Azm= ','A')
1878	# if angle has unneeded decimal places on aziumuth, remove them
1879	if file0[-3:] == '.00': file0 = file0[:-3]
1880	file0 = file0.replace('.','_')
1881	file0 = file0.replace(' ','_')
1882	return file0
1883
1884	def ExportSelect(self,AskFile='ask'):
1885	'''Selects histograms or phases when needed. Sets a default file name when
1886	requested in self.filename; always sets a default directory in self.dirname.
1887
1888	:param bool AskFile: Determines how this routine processes getting a
1889	location to store the current export(s).
1890
1891	* if AskFile is 'ask' (default option), get the name of the file to be written;
1892	self.filename and self.dirname are always set. In the case where
1893	multiple files must be generated, the export routine should do this
1894	based on self.filename as a template.
1895	* if AskFile is 'dir', get the name of the directory to be used;
1896	self.filename is not used, but self.dirname is always set. The export routine
1897	will always generate the file name.
1898	* if AskFile is 'single', get only the name of the directory to be used when
1899	multiple items will be written (as multiple files) are used
1900	or a complete file name is requested when a single file
1901	name is selected. self.dirname is always set and self.filename used
1902	only when a single file is selected.
1903	* if AskFile is 'default', creates a name of the file to be used from
1904	the name of the project (.gpx) file. If the project has not been saved,
1905	then the name of file is requested.
1906	self.filename and self.dirname are always set. In the case where
1907	multiple file names must be generated, the export routine should do this
1908	based on self.filename.
1909	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1910	file. If the project has not been saved, then a directory is requested.
1911	self.filename is not used.
1912
1913	:returns: True in case of an error
1914	'''
1915
1916	numselected = 1
1917	if self.currentExportType == 'phase':
1918	if len(self.Phases) == 0:
1919	self.G2frame.ErrorDialog(
1920	'Empty project',
1921	'Project does not contain any phases.')
1922	return True
1923	elif len(self.Phases) == 1:
1924	self.phasenam = self.Phases.keys()
1925	elif self.multiple:
1926	choices = sorted(self.Phases.keys())
1927	phasenum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1928	if phasenum is None: return True
1929	self.phasenam = [choices[i] for i in phasenum]
1930	if not self.phasenam: return True
1931	numselected = len(self.phasenam)
1932	else:
1933	choices = sorted(self.Phases.keys())
1934	phasenum = G2gd.ItemSelector(choices,self.G2frame)
1935	if phasenum is None: return True
1936	self.phasenam = [choices[phasenum]]
1937	numselected = len(self.phasenam)
1938	elif self.currentExportType == 'single':
1939	if len(self.xtalDict) == 0:
1940	self.G2frame.ErrorDialog(
1941	'Empty project',
1942	'Project does not contain any single crystal data.')
1943	return True
1944	elif len(self.xtalDict) == 1:
1945	self.histnam = self.xtalDict.values()
1946	elif self.multiple:
1947	choices = sorted(self.xtalDict.values())
1948	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1949	if not hnum: return True
1950	self.histnam = [choices[i] for i in hnum]
1951	numselected = len(self.histnam)
1952	else:
1953	choices = sorted(self.xtalDict.values())
1954	hnum = G2gd.ItemSelector(choices,self.G2frame)
1955	if hnum is None: return True
1956	self.histnam = [choices[hnum]]
1957	numselected = len(self.histnam)
1958	elif self.currentExportType == 'powder':
1959	if len(self.powderDict) == 0:
1960	self.G2frame.ErrorDialog(
1961	'Empty project',
1962	'Project does not contain any powder data.')
1963	return True
1964	elif len(self.powderDict) == 1:
1965	self.histnam = self.powderDict.values()
1966	elif self.multiple:
1967	choices = sorted(self.powderDict.values())
1968	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1969	if not hnum: return True
1970	self.histnam = [choices[i] for i in hnum]
1971	numselected = len(self.histnam)
1972	else:
1973	choices = sorted(self.powderDict.values())
1974	hnum = G2gd.ItemSelector(choices,self.G2frame)
1975	if hnum is None: return True
1976	self.histnam = [choices[hnum]]
1977	numselected = len(self.histnam)
1978	elif self.currentExportType == 'image':
1979	if len(self.Histograms) == 0:
1980	self.G2frame.ErrorDialog(
1981	'Empty project',
1982	'Project does not contain any images.')
1983	return True
1984	elif len(self.Histograms) == 1:
1985	self.histnam = self.Histograms.keys()
1986	else:
1987	choices = sorted(self.Histograms.keys())
1988	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1989	if self.multiple:
1990	if not hnum: return True
1991	self.histnam = [choices[i] for i in hnum]
1992	else:
1993	if hnum is None: return True
1994	self.histnam = [choices[hnum]]
1995	numselected = len(self.histnam)
1996	if self.currentExportType == 'map':
1997	# search for phases with maps
1998	mapPhases = []
1999	choices = []
2000	for phasenam in sorted(self.Phases):
2001	phasedict = self.Phases[phasenam] # pointer to current phase info
2002	if len(phasedict['General']['Map'].get('rho',[])):
2003	mapPhases.append(phasenam)
2004	if phasedict['General']['Map'].get('Flip'):
2005	choices.append('Charge flip map: '+str(phasenam))
2006	elif phasedict['General']['Map'].get('MapType'):
2007	choices.append(
2008	str(phasedict['General']['Map'].get('MapType'))
2009	+ ' map: ' + str(phasenam))
2010	else:
2011	choices.append('unknown map: '+str(phasenam))
2012	# select a map if needed
2013	if len(mapPhases) == 0:
2014	self.G2frame.ErrorDialog(
2015	'Empty project',
2016	'Project does not contain any maps.')
2017	return True
2018	elif len(mapPhases) == 1:
2019	self.phasenam = mapPhases
2020	else:
2021	phasenum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
2022	if self.multiple:
2023	if not phasenum: return True
2024	self.phasenam = [mapPhases[i] for i in phasenum]
2025	else:
2026	if phasenum is None: return True
2027	self.phasenam = [mapPhases[phasenum]]
2028	numselected = len(self.phasenam)
2029
2030	# items selected, now set self.dirname and usually self.filename
2031	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
2032	AskFile == 'default' and not self.G2frame.GSASprojectfile
2033	):
2034	filename = self.askSaveFile()
2035	if not filename: return True
2036	self.dirname,self.filename = os.path.split(filename)
2037	elif AskFile == 'dir' or AskFile == 'single' or (
2038	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
2039	):
2040	self.dirname = self.askSaveDirectory()
2041	if not self.dirname: return True
2042	elif AskFile == 'default-dir' or AskFile == 'default':
2043	self.dirname,self.filename = os.path.split(
2044	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
2045	)
2046	else:
2047	raise Exception('This should not happen!')
2048
2049	def loadParmDict(self):
2050	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
2051	refined values to those from the last cycle and set the uncertainties for the
2052	refined parameters in another dict (self.sigDict).
2053
2054	Expands the parm & sig dicts to include values derived from constraints.
2055	'''
2056	self.parmDict = {}
2057	self.sigDict = {}
2058	rigidbodyDict = {}
2059	covDict = {}
2060	consDict = {}
2061	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2062	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2063	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2064	while item:
2065	name = self.G2frame.PatternTree.GetItemText(item)
2066	if name == 'Rigid bodies':
2067	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
2068	elif name == 'Covariance':
2069	covDict = self.G2frame.PatternTree.GetItemPyData(item)
2070	elif name == 'Constraints':
2071	consDict = self.G2frame.PatternTree.GetItemPyData(item)
2072	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2073	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
2074	self.parmDict.update(rbDict)
2075	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
2076	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,maxSSwave = G2stIO.GetPhaseData(
2077	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
2078	self.parmDict.update(phaseDict)
2079	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
2080	Phases,Histograms,Print=False,resetRefList=False)
2081	self.parmDict.update(hapDict)
2082	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
2083	self.parmDict.update(histDict)
2084	self.parmDict.update(zip(
2085	covDict.get('varyList',[]),
2086	covDict.get('variables',[])))
2087	self.sigDict = dict(zip(
2088	covDict.get('varyList',[]),
2089	covDict.get('sig',[])))
2090	# expand to include constraints: first compile a list of constraints
2091	constList = []
2092	for item in consDict:
2093	if item.startswith('_'): continue
2094	constList += consDict[item]
2095	# now process the constraints
2096	G2mv.InitVars()
2097	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
2098	varyList = covDict.get('varyListStart')
2099	if varyList is None and len(constDict) == 0:
2100	# no constraints can use varyList
2101	varyList = covDict.get('varyList')
2102	elif varyList is None:
2103	# old GPX file from before pre-constraint varyList is saved
2104	print ' * Old refinement: Please use Calculate/Refine to redo *'
2105	raise Exception(' * Export aborted *')
2106	else:
2107	varyList = list(varyList)
2108	try:
2109	groups,parmlist = G2mv.GroupConstraints(constDict)
2110	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
2111	except:
2112	# this really should not happen
2113	print ' * ERROR - constraints are internally inconsistent *'
2114	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
2115	print 'Errors',errmsg
2116	if warnmsg: print 'Warnings',warnmsg
2117	raise Exception(' * CIF creation aborted *')
2118	# add the constrained values to the parameter dictionary
2119	G2mv.Dict2Map(self.parmDict,varyList)
2120	# and add their uncertainties into the esd dictionary (sigDict)
2121	if covDict.get('covMatrix') is not None:
2122	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
2123
2124	def loadTree(self):
2125	'''Load the contents of the data tree into a set of dicts
2126	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2127	& self.xtalDict)
2128
2129	* The childrenless data tree items are overall parameters/controls for the
2130	entire project and are placed in self.OverallParms
2131	* Phase items are placed in self.Phases
2132	* Data items are placed in self.Histogram. The key for these data items
2133	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2134	'''
2135	self.OverallParms = {}
2136	self.powderDict = {}
2137	self.xtalDict = {}
2138	self.Phases = {}
2139	self.Histograms = {}
2140	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2141	histType = None
2142	if self.currentExportType == 'phase':
2143	# if exporting phases load them here
2144	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2145	if not sub:
2146	print 'no phases found'
2147	return True
2148	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2149	while item:
2150	phaseName = self.G2frame.PatternTree.GetItemText(item)
2151	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2152	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2153	return
2154	elif self.currentExportType == 'single':
2155	histType = 'HKLF'
2156	elif self.currentExportType == 'powder':
2157	histType = 'PWDR'
2158	elif self.currentExportType == 'image':
2159	histType = 'IMG'
2160
2161	if histType: # Loading just one kind of tree entry
2162	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2163	while item:
2164	name = self.G2frame.PatternTree.GetItemText(item)
2165	if name.startswith(histType):
2166	if self.Histograms.get(name): # there is already an item with this name
2167	print('Histogram name '+str(name)+' is repeated. Renaming')
2168	if name[-1] == '9':
2169	name = name[:-1] + '10'
2170	elif name[-1] in '012345678':
2171	name = name[:-1] + str(int(name[-1])+1)
2172	else:
2173	name += '-1'
2174	self.Histograms[name] = {}
2175	# the main info goes into Data, but the 0th
2176	# element contains refinement results, carry
2177	# that over too now.
2178	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2179	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2180	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2181	while item2:
2182	child = self.G2frame.PatternTree.GetItemText(item2)
2183	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2184	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2185	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2186	# index powder and single crystal histograms by number
2187	for hist in self.Histograms:
2188	if hist.startswith("PWDR"):
2189	d = self.powderDict
2190	elif hist.startswith("HKLF"):
2191	d = self.xtalDict
2192	else:
2193	return
2194	i = self.Histograms[hist].get('hId')
2195	if i is None and not d.keys():
2196	i = 0
2197	elif i is None or i in d.keys():
2198	i = max(d.keys())+1
2199	d[i] = hist
2200	return
2201	# else standard load: using all interlinked phases and histograms
2202	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2203	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2204	while item:
2205	name = self.G2frame.PatternTree.GetItemText(item)
2206	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2207	if not item2:
2208	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2209	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2210	# index powder and single crystal histograms
2211	for hist in self.Histograms:
2212	i = self.Histograms[hist]['hId']
2213	if hist.startswith("PWDR"):
2214	self.powderDict[i] = hist
2215	elif hist.startswith("HKLF"):
2216	self.xtalDict[i] = hist
2217
2218	def dumpTree(self,mode='type'):
2219	'''Print out information on the data tree dicts loaded in loadTree
2220	'''
2221	print '\nOverall'
2222	if mode == 'type':
2223	def Show(arg): return type(arg)
2224	else:
2225	def Show(arg): return arg
2226	for key in self.OverallParms:
2227	print ' ',key,Show(self.OverallParms[key])
2228	print 'Phases'
2229	for key1 in self.Phases:
2230	print ' ',key1,Show(self.Phases[key1])
2231	print 'Histogram'
2232	for key1 in self.Histograms:
2233	print ' ',key1,Show(self.Histograms[key1])
2234	for key2 in self.Histograms[key1]:
2235	print ' ',key2,Show(self.Histograms[key1][key2])
2236
2237	def defaultSaveFile(self):
2238	return os.path.abspath(
2239	os.path.splitext(self.G2frame.GSASprojectfile
2240	)[0]+self.extension)
2241
2242	def askSaveFile(self):
2243	'''Ask the user to supply a file name
2244
2245	:returns: a file name (str) or None if Cancel is pressed
2246	'''
2247	defnam = os.path.splitext(
2248	os.path.split(self.G2frame.GSASprojectfile)[1]
2249	)[0]+self.extension
2250	dlg = wx.FileDialog(
2251	self.G2frame, 'Input name for file to write', '.', defnam,
2252	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2253	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2254	dlg.CenterOnParent()
2255	try:
2256	if dlg.ShowModal() == wx.ID_OK:
2257	filename = dlg.GetPath()
2258	# make sure extension is correct
2259	filename = os.path.splitext(filename)[0]+self.extension
2260	else:
2261	filename = None
2262	finally:
2263	dlg.Destroy()
2264	return filename
2265
2266	def askSaveDirectory(self):
2267	'''Ask the user to supply a directory name. Path name is used as the
2268	starting point for the next export path search.
2269
2270	:returns: a directory name (str) or None if Cancel is pressed
2271	'''
2272	if self.G2frame.exportDir:
2273	startdir = self.G2frame.exportDir
2274	elif self.G2frame.GSASprojectfile:
2275	startdir = os.path.split(self.G2frame.GSASprojectfile)[0]
2276	elif self.G2frame.dirname:
2277	startdir = self.G2frame.dirname
2278	else:
2279	startdir = ''
2280	dlg = wx.DirDialog(
2281	self.G2frame, 'Input directory where file(s) will be written', startdir,
2282	wx.DD_DEFAULT_STYLE)
2283	dlg.CenterOnParent()
2284	try:
2285	if dlg.ShowModal() == wx.ID_OK:
2286	filename = dlg.GetPath()
2287	self.G2frame.exportDir = filename
2288	else:
2289	filename = None
2290	finally:
2291	dlg.Destroy()
2292	return filename
2293
2294	# Tools for file writing.
2295	def OpenFile(self,fil=None,mode='w'):
2296	'''Open the output file
2297
2298	:param str fil: The name of the file to open. If None (default)
2299	the name defaults to self.dirname + self.filename.
2300	If an extension is supplied, it is not overridded,
2301	but if not, the default extension is used.
2302	:returns: the file object opened by the routine which is also
2303	saved as self.fp
2304	'''
2305	if not fil:
2306	if not os.path.splitext(self.filename)[1]:
2307	self.filename += self.extension
2308	fil = os.path.join(self.dirname,self.filename)
2309	self.fullpath = fil
2310	self.fp = open(fil,mode)
2311	return self.fp
2312
2313	def Write(self,line):
2314	'''write a line of output, attaching a line-end character
2315
2316	:param str line: the text to be written.
2317	'''
2318	self.fp.write(line+'\n')
2319	def CloseFile(self,fp=None):
2320	'''Close a file opened in OpenFile
2321
2322	:param file fp: the file object to be closed. If None (default)
2323	file object self.fp is closed.
2324	'''
2325	if fp is None:
2326	fp = self.fp
2327	self.fp = None
2328	fp.close()
2329	# Tools to pull information out of the data arrays
2330	def GetCell(self,phasenam):
2331	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2332
2333	:param str phasenam: the name for the selected phase
2334	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2335	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2336	cell values and `cellSig` has their uncertainties.
2337	"""
2338	phasedict = self.Phases[phasenam] # pointer to current phase info
2339	try:
2340	pfx = str(phasedict['pId'])+'::'
2341	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2342	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
2343	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2344	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2345	return cellList,cellSig
2346	except KeyError:
2347	cell = phasedict['General']['Cell'][1:]
2348	return cell,7*[0]
2349
2350	def GetAtoms(self,phasenam):
2351	"""Gets the atoms associated with a phase. Can be used with standard
2352	or macromolecular phases
2353
2354	:param str phasenam: the name for the selected phase
2355	:returns: a list of items for eac atom where each item is a list containing:
2356	label, typ, mult, xyz, and td, where
2357
2358	* label and typ are the atom label and the scattering factor type (str)
2359	* mult is the site multiplicity (int)
2360	* xyz is contains a list with four pairs of numbers:
2361	x, y, z and fractional occupancy and
2362	their standard uncertainty (or a negative value)
2363	* td is contains a list with either one or six pairs of numbers:
2364	if one number it is U\ :sub:`iso` and with six numbers it is
2365	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2366	paired with their standard uncertainty (or a negative value)
2367	"""
2368	phasedict = self.Phases[phasenam] # pointer to current phase info
2369	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2370	cfrac = cx+3
2371	fpfx = str(phasedict['pId'])+'::Afrac:'
2372	atomslist = []
2373	for i,at in enumerate(phasedict['Atoms']):
2374	if phasedict['General']['Type'] == 'macromolecular':
2375	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2376	else:
2377	label = at[ct-1]
2378	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2379	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2380	mult = at[cs+1]
2381	typ = at[ct]
2382	xyz = []
2383	for j,v in enumerate(('x','y','z')):
2384	val = at[cx+j]
2385	pfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2386	sig = self.sigDict.get(pfx,-0.000009)
2387	xyz.append((val,sig))
2388	xyz.append((fval,fsig))
2389	td = []
2390	if at[cia] == 'I':
2391	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2392	val = self.parmDict.get(pfx,at[cia+1])
2393	sig = self.sigDict.get(pfx,-0.0009)
2394	td.append((val,sig))
2395	else:
2396	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2397	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2398	val = self.parmDict.get(pfx,at[cia+2+i])
2399	sig = self.sigDict.get(pfx,-0.0009)
2400	td.append((val,sig))
2401	atomslist.append((label,typ,mult,xyz,td))
2402	return atomslist
2403	######################################################################
2404
2405	def ReadCIF(URLorFile):
2406	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2407	(from James Hester).
2408	The open routine gets confused with DOS names that begin with a letter and colon
2409	"C:\dir\" so this routine will try to open the passed name as a file and if that
2410	fails, try it as a URL
2411
2412	:param str URLorFile: string containing a URL or a file name. Code will try first
2413	to open it as a file and then as a URL.
2414
2415	:returns: a PyCifRW CIF object.
2416	'''
2417	import CifFile as cif # PyCifRW from James Hester
2418
2419	# alternate approach:
2420	#import urllib
2421	#ciffile = 'file:'+urllib.pathname2url(filename)
2422
2423	try:
2424	fp = open(URLorFile,'r')
2425	cf = cif.ReadCif(fp)
2426	fp.close()
2427	return cf
2428	except IOError:
2429	return cif.ReadCif(URLorFile)
2430
2431	if __name__ == '__main__':
2432	app = wx.PySimpleApp()
2433	frm = wx.Frame(None) # create a frame
2434	frm.Show(True)
2435	filename = '/tmp/notzip.zip'
2436	filename = '/tmp/all.zip'
2437	#filename = '/tmp/11bmb_7652.zip'
2438
2439	#selection=None, confirmoverwrite=True, parent=None
2440	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2441	print ExtractFileFromZip(filename,multipleselect=True)
2442	#confirmread=False, confirmoverwrite=False)
2443
2444	# choicelist=[ ('a','b','c'),
2445	# ('test1','test2'),('no choice',)]
2446	# titles = [ 'a, b or c', 'tests', 'No option here']
2447	# dlg = MultipleChoicesDialog(
2448	# choicelist,titles,
2449	# parent=frm)
2450	# if dlg.ShowModal() == wx.ID_OK:
2451	# print 'Got OK'

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