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source: trunk/GSASIIIO.py @ 1355

Last change on this file since 1355 was 1355, checked in by toby, 9 years ago
initial 10.9/Canopy fixes
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2014-05-20 16:49:19 +0000 (Tue, 20 May 2014) $
4	# $Author: toby $
5	# $Revision: 1355 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 1355 2014-05-20 16:49:19Z 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: 1355 $")
33	import GSASIIgrid as G2gd
34	import GSASIIspc as G2spc
35	import GSASIIlattice as G2lat
36	import GSASIIpwdGUI as G2pdG
37	import GSASIIElem as G2el
38	import GSASIIstrIO as G2stIO
39	import GSASIImapvars as G2mv
40	import os
41	import os.path as ospath
42
43	DEBUG = False #=True for various prints
44	TRANSP = False #=true to transpose images for testing
45	npsind = lambda x: np.sin(x*np.pi/180.)
46
47	def sfloat(S):
48	'Convert a string to float. An empty field is treated as zero'
49	if S.strip():
50	return float(S)
51	else:
52	return 0.0
53
54	def sint(S):
55	'Convert a string to int. An empty field is treated as zero'
56	if S.strip():
57	return int(S)
58	else:
59	return 0
60
61	def trim(val):
62	'''Simplify a string containing leading and trailing spaces
63	as well as newlines, tabs, repeated spaces etc. into a shorter and
64	more simple string, by replacing all ranges of whitespace
65	characters with a single space.
66
67	:param str val: the string to be simplified
68
69	:returns: the (usually) shortened version of the string
70	'''
71	return re.sub('\s+', ' ', val).strip()
72
73	def makeInstDict(names,data,codes):
74	inst = dict(zip(names,zip(data,data,codes)))
75	for item in inst:
76	inst[item] = list(inst[item])
77	return inst
78
79	def FileDlgFixExt(dlg,file):
80	'this is needed to fix a problem in linux wx.FileDialog'
81	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
82	if ext not in file:
83	file += ext
84	return file
85
86	def GetPowderPeaks(fileName):
87	'Read powder peaks from a file'
88	sind = lambda x: math.sin(x*math.pi/180.)
89	asind = lambda x: 180.*math.asin(x)/math.pi
90	Cuka = 1.54052
91	File = open(fileName,'Ur')
92	Comments = []
93	peaks = []
94	S = File.readline()
95	while S:
96	if S[:1] == '#':
97	Comments.append(S[:-1])
98	else:
99	item = S.split()
100	if len(item) == 1:
101	peaks.append([float(item[0]),1.0])
102	elif len(item) > 1:
103	peaks.append([float(item[0]),float(item[0])])
104	S = File.readline()
105	File.close()
106	if Comments:
107	print 'Comments on file:'
108	for Comment in Comments: print Comment
109	Peaks = []
110	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
111	for peak in peaks:
112	dsp = peak[0]
113	sth = Cuka/(2.0*dsp)
114	if sth < 1.0:
115	tth = 2.0*asind(sth)
116	else:
117	break
118	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
119	else: #2-thetas - assume Cuka (for now)
120	for peak in peaks:
121	tth = peak[0]
122	dsp = Cuka/(2.0*sind(tth/2.0))
123	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
124	return Comments,Peaks
125
126	def CheckImageFile(G2frame,imagefile):
127	'''Get an new image file name if the specified one does not
128	exist
129
130	:param wx.Frame G2frame: main GSAS-II Frame and data object
131
132	:param str imagefile: name of image file
133
134	:returns: imagefile, if it exists, or the name of a file
135	that does exist or False if the user presses Cancel
136
137	'''
138	if not ospath.exists(imagefile):
139	dlg = wx.FileDialog(G2frame, 'Bad image file name; choose name', '.', '',\
140	'Any image file (.edf;.tif;.tiff;.mar;.avg;.sum;.img)\
141	\|.edf;.tif;.tiff;.mar;.avg;.sum;.img\|\
142	European detector file (.edf)\|.edf\|\
143	Any detector tif (.tif;.tiff)\|.tif;.tiff\|\
144	MAR file (.mar)\|.mar\|\
145	GE Image (.avg;.sum)\|.avg;.sum\|\
146	ADSC Image (.img)\|.img\|\
147	All files (.)\|.',wx.OPEN\|wx.CHANGE_DIR)
148	try:
149	dlg.SetFilename(''+ospath.split(imagefile)[1])
150	if dlg.ShowModal() == wx.ID_OK:
151	imagefile = dlg.GetPath()
152	else:
153	imagefile = False
154	finally:
155	dlg.Destroy()
156	return imagefile
157
158	def EditImageParms(parent,Data,Comments,Image,filename):
159	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
160	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
161	def onClose(event):
162	dlg.EndModal(wx.ID_OK)
163	mainsizer = wx.BoxSizer(wx.VERTICAL)
164	h,w = Image.shape[:2]
165	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,
166	'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
167	0,wx.ALIGN_LEFT\|wx.ALL, 2)
168
169	vsizer = wx.BoxSizer(wx.HORIZONTAL)
170	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
171	0,wx.ALIGN_LEFT\|wx.ALL, 2)
172	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data,'wavelength')
173	vsizer.Add(wdgt)
174	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
175
176	vsizer = wx.BoxSizer(wx.HORIZONTAL)
177	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
178	0,wx.ALIGN_LEFT\|wx.ALL, 2)
179	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
180	size=(50,-1))
181	vsizer.Add(wdgt)
182	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),
183	wx.ALIGN_LEFT\|wx.ALL, 2)
184	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,
185	size=(50,-1))
186	vsizer.Add(wdgt)
187	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
188
189	vsizer = wx.BoxSizer(wx.HORIZONTAL)
190	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
191	0,wx.ALIGN_LEFT\|wx.ALL, 2)
192	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data,'distance')
193	vsizer.Add(wdgt)
194	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
195
196	vsizer = wx.BoxSizer(wx.HORIZONTAL)
197	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
198	0,wx.ALIGN_LEFT\|wx.ALL, 2)
199	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data['center'],0,
200	size=(75,-1))
201	vsizer.Add(wdgt)
202	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),
203	wx.ALIGN_LEFT\|wx.ALL, 2)
204	wdgt = G2gd.ValidatedTxtCtrl(dlg,Data['center'],1,
205	size=(75,-1))
206	vsizer.Add(wdgt)
207	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
208
209	vsizer = wx.BoxSizer(wx.HORIZONTAL)
210	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
211	0,wx.ALIGN_LEFT\|wx.ALL, 2)
212	wdgt = G2gd.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
213	vsizer.Add(wdgt)
214	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
215
216	btnsizer = wx.StdDialogButtonSizer()
217	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
218	OKbtn.SetDefault()
219	OKbtn.Bind(wx.EVT_BUTTON,onClose)
220	btnsizer.AddButton(OKbtn) # not sure why this is needed
221	btnsizer.Realize()
222	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
223	dlg.SetSizer(mainsizer)
224	dlg.CenterOnParent()
225	dlg.ShowModal()
226
227	def GetImageData(G2frame,imagefile,imageOnly=False):
228	'''Read an image with the file reader keyed by the
229	file extension
230
231	:param wx.Frame G2frame: main GSAS-II Frame and data object.
232
233	:param str imagefile: name of image file
234
235	:param bool imageOnly: If True return only the image,
236	otherwise (default) return more (see below)
237
238	:returns: an image as a numpy array or a list of four items:
239	Comments, Data, Npix and the Image, as selected by imageOnly
240
241	'''
242	ext = ospath.splitext(imagefile)[1]
243	Comments = []
244	if ext == '.tif' or ext == '.tiff':
245	Comments,Data,Npix,Image = GetTifData(imagefile)
246	if Npix == 0:
247	print("GetTifData failed to read "+str(filename)+" Trying PIL")
248	import scipy.misc
249	Image = scipy.misc.imread(imagefile,flatten=True)
250	Npix = Image.size
251	Comments = ['no metadata']
252	Data = {'wavelength': 0.1, 'pixelSize': [200, 200], 'distance': 100.0}
253	Data['size'] = list(Image.shape)
254	Data['center'] = [int(i/2) for i in Image.shape]
255	if not imageOnly:
256	EditImageParms(G2frame,Data,Comments,Image,imagefile)
257	elif ext == '.edf':
258	Comments,Data,Npix,Image = GetEdfData(imagefile)
259	elif ext == '.img':
260	Comments,Data,Npix,Image = GetImgData(imagefile)
261	Image[0][0] = 0
262	elif ext == '.mar3450' or ext == '.mar2300':
263	Comments,Data,Npix,Image = GetMAR345Data(imagefile)
264	elif ext in ['.sum','.avg','']:
265	Comments,Data,Npix,Image = GetGEsumData(imagefile)
266	elif ext == '.G2img':
267	Comments,Data,Npix,Image = GetG2Image(imagefile)
268	elif ext == '.png':
269	Comments,Data,Npix,Image = GetPNGData(imagefile)
270	if not imageOnly:
271	EditImageParms(G2frame,Data,Comments,Image,imagefile)
272	if imageOnly:
273	if TRANSP:
274	return Image.T
275	else:
276	return Image
277	else:
278	if TRANSP:
279	return Comments,Data,Npix,Image.T
280	else:
281	return Comments,Data,Npix,Image
282
283	def PutG2Image(filename,Comments,Data,Npix,image):
284	'Write an image as a python pickle'
285	File = open(filename,'wb')
286	cPickle.dump([Comments,Data,Npix,image],File,1)
287	File.close()
288	return
289
290	def GetG2Image(filename):
291	'Read an image as a python pickle'
292	File = open(filename,'rb')
293	Comments,Data,Npix,image = cPickle.load(File)
294	File.close()
295	return Comments,Data,Npix,image
296
297	def GetEdfData(filename,imageOnly=False):
298	'Read European detector data edf file'
299	import struct as st
300	import array as ar
301	if not imageOnly:
302	print 'Read European detector data edf file: ',filename
303	File = open(filename,'rb')
304	fileSize = os.stat(filename).st_size
305	head = File.read(3072)
306	lines = head.split('\n')
307	sizexy = [0,0]
308	pixSize = [0,0]
309	cent = [0,0]
310	head = ['European detector data',]
311	for line in lines:
312	fields = line.split()
313	if 'Dim_1' in line:
314	sizexy[0] = int(fields[2])
315	elif 'Dim_2' in line:
316	sizexy[1] = int(fields[2])
317	elif 'DataType' in line:
318	dType = fields[2]
319	elif 'refined_wavelength' in line:
320	wave = float(fields[2])
321	elif 'Size' in line:
322	imSize = int(fields[2])
323	elif 'DataType' in lines:
324	dType = fields[2]
325	elif 'pixel_size_x' in line:
326	pixSize[0] = float(fields[2])
327	elif 'pixel_size_y' in line:
328	pixSize[1] = float(fields[2])
329	elif 'beam_center_x' in line:
330	cent[0] = float(fields[2])
331	elif 'beam_center_y' in line:
332	cent[1] = float(fields[2])
333	elif 'refined_distance' in line:
334	dist = float(fields[2])
335	if line:
336	head.append(line)
337	File.seek(fileSize-imSize)
338	if dType == 'UnsignedShort':
339	image = np.array(ar.array('H',File.read(imSize)),dtype=np.int32)
340	elif dType == 'UnsignedInt':
341	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
342	image = np.reshape(image,(sizexy[1],sizexy[0]))
343	data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'size':sizexy}
344	Npix = sizexy[0]*sizexy[1]
345	File.close()
346	if imageOnly:
347	return image
348	else:
349	return head,data,Npix,image
350
351	def GetGEsumData(filename,imageOnly=False):
352	'Read SUM file as produced at 1-ID from G.E. images'
353	import struct as st
354	import array as ar
355	if not imageOnly:
356	print 'Read GE sum file: ',filename
357	File = open(filename,'rb')
358	if '.sum' in filename:
359	head = ['GE detector sum data from APS 1-ID',]
360	sizexy = [2048,2048]
361	elif '.avg' in filename:
362	head = ['GE detector avg data from APS 1-ID',]
363	sizexy = [2048,2048]
364	else:
365	head = ['GE detector raw data from APS 1-ID',]
366	File.seek(18)
367	size,nframes = st.unpack('<ih',File.read(6))
368	sizexy = [2048,2048]
369	pos = 8192
370	File.seek(pos)
371	Npix = sizexy[0]*sizexy[1]
372	if '.sum' in filename:
373	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.int32)
374	elif '.avg' in filename:
375	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
376	else:
377	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
378	while nframes > 1:
379	image += np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
380	nframes -= 1
381	image = np.reshape(image,(sizexy[1],sizexy[0]))
382	data = {'pixelSize':(200,200),'wavelength':0.15,'distance':250.0,'center':[204.8,204.8],'size':sizexy}
383	File.close()
384	if imageOnly:
385	return image
386	else:
387	return head,data,Npix,image
388
389	def GetImgData(filename,imageOnly=False):
390	'Read an ADSC image file'
391	import struct as st
392	import array as ar
393	if not imageOnly:
394	print 'Read ADSC img file: ',filename
395	File = open(filename,'rb')
396	head = File.read(511)
397	lines = head.split('\n')
398	head = []
399	center = [0,0]
400	for line in lines[1:-2]:
401	line = line.strip()[:-1]
402	if line:
403	if 'SIZE1' in line:
404	size = int(line.split('=')[1])
405	Npix = size*size
406	elif 'WAVELENGTH' in line:
407	wave = float(line.split('=')[1])
408	elif 'BIN' in line:
409	if line.split('=')[1] == '2x2':
410	pixel=(102,102)
411	else:
412	pixel = (51,51)
413	elif 'DISTANCE' in line:
414	distance = float(line.split('=')[1])
415	elif 'CENTER_X' in line:
416	center[0] = float(line.split('=')[1])
417	elif 'CENTER_Y' in line:
418	center[1] = float(line.split('=')[1])
419	head.append(line)
420	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center,'size':[size,size]}
421	image = []
422	row = 0
423	pos = 512
424	File.seek(pos)
425	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
426	image = np.reshape(image,(sizexy[1],sizexy[0]))
427	# image = np.zeros(shape=(size,size),dtype=np.int32)
428	# while row < size:
429	# File.seek(pos)
430	# line = ar.array('H',File.read(2*size))
431	# image[row] = np.asarray(line)
432	# row += 1
433	# pos += 2*size
434	File.close()
435	if imageOnly:
436	return image
437	else:
438	return lines[1:-2],data,Npix,image
439
440	def GetMAR345Data(filename,imageOnly=False):
441	'Read a MAR-345 image plate image'
442	import array as ar
443	import struct as st
444	try:
445	import pack_f as pf
446	except:
447	msg = wx.MessageDialog(None, message="Unable to load the GSAS MAR image decompression, pack_f",
448	caption="Import Error",
449	style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
450	msg.ShowModal()
451	return None,None,None,None
452
453	if not imageOnly:
454	print 'Read Mar345 file: ',filename
455	File = open(filename,'rb')
456	head = File.read(4095)
457	numbers = st.unpack('<iiiiiiiiii',head[:40])
458	lines = head[128:].split('\n')
459	head = []
460	for line in lines:
461	line = line.strip()
462	if 'PIXEL' in line:
463	values = line.split()
464	pixel = (int(values[2]),int(values[4])) #in microns
465	elif 'WAVELENGTH' in line:
466	wave = float(line.split()[1])
467	elif 'DISTANCE' in line:
468	distance = float(line.split()[1]) #in mm
469	elif 'CENTER' in line:
470	values = line.split()
471	center = [float(values[2])/10.,float(values[4])/10.] #make in mm from pixels
472	if line:
473	head.append(line)
474	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center}
475	for line in head:
476	if 'FORMAT' in line[0:6]:
477	items = line.split()
478	size = int(items[1])
479	Npix = size*size
480	pos = 4096
481	data['size'] = [size,size]
482	File.seek(pos)
483	line = File.read(8)
484	while 'CCP4' not in line: #get past overflow list for now
485	line = File.read(8)
486	pos += 8
487	pos += 37
488	File.seek(pos)
489	raw = File.read()
490	File.close()
491	image = np.zeros(shape=(size,size),dtype=np.int32)
492	image = np.flipud(pf.pack_f(len(raw),raw,size,image).T) #transpose to get it right way around & flip
493	if imageOnly:
494	return image
495	else:
496	return head,data,Npix,image
497
498	def GetPNGData(filename,imageOnly=False):
499	'''Read an image in a png format, assumes image is converted from CheMin tif file
500	so default parameters are that machine.
501	'''
502	import scipy.misc
503	Image = scipy.misc.imread(filename,flatten=True)
504	Npix = Image.size
505	Comments = ['no metadata']
506	pixy = list(Image.shape)
507	sizexy = [40,40]
508	Data = {'wavelength': 1.78892, 'pixelSize': sizexy, 'distance': 18.0,'size':pixy}
509	Data['center'] = [pixy[0]sizexy[0]/1000,pixy[1]sizexy[1]/2000]
510	if imageOnly:
511	return Image.T
512	else:
513	return Comments,Data,Npix,Image.T
514
515	def GetTifData(filename,imageOnly=False):
516	'''Read an image in a pseudo-tif format,
517	as produced by a wide variety of software, almost always
518	incorrectly in some way.
519	'''
520	import struct as st
521	import Image as Im
522	import array as ar
523	import ReadMarCCDFrame as rmf
524	File = open(filename,'rb')
525	dataType = 5
526	center = [None,None]
527	wavelength = None
528	distance = None
529	try:
530	Meta = open(filename+'.metadata','Ur')
531	head = Meta.readlines()
532	for line in head:
533	line = line.strip()
534	if 'dataType=' in line:
535	dataType = int(line.split('=')[1])
536	Meta.close()
537	except IOError:
538	print 'no metadata file found - will try to read file anyway'
539	head = ['no metadata file found',]
540
541	tag = File.read(2)
542	byteOrd = '<'
543	if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
544	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
545	elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
546	byteOrd = '>'
547	IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
548	else:
549	lines = ['not a detector tiff file',]
550	return lines,0,0,0
551	File.seek(IFD) #get number of directory entries
552	NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
553	IFD = {}
554	nSlice = 1
555	for ied in range(NED):
556	Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
557	nVal = st.unpack(byteOrd+'i',File.read(4))[0]
558	if DEBUG: print 'Try:',Tag,Type,nVal
559	if Type == 1:
560	Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
561	elif Type == 2:
562	Value = st.unpack(byteOrd+'i',File.read(4))
563	elif Type == 3:
564	Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
565	x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
566	elif Type == 4:
567	if Tag in [273,279]:
568	nSlice = nVal
569	nVal = 1
570	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
571	elif Type == 5:
572	Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
573	elif Type == 11:
574	Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
575	IFD[Tag] = [Type,nVal,Value]
576	if DEBUG: print Tag,IFD[Tag]
577	sizexy = [IFD[256][2][0],IFD[257][2][0]]
578	[nx,ny] = sizexy
579	Npix = nx*ny
580	if 34710 in IFD:
581	if not imageOnly:
582	print 'Read MAR CCD tiff file: ',filename
583	marFrame = rmf.marFrame(File,byteOrd,IFD)
584	image = np.flipud(np.array(np.asarray(marFrame.image),dtype=np.int32))
585	tifType = marFrame.filetitle
586	pixy = (marFrame.pixelsizeX/1000.0,marFrame.pixelsizeY/1000.0)
587	head = marFrame.outputHead()
588	# extract resonable wavelength from header
589	wavelength = marFrame.sourceWavelength*1e-5
590	wavelength = (marFrame.opticsWavelength > 0) and marFrame.opticsWavelength*1e-5 or wavelength
591	wavelength = (wavelength <= 0) and None or wavelength
592	# extract resonable distance from header
593	distance = (marFrame.startXtalToDetector+marFrame.endXtalToDetector)*5e-4
594	distance = (distance <= 0) and marFrame.xtalToDetector*1e-3 or distance
595	distance = (distance <= 0) and None or distance
596	# extract resonable center from header
597	center = [marFrame.beamXmarFrame.pixelsizeX1e-9,marFrame.beamYmarFrame.pixelsizeY1e-9]
598	center = (center[0] != 0 and center[1] != 0) and center or [None,None]
599	#print head,tifType,pixy
600	elif nSlice > 1: #CheMin multislice tif file!
601	tifType = 'CheMin'
602	pixy = [40,40]
603	image = np.flipud(np.array(Im.open(filename)))*10.
604	distance = 18.0
605	center = [pixy[0]*sizexy[0]/2000,0] #the CheMin beam stop is here
606	wavelength = 1.78892
607	elif 272 in IFD:
608	ifd = IFD[272]
609	File.seek(ifd[2][0])
610	S = File.read(ifd[1])
611	if 'PILATUS' in S:
612	tifType = 'Pilatus'
613	dataType = 0
614	pixy = (172,172)
615	File.seek(4096)
616	if not imageOnly:
617	print 'Read Pilatus tiff file: ',filename
618	image = ar.array('L',File.read(4*Npix))
619	image = np.array(np.asarray(image),dtype=np.int32)
620	else:
621	if IFD[258][2][0] == 16:
622	tifType = 'GE'
623	pixy = (200,200)
624	File.seek(8)
625	if not imageOnly:
626	print 'Read GE-detector tiff file: ',filename
627	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
628	elif IFD[258][2][0] == 32:
629	tifType = 'CHESS'
630	pixy = (200,200)
631	File.seek(8)
632	if not imageOnly:
633	print 'Read CHESS-detector tiff file: ',filename
634	image = np.array(ar.array('L',File.read(4*Npix)),dtype=np.int32)
635
636	elif 262 in IFD and IFD[262][2][0] > 4:
637	tifType = 'DND'
638	pixy = (158,158)
639	File.seek(512)
640	if not imageOnly:
641	print 'Read DND SAX/WAX-detector tiff file: ',filename
642	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
643	elif sizexy == [1536,1536]:
644	tifType = 'APS Gold'
645	pixy = (150,150)
646	File.seek(64)
647	if not imageOnly:
648	print 'Read Gold tiff file:',filename
649	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
650	elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
651	if IFD[273][2][0] == 8:
652	if IFD[258][2][0] == 32:
653	tifType = 'PE'
654	pixy = (200,200)
655	File.seek(8)
656	if not imageOnly:
657	print 'Read APS PE-detector tiff file: ',filename
658	if dataType == 5:
659	image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
660	else:
661	image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
662
663	elif IFD[273][2][0] == 4096:
664	if sizexy[0] == 3072:
665	pixy = (73,73)
666	tifType = 'MAR225'
667	else:
668	pixy = (158,158)
669	tifType = 'MAR325'
670	File.seek(4096)
671	if not imageOnly:
672	print 'Read MAR CCD tiff file: ',filename
673	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
674	elif IFD[273][2][0] == 512:
675	tiftype = '11-ID-C'
676	pixy = [200,200]
677	File.seek(512)
678	if not imageOnly:
679	print 'Read 11-ID-C tiff file: ',filename
680	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
681	elif sizexy == [4096,4096]:
682	if IFD[273][2][0] == 8:
683	if IFD[258][2][0] == 16:
684	tifType = 'scanCCD'
685	pixy = (9,9)
686	File.seek(8)
687	if not imageOnly:
688	print 'Read APS scanCCD tiff file: ',filename
689	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
690	elif IFD[273][2][0] == 4096:
691	tifType = 'Rayonix'
692	pixy = (73.242,73.242)
693	File.seek(4096)
694	if not imageOnly:
695	print 'Read Rayonix MX300HE tiff file: ',filename
696	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
697	# elif sizexy == [960,960]:
698	# tiftype = 'PE-BE'
699	# pixy = (200,200)
700	# File.seek(8)
701	# if not imageOnly:
702	# print 'Read Gold tiff file:',filename
703	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
704
705	else:
706	lines = ['not a known detector tiff file',]
707	return lines,0,0,0
708
709	image = np.reshape(image,(sizexy[1],sizexy[0]))
710	center = (not center[0]) and [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000] or center
711	wavelength = (not wavelength) and 0.10 or wavelength
712	distance = (not distance) and 100.0 or distance
713	data = {'pixelSize':pixy,'wavelength':wavelength,'distance':distance,'center':center,'size':sizexy}
714	File.close()
715	if imageOnly:
716	return image
717	else:
718	return head,data,Npix,image
719
720	#def GetTifData(filename,imageOnly=False):
721	# import struct as st
722	# import array as ar
723	# File = open(filename,'rb')
724	# dataType = 5
725	# try:
726	# Meta = open(filename+'.metadata','Ur')
727	# head = Meta.readlines()
728	# for line in head:
729	# line = line.strip()
730	# if 'dataType=' in line:
731	# dataType = int(line.split('=')[1])
732	# Meta.close()
733	# except IOError:
734	# print 'no metadata file found - will try to read file anyway'
735	# head = ['no metadata file found',]
736	#
737	# tag = File.read(2)
738	# byteOrd = '<'
739	# if tag == 'II' and int(st.unpack('<h',File.read(2))[0]) == 42: #little endian
740	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
741	# elif tag == 'MM' and int(st.unpack('>h',File.read(2))[0]) == 42: #big endian
742	# byteOrd = '>'
743	# IFD = int(st.unpack(byteOrd+'i',File.read(4))[0])
744	# else:
745	# lines = ['not a detector tiff file',]
746	# return lines,0,0,0
747	# File.seek(IFD) #get number of directory entries
748	# NED = int(st.unpack(byteOrd+'h',File.read(2))[0])
749	# IFD = {}
750	# for ied in range(NED):
751	# Tag,Type = st.unpack(byteOrd+'Hh',File.read(4))
752	# nVal = st.unpack(byteOrd+'i',File.read(4))[0]
753	# if Type == 1:
754	# Value = st.unpack(byteOrd+nVal*'b',File.read(nVal))
755	# elif Type == 2:
756	# Value = st.unpack(byteOrd+'i',File.read(4))
757	# elif Type == 3:
758	# Value = st.unpack(byteOrd+nVal'h',File.read(nVal2))
759	# x = st.unpack(byteOrd+nVal'h',File.read(nVal2))
760	# elif Type == 4:
761	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
762	# elif Type == 5:
763	# Value = st.unpack(byteOrd+nVal'i',File.read(nVal4))
764	# elif Type == 11:
765	# Value = st.unpack(byteOrd+nVal'f',File.read(nVal4))
766	# IFD[Tag] = [Type,nVal,Value]
767	## print Tag,IFD[Tag]
768	# sizexy = [IFD[256][2][0],IFD[257][2][0]]
769	# [nx,ny] = sizexy
770	# Npix = nx*ny
771	# if 272 in IFD:
772	# ifd = IFD[272]
773	# File.seek(ifd[2][0])
774	# S = File.read(ifd[1])
775	# if 'PILATUS' in S:
776	# tifType = 'Pilatus'
777	# dataType = 0
778	# pixy = (172,172)
779	# File.seek(4096)
780	# if not imageOnly:
781	# print 'Read Pilatus tiff file: ',filename
782	# image = ar.array('L',File.read(4*Npix))
783	# image = np.array(np.asarray(image),dtype=np.int32)
784	# elif 262 in IFD and IFD[262][2][0] > 4:
785	# tifType = 'DND'
786	# pixy = (158,158)
787	# File.seek(512)
788	# if not imageOnly:
789	# print 'Read DND SAX/WAX-detector tiff file: ',filename
790	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
791	# elif sizexy == [1536,1536]:
792	# tifType = 'APS Gold'
793	# pixy = (150,150)
794	# File.seek(64)
795	# if not imageOnly:
796	# print 'Read Gold tiff file:',filename
797	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
798	# elif sizexy == [2048,2048] or sizexy == [1024,1024] or sizexy == [3072,3072]:
799	# if IFD[273][2][0] == 8:
800	# if IFD[258][2][0] == 32:
801	# tifType = 'PE'
802	# pixy = (200,200)
803	# File.seek(8)
804	# if not imageOnly:
805	# print 'Read APS PE-detector tiff file: ',filename
806	# if dataType == 5:
807	# image = np.array(ar.array('f',File.read(4*Npix)),dtype=np.float32)
808	# else:
809	# image = np.array(ar.array('I',File.read(4*Npix)),dtype=np.int32)
810	# elif IFD[273][2][0] == 4096:
811	# if sizexy[0] == 3072:
812	# pixy = (73,73)
813	# tifType = 'MAR225'
814	# else:
815	# pixy = (158,158)
816	# tifType = 'MAR325'
817	# File.seek(4096)
818	# if not imageOnly:
819	# print 'Read MAR CCD tiff file: ',filename
820	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
821	# elif IFD[273][2][0] == 512:
822	# tiftype = '11-ID-C'
823	# pixy = [200,200]
824	# File.seek(512)
825	# if not imageOnly:
826	# print 'Read 11-ID-C tiff file: ',filename
827	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
828	# elif sizexy == [4096,4096]:
829	# if IFD[273][2][0] == 8:
830	# if IFD[258][2][0] == 16:
831	# tifType = 'scanCCD'
832	# pixy = (9,9)
833	# File.seek(8)
834	# if not imageOnly:
835	# print 'Read APS scanCCD tiff file: ',filename
836	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
837	# elif IFD[273][2][0] == 4096:
838	# tifType = 'Rayonix'
839	# pixy = (73.242,73.242)
840	# File.seek(4096)
841	# if not imageOnly:
842	# print 'Read Rayonix MX300HE tiff file: ',filename
843	# image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
844	## elif sizexy == [960,960]:
845	## tiftype = 'PE-BE'
846	## pixy = (200,200)
847	## File.seek(8)
848	## if not imageOnly:
849	## print 'Read Gold tiff file:',filename
850	## image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
851	#
852	# else:
853	# lines = ['not a known detector tiff file',]
854	# return lines,0,0,0
855	#
856	# image = np.reshape(image,(sizexy[1],sizexy[0]))
857	# center = [pixy[0]sizexy[0]/2000,pixy[1]sizexy[1]/2000]
858	# data = {'pixelSize':pixy,'wavelength':0.10,'distance':100.0,'center':center,'size':sizexy}
859	# File.close()
860	# if imageOnly:
861	# return image
862	# else:
863	# return head,data,Npix,image
864	#
865	def ProjFileOpen(G2frame):
866	'Read a GSAS-II project file and load into the G2 data tree'
867	if not os.path.exists(G2frame.GSASprojectfile):
868	print ('\n*** Error attempt to open project file that does not exist:\n '+
869	str(G2frame.GSASprojectfile))
870	return
871	file = open(G2frame.GSASprojectfile,'rb')
872	print 'load from file: ',G2frame.GSASprojectfile
873	G2frame.SetTitle("GSAS-II data tree: "+
874	os.path.split(G2frame.GSASprojectfile)[1])
875	wx.BeginBusyCursor()
876	try:
877	while True:
878	try:
879	data = cPickle.load(file)
880	except EOFError:
881	break
882	datum = data[0]
883
884	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=datum[0])
885	if 'PWDR' in datum[0]:
886	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
887	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
888	G2frame.PatternTree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
889	elif datum[0].startswith('HKLF'):
890	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
891	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
892	G2frame.PatternTree.SetItemPyData(Id,datum[1])
893	else:
894	G2frame.PatternTree.SetItemPyData(Id,datum[1])
895	for datus in data[1:]:
896	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
897	#patch
898	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
899	if 'PWDR' in datum[0]:
900	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
901	else:
902	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
903	for item in datus[1][0]: #zip makes tuples - now make lists!
904	datus[1][0][item] = list(datus[1][0][item])
905	#end patch
906	G2frame.PatternTree.SetItemPyData(sub,datus[1])
907	if 'IMG' in datum[0]: #retrieve image default flag & data if set
908	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
909	if Data['setDefault']:
910	G2frame.imageDefault = Data
911	file.close()
912	print('project load successful')
913	G2frame.NewPlot = True
914	except:
915	msg = wx.MessageDialog(G2frame,message="Error reading file "+
916	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
917	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
918	msg.ShowModal()
919	finally:
920	wx.EndBusyCursor()
921
922	def ProjFileSave(G2frame):
923	'Save a GSAS-II project file'
924	if not G2frame.PatternTree.IsEmpty():
925	file = open(G2frame.GSASprojectfile,'wb')
926	print 'save to file: ',G2frame.GSASprojectfile
927	wx.BeginBusyCursor()
928	try:
929	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
930	while item:
931	data = []
932	name = G2frame.PatternTree.GetItemText(item)
933	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
934	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
935	while item2:
936	name = G2frame.PatternTree.GetItemText(item2)
937	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
938	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
939	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
940	cPickle.dump(data,file,1)
941	file.close()
942	finally:
943	wx.EndBusyCursor()
944	print('project save successful')
945
946	def SaveIntegration(G2frame,PickId,data):
947	'Save image integration results as powder pattern(s)'
948	azms = G2frame.Integrate[1]
949	X = G2frame.Integrate[2][:-1]
950	N = len(X)
951	Id = G2frame.PatternTree.GetItemParent(PickId)
952	name = G2frame.PatternTree.GetItemText(Id)
953	name = name.replace('IMG ',data['type']+' ')
954	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
955	if 'PWDR' in name:
956	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
957	codes = [0 for i in range(11)]
958	elif 'SASD' in name:
959	names = ['Type','Lam','Zero','Azimuth']
960	codes = [0 for i in range(4)]
961	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
962	Xminmax = [X[0],X[-1]]
963	LRazm = data['LRazimuth']
964	Azms = []
965	if data['fullIntegrate'] and data['outAzimuths'] == 1:
966	Azms = [45.0,] #a poor man's average?
967	else:
968	for i,azm in enumerate(azms[:-1]):
969	Azms.append((azms[i+1]+azm)/2.)
970	for i,azm in enumerate(azms[:-1]):
971	name += " Azm= %.2f"%(Azms[i])
972	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
973	nOcc = 0
974	while item:
975	Name = G2frame.PatternTree.GetItemText(item)
976	if name in Name:
977	nOcc += 1
978	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
979	if nOcc:
980	name += '(%d)'%(nOcc)
981	Sample = G2pdG.SetDefaultSample()
982	Sample['Gonio. radius'] = data['distance']
983	Sample['Omega'] = data['GonioAngles'][0]
984	Sample['Chi'] = data['GonioAngles'][1]
985	Sample['Phi'] = data['GonioAngles'][2]
986	if 'PWDR' in name:
987	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!
988	elif 'SASD' in name:
989	Sample['Trans'] = data['SampleAbs'][0]
990	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
991	Y = G2frame.Integrate[0][i]
992	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
993	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=name)
994	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
995	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
996	if 'PWDR' in name:
997	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
998	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
999	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
1000	for item in inst[0]:
1001	inst[0][item] = list(inst[0][item])
1002	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
1003	if 'PWDR' in name:
1004	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1005	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),[])
1006	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[])
1007	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
1008	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
1009	elif 'SASD' in name:
1010	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
1011	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1012	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
1013	valuesdict = {
1014	'wtFactor':1.0,
1015	'Dummy':False,
1016	'ranId':ran.randint(0,sys.maxint),
1017	}
1018	G2frame.PatternTree.SetItemPyData(
1019	Id,[valuesdict,
1020	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
1021	return Id #last powder pattern generated
1022
1023	# def powderFxyeSave(G2frame,exports,powderfile):
1024	# 'Save a powder histogram as a GSAS FXYE file'
1025	# head,tail = ospath.split(powderfile)
1026	# name,ext = tail.split('.')
1027	# for i,export in enumerate(exports):
1028	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1029	# prmname = filename.strip(ext)+'prm'
1030	# prm = open(prmname,'w') #old style GSAS parm file
1031	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1032	# Inst = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, \
1033	# PickId, 'Instrument Parameters'))[0]
1034	# prm.write( ' 123456789012345678901234567890123456789012345678901234567890 '+'\n')
1035	# prm.write( 'INS BANK 1 '+'\n')
1036	# prm.write(('INS HTYPE %sR '+'\n')%(Inst['Type'][0]))
1037	# if 'Lam1' in Inst: #Ka1 & Ka2
1038	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam1'][0],Inst['Lam2'][0]))
1039	# elif 'Lam' in Inst: #single wavelength
1040	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam'][1],0.0))
1041	# prm.write( 'INS 1 IRAD 0 '+'\n')
1042	# prm.write( 'INS 1I HEAD '+'\n')
1043	# prm.write( 'INS 1I ITYP 0 0.0000 180.0000 1 '+'\n')
1044	# prm.write(('INS 1DETAZM%10.3f '+'\n')%(Inst['Azimuth'][0]))
1045	# prm.write( 'INS 1PRCF1 3 8 0.00100 '+'\n')
1046	# prm.write(('INS 1PRCF11 %15.6g%15.6g%15.6g%15.6g '+'\n')%(Inst['U'][1],Inst['V'][1],Inst['W'][1],0.0))
1047	# 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.))
1048	# prm.close()
1049	# file = open(filename,'w')
1050	# print 'save powder pattern to file: ',filename
1051	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1052	# file.write(powderfile+'\n')
1053	# file.write('Instrument parameter file:'+ospath.split(prmname)[1]+'\n')
1054	# file.write('BANK 1 %d %d CONS %.2f %.2f 0 0 FXYE\n'%(len(x),len(x),\
1055	# 100.x[0],100.(x[1]-x[0])))
1056	# s = list(np.sqrt(1./np.array(w)))
1057	# XYW = zip(x,y,s)
1058	# for X,Y,S in XYW:
1059	# file.write("%15.6g %15.6g %15.6g\n" % (100.*X,Y,max(S,1.0)))
1060	# file.close()
1061	# print 'powder pattern file '+filename+' written'
1062
1063	# def powderXyeSave(G2frame,exports,powderfile):
1064	# 'Save a powder histogram as a Topas XYE file'
1065	# head,tail = ospath.split(powderfile)
1066	# name,ext = tail.split('.')
1067	# for i,export in enumerate(exports):
1068	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1069	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1070	# file = open(filename,'w')
1071	# file.write('#%s\n'%(export))
1072	# print 'save powder pattern to file: ',filename
1073	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1074	# s = list(np.sqrt(1./np.array(w)))
1075	# XYW = zip(x,y,s)
1076	# for X,Y,W in XYW:
1077	# file.write("%15.6g %15.6g %15.6g\n" % (X,Y,W))
1078	# file.close()
1079	# print 'powder pattern file '+filename+' written'
1080
1081	def PDFSave(G2frame,exports):
1082	'Save a PDF G(r) and S(Q) in column formats'
1083	for export in exports:
1084	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1085	SQname = 'S(Q)'+export[4:]
1086	GRname = 'G(R)'+export[4:]
1087	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
1088	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
1089	sqId = G2gd.GetPatternTreeItemId(G2frame, PickId, SQname)
1090	grId = G2gd.GetPatternTreeItemId(G2frame, PickId, GRname)
1091	sqdata = np.array(G2frame.PatternTree.GetItemPyData(sqId)[1][:2]).T
1092	grdata = np.array(G2frame.PatternTree.GetItemPyData(grId)[1][:2]).T
1093	sqfile = open(sqfilename,'w')
1094	grfile = open(grfilename,'w')
1095	sqfile.write('#T S(Q) %s\n'%(export))
1096	grfile.write('#T G(R) %s\n'%(export))
1097	sqfile.write('#L Q S(Q)\n')
1098	grfile.write('#L R G(R)\n')
1099	for q,sq in sqdata:
1100	sqfile.write("%15.6g %15.6g\n" % (q,sq))
1101	sqfile.close()
1102	for r,gr in grdata:
1103	grfile.write("%15.6g %15.6g\n" % (r,gr))
1104	grfile.close()
1105
1106	def PeakListSave(G2frame,file,peaks):
1107	'Save powder peaks to a data file'
1108	print 'save peak list to file: ',G2frame.peaklistfile
1109	if not peaks:
1110	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1111	try:
1112	result = dlg.ShowModal()
1113	finally:
1114	dlg.Destroy()
1115	return
1116	for peak in peaks:
1117	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1118	(peak[0],peak[2],peak[4],peak[6]))
1119	print 'peak list saved'
1120
1121	def IndexPeakListSave(G2frame,peaks):
1122	'Save powder peaks from the indexing list'
1123	file = open(G2frame.peaklistfile,'wa')
1124	print 'save index peak list to file: ',G2frame.peaklistfile
1125	wx.BeginBusyCursor()
1126	try:
1127	if not peaks:
1128	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1129	try:
1130	result = dlg.ShowModal()
1131	finally:
1132	dlg.Destroy()
1133	return
1134	for peak in peaks:
1135	file.write("%12.6f\n" % (peak[7]))
1136	file.close()
1137	finally:
1138	wx.EndBusyCursor()
1139	print 'index peak list saved'
1140
1141	def SetNewPhase(Name='New Phase',SGData=None,cell=None):
1142	'''Create a new phase dict with default values for various parameters
1143
1144	:param str Name: Name for new Phase
1145
1146	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1147	defaults to data for P 1
1148
1149	:param list cell: unit cell parameter list; defaults to
1150	[1.0,1.0,1.0,90.,90,90.,1.]
1151
1152	'''
1153	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1154	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1155	phaseData = {
1156	'ranId':ran.randint(0,sys.maxint),
1157	'General':{
1158	'Name':Name,
1159	'Type':'nuclear',
1160	'AtomPtrs':[3,1,7,9],
1161	'SGData':SGData,
1162	'Cell':[False,]+cell,
1163	'Pawley dmin':1.0,
1164	'Data plot type':'None',
1165	'SH Texture':{
1166	'Order':0,
1167	'Model':'cylindrical',
1168	'Sample omega':[False,0.0],
1169	'Sample chi':[False,0.0],
1170	'Sample phi':[False,0.0],
1171	'SH Coeff':[False,{}],
1172	'SHShow':False,
1173	'PFhkl':[0,0,1],
1174	'PFxyz':[0,0,1],
1175	'PlotType':'Pole figure'}},
1176	'Atoms':[],
1177	'Drawing':{},
1178	'Histograms':{},
1179	'Pawley ref':[],
1180	'RBModels':{},
1181	}
1182	return phaseData
1183
1184	class MultipleChoicesDialog(wx.Dialog):
1185	'''A dialog that offers a series of choices, each with a
1186	title and a wx.Choice widget. Intended to be used Modally.
1187	typical input:
1188
1189	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1190	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1191
1192	selections are placed in self.chosen when OK is pressed
1193	'''
1194	def __init__(self,choicelist,headinglist,
1195	head='Select options',
1196	title='Please select from options below',
1197	parent=None):
1198	self.chosen = []
1199	wx.Dialog.__init__(
1200	self,parent,wx.ID_ANY,head,
1201	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1202	panel = wx.Panel(self)
1203	mainSizer = wx.BoxSizer(wx.VERTICAL)
1204	mainSizer.Add((10,10),1)
1205	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1206	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1207	self.ChItems = []
1208	for choice,lbl in zip(choicelist,headinglist):
1209	mainSizer.Add((10,10),1)
1210	self.chosen.append(0)
1211	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1212	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1213	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1214	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1215
1216	OkBtn = wx.Button(panel,-1,"Ok")
1217	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1218	cancelBtn = wx.Button(panel,-1,"Cancel")
1219	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1220	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1221	btnSizer.Add((20,20),1)
1222	btnSizer.Add(OkBtn)
1223	btnSizer.Add((20,20),1)
1224	btnSizer.Add(cancelBtn)
1225	btnSizer.Add((20,20),1)
1226	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1227	panel.SetSizer(mainSizer)
1228	panel.Fit()
1229	self.Fit()
1230
1231	def OnOk(self,event):
1232	parent = self.GetParent()
1233	if parent is not None: parent.Raise()
1234	# save the results from the choice widgets
1235	self.chosen = []
1236	for w in self.ChItems:
1237	self.chosen.append(w.GetSelection())
1238	self.EndModal(wx.ID_OK)
1239
1240	def OnCancel(self,event):
1241	parent = self.GetParent()
1242	if parent is not None: parent.Raise()
1243	self.chosen = []
1244	self.EndModal(wx.ID_CANCEL)
1245
1246	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1247	confirmoverwrite=True, parent=None,
1248	multipleselect=False):
1249	'''If the filename is a zip file, extract a file from that
1250	archive.
1251
1252	:param list Selection: used to predefine the name of the file
1253	to be extracted. Filename case and zip directory name are
1254	ignored in selection; the first matching file is used.
1255
1256	:param bool confirmread: if True asks the user to confirm before expanding
1257	the only file in a zip
1258
1259	:param bool confirmoverwrite: if True asks the user to confirm
1260	before overwriting if the extracted file already exists
1261
1262	:param bool multipleselect: if True allows more than one zip
1263	file to be extracted, a list of file(s) is returned.
1264	If only one file is present, do not ask which one, otherwise
1265	offer a list of choices (unless selection is used).
1266
1267	:returns: the name of the file that has been created or a
1268	list of files (see multipleselect)
1269
1270	If the file is not a zipfile, return the name of the input file.
1271	If the zipfile is empty or no file has been selected, return None
1272	'''
1273	import zipfile # do this now, since we can save startup time by doing this only on need
1274	import shutil
1275	zloc = os.path.split(filename)[0]
1276	if not zipfile.is_zipfile(filename):
1277	#print("not zip")
1278	return filename
1279
1280	z = zipfile.ZipFile(filename,'r')
1281	zinfo = z.infolist()
1282
1283	if len(zinfo) == 0:
1284	#print('Zip has no files!')
1285	zlist = [-1]
1286	if selection:
1287	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1288	if selection.lower() in choices:
1289	zlist = [choices.index(selection.lower())]
1290	else:
1291	print('debug: file '+str(selection)+' was not found in '+str(filename))
1292	zlist = [-1]
1293	elif len(zinfo) == 1 and confirmread:
1294	result = wx.ID_NO
1295	dlg = wx.MessageDialog(
1296	parent,
1297	'Is file '+str(zinfo[0].filename)+
1298	' what you want to extract from '+
1299	str(os.path.split(filename)[1])+'?',
1300	'Confirm file',
1301	wx.YES_NO \| wx.ICON_QUESTION)
1302	try:
1303	result = dlg.ShowModal()
1304	finally:
1305	dlg.Destroy()
1306	if result == wx.ID_NO:
1307	zlist = [-1]
1308	else:
1309	zlist = [0]
1310	elif len(zinfo) == 1:
1311	zlist = [0]
1312	elif multipleselect:
1313	# select one or more from a from list
1314	choices = [i.filename for i in zinfo]
1315	dlg = G2gd.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1316	'Choose file(s)',choices)
1317	if dlg.ShowModal() == wx.ID_OK:
1318	zlist = dlg.GetSelections()
1319	else:
1320	zlist = []
1321	dlg.Destroy()
1322	else:
1323	# select one from a from list
1324	choices = [i.filename for i in zinfo]
1325	dlg = wx.SingleChoiceDialog(parent,
1326	'Select file to extract from zip file'+str(filename),'Choose file',
1327	choices,)
1328	if dlg.ShowModal() == wx.ID_OK:
1329	zlist = [dlg.GetSelection()]
1330	else:
1331	zlist = [-1]
1332	dlg.Destroy()
1333
1334	outlist = []
1335	for zindex in zlist:
1336	if zindex >= 0:
1337	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1338	if os.path.exists(efil) and confirmoverwrite:
1339	result = wx.ID_NO
1340	dlg = wx.MessageDialog(parent,
1341	'File '+str(efil)+' already exists. OK to overwrite it?',
1342	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1343	try:
1344	result = dlg.ShowModal()
1345	finally:
1346	dlg.Destroy()
1347	if result == wx.ID_NO:
1348	zindex = -1
1349	if zindex >= 0:
1350	# extract the file to the current directory, regardless of it's original path
1351	#z.extract(zinfo[zindex],zloc)
1352	eloc,efil = os.path.split(zinfo[zindex].filename)
1353	outfile = os.path.join(zloc, efil)
1354	fpin = z.open(zinfo[zindex])
1355	fpout = file(outfile, "wb")
1356	shutil.copyfileobj(fpin, fpout)
1357	fpin.close()
1358	fpout.close()
1359	outlist.append(outfile)
1360	z.close()
1361	if multipleselect and len(outlist) >= 1:
1362	return outlist
1363	elif len(outlist) == 1:
1364	return outlist[0]
1365	else:
1366	return None
1367
1368	######################################################################
1369	# base classes for reading various types of data files
1370	# not used directly, only by subclassing
1371	######################################################################
1372	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1373	P1SGData = SGData
1374	class ImportBaseclass(object):
1375	'''Defines a base class for the reading of input files (diffraction
1376	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1377	for an explanation on how to use a subclass of this class.
1378	'''
1379	class ImportException(Exception):
1380	'''Defines an Exception that is used when an import routine hits an expected error,
1381	usually in .Reader.
1382
1383	Good practice is that the Reader should define a value in self.errors that
1384	tells the user some information about what is wrong with their file.
1385	'''
1386	pass
1387
1388	def __init__(self,
1389	formatName,
1390	longFormatName=None,
1391	extensionlist=[],
1392	strictExtension=False,
1393	):
1394	self.formatName = formatName # short string naming file type
1395	if longFormatName: # longer string naming file type
1396	self.longFormatName = longFormatName
1397	else:
1398	self.longFormatName = formatName
1399	# define extensions that are allowed for the file type
1400	# for windows, remove any extensions that are duplicate, as case is ignored
1401	if sys.platform == 'windows' and extensionlist:
1402	extensionlist = list(set([s.lower() for s in extensionlist]))
1403	self.extensionlist = extensionlist
1404	# If strictExtension is True, the file will not be read, unless
1405	# the extension matches one in the extensionlist
1406	self.strictExtension = strictExtension
1407	self.errors = ''
1408	self.warnings = ''
1409	# used for readers that will use multiple passes to read
1410	# more than one data block
1411	self.repeat = False
1412	self.repeatcount = 0
1413	self.readfilename = '?'
1414	#print 'created',self.__class__
1415
1416	def ReInitialize(self):
1417	'Reinitialize the Reader to initial settings'
1418	self.errors = ''
1419	self.warnings = ''
1420	self.repeat = False
1421	self.repeatcount = 0
1422	self.readfilename = '?'
1423
1424	def BlockSelector(self, ChoiceList, ParentFrame=None,
1425	title='Select a block',
1426	size=None, header='Block Selector',
1427	useCancel=True):
1428	''' Provide a wx dialog to select a block if the file contains more
1429	than one set of data and one must be selected
1430	'''
1431	if useCancel:
1432	dlg = wx.SingleChoiceDialog(
1433	ParentFrame,title, header,ChoiceList)
1434	else:
1435	dlg = wx.SingleChoiceDialog(
1436	ParentFrame,title, header,ChoiceList,
1437	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1438	if size: dlg.SetSize(size)
1439	dlg.CenterOnParent()
1440	if dlg.ShowModal() == wx.ID_OK:
1441	sel = dlg.GetSelection()
1442	return sel
1443	else:
1444	return None
1445	dlg.Destroy()
1446
1447	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1448	title='Select a block',size=None, header='Block Selector'):
1449	'''Provide a wx dialog to select a block of data if the
1450	file contains more than one set of data and one must be
1451	selected.
1452
1453	:returns: a list of the selected blocks
1454	'''
1455	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1456	wx.CHOICEDLG_STYLE)
1457	dlg.CenterOnParent()
1458	if size: dlg.SetSize(size)
1459	if dlg.ShowModal() == wx.ID_OK:
1460	sel = dlg.GetSelections()
1461	else:
1462	return []
1463	dlg.Destroy()
1464	selected = []
1465	if len(ChoiceList) in sel:
1466	return range(len(ChoiceList))
1467	else:
1468	return sel
1469	return selected
1470
1471	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1472	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1473	widget. Typical input:
1474
1475	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1476
1477	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1478
1479	optional keyword parameters are: head (window title) and title
1480	returns a list of selected indicies for each choice (or None)
1481	'''
1482	result = None
1483	dlg = MultipleChoicesDialog(choicelist,headinglist,
1484	parent=ParentFrame, **kwargs)
1485	dlg.CenterOnParent()
1486	if dlg.ShowModal() == wx.ID_OK:
1487	result = dlg.chosen
1488	dlg.Destroy()
1489	return result
1490
1491	def ShowBusy(self):
1492	wx.BeginBusyCursor()
1493	wx.Yield() # make it happen now!
1494
1495	def DoneBusy(self):
1496	wx.EndBusyCursor()
1497	wx.Yield() # make it happen now!
1498
1499	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1500	# '''This method must be supplied in the child class to read the file.
1501	# if the read fails either return False or raise an Exception
1502	# preferably of type ImportException.
1503	# '''
1504	# #start reading
1505	# raise ImportException("Error occurred while...")
1506	# self.errors += "Hint for user on why the error occur
1507	# return False # if an error occurs
1508	# return True # if read OK
1509
1510	def ExtensionValidator(self, filename):
1511	'''This methods checks if the file has the correct extension
1512	Return False if this filename will not be supported by this reader
1513	Return True if the extension matches the list supplied by the reader
1514	Return None if the reader allows un-registered extensions
1515	'''
1516	if filename:
1517	ext = os.path.splitext(filename)[1]
1518	if sys.platform == 'windows': ext = ext.lower()
1519	if ext in self.extensionlist: return True
1520	if self.strictExtension: return False
1521	return None
1522
1523	def ContentsValidator(self, filepointer):
1524	'''This routine will attempt to determine if the file can be read
1525	with the current format.
1526	This will typically be overridden with a method that
1527	takes a quick scan of [some of]
1528	the file contents to do a "sanity" check if the file
1529	appears to match the selected format.
1530	Expected to be called via self.Validator()
1531	'''
1532	#filepointer.seek(0) # rewind the file pointer
1533	return True
1534
1535	def CIFValidator(self, filepointer):
1536	'''A :meth:`ContentsValidator` for use to validate CIF files.
1537	'''
1538	for i,l in enumerate(filepointer):
1539	if i >= 1000: return True
1540	'''Encountered only blank lines or comments in first 1000
1541	lines. This is unlikely, but assume it is CIF anyway, since we are
1542	even less likely to find a file with nothing but hashes and
1543	blank lines'''
1544	line = l.strip()
1545	if len(line) == 0: # ignore blank lines
1546	continue
1547	elif line.startswith('#'): # ignore comments
1548	continue
1549	elif line.startswith('data_'): # on the right track, accept this file
1550	return True
1551	else: # found something invalid
1552	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1553	self.errors += ' '+str(l)
1554	self.errors += ' Note: a CIF should only have blank lines or comments before'
1555	self.errors += ' a data_ statement begins a block.'
1556	return False
1557
1558	class ImportPhase(ImportBaseclass):
1559	'''Defines a base class for the reading of files with coordinates
1560
1561	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1562	in :meth:`GSASII.GSASII.OnImportPhase`.
1563	See :ref:`Writing a Import Routine<Import_Routines>`
1564	for an explanation on how to use this class.
1565
1566	'''
1567	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1568	strictExtension=False,):
1569	# call parent __init__
1570	ImportBaseclass.__init__(self,formatName,longFormatName,
1571	extensionlist,strictExtension)
1572	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1573	self.Constraints = None
1574
1575	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1576	title='Select a phase', size=None,header='Phase Selector'):
1577	''' Provide a wx dialog to select a phase if the file contains more
1578	than one phase
1579	'''
1580	return self.BlockSelector(ChoiceList,ParentFrame,title,
1581	size,header)
1582
1583	class ImportStructFactor(ImportBaseclass):
1584	'''Defines a base class for the reading of files with tables
1585	of structure factors.
1586
1587	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1588	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1589	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1590	:meth:`Reader`.
1591
1592	See :ref:`Writing a Import Routine<Import_Routines>`
1593	for an explanation on how to use import classes in general. The specifics
1594	for reading a structure factor histogram require that
1595	the ``Reader()`` routine in the import
1596	class need to do only a few things: It
1597	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1598	and set :attr:`Parameters` with the instrument parameters
1599	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1600	Also, set :attr:`Controls`,
1601	which specifies how the histogram is plotted
1602	(initialized with :meth:`InitControls` and set with :meth:`UpdateControls`).
1603	'''
1604	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1605	strictExtension=False,):
1606	ImportBaseclass.__init__(self,formatName,longFormatName,
1607	extensionlist,strictExtension)
1608
1609	# define contents of Structure Factor entry
1610	self.Parameters = []
1611	'self.Parameters is a list with two dicts for data parameter settings'
1612	self.InitParameters()
1613	self.Controls = {}
1614	'self.Controls is a dict with plotting controls'
1615	self.InitControls() # initialize the above
1616	self.RefDict = {'RefList':[],'FF':[]}
1617	'''self.RefDict is a dict containing the reflection information, as read from the file.
1618	Item 'RefList' contains the reflection information. See the
1619	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1620	for the contents of each row. Dict element 'FF'
1621	contains the form factor values for each element type; if this entry
1622	is left as initialized (an empty list) it will be initialized as needed later.
1623	'''
1624	def ReInitialize(self):
1625	'Reinitialize the Reader to initial settings'
1626	ImportBaseclass.ReInitialize(self)
1627	self.InitParameters()
1628	self.InitControls()
1629	self.RefDict = {'RefList':[],'FF':[]}
1630
1631
1632	def InitControls(self):
1633	'initialize the controls structure'
1634	self.Controls = { # dictionary with plotting controls
1635	'Type' : 'Fosq',
1636	'ifFc' : False, #
1637	'HKLmax' : [None,None,None],
1638	'HKLmin' : [None,None,None],
1639	'FoMax' : None, # maximum observed structure factor as Fo
1640	'Zone' : '001',
1641	'Layer' : 0,
1642	'Scale' : 1.0,
1643	}
1644
1645	def InitParameters(self):
1646	'initialize the instrument parameters structure'
1647	Lambda = 0.70926
1648	HistType = 'SXC'
1649	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1650	'Lam':[Lambda,Lambda]
1651	}, {}]
1652	'Parameters is a list with two dicts for data parameter settings'
1653
1654	def UpdateParameters(self,Type=None,Wave=None):
1655	'Revise the instrument parameters'
1656	if Type is not None:
1657	self.Parameters[0]['Type'] = [Type,Type]
1658	if Wave is not None:
1659	self.Parameters[0]['Lam'] = [Wave,Wave]
1660
1661	def UpdateControls(self,Type='Fosq',FcalcPresent=False):
1662	'''Scan through the reflections to update the Controls dictionary
1663	'''
1664	self.Controls['Type'] = Type
1665	self.Controls['ifFc'] = FcalcPresent
1666	HKLmax = [None,None,None]
1667	HKLmin = [None,None,None]
1668	Fo2max = None
1669	for refl in self.RefDict['RefList']:
1670	HKL = refl[:3]
1671	if Fo2max is None:
1672	Fo2max = refl[8]
1673	else:
1674	Fo2max = max(Fo2max,refl[8])
1675	for i,hkl in enumerate(HKL):
1676	if HKLmax[i] is None:
1677	HKLmax[i] = hkl
1678	HKLmin[i] = hkl
1679	else:
1680	HKLmax[i] = max(HKLmax[i],hkl)
1681	HKLmin[i] = min(HKLmin[i],hkl)
1682	self.Controls['HKLmax'] = HKLmax
1683	self.Controls['HKLmin'] = HKLmin
1684	if Type == 'Fosq':
1685	self.Controls['FoMax'] = np.sqrt(Fo2max)
1686	elif Type == 'Fo':
1687	self.Controls['FoMax'] = Fo2max
1688	else:
1689	print "Unsupported Struct Fact type in ImportStructFactor.UpdateControls"
1690	raise Exception,"Unsupported Struct Fact type in ImportStructFactor.UpdateControls"
1691
1692	######################################################################
1693	class ImportPowderData(ImportBaseclass):
1694	'''Defines a base class for the reading of files with powder data.
1695
1696	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1697	in :meth:`GSASII.GSASII.OnImportPowder`.
1698	See :ref:`Writing a Import Routine<Import_Routines>`
1699	for an explanation on how to use this class.
1700	'''
1701	# define some default instrument parameter files
1702	# just like GSAS, sigh
1703	defaultIparm_lbl = []
1704	defaultIparms = []
1705	defaultIparm_lbl.append('CuKa lab data')
1706	defaultIparms.append({
1707	'INS HTYPE ':'PXC ',
1708	'INS 1 ICONS':' 1.540500 1.544300 0.0 0 0.7 0 0.5 ',
1709	'INS 1PRCF1 ':' 3 8 0.01 ',
1710	'INS 1PRCF11':' 2.000000E+00 -2.000000E+00 5.000000E+00 0.000000E+00 ',
1711	'INS 1PRCF12':' 0.000000E+00 0.000000E+00 0.150000E-01 0.150000E-01 ',
1712	})
1713	defaultIparm_lbl.append('0.6A synch')
1714	defaultIparms.append({
1715	'INS HTYPE ':'PXC ',
1716	'INS 1 ICONS':' 0.600000 0.000000 0.0 0 0.99 0 0.5 ',
1717	'INS 1PRCF1 ':' 3 8 0.01 ',
1718	'INS 1PRCF11':' 1.000000E+00 -1.000000E+00 0.300000E+00 0.000000E+00 ',
1719	'INS 1PRCF12':' 0.000000E+00 0.000000E+00 0.100000E-01 0.100000E-01 ',
1720	})
1721	defaultIparm_lbl.append('1.5A CW neutron data')
1722	defaultIparms.append({
1723	'INS HTYPE ':'PNC',
1724	'INS 1 ICONS':' 1.54020 0.00000 0.04000 0',
1725	'INS 1PRCF1 ':' 3 8 0.005',
1726	'INS 1PRCF11':' 0.239700E+03 -0.298200E+03 0.180800E+03 0.000000E+00',
1727	'INS 1PRCF12':' 0.000000E+00 0.000000E+00 0.400000E-01 0.300000E-01',
1728	})
1729	defaultIparm_lbl.append('10m TOF backscattering bank')
1730	defaultIparms.append({
1731	'INS HTYPE ':'PNT',
1732	'INS 1 ICONS':' 5000.00 0.00 0.00',
1733	'INS 1BNKPAR':' 1.0000 150.000',
1734	'INS 1PRCF1 ':' 1 8 0.01000',
1735	'INS 1PRCF11':' 0.000000E+00 5.000000E+00 3.000000E-02 1.000000E-03',
1736	'INS 1PRCF12':' 0.000000E+00 4.000000E+01 0.000000E+00 0.000000E+00',
1737	})
1738	defaultIparm_lbl.append('10m TOF 90deg bank')
1739	defaultIparms.append({
1740	'INS HTYPE ':'PNT',
1741	'INS 1 ICONS':' 3500.00 0.00 0.00',
1742	'INS 1BNKPAR':' 1.0000 90.000',
1743	'INS 1PRCF1 ':' 1 8 0.01000',
1744	'INS 1PRCF11':' 0.000000E+00 5.000000E+00 3.000000E-02 4.000000E-03',
1745	'INS 1PRCF12':' 0.000000E+00 8.000000E+01 0.000000E+00 0.000000E+00',
1746	})
1747	defaultIparm_lbl.append('63m POWGEN 90deg bank')
1748	defaultIparms.append({
1749	'INS HTYPE ':'PNT',
1750	'INS 1 ICONS':' 22585.80 0.00 0.00',
1751	'INS 1BNKPAR':' 1.0000 90.000',
1752	'INS 1PRCF1 ':' 1 8 0.01000',
1753	'INS 1PRCF11':' 0.000000E+00 1.000000E+00 3.000000E-02 4.000000E-03',
1754	'INS 1PRCF12':' 0.000000E+00 8.000000E+01 0.000000E+00 0.000000E+00',
1755	})
1756	def __init__(self,
1757	formatName,
1758	longFormatName=None,
1759	extensionlist=[],
1760	strictExtension=False,
1761	):
1762	ImportBaseclass.__init__(self,formatName,
1763	longFormatName,
1764	extensionlist,
1765	strictExtension)
1766	self.clockWd = None # used in TOF
1767	self.ReInitialize()
1768
1769	def ReInitialize(self):
1770	'Reinitialize the Reader to initial settings'
1771	ImportBaseclass.ReInitialize(self)
1772	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1773	self.powderdata = [] # Powder dataset
1774	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1775	np.array(x), # x-axis values
1776	np.array(y), # powder pattern intensities
1777	np.array(w), # 1/sig(intensity)^2 values (weights)
1778	np.array(yc), # calc. intensities (zero)
1779	np.array(yb), # calc. background (zero)
1780	np.array(yd), # obs-calc profiles
1781	'''
1782	self.comments = []
1783	self.idstring = ''
1784	self.Sample = G2pdG.SetDefaultSample()
1785	self.GSAS = None # used in TOF
1786	self.repeat_instparm = True # Should a parm file be
1787	# used for multiple histograms?
1788	self.instparm = None # name hint from file of instparm to use
1789	self.instfile = '' # full path name to instrument parameter file
1790	self.instbank = '' # inst parm bank number
1791	self.instmsg = '' # a label that gets printed to show
1792	# where instrument parameters are from
1793	self.numbanks = 1
1794	self.instdict = {} # place items here that will be transferred to the instrument parameters
1795	######################################################################
1796	class ImportSmallAngleData(ImportBaseclass):
1797	'''Defines a base class for the reading of files with small angle data.
1798	See :ref:`Writing a Import Routine<Import_Routines>`
1799	for an explanation on how to use this class.
1800	'''
1801	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1802	strictExtension=False,):
1803
1804	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1805	strictExtension)
1806	self.ReInitialize()
1807
1808	def ReInitialize(self):
1809	'Reinitialize the Reader to initial settings'
1810	ImportBaseclass.ReInitialize(self)
1811	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1812	self.smallangledata = [] # SASD dataset
1813	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1814	np.array(x), # x-axis values
1815	np.array(y), # powder pattern intensities
1816	np.array(w), # 1/sig(intensity)^2 values (weights)
1817	np.array(yc), # calc. intensities (zero)
1818	np.array(yd), # obs-calc profiles
1819	np.array(yb), # preset bkg
1820	'''
1821	self.comments = []
1822	self.idstring = ''
1823	self.Sample = G2pdG.SetDefaultSample()
1824	self.GSAS = None # used in TOF
1825	self.clockWd = None # used in TOF
1826	self.numbanks = 1
1827	self.instdict = {} # place items here that will be transferred to the instrument parameters
1828	######################################################################
1829	class ExportBaseclass(object):
1830	'''Defines a base class for the exporting of GSAS-II results.
1831
1832	This class is subclassed in the various exports/G2export_*.py files. Those files
1833	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
1834	appropriate menu items for each one and the .Exporter method is called
1835	directly from the menu item.
1836
1837	'''
1838	def __init__(self,
1839	G2frame,
1840	formatName,
1841	extension,
1842	longFormatName=None,
1843	):
1844	self.G2frame = G2frame
1845	self.formatName = formatName # short string naming file type
1846	self.extension = extension
1847	if longFormatName: # longer string naming file type
1848	self.longFormatName = longFormatName
1849	else:
1850	self.longFormatName = formatName
1851	self.OverallParms = {}
1852	self.Phases = {}
1853	self.Histograms = {}
1854	self.powderDict = {}
1855	self.xtalDict = {}
1856	self.parmDict = {}
1857	self.sigDict = {}
1858	# updated in InitExport:
1859	self.currentExportType = None # type of export that has been requested
1860	# updated in ExportSelect (when used):
1861	self.phasenam = None # a list of selected phases
1862	self.histnam = None # a list of selected histograms
1863	self.filename = None # name of file to be written (single export) or template (multiple files)
1864	self.dirname = '' # name of directory where file(s) will be written
1865	self.fullpath = '' # name of file being written -- full path
1866
1867	# items that should be defined in a subclass of this class
1868	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1869	# The following types are defined: 'project', "phase", "powder", "single"
1870	self.multiple = False # set as True if the class can export multiple phases or histograms
1871	# self.multiple is ignored for "project" exports
1872
1873	def InitExport(self,event):
1874	'''Determines the type of menu that called the Exporter and
1875	misc initialization.
1876	'''
1877	self.filename = None # name of file to be written (single export)
1878	self.dirname = '' # name of file to be written (multiple export)
1879	if event:
1880	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1881
1882	def MakePWDRfilename(self,hist):
1883	'''Make a filename root (no extension) from a PWDR histogram name
1884
1885	:param str hist: the histogram name in data tree (starts with "PWDR ")
1886	'''
1887	file0 = ''
1888	file1 = hist[5:]
1889	# replace repeated blanks
1890	while file1 != file0:
1891	file0 = file1
1892	file1 = file0.replace(' ',' ').strip()
1893	file0 = file1.replace('Azm= ','A')
1894	# if angle has unneeded decimal places on aziumuth, remove them
1895	if file0[-3:] == '.00': file0 = file0[:-3]
1896	file0 = file0.replace('.','_')
1897	file0 = file0.replace(' ','_')
1898	return file0
1899
1900	def ExportSelect(self,AskFile='ask'):
1901	'''Selects histograms or phases when needed. Sets a default file name when
1902	requested in self.filename; always sets a default directory in self.dirname.
1903
1904	:param bool AskFile: Determines how this routine processes getting a
1905	location to store the current export(s).
1906
1907	* if AskFile is 'ask' (default option), get the name of the file to be written;
1908	self.filename and self.dirname are always set. In the case where
1909	multiple files must be generated, the export routine should do this
1910	based on self.filename as a template.
1911	* if AskFile is 'dir', get the name of the directory to be used;
1912	self.filename is not used, but self.dirname is always set. The export routine
1913	will always generate the file name.
1914	* if AskFile is 'single', get only the name of the directory to be used when
1915	multiple items will be written (as multiple files) are used
1916	or a complete file name is requested when a single file
1917	name is selected. self.dirname is always set and self.filename used
1918	only when a single file is selected.
1919	* if AskFile is 'default', creates a name of the file to be used from
1920	the name of the project (.gpx) file. If the project has not been saved,
1921	then the name of file is requested.
1922	self.filename and self.dirname are always set. In the case where
1923	multiple file names must be generated, the export routine should do this
1924	based on self.filename.
1925	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1926	file. If the project has not been saved, then a directory is requested.
1927	self.filename is not used.
1928
1929	:returns: True in case of an error
1930	'''
1931
1932	numselected = 1
1933	if self.currentExportType == 'phase':
1934	if len(self.Phases) == 0:
1935	self.G2frame.ErrorDialog(
1936	'Empty project',
1937	'Project does not contain any phases.')
1938	return True
1939	elif len(self.Phases) == 1:
1940	self.phasenam = self.Phases.keys()
1941	elif self.multiple:
1942	choices = sorted(self.Phases.keys())
1943	phasenum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1944	if phasenum is None: return True
1945	self.phasenam = [choices[i] for i in phasenum]
1946	if not self.phasenam: return True
1947	numselected = len(self.phasenam)
1948	else:
1949	choices = sorted(self.Phases.keys())
1950	phasenum = G2gd.ItemSelector(choices,self.G2frame)
1951	if phasenum is None: return True
1952	self.phasenam = [choices[phasenum]]
1953	numselected = len(self.phasenam)
1954	elif self.currentExportType == 'single':
1955	if len(self.xtalDict) == 0:
1956	self.G2frame.ErrorDialog(
1957	'Empty project',
1958	'Project does not contain any single crystal data.')
1959	return True
1960	elif len(self.xtalDict) == 1:
1961	self.histnam = self.xtalDict.values()
1962	elif self.multiple:
1963	choices = sorted(self.xtalDict.values())
1964	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1965	if not hnum: return True
1966	self.histnam = [choices[i] for i in hnum]
1967	numselected = len(self.histnam)
1968	else:
1969	choices = sorted(self.xtalDict.values())
1970	hnum = G2gd.ItemSelector(choices,self.G2frame)
1971	if hnum is None: return True
1972	self.histnam = [choices[hnum]]
1973	numselected = len(self.histnam)
1974	elif self.currentExportType == 'powder':
1975	if len(self.powderDict) == 0:
1976	self.G2frame.ErrorDialog(
1977	'Empty project',
1978	'Project does not contain any powder data.')
1979	return True
1980	elif len(self.powderDict) == 1:
1981	self.histnam = self.powderDict.values()
1982	elif self.multiple:
1983	choices = sorted(self.powderDict.values())
1984	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=True)
1985	if not hnum: return True
1986	self.histnam = [choices[i] for i in hnum]
1987	numselected = len(self.histnam)
1988	else:
1989	choices = sorted(self.powderDict.values())
1990	hnum = G2gd.ItemSelector(choices,self.G2frame)
1991	if hnum is None: return True
1992	self.histnam = [choices[hnum]]
1993	numselected = len(self.histnam)
1994	elif self.currentExportType == 'image':
1995	if len(self.Histograms) == 0:
1996	self.G2frame.ErrorDialog(
1997	'Empty project',
1998	'Project does not contain any images.')
1999	return True
2000	elif len(self.Histograms) == 1:
2001	self.histnam = self.Histograms.keys()
2002	else:
2003	choices = sorted(self.Histograms.keys())
2004	hnum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
2005	if self.multiple:
2006	if not hnum: return True
2007	self.histnam = [choices[i] for i in hnum]
2008	else:
2009	if hnum is None: return True
2010	self.histnam = [choices[hnum]]
2011	numselected = len(self.histnam)
2012	if self.currentExportType == 'map':
2013	# search for phases with maps
2014	mapPhases = []
2015	choices = []
2016	for phasenam in sorted(self.Phases):
2017	phasedict = self.Phases[phasenam] # pointer to current phase info
2018	if len(phasedict['General']['Map'].get('rho',[])):
2019	mapPhases.append(phasenam)
2020	if phasedict['General']['Map'].get('Flip'):
2021	choices.append('Charge flip map: '+str(phasenam))
2022	elif phasedict['General']['Map'].get('MapType'):
2023	choices.append(
2024	str(phasedict['General']['Map'].get('MapType'))
2025	+ ' map: ' + str(phasenam))
2026	else:
2027	choices.append('unknown map: '+str(phasenam))
2028	# select a map if needed
2029	if len(mapPhases) == 0:
2030	self.G2frame.ErrorDialog(
2031	'Empty project',
2032	'Project does not contain any maps.')
2033	return True
2034	elif len(mapPhases) == 1:
2035	self.phasenam = mapPhases
2036	else:
2037	phasenum = G2gd.ItemSelector(choices,self.G2frame,multiple=self.multiple)
2038	if self.multiple:
2039	if not phasenum: return True
2040	self.phasenam = [mapPhases[i] for i in phasenum]
2041	else:
2042	if phasenum is None: return True
2043	self.phasenam = [mapPhases[phasenum]]
2044	numselected = len(self.phasenam)
2045
2046	# items selected, now set self.dirname and usually self.filename
2047	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
2048	AskFile == 'default' and not self.G2frame.GSASprojectfile
2049	):
2050	filename = self.askSaveFile()
2051	if not filename: return True
2052	self.dirname,self.filename = os.path.split(filename)
2053	elif AskFile == 'dir' or AskFile == 'single' or (
2054	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
2055	):
2056	self.dirname = self.askSaveDirectory()
2057	if not self.dirname: return True
2058	elif AskFile == 'default-dir' or AskFile == 'default':
2059	self.dirname,self.filename = os.path.split(
2060	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
2061	)
2062	else:
2063	raise Exception('This should not happen!')
2064
2065	def loadParmDict(self):
2066	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
2067	refined values to those from the last cycle and set the uncertainties for the
2068	refined parameters in another dict (self.sigDict).
2069
2070	Expands the parm & sig dicts to include values derived from constraints.
2071	'''
2072	self.parmDict = {}
2073	self.sigDict = {}
2074	rigidbodyDict = {}
2075	covDict = {}
2076	consDict = {}
2077	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2078	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2079	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2080	while item:
2081	name = self.G2frame.PatternTree.GetItemText(item)
2082	if name == 'Rigid bodies':
2083	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
2084	elif name == 'Covariance':
2085	covDict = self.G2frame.PatternTree.GetItemPyData(item)
2086	elif name == 'Constraints':
2087	consDict = self.G2frame.PatternTree.GetItemPyData(item)
2088	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2089	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
2090	self.parmDict.update(rbDict)
2091	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
2092	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables = G2stIO.GetPhaseData(
2093	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
2094	self.parmDict.update(phaseDict)
2095	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
2096	Phases,Histograms,Print=False,resetRefList=False)
2097	self.parmDict.update(hapDict)
2098	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
2099	self.parmDict.update(histDict)
2100	self.parmDict.update(zip(
2101	covDict.get('varyList',[]),
2102	covDict.get('variables',[])))
2103	self.sigDict = dict(zip(
2104	covDict.get('varyList',[]),
2105	covDict.get('sig',[])))
2106	# expand to include constraints: first compile a list of constraints
2107	constList = []
2108	for item in consDict:
2109	if item.startswith('_'): continue
2110	constList += consDict[item]
2111	# now process the constraints
2112	G2mv.InitVars()
2113	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
2114	varyList = covDict.get('varyListStart')
2115	if varyList is None and len(constDict) == 0:
2116	# no constraints can use varyList
2117	varyList = covDict.get('varyList')
2118	elif varyList is None:
2119	# old GPX file from before pre-constraint varyList is saved
2120	print ' * Old refinement: Please use Calculate/Refine to redo *'
2121	raise Exception(' * Export aborted *')
2122	else:
2123	varyList = list(varyList)
2124	try:
2125	groups,parmlist = G2mv.GroupConstraints(constDict)
2126	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
2127	except:
2128	# this really should not happen
2129	print ' * ERROR - constraints are internally inconsistent *'
2130	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
2131	print 'Errors',errmsg
2132	if warnmsg: print 'Warnings',warnmsg
2133	raise Exception(' * CIF creation aborted *')
2134	# add the constrained values to the parameter dictionary
2135	G2mv.Dict2Map(self.parmDict,varyList)
2136	# and add their uncertainties into the esd dictionary (sigDict)
2137	if covDict.get('covMatrix') is not None:
2138	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
2139
2140	def loadTree(self):
2141	'''Load the contents of the data tree into a set of dicts
2142	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2143	& self.xtalDict)
2144
2145	* The childrenless data tree items are overall parameters/controls for the
2146	entire project and are placed in self.OverallParms
2147	* Phase items are placed in self.Phases
2148	* Data items are placed in self.Histogram. The key for these data items
2149	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2150	'''
2151	self.OverallParms = {}
2152	self.powderDict = {}
2153	self.xtalDict = {}
2154	self.Phases = {}
2155	self.Histograms = {}
2156	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2157	histType = None
2158	if self.currentExportType == 'phase':
2159	# if exporting phases load them here
2160	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2161	if not sub:
2162	print 'no phases found'
2163	return True
2164	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2165	while item:
2166	phaseName = self.G2frame.PatternTree.GetItemText(item)
2167	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2168	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2169	return
2170	elif self.currentExportType == 'single':
2171	histType = 'HKLF'
2172	elif self.currentExportType == 'powder':
2173	histType = 'PWDR'
2174	elif self.currentExportType == 'image':
2175	histType = 'IMG'
2176
2177	if histType: # Loading just one kind of tree entry
2178	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2179	while item:
2180	name = self.G2frame.PatternTree.GetItemText(item)
2181	if name.startswith(histType):
2182	if self.Histograms.get(name): # there is already an item with this name
2183	print('Histogram name '+str(name)+' is repeated. Renaming')
2184	if name[-1] == '9':
2185	name = name[:-1] + '10'
2186	elif name[-1] in '012345678':
2187	name = name[:-1] + str(int(name[-1])+1)
2188	else:
2189	name += '-1'
2190	self.Histograms[name] = {}
2191	# the main info goes into Data, but the 0th
2192	# element contains refinement results, carry
2193	# that over too now.
2194	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2195	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2196	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2197	while item2:
2198	child = self.G2frame.PatternTree.GetItemText(item2)
2199	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2200	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2201	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2202	# index powder and single crystal histograms by number
2203	for hist in self.Histograms:
2204	if hist.startswith("PWDR"):
2205	d = self.powderDict
2206	elif hist.startswith("HKLF"):
2207	d = self.xtalDict
2208	else:
2209	return
2210	i = self.Histograms[hist].get('hId')
2211	if i is None and not d.keys():
2212	i = 0
2213	elif i is None or i in d.keys():
2214	i = max(d.keys())+1
2215	d[i] = hist
2216	return
2217	# else standard load: using all interlinked phases and histograms
2218	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2219	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2220	while item:
2221	name = self.G2frame.PatternTree.GetItemText(item)
2222	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2223	if not item2:
2224	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2225	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2226	# index powder and single crystal histograms
2227	for hist in self.Histograms:
2228	i = self.Histograms[hist]['hId']
2229	if hist.startswith("PWDR"):
2230	self.powderDict[i] = hist
2231	elif hist.startswith("HKLF"):
2232	self.xtalDict[i] = hist
2233
2234	def dumpTree(self,mode='type'):
2235	'''Print out information on the data tree dicts loaded in loadTree
2236	'''
2237	print '\nOverall'
2238	if mode == 'type':
2239	def Show(arg): return type(arg)
2240	else:
2241	def Show(arg): return arg
2242	for key in self.OverallParms:
2243	print ' ',key,Show(self.OverallParms[key])
2244	print 'Phases'
2245	for key1 in self.Phases:
2246	print ' ',key1,Show(self.Phases[key1])
2247	print 'Histogram'
2248	for key1 in self.Histograms:
2249	print ' ',key1,Show(self.Histograms[key1])
2250	for key2 in self.Histograms[key1]:
2251	print ' ',key2,Show(self.Histograms[key1][key2])
2252
2253	def defaultSaveFile(self):
2254	return os.path.abspath(
2255	os.path.splitext(self.G2frame.GSASprojectfile
2256	)[0]+self.extension)
2257
2258	def askSaveFile(self):
2259	'''Ask the user to supply a file name
2260
2261	:returns: a file name (str) or None if Cancel is pressed
2262	'''
2263	defnam = os.path.splitext(
2264	os.path.split(self.G2frame.GSASprojectfile)[1]
2265	)[0]+self.extension
2266	dlg = wx.FileDialog(
2267	self.G2frame, 'Input name for file to write', '.', defnam,
2268	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2269	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2270	dlg.CenterOnParent()
2271	try:
2272	if dlg.ShowModal() == wx.ID_OK:
2273	filename = dlg.GetPath()
2274	# make sure extension is correct
2275	filename = os.path.splitext(filename)[0]+self.extension
2276	else:
2277	filename = None
2278	finally:
2279	dlg.Destroy()
2280	return filename
2281
2282	def askSaveDirectory(self):
2283	'''Ask the user to supply a directory name. Path name is used as the
2284	starting point for the next export path search.
2285
2286	:returns: a directory name (str) or None if Cancel is pressed
2287	'''
2288	if self.G2frame.exportDir:
2289	startdir = self.G2frame.exportDir
2290	elif self.G2frame.GSASprojectfile:
2291	startdir = os.path.split(self.G2frame.GSASprojectfile)[0]
2292	elif self.G2frame.dirname:
2293	startdir = self.G2frame.dirname
2294	else:
2295	startdir = ''
2296	dlg = wx.DirDialog(
2297	self.G2frame, 'Input directory where file(s) will be written', startdir,
2298	wx.DD_DEFAULT_STYLE)
2299	dlg.CenterOnParent()
2300	try:
2301	if dlg.ShowModal() == wx.ID_OK:
2302	filename = dlg.GetPath()
2303	self.G2frame.exportDir = filename
2304	else:
2305	filename = None
2306	finally:
2307	dlg.Destroy()
2308	return filename
2309
2310	# Tools for file writing.
2311	def OpenFile(self,fil=None,mode='w'):
2312	'''Open the output file
2313
2314	:param str fil: The name of the file to open. If None (default)
2315	the name defaults to self.dirname + self.filename.
2316	If an extension is supplied, it is not overridded,
2317	but if not, the default extension is used.
2318	:returns: the file object opened by the routine which is also
2319	saved as self.fp
2320	'''
2321	if not fil:
2322	if not os.path.splitext(self.filename)[1]:
2323	self.filename += self.extension
2324	fil = os.path.join(self.dirname,self.filename)
2325	self.fullpath = fil
2326	self.fp = open(fil,mode)
2327	return self.fp
2328
2329	def Write(self,line):
2330	'''write a line of output, attaching a line-end character
2331
2332	:param str line: the text to be written.
2333	'''
2334	self.fp.write(line+'\n')
2335	def CloseFile(self,fp=None):
2336	'''Close a file opened in OpenFile
2337
2338	:param file fp: the file object to be closed. If None (default)
2339	file object self.fp is closed.
2340	'''
2341	if fp is None:
2342	fp = self.fp
2343	self.fp = None
2344	fp.close()
2345	# Tools to pull information out of the data arrays
2346	def GetCell(self,phasenam):
2347	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2348
2349	:param str phasenam: the name for the selected phase
2350	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2351	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2352	cell values and `cellSig` has their uncertainties.
2353	"""
2354	phasedict = self.Phases[phasenam] # pointer to current phase info
2355	try:
2356	pfx = str(phasedict['pId'])+'::'
2357	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2358	cellSig = G2stIO.getCellEsd(pfx,
2359	phasedict['General']['SGData'],A,
2360	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2361	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2362	return cellList,cellSig
2363	except KeyError:
2364	cell = phasedict['General']['Cell'][1:]
2365	return cell,7*[0]
2366
2367	def GetAtoms(self,phasenam):
2368	"""Gets the atoms associated with a phase. Can be used with standard
2369	or macromolecular phases
2370
2371	:param str phasenam: the name for the selected phase
2372	:returns: a list of items for eac atom where each item is a list containing:
2373	label, typ, mult, xyz, and td, where
2374
2375	* label and typ are the atom label and the scattering factor type (str)
2376	* mult is the site multiplicity (int)
2377	* xyz is contains a list with four pairs of numbers:
2378	x, y, z and fractional occupancy and
2379	their standard uncertainty (or a negative value)
2380	* td is contains a list with either one or six pairs of numbers:
2381	if one number it is U\ :sub:`iso` and with six numbers it is
2382	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2383	paired with their standard uncertainty (or a negative value)
2384	"""
2385	phasedict = self.Phases[phasenam] # pointer to current phase info
2386	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2387	cfrac = cx+3
2388	fpfx = str(phasedict['pId'])+'::Afrac:'
2389	atomslist = []
2390	for i,at in enumerate(phasedict['Atoms']):
2391	if phasedict['General']['Type'] == 'macromolecular':
2392	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2393	else:
2394	label = at[ct-1]
2395	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2396	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2397	mult = at[cs+1]
2398	typ = at[ct]
2399	xyz = []
2400	for j,v in enumerate(('x','y','z')):
2401	val = at[cx+j]
2402	pfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2403	sig = self.sigDict.get(pfx,-0.000009)
2404	xyz.append((val,sig))
2405	xyz.append((fval,fsig))
2406	td = []
2407	if at[cia] == 'I':
2408	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2409	val = self.parmDict.get(pfx,at[cia+1])
2410	sig = self.sigDict.get(pfx,-0.0009)
2411	td.append((val,sig))
2412	else:
2413	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2414	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2415	val = self.parmDict.get(pfx,at[cia+2+i])
2416	sig = self.sigDict.get(pfx,-0.0009)
2417	td.append((val,sig))
2418	atomslist.append((label,typ,mult,xyz,td))
2419	return atomslist
2420	######################################################################
2421
2422	def ReadCIF(URLorFile):
2423	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2424	(from James Hester).
2425	The open routine gets confused with DOS names that begin with a letter and colon
2426	"C:\dir\" so this routine will try to open the passed name as a file and if that
2427	fails, try it as a URL
2428
2429	:param str URLorFile: string containing a URL or a file name. Code will try first
2430	to open it as a file and then as a URL.
2431
2432	:returns: a PyCifRW CIF object.
2433	'''
2434	import CifFile as cif # PyCifRW from James Hester
2435
2436	# alternate approach:
2437	#import urllib
2438	#ciffile = 'file:'+urllib.pathname2url(filename)
2439
2440	try:
2441	fp = open(URLorFile,'r')
2442	cf = cif.ReadCif(fp)
2443	fp.close()
2444	return cf
2445	except IOError:
2446	return cif.ReadCif(URLorFile)
2447
2448	if __name__ == '__main__':
2449	app = wx.PySimpleApp()
2450	frm = wx.Frame(None) # create a frame
2451	frm.Show(True)
2452	filename = '/tmp/notzip.zip'
2453	filename = '/tmp/all.zip'
2454	#filename = '/tmp/11bmb_7652.zip'
2455
2456	#selection=None, confirmoverwrite=True, parent=None
2457	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2458	print ExtractFileFromZip(filename,multipleselect=True)
2459	#confirmread=False, confirmoverwrite=False)
2460
2461	# choicelist=[ ('a','b','c'),
2462	# ('test1','test2'),('no choice',)]
2463	# titles = [ 'a, b or c', 'tests', 'No option here']
2464	# dlg = MultipleChoicesDialog(
2465	# choicelist,titles,
2466	# parent=frm)
2467	# if dlg.ShowModal() == wx.ID_OK:
2468	# print 'Got OK'

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