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source: trunk/GSASII.py @ 1304

Last change on this file since 1304 was 1304, checked in by vondreele, 9 years ago
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1	#!/usr/bin/env python
2	# -- coding: utf-8 --
3	#GSASII
4	########### SVN repository information ###################
5	# $Date: 2014-04-25 20:09:03 +0000 (Fri, 25 Apr 2014) $
6	# $Author: vondreele $
7	# $Revision: 1304 $
8	# $URL: trunk/GSASII.py $
9	# $Id: GSASII.py 1304 2014-04-25 20:09:03Z vondreele $
10	########### SVN repository information ###################
11	'''
12	GSAS-II Main Module
13	=====================
14
15	Main routines for the GSAS-II program
16	'''
17
18	import os
19	import sys
20	import math
21	import copy
22	import random as ran
23	import time
24	import copy
25	import glob
26	import imp
27	import inspect
28	import numpy as np
29	import scipy as sp
30	import wx
31	import matplotlib as mpl
32	try:
33	import OpenGL as ogl
34	except ImportError:
35	print('*******************************************************')
36	print('PyOpenGL is missing from your python installation')
37	print(' - we will try to install it')
38	print('*******************************************************')
39	def install_with_easyinstall(package):
40	try:
41	print "trying a system-wide PyOpenGl install"
42	easy_install.main(['-f',os.path.split(__file__)[0],package])
43	return
44	except:
45	pass
46	try:
47	print "trying a user level PyOpenGl install"
48	easy_install.main(['-f',os.path.split(__file__)[0],'--user',package])
49	return
50	except:
51	print "Install of '+package+' failed. Please report this information:"
52	import traceback
53	print traceback.format_exc()
54	sys.exit()
55	from setuptools.command import easy_install
56	install_with_easyinstall('PyOpenGl')
57	print('*******************************************************')
58	print('OpenGL has been installed. Please restart GSAS-II')
59	print('*******************************************************')
60	sys.exit()
61
62	# load the GSAS routines
63	import GSASIIpath
64	GSASIIpath.SetVersionNumber("$Revision: 1304 $")
65	import GSASIIIO as G2IO
66	import GSASIIgrid as G2gd
67	import GSASIIplot as G2plt
68	import GSASIIpwd as G2pwd
69	import GSASIIpwdGUI as G2pdG
70	import GSASIIspc as G2spc
71	import GSASIIstrMain as G2stMn
72	import GSASIIstrIO as G2stIO
73	import GSASIImapvars as G2mv
74	import GSASIIobj as G2obj
75	import GSASIIlattice as G2lat
76
77	#wx inspector - use as needed
78	wxInspector = False
79
80	# print versions
81	print "Python module versions loaded:"
82	print "python: ",sys.version[:5]
83	print "wxpython: ",wx.__version__
84	print "matplotlib: ",mpl.__version__
85	print "numpy: ",np.__version__
86	print "scipy: ",sp.__version__
87	print "OpenGL: ",ogl.__version__
88	try:
89	import mkl
90	print "Max threads ",mkl.get_max_threads()
91	except:
92	pass
93	# print "MKL module not present"
94	__version__ = '0.2.0'
95	G2gd.__version__ = __version__
96	print "This is GSAS-II version: ",__version__,' revision '+str(GSASIIpath.GetVersionNumber())
97
98	# useful degree trig functions
99	sind = lambda x: math.sin(x*math.pi/180.)
100	cosd = lambda x: math.cos(x*math.pi/180.)
101	tand = lambda x: math.tan(x*math.pi/180.)
102	asind = lambda x: 180.*math.asin(x)/math.pi
103	acosd = lambda x: 180.*math.acos(x)/math.pi
104	atan2d = lambda x,y: 180.*math.atan2(y,x)/math.pi
105
106	def create(parent):
107	return GSASII(parent)
108
109	class GSASII(wx.Frame):
110	'''Define the main GSAS-II frame and its associated menu items
111	'''
112	def _Add_FileMenuItems(self, parent):
113	item = parent.Append(
114	help='Open a GSAS-II project file (*.gpx)', id=wx.ID_ANY,
115	kind=wx.ITEM_NORMAL,text='&Open project...')
116	self.Bind(wx.EVT_MENU, self.OnFileOpen, id=item.GetId())
117	item = parent.Append(
118	help='Save project under current name', id=wx.ID_ANY,
119	kind=wx.ITEM_NORMAL,text='&Save project')
120	self.Bind(wx.EVT_MENU, self.OnFileSave, id=item.GetId())
121	item = parent.Append(
122	help='Save current project to new file', id=wx.ID_ANY,
123	kind=wx.ITEM_NORMAL,text='Save project as...')
124	self.Bind(wx.EVT_MENU, self.OnFileSaveas, id=item.GetId())
125	item = parent.Append(
126	help='Create empty new project, saving current is optional', id=wx.ID_ANY,
127	kind=wx.ITEM_NORMAL,text='&New project')
128	self.Bind(wx.EVT_MENU, self.OnFileClose, id=item.GetId())
129	item = parent.Append(
130	help='Exit from GSAS-II', id=wx.ID_ANY,
131	kind=wx.ITEM_NORMAL,text='&Exit')
132	self.Bind(wx.EVT_MENU, self.OnFileExit, id=item.GetId())
133
134	def _Add_DataMenuItems(self,parent):
135	item = parent.Append(
136	help='',id=wx.ID_ANY,
137	kind=wx.ITEM_NORMAL,
138	text='Read image data...')
139	self.Bind(wx.EVT_MENU, self.OnImageRead, id=item.GetId())
140	item = parent.Append(
141	help='',id=wx.ID_ANY,
142	kind=wx.ITEM_NORMAL,
143	text='Read Powder Pattern Peaks...')
144	self.Bind(wx.EVT_MENU, self.OnReadPowderPeaks, id=item.GetId())
145	item = parent.Append(
146	help='',id=wx.ID_ANY,
147	kind=wx.ITEM_NORMAL,
148	text='Sum powder data')
149	self.Bind(wx.EVT_MENU, self.OnPwdrSum, id=item.GetId())
150	item = parent.Append(
151	help='',id=wx.ID_ANY,
152	kind=wx.ITEM_NORMAL,
153	text='Sum image data')
154	self.Bind(wx.EVT_MENU, self.OnImageSum, id=item.GetId())
155	item = parent.Append(
156	help='',id=wx.ID_ANY,
157	kind=wx.ITEM_NORMAL,
158	text='Add phase')
159	self.Bind(wx.EVT_MENU, self.OnAddPhase, id=item.GetId())
160	item = parent.Append(
161	help='',id=wx.ID_ANY,
162	kind=wx.ITEM_NORMAL,
163	text='Delete phase')
164	self.Bind(wx.EVT_MENU, self.OnDeletePhase, id=item.GetId())
165	item = parent.Append(
166	help='',id=wx.ID_ANY,
167	kind=wx.ITEM_NORMAL,
168	text='Rename data')
169	self.Bind(wx.EVT_MENU, self.OnRenameData, id=item.GetId())
170	item = parent.Append(
171	help='',id=wx.ID_ANY,
172	kind=wx.ITEM_NORMAL,
173	text='Delete data')
174	self.Bind(wx.EVT_MENU, self.OnDataDelete, id=item.GetId())
175
176	def _Add_CalculateMenuItems(self,parent):
177	item = parent.Append(help='Make new PDFs from selected powder patterns',
178	id=wx.ID_ANY, kind=wx.ITEM_NORMAL,text='Make new PDFs')
179	self.MakePDF.append(item)
180	# item.Enable(False)
181	self.Bind(wx.EVT_MENU, self.OnMakePDFs, id=item.GetId())
182
183	item = parent.Append(help='View least squares parameters',
184	id=wx.ID_ANY, kind=wx.ITEM_NORMAL,text='&View LS parms')
185	self.Bind(wx.EVT_MENU, self.ShowLSParms, id=item.GetId())
186
187	item = parent.Append(help='', id=wx.ID_ANY, kind=wx.ITEM_NORMAL,
188	text='&Refine')
189	if len(self.Refine): # extend state for new menus to match main (on mac)
190	state = self.Refine[0].IsEnabled()
191	else:
192	state = False
193	item.Enable(state)
194	self.Refine.append(item)
195	self.Bind(wx.EVT_MENU, self.OnRefine, id=item.GetId())
196
197	item = parent.Append(help='', id=wx.ID_ANY, kind=wx.ITEM_NORMAL,
198	text='Sequential refine')
199	if len(self.SeqRefine): # extend state for new menus to match main (on mac)
200	state = self.SeqRefine[0].IsEnabled()
201	else:
202	state = False
203	item.Enable(state)
204	self.SeqRefine.append(item) # save menu obj for use in self.EnableSeqRefineMenu
205	self.Bind(wx.EVT_MENU, self.OnSeqRefine, id=item.GetId())
206
207	def _init_Imports(self):
208	'''import all the G2phase.py & G2sfact.py & G2pwd*.py files that
209	are found in the path
210	'''
211
212	self.ImportPhaseReaderlist = []
213	self._init_Import_routines('phase',self.ImportPhaseReaderlist,'Phase')
214	self.ImportSfactReaderlist = []
215	self._init_Import_routines('sfact',self.ImportSfactReaderlist,'Struct_Factor')
216	self.ImportPowderReaderlist = []
217	self._init_Import_routines('pwd',self.ImportPowderReaderlist,'Powder_Data')
218	self.ImportSmallAngleReaderlist = []
219	self._init_Import_routines('sad',self.ImportSmallAngleReaderlist,'SmallAngle_Data')
220	self.ImportMenuId = {}
221
222	def _init_Import_routines(self,prefix,readerlist,errprefix):
223	'''import all the import readers matching the prefix
224	'''
225	#path2GSAS2 = os.path.dirname(os.path.realpath(__file__)) # location of this file
226	#pathlist = sys.path[:]
227	#if path2GSAS2 not in pathlist: pathlist.append(path2GSAS2)
228	#path2GSAS2 = os.path.join(
229	# os.path.dirname(os.path.realpath(__file__)), # location of this file
230	# 'imports')
231	pathlist = sys.path[:]
232	#if path2GSAS2 not in pathlist: pathlist.append(path2GSAS2)
233
234	filelist = []
235	for path in pathlist:
236	for filename in glob.iglob(os.path.join(
237	path,
238	"G2"+prefix+"*.py")):
239	filelist.append(filename)
240	#print 'debug: found',filename
241	filelist = sorted(list(set(filelist))) # remove duplicates
242	for filename in filelist:
243	path,rootname = os.path.split(filename)
244	pkg = os.path.splitext(rootname)[0]
245	try:
246	fp = None
247	fp, fppath,desc = imp.find_module(pkg,[path,])
248	pkg = imp.load_module(pkg,fp,fppath,desc)
249	for clss in inspect.getmembers(pkg): # find classes defined in package
250	if clss[0].startswith('_'): continue
251	if inspect.isclass(clss[1]):
252	# check if we have the required methods
253	for m in 'Reader','ExtensionValidator','ContentsValidator':
254	if not hasattr(clss[1],m): break
255	if not callable(getattr(clss[1],m)): break
256	else:
257	reader = clss[1]() # create an import instance
258	readerlist.append(reader)
259	except AttributeError:
260	print 'Import_'+errprefix+': Attribute Error '+str(filename)
261	pass
262	except ImportError:
263	print 'Import_'+errprefix+': Error importing file '+str(filename)
264	pass
265	if fp: fp.close()
266
267	def EnableSeqRefineMenu(self):
268	'''Enable or disable the sequential refinement menu items based on the
269	contents of the Controls 'Seq Data' item (if present)
270	'''
271	controls = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.root, 'Controls'))
272	if controls.get('Seq Data'):
273	for i in self.SeqRefine: i.Enable(True)
274	else:
275	for i in self.SeqRefine: i.Enable(False)
276
277	def OnImportGeneric(self,reader,readerlist,label,multiple=False,usedRanIdList=[]):
278	'''Used to import Phases, powder dataset or single
279	crystal datasets (structure factor tables) using reader objects
280	subclassed from :class:`GSASIIIO.ImportPhase`, :class:`GSASIIIO.ImportStructFactor`
281	or :class:`GSASIIIO.ImportPowderData`. If a reader is specified, only
282	that will be attempted, but if no reader is specified, every one
283	that is potentially compatible (by file extension) will
284	be tried on the selected file(s).
285
286	:param readerobject reader: This will be a reference to
287	a particular object to be used to read a file or None,
288	if every appropriate reader should be used.
289
290	:param list readerlist: a list of reader objects appropriate for
291	the current read attempt. At present, this will be either
292	self.ImportPhaseReaderlist, self.ImportSfactReaderlist or
293	self.ImportPowderReaderlist (defined in _init_Imports from
294	the files found in the path), but in theory this list could
295	be tailored. Used only when reader is None.
296
297	:param str label: string to place on the open file dialog:
298	Open `label` input file
299
300	:param bool multiple: True if multiple files can be selected
301	in the file dialog. False is default. At present True is used
302	only for reading of powder data.
303
304	:param list usedRanIdList: an optional list of random Ids that
305	have been used and should not be reused
306
307	:returns: a list of reader objects (rd_list) that were able
308	to read the specified file(s). This list may be empty.
309	'''
310	self.lastimport = ''
311	self.zipfile = None
312	singlereader = True
313	if reader is None:
314	singlereader = False
315	multiple = False
316	#print "use all formats"
317	choices = "any file (.)\|."
318	choices += "\|zip archive (.zip)\|*.zip"
319	extdict = {}
320	# compile a list of allowed extensions
321	for rd in readerlist:
322	fmt = rd.formatName
323	for extn in rd.extensionlist:
324	if not extdict.get(extn): extdict[extn] = []
325	extdict[extn] += [fmt,]
326	for extn in sorted(extdict.keys(),cmp=lambda x,y: cmp(x.lower(), y.lower())):
327	fmt = ''
328	for f in extdict[extn]:
329	if fmt != "": fmt += ', '
330	fmt += f
331	choices += "\|" + fmt + " file (" + extn + ")\|" + extn
332	else:
333	readerlist = [reader,]
334	# compile a list of allowed extensions
335	choices = reader.formatName + " file ("
336	w = ""
337	for extn in reader.extensionlist:
338	if w != "": w += ";"
339	w += "*" + extn
340	choices += w + ")\|" + w
341	choices += "\|zip archive (.zip)\|*.zip"
342	if not reader.strictExtension:
343	choices += "\|any file (.)\|."
344	# get the file(s)
345	if multiple:
346	mode = style=wx.OPEN \| wx.CHANGE_DIR \| wx.MULTIPLE
347	else:
348	mode = style=wx.OPEN \| wx.CHANGE_DIR
349	dlg = wx.FileDialog(self, message="Choose "+label+" input file",
350	defaultFile="",wildcard=choices, style=mode)
351	if self.Tutorials:
352	dlg.SetDirectory(os.path.join(GSASIIpath.path2GSAS2,'Exercises'))
353	self.Tutorials = False
354	try:
355	if dlg.ShowModal() == wx.ID_OK:
356	if multiple:
357	filelist = dlg.GetPaths()
358	if len(filelist) == 0: return []
359	else:
360	filename = dlg.GetPath()
361	filelist = [filename,]
362	os.chdir(dlg.GetDirectory()) # to get Mac/Linux to change directory!
363	else: # cancel was pressed
364	return []
365	finally:
366	dlg.Destroy()
367	rd_list = []
368	filelist1 = []
369	for filename in filelist:
370	# is this a zip file?
371	if os.path.splitext(filename)[1].lower() == '.zip':
372	extractedfiles = G2IO.ExtractFileFromZip(
373	filename,parent=self,
374	multipleselect=True)
375	if extractedfiles is None: continue # error or Cancel
376	if extractedfiles != filename:
377	self.zipfile = filename # save zip name
378	filelist1 += extractedfiles
379	continue
380	filelist1.append(filename)
381	filelist = filelist1
382	for filename in filelist:
383	# is this a zip file?
384	if os.path.splitext(filename)[1].lower() == '.zip':
385	extractedfile = G2IO.ExtractFileFromZip(filename,parent=self)
386	if extractedfile is None: continue # error or Cancel
387	if extractedfile != filename:
388	filename,self.zipfile = extractedfile,filename # now use the file that was created
389	# set what formats are compatible with this file
390	primaryReaders = []
391	secondaryReaders = []
392	for rd in readerlist:
393	flag = rd.ExtensionValidator(filename)
394	if flag is None:
395	secondaryReaders.append(rd)
396	elif flag:
397	primaryReaders.append(rd)
398	if len(secondaryReaders) + len(primaryReaders) == 0:
399	self.ErrorDialog('No Format','No matching format for file '+filename)
400	return []
401
402	fp = None
403	msg = ''
404	try:
405	fp = open(filename,'Ur')
406	if len(filelist) == 1:
407	# confirm we have the right file
408	rdmsg = 'File '+str(filename)+' begins:\n\n'
409	for i in range(3):
410	rdmsg += fp.readline()
411	rdmsg += '\n\nDo you want to read this file?'
412	if not all([ord(c) < 128 and ord(c) != 0 for c in rdmsg]): # show only if ASCII
413	rdmsg = 'File '+str(
414	filename)+' is a binary file. Do you want to read this file?'
415	result = wx.ID_NO
416	# it would be better to use something that
417	# would resize better, but this will do for now
418	dlg = wx.MessageDialog(
419	self, rdmsg,
420	'Is this the file you want?',
421	wx.YES_NO \| wx.ICON_QUESTION,
422	)
423	dlg.SetSize((700,300)) # does not resize on Mac
424	try:
425	result = dlg.ShowModal()
426	finally:
427	dlg.Destroy()
428	if result == wx.ID_NO: return []
429
430	self.lastimport = filename # this is probably not what I want to do -- it saves only the
431	# last name in a series. See rd.readfilename for a better name.
432
433	# try the file first with Readers that specify the
434	# file's extension and later with ones that merely allow it
435	errorReport = ''
436	for rd in primaryReaders+secondaryReaders:
437	rd.ReInitialize() # purge anything from a previous read
438	fp.seek(0) # rewind
439	rd.errors = "" # clear out any old errors
440	if not rd.ContentsValidator(fp): # rejected on cursory check
441	errorReport += "\n "+rd.formatName + ' validator error'
442	if rd.errors:
443	errorReport += ': '+rd.errors
444	continue
445	repeat = True
446	rdbuffer = {} # create temporary storage for file reader
447	block = 0
448	while repeat: # loop if the reader asks for another pass on the file
449	block += 1
450	repeat = False
451	fp.seek(0) # rewind
452	rd.objname = os.path.basename(filename)
453	flag = False
454	try:
455	flag = rd.Reader(filename,fp,self,
456	buffer=rdbuffer,
457	blocknum=block,
458	usedRanIdList=usedRanIdList,
459	)
460	except rd.ImportException as detail:
461	rd.errors += "\n Read exception: "+str(detail)
462	except Exception as detail:
463	rd.errors += "\n Unhandled read exception: "+str(detail)
464	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
465	if flag: # this read succeeded
466	rd.readfilename = filename
467	rd_list.append(copy.deepcopy(rd)) # save the result before it is written over
468	if rd.repeat:
469	repeat = True
470	continue
471	errorReport += '\n'+rd.formatName + ' read error'
472	if rd.errors:
473	errorReport += ': '+rd.errors
474	if rd_list: # read succeeded, was there a warning or any errors?
475	if rd.warnings:
476	self.ErrorDialog('Read Warning','The '+ rd.formatName+
477	' reader reported a warning message:\n\n'+
478	rd.warnings)
479	break # success in reading, try no further
480	else:
481	if singlereader:
482	self.ErrorDialog('Read Error','The '+ rd.formatName+
483	' reader was not able to read file '+filename+msg+
484	'\n\nError message(s):\n'+errorReport
485	)
486	else:
487	self.ErrorDialog('Read Error','No reader was able to read file '+filename+msg+
488	'\n\nError messages:\n'+errorReport
489	)
490	except:
491	import traceback
492	print traceback.format_exc()
493	self.ErrorDialog('Open Error','Unexpected error trying to open or read file '+filename)
494	if fp: fp.close()
495	return rd_list
496
497	def _Add_ImportMenu_Phase(self,parent):
498	'''configure the Import Phase menus accord to the readers found in _init_Imports
499	'''
500	submenu = wx.Menu()
501	item = parent.AppendMenu(wx.ID_ANY, 'Phase',
502	submenu, help='Import phase data')
503	for reader in self.ImportPhaseReaderlist:
504	item = submenu.Append(wx.ID_ANY,help=reader.longFormatName,
505	kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file')
506	self.ImportMenuId[item.GetId()] = reader
507	self.Bind(wx.EVT_MENU, self.OnImportPhase, id=item.GetId())
508	item = submenu.Append(wx.ID_ANY,
509	help='Import phase data, use file to try to determine format',
510	kind=wx.ITEM_NORMAL,
511	text='guess format from file')
512	self.Bind(wx.EVT_MENU, self.OnImportPhase, id=item.GetId())
513
514	def OnImportPhase(self,event):
515	'''Called in response to an Import/Phase/... menu item
516	to read phase information.
517	dict self.ImportMenuId is used to look up the specific
518	reader item associated with the menu item, which will be
519	None for the last menu item, which is the "guess" option
520	where all appropriate formats will be tried.
521	'''
522	# look up which format was requested
523	reqrdr = self.ImportMenuId.get(event.GetId())
524
525	# make a list of phase names, ranId's and the histograms used in those phases
526	phaseRIdList,usedHistograms = self.GetPhaseInfofromTree()
527	phaseNameList = usedHistograms.keys() # phase names in use
528	usedHKLFhists = [] # used single-crystal histograms
529	for p in usedHistograms:
530	for h in usedHistograms[p]:
531	if h.startswith('HKLF ') and h not in usedHKLFhists:
532	usedHKLFhists.append(h)
533	rdlist = self.OnImportGeneric(reqrdr,
534	self.ImportPhaseReaderlist,
535	'phase',usedRanIdList=phaseRIdList)
536	if len(rdlist) == 0: return
537	# for now rdlist is only expected to have one element
538	# but below will allow multiple phases to be imported
539	# if ever the import routines ever implement multiple phase reads.
540	self.CheckNotebook()
541	newPhaseList = []
542	for rd in rdlist:
543	dlg = wx.TextEntryDialog( # allow editing of phase name
544	self, 'Enter the name for the new phase',
545	'Edit phase name', rd.Phase['General']['Name'],
546	style=wx.OK)
547	dlg.CenterOnParent()
548	if dlg.ShowModal() == wx.ID_OK:
549	rd.Phase['General']['Name'] = dlg.GetValue()
550	dlg.Destroy()
551	# make new phase names unique
552	rd.Phase['General']['Name'] = G2obj.MakeUniqueLabel(rd.Phase['General']['Name'],phaseNameList)
553	PhaseName = rd.Phase['General']['Name']
554	newPhaseList.append(PhaseName)
555	print 'Read phase '+str(PhaseName)+' from file '+str(self.lastimport)
556	if not G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
557	sub = self.PatternTree.AppendItem(parent=self.root,text='Phases')
558	else:
559	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
560	psub = self.PatternTree.AppendItem(parent=sub,text=PhaseName)
561	self.PatternTree.SetItemPyData(psub,rd.Phase)
562	self.PatternTree.Expand(self.root) # make sure phases are seen
563	self.PatternTree.Expand(sub)
564	self.PatternTree.Expand(psub)
565	self.PatternTree.SelectItem(psub) # show the page to complete the initialization (yuk!)
566	wx.Yield() # make sure call of GSASII.OnPatternTreeSelChanged happens before we go on
567
568	if rd.Constraints:
569	sub = G2gd.GetPatternTreeItemId(self,self.root,'Constraints') # was created in CheckNotebook if needed
570	Constraints = self.PatternTree.GetItemPyData(sub)
571	# TODO: make sure that NEWVAR names are unique here?
572	for i in rd.Constraints:
573	if type(i) is dict:
574	#for j in i: print j,' --> ',i[j]
575	if '_Explain' not in Constraints: Constraints['_Explain'] = {}
576	Constraints['_Explain'].update(i)
577	continue
578	Constraints['Phase'].append(i)
579	if not newPhaseList: return # somehow, no new phases
580	# get a list of existing histograms
581	PWDRlist = []
582	HKLFlist = []
583	if self.PatternTree.GetCount():
584	item, cookie = self.PatternTree.GetFirstChild(self.root)
585	while item:
586	name = self.PatternTree.GetItemText(item)
587	if name.startswith('PWDR ') and name not in PWDRlist:
588	PWDRlist.append(name)
589	if name.startswith('HKLF ') and name not in HKLFlist:
590	HKLFlist.append(name)
591	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
592	TextList = PWDRlist + HKLFlist
593	if not len(TextList): return # no data loaded yet
594	header = 'Select histogram(s) to add to new phase(s):'
595	for phaseName in newPhaseList:
596	header += '\n '+str(phaseName)
597
598	notOK = True
599	while notOK:
600	result = G2gd.ItemSelector(TextList,self,header,header='Add histogram(s)',multiple=True)
601	if not result: return
602	# check that selected single crystal histograms are not already in use!
603	used = [TextList[i] for i in result if TextList[i] in usedHKLFhists]
604	#for i in result:
605	# if TextList[i] in usedHKLFhists: used.append(TextList[i])
606	if used:
607	msg = 'The following single crystal histogram(s) are already in use'
608	for i in used:
609	msg += '\n '+str(i)
610	msg += '\nAre you sure you want to add them to this phase? '
611	msg += 'Associating a single crystal dataset to >1 histogram is usually an error, '
612	msg += 'so No is suggested here.'
613	if self.ErrorDialog('Likely error',msg,self,wtype=wx.YES_NO) == wx.ID_YES: notOK = False
614	else:
615	notOK = False
616	# connect new phases to histograms
617	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
618	if not sub:
619	raise Exception('ERROR -- why are there no phases here?')
620	wx.BeginBusyCursor()
621	item, cookie = self.PatternTree.GetFirstChild(sub)
622	while item: # loop over (new) phases
623	phaseName = self.PatternTree.GetItemText(item)
624	data = self.PatternTree.GetItemPyData(item)
625	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
626	if phaseName not in newPhaseList: continue
627	generalData = data['General']
628	SGData = generalData['SGData']
629	UseList = data['Histograms']
630	NShkl = len(G2spc.MustrainNames(SGData))
631	NDij = len(G2spc.HStrainNames(SGData))
632	for i in result:
633	histoName = TextList[i]
634	if histoName in HKLFlist:
635	UseList[histoName] = {
636	'Histogram':histoName,'Show':False,'Scale':[1.0,True],
637	'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]},
638	'Extinction':['Lorentzian','None', {'Tbar':0.1,'Cos2TM':0.955,
639	'Eg':[1.e-10,False],
640	'Es':[1.e-10,False],
641	'Ep':[1.e-10,False]},]
642	}
643	#redo UpdateHKLFdata(histoName) here:
644	Id = G2gd.GetPatternTreeItemId(self,self.root,histoName)
645	refDict,reflData = self.PatternTree.GetItemPyData(Id)
646	G,g = G2lat.cell2Gmat(generalData['Cell'][1:7])
647	for iref,ref in enumerate(reflData['RefList']):
648	H = list(ref[:3])
649	ref[4] = np.sqrt(1./G2lat.calc_rDsq2(H,G))
650	iabsnt,ref[3],Uniq,phi = G2spc.GenHKLf(H,SGData)
651	elif histoName in PWDRlist:
652	UseList[histoName] = {
653	'Histogram':histoName,'Show':False,
654	'Scale':[1.0,False],'Pref.Ori.':['MD',1.0,False,[0,0,1],0,{}],
655	'Size':['isotropic',[1.,1.,1.],[False,False,False],[0,0,1],
656	[1.,1.,1.,0.,0.,0.],6*[False,]],
657	'Mustrain':['isotropic',[1000.0,1000.0,1.0],[False,False,False],[0,0,1],
658	NShkl[0.01,],NShkl[False,]],
659	'HStrain':[NDij[0.0,],NDij[False,]],
660	'Extinction':[0.0,False],'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}}
661	Id = G2gd.GetPatternTreeItemId(self,self.root,histoName)
662	refList = self.PatternTree.GetItemPyData(
663	G2gd.GetPatternTreeItemId(self,Id,'Reflection Lists'))
664	refList[generalData['Name']] = []
665	else:
666	raise Exception('Unexpected histogram '+str(histoName))
667	wx.EndBusyCursor()
668	return # success
669
670	def _Add_ImportMenu_Sfact(self,parent):
671	'''configure the Import Structure Factor menus accord to the readers found in _init_Imports
672	'''
673	submenu = wx.Menu()
674	item = parent.AppendMenu(wx.ID_ANY, 'Structure Factor',
675	submenu, help='Import Structure Factor data')
676	for reader in self.ImportSfactReaderlist:
677	item = submenu.Append(wx.ID_ANY,help=reader.longFormatName,
678	kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file')
679	self.ImportMenuId[item.GetId()] = reader
680	self.Bind(wx.EVT_MENU, self.OnImportSfact, id=item.GetId())
681	item = submenu.Append(wx.ID_ANY,
682	help='Import Structure Factor, use file to try to determine format',
683	kind=wx.ITEM_NORMAL,
684	text='guess format from file')
685	self.Bind(wx.EVT_MENU, self.OnImportSfact, id=item.GetId())
686
687	def OnImportSfact(self,event):
688	'''Called in response to an Import/Structure Factor/... menu item
689	to read single crystal datasets.
690	dict self.ImportMenuId is used to look up the specific
691	reader item associated with the menu item, which will be
692	None for the last menu item, which is the "guess" option
693	where all appropriate formats will be tried.
694	'''
695	# get a list of existing histograms
696	HKLFlist = []
697	if self.PatternTree.GetCount():
698	item, cookie = self.PatternTree.GetFirstChild(self.root)
699	while item:
700	name = self.PatternTree.GetItemText(item)
701	if name.startswith('HKLF ') and name not in HKLFlist:
702	HKLFlist.append(name)
703	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
704	# look up which format was requested
705	reqrdr = self.ImportMenuId.get(event.GetId())
706	rdlist = self.OnImportGeneric(reqrdr,self.ImportSfactReaderlist,
707	'Structure Factor')
708	if len(rdlist) == 0: return
709	self.CheckNotebook()
710	newHistList = []
711	for rd in rdlist:
712	HistName = rd.objname
713	if len(rdlist) <= 2:
714	dlg = wx.TextEntryDialog( # allow editing of Structure Factor name
715	self, 'Enter the name for the new Structure Factor',
716	'Edit Structure Factor name', HistName,
717	style=wx.OK)
718	dlg.CenterOnParent()
719	if dlg.ShowModal() == wx.ID_OK:
720	HistName = dlg.GetValue()
721	dlg.Destroy()
722	HistName = 'HKLF '+HistName
723	# make new histogram names unique
724	HistName = G2obj.MakeUniqueLabel(HistName,HKLFlist)
725	print 'Read structure factor table '+str(HistName)+' from file '+str(self.lastimport)
726	if not rd.RefDict.get('FF'):
727	rd.RefDict['FF'] = [{} for i in range(len(rd.RefDict['RefList']))]
728	Id = self.PatternTree.AppendItem(parent=self.root,text=HistName)
729	valuesdict = {
730	'wtFactor':1.0,
731	'Dummy':False,
732	'ranId':ran.randint(0,sys.maxint),
733	}
734	self.PatternTree.SetItemPyData(Id,[valuesdict,rd.RefDict])
735	Sub = self.PatternTree.AppendItem(Id,text='Instrument Parameters')
736	self.PatternTree.SetItemPyData(Sub,rd.Parameters)
737	self.PatternTree.SetItemPyData(
738	self.PatternTree.AppendItem(Id,text='HKL Plot Controls'),
739	rd.Controls)
740	self.PatternTree.SetItemPyData(
741	self.PatternTree.AppendItem(Id,text='Reflection List'),[]) #dummy entry for GUI use
742	self.PatternTree.SelectItem(Id)
743	self.PatternTree.Expand(Id)
744	self.Sngl = True
745	newHistList.append(HistName)
746
747	if not newHistList: return # somehow, no new histograms
748	# make a list of phase names
749	phaseRIdList,usedHistograms = self.GetPhaseInfofromTree()
750	phaseNameList = usedHistograms.keys() # phase names in use
751	if not phaseNameList: return # no phases yet, nothing to do
752	header = 'Select phase(s) to add the new\nsingle crystal dataset(s) to:'
753	for Name in newHistList:
754	header += '\n '+str(Name)
755	result = G2gd.ItemSelector(phaseNameList,self,header,header='Add to phase(s)',multiple=True)
756	if not result: return
757	# connect new phases to histograms
758	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
759	if not sub:
760	raise Exception('ERROR -- why are there no phases here?')
761	wx.BeginBusyCursor()
762	item, cookie = self.PatternTree.GetFirstChild(sub)
763	iph = -1
764	while item: # loop over (new) phases
765	iph += 1
766	phaseName = self.PatternTree.GetItemText(item)
767	data = self.PatternTree.GetItemPyData(item)
768	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
769	if iph not in result: continue
770	generalData = data['General']
771	SGData = generalData['SGData']
772	UseList = data['Histograms']
773	NShkl = len(G2spc.MustrainNames(SGData))
774	NDij = len(G2spc.HStrainNames(SGData))
775	for histoName in newHistList:
776	UseList[histoName] = {
777	'Histogram':histoName,'Show':False,'Scale':[1.0,True],
778	'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]},
779	'Extinction':['Lorentzian','None', {'Tbar':0.1,'Cos2TM':0.955,
780	'Eg':[1.e-10,False],
781	'Es':[1.e-10,False],
782	'Ep':[1.e-10,False]},]
783	}
784	#redo UpdateHKLFdata(histoName) here:
785	Id = G2gd.GetPatternTreeItemId(self,self.root,histoName)
786	refDict,reflData = self.PatternTree.GetItemPyData(Id)
787	G,g = G2lat.cell2Gmat(generalData['Cell'][1:7])
788	for iref,ref in enumerate(reflData['RefList']):
789	H = list(ref[:3])
790	ref[4] = np.sqrt(1./G2lat.calc_rDsq2(H,G))
791	iabsnt,ref[3],Uniq,phi = G2spc.GenHKLf(H,SGData)
792	wx.EndBusyCursor()
793
794	return # success
795
796	def _Add_ImportMenu_powder(self,parent):
797	'''configure the Powder Data menus accord to the readers found in _init_Imports
798	'''
799	submenu = wx.Menu()
800	item = parent.AppendMenu(wx.ID_ANY, 'Powder Data',
801	submenu, help='Import Powder data')
802	for reader in self.ImportPowderReaderlist:
803	item = submenu.Append(wx.ID_ANY,help=reader.longFormatName,
804	kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file')
805	self.ImportMenuId[item.GetId()] = reader
806	self.Bind(wx.EVT_MENU, self.OnImportPowder, id=item.GetId())
807	item = submenu.Append(wx.ID_ANY,
808	help='Import powder data, use file to try to determine format',
809	kind=wx.ITEM_NORMAL,text='guess format from file')
810	self.Bind(wx.EVT_MENU, self.OnImportPowder, id=item.GetId())
811	submenu.AppendSeparator()
812	item = submenu.Append(wx.ID_ANY,
813	help='Create a powder data set entry that will be simulated',
814	kind=wx.ITEM_NORMAL,text='Simulate a dataset')
815	self.Bind(wx.EVT_MENU, self.OnDummyPowder, id=item.GetId())
816
817	def ReadPowderInstprm(self,instfile): #fix the write routine for [inst1,inst2] style
818	'''Read a GSAS-II (new) instrument parameter file
819
820	:param str instfile: name of instrument parameter file
821
822	'''
823	if os.path.splitext(instfile)[1].lower() != '.instprm': # invalid file
824	return None
825	if not os.path.exists(instfile): # no such file
826	return None
827	File = open(instfile,'r')
828	S = File.readline()
829	if not S.startswith('#GSAS-II'): # not a valid file
830	File.close()
831	return None
832	newItems = []
833	newVals = []
834	while S:
835	if S[0] == '#':
836	S = File.readline()
837	continue
838	[item,val] = S[:-1].split(':')
839	newItems.append(item)
840	try:
841	newVals.append(float(val))
842	except ValueError:
843	newVals.append(val)
844	S = File.readline()
845	File.close()
846	# add a second MT dict here. TOF parms? (BHT)
847	return G2IO.makeInstDict(newItems,newVals,len(newVals)*[False,]),{}
848
849	def ReadPowderIparm(self,instfile,bank,databanks,rd):
850	'''Read a GSAS (old) instrument parameter file
851
852	:param str instfile: name of instrument parameter file
853
854	:param int bank: the bank number read in the raw data file
855
856	:param int databanks: the number of banks in the raw data file.
857	If the number of banks in the data and instrument parameter files
858	agree, then the sets of banks are assumed to match up and bank
859	is used to select the instrument parameter file. If not, the user
860	is asked to make a selection.
861
862	:param obj rd: the raw data (histogram) data object. This
863	sets rd.instbank.
864
865	'''
866	if not os.path.exists(instfile): # no such file
867	return {}
868	fp = 0
869	try:
870	fp = open(instfile,'Ur')
871	Iparm = {}
872	for S in fp:
873	Iparm[S[:12]] = S[12:-1]
874	except IOError:
875	print('Error reading file:'+str(instfile))
876	if fp:
877	fp.close()
878
879	ibanks = int(Iparm.get('INS BANK ','1').strip())
880	hType = Iparm['INS HTYPE '].strip()
881	if ibanks == 1: # there is only one bank here, return it
882	rd.instbank = 1
883	return Iparm
884	if 'PNT' in hType:
885	rd.instbank = bank
886	elif ibanks != databanks:
887	# number of banks in data and prm file not not agree, need a
888	# choice from a human here
889	choices = []
890	for i in range(1,1+ibanks):
891	choices.append('Bank '+str(i))
892	bank = rd.BlockSelector(
893	choices, self,
894	title='Select an instrument parameter bank for '+
895	os.path.split(rd.powderentry[0])[1]+' BANK '+str(bank)+
896	'\nOr use Cancel to select from the default parameter sets',
897	header='Block Selector')
898	if bank is None: return {}
899	# pull out requested bank # bank from the data, and change the bank to 1
900	IparmS = {}
901	for key in Iparm:
902	if key[4:6] == " ":
903	IparmS[key] = Iparm[key]
904	elif int(key[4:6].strip()) == bank:
905	IparmS[key[:4]+' 1'+key[6:]] = Iparm[key]
906	rd.instbank = bank
907	return IparmS
908
909	def GetPowderIparm(self,rd, prevIparm, lastIparmfile, lastdatafile):
910	'''Open and read an instrument parameter file for a data file
911	Returns the list of parameters used in the data tree
912
913	:param obj rd: the raw data (histogram) data object.
914
915	:param str prevIparm: not used
916
917	:param str lastIparmfile: Name of last instrument parameter
918	file that was read, or a empty string.
919
920	:param str lastdatafile: Name of last data file that was read.
921
922	:returns: a list of two dicts, the first containing instrument parameters
923	and the second used for future TOF datasets (timemaps?)
924
925	'''
926	def SetPowderInstParms(Iparm, rd):
927	'''extracts values from instrument parameters in rd.instdict
928	or in array Iparm.
929	Create and return the contents of the instrument parameter tree entry.
930	'''
931	DataType = Iparm['INS HTYPE '].strip()[:3] # take 1st 3 chars
932	# override inst values with values read from data file
933	if rd.instdict.get('type'):
934	DataType = rd.instdict.get('type')
935	data = [DataType,]
936	instname = Iparm.get('INS 1INAME ')
937	if instname:
938	rd.Sample['InstrName'] = instname.strip()
939	if 'C' in DataType:
940	wave1 = None
941	wave2 = 0.0
942	if rd.instdict.get('wave'):
943	wl = rd.instdict.get('wave')
944	wave1 = wl[0]
945	if len(wl) > 1: wave2 = wl[1]
946	s = Iparm['INS 1 ICONS']
947	if not wave1:
948	wave1 = G2IO.sfloat(s[:10])
949	wave2 = G2IO.sfloat(s[10:20])
950	v = (wave1,wave2,
951	G2IO.sfloat(s[20:30]),G2IO.sfloat(s[55:65]),G2IO.sfloat(s[40:50])) #get lam1, lam2, zero, pola & ratio
952	if not v[1]:
953	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
954	v = (v[0],v[2],v[4])
955	codes = [0,0,0,0]
956	else:
957	names = ['Type','Lam1','Lam2','Zero','I(L2)/I(L1)','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
958	codes = [0,0,0,0,0,0]
959	data.extend(v)
960	v1 = Iparm['INS 1PRCF1 '].split()
961	v = Iparm['INS 1PRCF11'].split()
962	data.extend([float(v[0]),float(v[1]),float(v[2])]) #get GU, GV & GW - always here
963	azm = float(Iparm.get('INS 1DETAZM','0.0'))
964	v = Iparm['INS 1PRCF12'].split()
965	if v1[0] == 3:
966	data.extend([float(v[0]),float(v[1]),float(v[2])+float(v[3],azm)]) #get LX, LY, S+H/L & azimuth
967	else:
968	data.extend([0.0,0.0,0.002,azm]) #OK defaults if fxn #3 not 1st in iprm file
969	codes.extend([0,0,0,0,0,0,0])
970	return [G2IO.makeInstDict(names,data,codes),{}]
971	elif 'T' in DataType:
972	names = ['Type','2-theta','difC','difA','Zero','alpha','beta-0','beta-1',
973	'beta-q','sig-0','sig-1','sig-q','X','Y','Azimuth']
974	codes = [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
975	azm = 0.
976	if 'INS 1DETAZM' in Iparm:
977	azm = float(Iparm['INS 1DETAZM'])
978	s = Iparm['INS 1BNKPAR'].split()
979	data.extend([G2IO.sfloat(s[1]),]) #2-theta for bank
980	s = Iparm['INS 1 ICONS'].split()
981	data.extend([G2IO.sfloat(s[0]),G2IO.sfloat(s[1]),G2IO.sfloat(s[2])]) #difC, difA, Zero
982	s = Iparm['INS 1PRCF1 '].split()
983	pfType = int(s[0])
984	s = Iparm['INS 1PRCF11'].split()
985	if abs(pfType) == 1:
986	data.extend([G2IO.sfloat(s[1]),G2IO.sfloat(s[2]),G2IO.sfloat(s[3])])
987	s = Iparm['INS 1PRCF12'].split()
988	data.extend([0.0,0.0,G2IO.sfloat(s[1]),0.0,0.0,0.0,azm])
989	elif abs(pfType) in [3,4,5]:
990	data.extend([G2IO.sfloat(s[0]),G2IO.sfloat(s[1]),G2IO.sfloat(s[2])])
991	if abs(pfType) == 4:
992	data.extend([0.0,0.0,G2IO.sfloat(s[3]),0.0,0.0,0.0,azm])
993	else:
994	s = Iparm['INS 1PRCF12'].split()
995	data.extend([0.0,0.0,G2IO.sfloat(s[0]),0.0,0.0,0.0,azm])
996	Inst1 = G2IO.makeInstDict(names,data,codes)
997	Inst2 = {}
998	if pfType < 0:
999	Ipab = 'INS 1PAB'+str(-pfType)
1000	Npab = int(Iparm[Ipab+' '].strip())
1001	Inst2['Pdabc'] = []
1002	for i in range(Npab):
1003	k = Ipab+str(i+1).rjust(2)
1004	s = Iparm[k].split()
1005	Inst2['Pdabc'].append([float(t) for t in s])
1006	Inst2['Pdabc'] = np.array(Inst2['Pdabc'])
1007	Inst2['Pdabc'].T[3] += Inst2['Pdabc'].T[0]*Inst1['difC'][0] #turn 3rd col into TOF
1008	if 'INS 1I ITYP' in Iparm:
1009	s = Iparm['INS 1I ITYP'].split()
1010	Ityp = int(s[0])
1011	Tminmax = [float(s[1])1000.,float(s[2])1000.]
1012	Itypes = ['Exponential','Maxwell/Exponential','','Maxwell/Chebyschev','']
1013	if Ityp in [1,2,4]:
1014	Inst2['Itype'] = Itypes[Ityp-1]
1015	Inst2['Tminmax'] = Tminmax
1016	Icoeff = []
1017	Iesd = []
1018	Icovar = []
1019	for i in range(3):
1020	s = Iparm['INS 1ICOFF'+str(i+1)].split()
1021	Icoeff += [float(S) for S in s]
1022	s = Iparm['INS 1IECOF'+str(i+1)].split()
1023	Iesd += [float(S) for S in s]
1024	for i in range(8):
1025	s = Iparm['INS 1IECOR'+str(i+1)].split()
1026	Icovar += [float(S) for S in s]
1027	Inst2['Icoeff'] = Icoeff
1028	Inst2['Iesd'] = Iesd
1029	Inst2['Icovar'] = Icovar
1030	return [Inst1,Inst2]
1031
1032	# stuff we might need from the reader
1033	filename = rd.powderentry[0]
1034	bank = rd.powderentry[2]
1035	numbanks = rd.numbanks
1036	# is there an instrument parameter file defined for the current data set?
1037	# or if this is a read on a set of set of files, use the last one again
1038	#if rd.instparm or (lastdatafile == filename and lastIparmfile):
1039	if rd.instparm or lastIparmfile:
1040	if rd.instparm:
1041	instfile = os.path.join(os.path.split(filename)[0],
1042	rd.instparm)
1043	else:
1044	# for multiple reads of one data file, reuse the inst parm file
1045	instfile = lastIparmfile
1046	if os.path.exists(instfile):
1047	#print 'debug: try read',instfile
1048	instParmList = self.ReadPowderInstprm(instfile)
1049	if instParmList is not None:
1050	rd.instfile = instfile
1051	rd.instmsg = 'GSAS-II file '+instfile
1052	return instParmList
1053	Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd)
1054	if Iparm:
1055	#print 'debug: success'
1056	rd.instfile = instfile
1057	rd.instmsg = instfile + ' bank ' + str(rd.instbank)
1058	return SetPowderInstParms(Iparm,rd)
1059	else:
1060	self.ErrorDialog('Open Error','Error opening instrument parameter file '
1061	+str(instfile)+' requested by file '+ filename)
1062	# is there an instrument parameter file matching the current file
1063	# with extension .inst or .prm? If so read it
1064	basename = os.path.splitext(filename)[0]
1065	for ext in '.instprm','.prm','.inst','.ins':
1066	instfile = basename + ext
1067	instParmList = self.ReadPowderInstprm(instfile)
1068	if instParmList is not None:
1069	rd.instfile = instfile
1070	rd.instmsg = 'GSAS-II file '+instfile
1071	return instParmList
1072	Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd)
1073	if Iparm:
1074	#print 'debug: success'
1075	rd.instfile = instfile
1076	rd.instmsg = instfile + ' bank ' + str(rd.instbank)
1077	return SetPowderInstParms(Iparm,rd)
1078	else:
1079	#print 'debug: open/read failed',instfile
1080	pass # fail silently
1081
1082	# did we read the data file from a zip? If so, look there for a
1083	# instrument parameter file
1084	if self.zipfile:
1085	for ext in '.instprm','.prm','.inst','.ins':
1086	instfile = G2IO.ExtractFileFromZip(
1087	self.zipfile,
1088	selection=os.path.split(basename + ext)[1],
1089	parent=self)
1090	if instfile is not None and instfile != self.zipfile:
1091	print 'debug:',instfile,'created from ',self.zipfile
1092	instParmList = self.ReadPowderInstprm(instfile)
1093	if instParmList is not None:
1094	rd.instfile = instfile
1095	rd.instmsg = 'GSAS-II file '+instfile
1096	return instParmList
1097	Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd)
1098	if Iparm:
1099	rd.instfile = instfile
1100	rd.instmsg = instfile + ' bank ' + str(rd.instbank)
1101	return SetPowderInstParms(Iparm,rd)
1102	else:
1103	#print 'debug: open/read for',instfile,'from',self.zipfile,'failed'
1104	pass # fail silently
1105
1106	while True: # loop until we get a file that works or we get a cancel
1107	instfile = ''
1108	dlg = wx.FileDialog(
1109	self,
1110	'Choose inst. param file for "'
1111	+rd.idstring
1112	+'" (or Cancel for default)',
1113	'.', '',
1114	'GSAS iparm file (.prm,.inst,.ins)\|.prm;.inst;.ins\|'
1115	'GSAS-II iparm file (.instprm)\|.instprm\|'
1116	'All files (.)\|.',
1117	wx.OPEN\|wx.CHANGE_DIR)
1118	if os.path.exists(lastIparmfile):
1119	dlg.SetFilename(lastIparmfile)
1120	if dlg.ShowModal() == wx.ID_OK:
1121	instfile = dlg.GetPath()
1122	dlg.Destroy()
1123	if not instfile: break
1124	instParmList = self.ReadPowderInstprm(instfile)
1125	if instParmList is not None:
1126	rd.instfile = instfile
1127	rd.instmsg = 'GSAS-II file '+instfile
1128	return instParmList
1129	Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd)
1130	if Iparm:
1131	#print 'debug: success with',instfile
1132	rd.instfile = instfile
1133	rd.instmsg = instfile + ' bank ' + str(rd.instbank)
1134	return SetPowderInstParms(Iparm,rd)
1135	else:
1136	self.ErrorDialog('Read Error',
1137	'Error opening/reading file '+str(instfile))
1138
1139	# still no success: offer user choice of defaults
1140	while True: # loop until we get a choice
1141	choices = []
1142	head = 'Select from default instrument parameters for '+rd.idstring
1143
1144	for l in rd.defaultIparm_lbl:
1145	choices.append('Defaults for '+l)
1146	res = rd.BlockSelector(
1147	choices,
1148	ParentFrame=self,
1149	title=head,
1150	header='Select default inst parms',
1151	useCancel=False)
1152	if res is None: continue
1153	rd.instfile = ''
1154	rd.instmsg = 'default: '+rd.defaultIparm_lbl[res]
1155	return SetPowderInstParms(rd.defaultIparms[res],rd)
1156
1157	def OnImportPowder(self,event):
1158	'''Called in response to an Import/Powder Data/... menu item
1159	to read a powder diffraction data set.
1160	dict self.ImportMenuId is used to look up the specific
1161	reader item associated with the menu item, which will be
1162	None for the last menu item, which is the "guess" option
1163	where all appropriate formats will be tried.
1164
1165	Also reads an instrument parameter file for each dataset.
1166	'''
1167	# get a list of existing histograms
1168	PWDRlist = []
1169	if self.PatternTree.GetCount():
1170	item, cookie = self.PatternTree.GetFirstChild(self.root)
1171	while item:
1172	name = self.PatternTree.GetItemText(item)
1173	if name.startswith('PWDR ') and name not in PWDRlist:
1174	PWDRlist.append(name)
1175	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
1176	# look up which format was requested
1177	reqrdr = self.ImportMenuId.get(event.GetId())
1178	rdlist = self.OnImportGeneric(
1179	reqrdr,self.ImportPowderReaderlist,'Powder Data',multiple=True)
1180	if len(rdlist) == 0: return
1181	self.CheckNotebook()
1182	Iparm = None
1183	lastIparmfile = ''
1184	lastdatafile = ''
1185	newHistList = []
1186	self.EnablePlot = False
1187	for rd in rdlist:
1188	# get instrument parameters for each dataset
1189	Iparm1,Iparm2 = self.GetPowderIparm(rd, Iparm, lastIparmfile, lastdatafile)
1190	if rd.repeat_instparm:
1191	lastIparmfile = rd.instfile
1192	lastdatafile = rd.powderentry[0]
1193	HistName = rd.idstring
1194	HistName = 'PWDR '+HistName
1195	# make new histogram names unique
1196	HistName = G2obj.MakeUniqueLabel(HistName,PWDRlist)
1197	print 'Read powder data '+str(HistName)+ \
1198	' from file '+str(rd.readfilename) + \
1199	' with parameters from '+str(rd.instmsg)
1200	# data are read, now store them in the tree
1201	Id = self.PatternTree.AppendItem(parent=self.root,text=HistName)
1202	if 'T' in Iparm1['Type'][0]:
1203	if not rd.clockWd and rd.GSAS:
1204	rd.powderdata[0] *= 100. #put back the CW centideg correction
1205	cw = np.diff(rd.powderdata[0])
1206	rd.powderdata[0] = rd.powderdata[0][:-1]+cw/2.
1207	rd.powderdata[1] = rd.powderdata[1][:-1]/cw
1208	rd.powderdata[2] = rd.powderdata[2][:-1]cw*2 #1/var=w at this point
1209	if 'Itype' in Iparm2:
1210	Ibeg = np.searchsorted(rd.powderdata[0],Iparm2['Tminmax'][0])
1211	Ifin = np.searchsorted(rd.powderdata[0],Iparm2['Tminmax'][1])
1212	rd.powderdata[0] = rd.powderdata[0][Ibeg:Ifin]
1213	YI,WYI = G2pwd.calcIncident(Iparm2,rd.powderdata[0])
1214	rd.powderdata[1] = rd.powderdata[1][Ibeg:Ifin]/YI
1215	var = 1./rd.powderdata[2][Ibeg:Ifin]
1216	var += WYIrd.powderdata[1]*2
1217	var /= YI**2
1218	rd.powderdata[2] = 1./var
1219	rd.powderdata[3] = np.zeros_like(rd.powderdata[0])
1220	rd.powderdata[4] = np.zeros_like(rd.powderdata[0])
1221	rd.powderdata[5] = np.zeros_like(rd.powderdata[0])
1222	Tmin = min(rd.powderdata[0])
1223	Tmax = max(rd.powderdata[0])
1224	valuesdict = {
1225	'wtFactor':1.0,
1226	'Dummy':False,
1227	'ranId':ran.randint(0,sys.maxint),
1228	}
1229	rd.Sample['ranId'] = valuesdict['ranId'] # this should be removed someday
1230	self.PatternTree.SetItemPyData(Id,[valuesdict,rd.powderdata])
1231	self.PatternTree.SetItemPyData(
1232	self.PatternTree.AppendItem(Id,text='Comments'),
1233	rd.comments)
1234	self.PatternTree.SetItemPyData(
1235	self.PatternTree.AppendItem(Id,text='Limits'),
1236	[(Tmin,Tmax),[Tmin,Tmax]])
1237	self.PatternId = G2gd.GetPatternTreeItemId(self,Id,'Limits')
1238	self.PatternTree.SetItemPyData(
1239	self.PatternTree.AppendItem(Id,text='Background'),
1240	[['chebyschev',True,3,1.0,0.0,0.0],
1241	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
1242	self.PatternTree.SetItemPyData(
1243	self.PatternTree.AppendItem(Id,text='Instrument Parameters'),
1244	[Iparm1,Iparm2])
1245	self.PatternTree.SetItemPyData(
1246	self.PatternTree.AppendItem(Id,text='Sample Parameters'),
1247	rd.Sample)
1248	self.PatternTree.SetItemPyData(
1249	self.PatternTree.AppendItem(Id,text='Peak List')
1250	,[])
1251	self.PatternTree.SetItemPyData(
1252	self.PatternTree.AppendItem(Id,text='Index Peak List'),
1253	[])
1254	self.PatternTree.SetItemPyData(
1255	self.PatternTree.AppendItem(Id,text='Unit Cells List'),
1256	[])
1257	self.PatternTree.SetItemPyData(
1258	self.PatternTree.AppendItem(Id,text='Reflection Lists'),
1259	{})
1260	newHistList.append(HistName)
1261	else:
1262	self.EnablePlot = True
1263	self.PatternTree.Expand(Id)
1264	self.PatternTree.SelectItem(Id)
1265
1266	if not newHistList: return # somehow, no new histograms
1267	# make a list of phase names
1268	phaseRIdList,usedHistograms = self.GetPhaseInfofromTree()
1269	phaseNameList = usedHistograms.keys() # phase names in use
1270	if not phaseNameList: return # no phases yet, nothing to do
1271	header = 'Select phase(s) to add the new\npowder dataset(s) to:'
1272	for Name in newHistList:
1273	header += '\n '+str(Name)
1274
1275	result = G2gd.ItemSelector(phaseNameList,self,header,header='Add to phase(s)',multiple=True)
1276	if not result: return
1277	# connect new phases to histograms
1278	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
1279	if not sub:
1280	raise Exception('ERROR -- why are there no phases here?')
1281	item, cookie = self.PatternTree.GetFirstChild(sub)
1282	iph = -1
1283	while item: # loop over (new) phases
1284	iph += 1
1285	phaseName = self.PatternTree.GetItemText(item)
1286	data = self.PatternTree.GetItemPyData(item)
1287	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
1288	if iph not in result: continue
1289	generalData = data['General']
1290	SGData = generalData['SGData']
1291	UseList = data['Histograms']
1292	NShkl = len(G2spc.MustrainNames(SGData))
1293	NDij = len(G2spc.HStrainNames(SGData))
1294	for histoName in newHistList:
1295	UseList[histoName] = {
1296	'Histogram':histoName,'Show':False,
1297	'Scale':[1.0,False],'Pref.Ori.':['MD',1.0,False,[0,0,1],0,{}],
1298	'Size':['isotropic',[1.,1.,1.],[False,False,False],[0,0,1],
1299	[1.,1.,1.,0.,0.,0.],6*[False,]],
1300	'Mustrain':['isotropic',[1000.0,1000.0,1.0],[False,False,False],[0,0,1],
1301	NShkl[0.01,],NShkl[False,]],
1302	'HStrain':[NDij[0.0,],NDij[False,]],
1303	'Extinction':[0.0,False],'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}}
1304	Id = G2gd.GetPatternTreeItemId(self,self.root,histoName)
1305	refList = self.PatternTree.GetItemPyData(
1306	G2gd.GetPatternTreeItemId(self,Id,'Reflection Lists'))
1307	refList[generalData['Name']] = []
1308	return # success
1309
1310	def OnDummyPowder(self,event):
1311	'''Called in response to Import/Powder Data/Simulate menu item
1312	to create a Dummy powder diffraction data set.
1313
1314	Reads an instrument parameter file and then gets input from the user
1315	'''
1316	# get a list of existing histograms
1317	PWDRlist = []
1318	if self.PatternTree.GetCount():
1319	item, cookie = self.PatternTree.GetFirstChild(self.root)
1320	while item:
1321	name = self.PatternTree.GetItemText(item)
1322	if name.startswith('PWDR ') and name not in PWDRlist:
1323	PWDRlist.append(name)
1324	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
1325	# Initialize a base class reader
1326	rd = G2IO.ImportPowderData(
1327	extensionlist=tuple(),
1328	strictExtension=False,
1329	formatName = 'Simulate dataset',
1330	longFormatName = 'Compute a simulated pattern')
1331	rd.powderentry[0] = '' # no filename
1332	# #self.powderentry[1] = pos # bank offset (N/A here)
1333	rd.powderentry[2] = 1 # only one bank
1334	rd.comments.append('This is a dummy dataset for powder pattern simulation')
1335	self.CheckNotebook()
1336	Iparm = None
1337	lastIparmfile = ''
1338	lastdatafile = ''
1339	self.zipfile = None
1340	# get instrument parameters for it
1341	Iparm1,Iparm2 = self.GetPowderIparm(rd, Iparm, lastIparmfile, lastdatafile)
1342	if 'T' in Iparm1['Type'][0]:
1343	print('TOF simulation not supported yet')
1344	return False
1345	else:
1346	# need to get name, 2theta start, end, step
1347	rd.idstring = ' CW'
1348	if 'X' in Iparm1['Type'][0]:
1349	rd.idstring = 'CW x-ray simulation'
1350	else:
1351	rd.idstring = 'CW neutron simulation'
1352	# base initial range on wavelength
1353	wave = Iparm1.get('Lam')
1354	if wave:
1355	wave = wave[0]
1356	else:
1357	wave = Iparm1.get('Lam1')
1358	if wave:
1359	wave = wave[0]
1360	N = 0
1361	while (N < 3): # insist on a dataset with a few points
1362	names = ('dataset name', 'start angle', 'end angle', 'step size')
1363	if not wave or wave < 1.0:
1364	inp = [rd.idstring, 10.,40.,0.005] # see names for what's what
1365	else:
1366	inp = [rd.idstring, 10.,80.,0.01] # see names for what's what
1367	dlg = G2gd.ScrolledMultiEditor(
1368	self,[inp] * len(inp),range(len(inp)),names,
1369	header='Enter simulation name and range',
1370	minvals=(None,0.001,0.001,0.0001),
1371	maxvals=(None,180.,180.,.1),
1372	sizevals=((225,-1),)
1373	)
1374	dlg.CenterOnParent()
1375	if dlg.ShowModal() == wx.ID_OK:
1376	if inp[1] > inp[2]:
1377	end,start,step = inp[1:]
1378	else:
1379	start,end,step = inp[1:]
1380	step = abs(step)
1381	else:
1382	return False
1383	N = int((end-start)/step)+1
1384	x = np.linspace(start,end,N,True)
1385	N = len(x)
1386	rd.powderdata = [
1387	np.array(x), # x-axis values
1388	np.zeros_like(x), # powder pattern intensities
1389	np.ones_like(x), # 1/sig(intensity)^2 values (weights)
1390	np.zeros_like(x), # calc. intensities (zero)
1391	np.zeros_like(x), # calc. background (zero)
1392	np.zeros_like(x), # obs-calc profiles
1393	]
1394	Tmin = rd.powderdata[0][0]
1395	Tmax = rd.powderdata[0][-1]
1396	# data are read, now store them in the tree
1397	HistName = inp[0]
1398	HistName = 'PWDR '+HistName
1399	HistName = G2obj.MakeUniqueLabel(HistName,PWDRlist) # make new histogram names unique
1400	Id = self.PatternTree.AppendItem(parent=self.root,text=HistName)
1401	valuesdict = {
1402	'wtFactor':1.0,
1403	'Dummy':True,
1404	'ranId':ran.randint(0,sys.maxint),
1405	}
1406	self.PatternTree.SetItemPyData(Id,[valuesdict,rd.powderdata])
1407	self.PatternTree.SetItemPyData(
1408	self.PatternTree.AppendItem(Id,text='Comments'),
1409	rd.comments)
1410	self.PatternTree.SetItemPyData(
1411	self.PatternTree.AppendItem(Id,text='Limits'),
1412	[(Tmin,Tmax),[Tmin,Tmax]])
1413	self.PatternId = G2gd.GetPatternTreeItemId(self,Id,'Limits')
1414	self.PatternTree.SetItemPyData(
1415	self.PatternTree.AppendItem(Id,text='Background'),
1416	[['chebyschev',True,3,1.0,0.0,0.0],
1417	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
1418	self.PatternTree.SetItemPyData(
1419	self.PatternTree.AppendItem(Id,text='Instrument Parameters'),
1420	[Iparm1,Iparm2])
1421	self.PatternTree.SetItemPyData(
1422	self.PatternTree.AppendItem(Id,text='Sample Parameters'),
1423	rd.Sample)
1424	self.PatternTree.SetItemPyData(
1425	self.PatternTree.AppendItem(Id,text='Peak List')
1426	,[])
1427	self.PatternTree.SetItemPyData(
1428	self.PatternTree.AppendItem(Id,text='Index Peak List'),
1429	[])
1430	self.PatternTree.SetItemPyData(
1431	self.PatternTree.AppendItem(Id,text='Unit Cells List'),
1432	[])
1433	self.PatternTree.SetItemPyData(
1434	self.PatternTree.AppendItem(Id,text='Reflection Lists'),
1435	{})
1436	self.PatternTree.Expand(Id)
1437	self.PatternTree.SelectItem(Id)
1438	print('Added simulation powder data '+str(HistName)+
1439	' with parameters from '+str(rd.instmsg))
1440
1441	# make a list of phase names
1442	phaseRIdList,usedHistograms = self.GetPhaseInfofromTree()
1443	phaseNameList = usedHistograms.keys() # phase names in use
1444	if not phaseNameList: return # no phases yet, nothing to do
1445	header = 'Select phase(s) to add the new\npowder simulation (dummy) dataset to:'
1446	result = G2gd.ItemSelector(phaseNameList,self,header,header='Add to phase(s)',multiple=True)
1447	if not result: return
1448	# connect new phases to histograms
1449	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
1450	if not sub:
1451	raise Exception('ERROR -- why are there no phases here?')
1452	item, cookie = self.PatternTree.GetFirstChild(sub)
1453	iph = -1
1454	while item: # loop over (new) phases
1455	iph += 1
1456	phaseName = self.PatternTree.GetItemText(item)
1457	data = self.PatternTree.GetItemPyData(item)
1458	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
1459	if iph not in result: continue
1460	generalData = data['General']
1461	SGData = generalData['SGData']
1462	UseList = data['Histograms']
1463	NShkl = len(G2spc.MustrainNames(SGData))
1464	NDij = len(G2spc.HStrainNames(SGData))
1465	UseList[HistName] = {
1466	'Histogram':HistName,'Show':False,
1467	'Scale':[1.0,False],'Pref.Ori.':['MD',1.0,False,[0,0,1],0,{}],
1468	'Size':['isotropic',[1.,1.,1.],[False,False,False],[0,0,1],
1469	[1.,1.,1.,0.,0.,0.],6*[False,]],
1470	'Mustrain':['isotropic',[1000.0,1000.0,1.0],[False,False,False],[0,0,1],
1471	NShkl[0.01,],NShkl[False,]],
1472	'HStrain':[NDij[0.0,],NDij[False,]],
1473	'Extinction':[0.0,False],'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}}
1474	Id = G2gd.GetPatternTreeItemId(self,self.root,HistName)
1475	refList = self.PatternTree.GetItemPyData(
1476	G2gd.GetPatternTreeItemId(self,Id,'Reflection Lists'))
1477	refList[generalData['Name']] = []
1478	return # success
1479
1480	def _Add_ImportMenu_smallangle(self,parent):
1481	'''configure the Small Angle Data menus accord to the readers found in _init_Imports
1482	'''
1483	submenu = wx.Menu()
1484	item = parent.AppendMenu(wx.ID_ANY, 'Small Angle Data',
1485	submenu, help='Import small angle data')
1486	for reader in self.ImportSmallAngleReaderlist:
1487	item = submenu.Append(wx.ID_ANY,help=reader.longFormatName,
1488	kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file')
1489	self.ImportMenuId[item.GetId()] = reader
1490	self.Bind(wx.EVT_MENU, self.OnImportSmallAngle, id=item.GetId())
1491	# item = submenu.Append(wx.ID_ANY,
1492	# help='Import small angle data, use file to try to determine format',
1493	# kind=wx.ITEM_NORMAL,text='guess format from file')
1494	# self.Bind(wx.EVT_MENU, self.OnImportSmallAngle, id=item.GetId())
1495
1496	def OnImportSmallAngle(self,event):
1497	'''Called in response to an Import/Small Angle Data/... menu item
1498	to read a small angle diffraction data set.
1499	dict self.ImportMenuId is used to look up the specific
1500	reader item associated with the menu item, which will be
1501	None for the last menu item, which is the "guess" option
1502	where all appropriate formats will be tried.
1503
1504	'''
1505
1506	def GetSASDIparm(reader):
1507	parm = reader.instdict
1508	Iparm = {'Type':[parm['type'],parm['type'],0],'Lam':[parm['wave'],
1509	parm['wave'],0],'Azimuth':[0.,0.,0]}
1510	return Iparm,{}
1511
1512	# get a list of existing histograms
1513	SASDlist = []
1514	if self.PatternTree.GetCount():
1515	item, cookie = self.PatternTree.GetFirstChild(self.root)
1516	while item:
1517	name = self.PatternTree.GetItemText(item)
1518	if name.startswith('SASD ') and name not in SASDlist:
1519	SASDlist.append(name)
1520	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
1521	# look up which format was requested
1522	reqrdr = self.ImportMenuId.get(event.GetId())
1523	rdlist = self.OnImportGeneric(
1524	reqrdr,self.ImportSmallAngleReaderlist,'Small Angle Data',multiple=True)
1525	if len(rdlist) == 0: return
1526	self.CheckNotebook()
1527	Iparm = None
1528	lastdatafile = ''
1529	newHistList = []
1530	self.EnablePlot = False
1531	for rd in rdlist:
1532	lastdatafile = rd.smallangleentry[0]
1533	HistName = rd.idstring
1534	HistName = 'SASD '+HistName
1535	# make new histogram names unique
1536	HistName = G2obj.MakeUniqueLabel(HistName,SASDlist)
1537	print 'Read small angle data '+str(HistName)+ \
1538	' from file '+str(self.lastimport)
1539	# data are read, now store them in the tree
1540	Id = self.PatternTree.AppendItem(parent=self.root,text=HistName)
1541	Iparm1,Iparm2 = GetSASDIparm(rd)
1542	# if 'T' in Iparm1['Type'][0]:
1543	# if not rd.clockWd and rd.GSAS:
1544	# rd.powderdata[0] *= 100. #put back the CW centideg correction
1545	# cw = np.diff(rd.powderdata[0])
1546	# rd.powderdata[0] = rd.powderdata[0][:-1]+cw/2.
1547	# rd.powderdata[1] = rd.powderdata[1][:-1]/cw
1548	# rd.powderdata[2] = rd.powderdata[2][:-1]cw*2 #1/var=w at this point
1549	# if 'Itype' in Iparm2:
1550	# Ibeg = np.searchsorted(rd.powderdata[0],Iparm2['Tminmax'][0])
1551	# Ifin = np.searchsorted(rd.powderdata[0],Iparm2['Tminmax'][1])
1552	# rd.powderdata[0] = rd.powderdata[0][Ibeg:Ifin]
1553	# YI,WYI = G2pwd.calcIncident(Iparm2,rd.powderdata[0])
1554	# rd.powderdata[1] = rd.powderdata[1][Ibeg:Ifin]/YI
1555	# var = 1./rd.powderdata[2][Ibeg:Ifin]
1556	# var += WYIrd.powderdata[1]*2
1557	# var /= YI**2
1558	# rd.powderdata[2] = 1./var
1559	# rd.powderdata[3] = np.zeros_like(rd.powderdata[0])
1560	# rd.powderdata[4] = np.zeros_like(rd.powderdata[0])
1561	# rd.powderdata[5] = np.zeros_like(rd.powderdata[0])
1562	Tmin = min(rd.smallangledata[0])
1563	Tmax = max(rd.smallangledata[0])
1564	valuesdict = {
1565	'wtFactor':1.0,
1566	'Dummy':False,
1567	'ranId':ran.randint(0,sys.maxint),
1568	}
1569	rd.Sample['ranId'] = valuesdict['ranId'] # this should be removed someday
1570	self.PatternTree.SetItemPyData(Id,[valuesdict,rd.smallangledata])
1571	self.PatternTree.SetItemPyData(
1572	self.PatternTree.AppendItem(Id,text='Comments'),
1573	rd.comments)
1574	self.PatternTree.SetItemPyData(
1575	self.PatternTree.AppendItem(Id,text='Limits'),
1576	[(Tmin,Tmax),[Tmin,Tmax]])
1577	self.PatternId = G2gd.GetPatternTreeItemId(self,Id,'Limits')
1578	self.PatternTree.SetItemPyData(
1579	self.PatternTree.AppendItem(Id,text='Instrument Parameters'),
1580	[Iparm1,Iparm2])
1581	self.PatternTree.SetItemPyData(
1582	self.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
1583	self.PatternTree.SetItemPyData(
1584	self.PatternTree.AppendItem(Id,text='Sample Parameters'),
1585	rd.Sample)
1586	self.PatternTree.SetItemPyData(
1587	self.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
1588	newHistList.append(HistName)
1589	else:
1590	self.EnablePlot = True
1591	self.PatternTree.Expand(Id)
1592	self.PatternTree.SelectItem(Id)
1593
1594	if not newHistList: return # somehow, no new histograms
1595	return # success
1596
1597	def _init_Exports(self,menu):
1598	'''Find exporter routines and add them into menus
1599	'''
1600	# set up the top-level menus
1601	projectmenu = wx.Menu()
1602	item = menu.AppendMenu(
1603	wx.ID_ANY, 'Entire project as',
1604	projectmenu, help='Export entire project')
1605
1606	phasemenu = wx.Menu()
1607	item = menu.AppendMenu(
1608	wx.ID_ANY, 'Phase as',
1609	phasemenu, help='Export phase or sometimes phases')
1610
1611	powdermenu = wx.Menu()
1612	item = menu.AppendMenu(
1613	wx.ID_ANY, 'Powder data as',
1614	powdermenu, help='Export powder diffraction histogram(s)')
1615
1616	singlemenu = wx.Menu()
1617	item = menu.AppendMenu(
1618	wx.ID_ANY, 'Single crystal data as',
1619	singlemenu, help='Export single crystal histogram(s)')
1620
1621	imagemenu = wx.Menu()
1622	item = menu.AppendMenu(
1623	wx.ID_ANY, 'Image data as',
1624	imagemenu, help='Export powder image(s) data')
1625
1626	mapmenu = wx.Menu()
1627	item = menu.AppendMenu(
1628	wx.ID_ANY, 'Maps as',
1629	mapmenu, help='Export density map(s)')
1630
1631	# pdfmenu = wx.Menu()
1632	# item = menu.AppendMenu(
1633	# wx.ID_ANY, 'PDFs as',
1634	# pdfmenu, help='Export pair distribution function(s)')
1635
1636	# find all the exporter files
1637	pathlist = sys.path
1638	filelist = []
1639	for path in pathlist:
1640	for filename in glob.iglob(os.path.join(
1641	path,
1642	"G2export*.py")):
1643	filelist.append(filename)
1644	filelist = sorted(list(set(filelist))) # remove duplicates
1645	exporterlist = []
1646	# go through the routines and import them, saving objects that
1647	# have export routines (method Exporter)
1648	for filename in filelist:
1649	path,rootname = os.path.split(filename)
1650	pkg = os.path.splitext(rootname)[0]
1651	try:
1652	fp = None
1653	fp, fppath,desc = imp.find_module(pkg,[path,])
1654	pkg = imp.load_module(pkg,fp,fppath,desc)
1655	for clss in inspect.getmembers(pkg): # find classes defined in package
1656	if clss[0].startswith('_'): continue
1657	if inspect.isclass(clss[1]):
1658	# check if we have the required methods
1659	for m in 'Exporter','loadParmDict':
1660	if not hasattr(clss[1],m): break
1661	if not callable(getattr(clss[1],m)): break
1662	else:
1663	exporter = clss[1](self) # create an export instance
1664	exporterlist.append(exporter)
1665	except AttributeError:
1666	print 'Import_'+errprefix+': Attribute Error'+str(filename)
1667	pass
1668	except ImportError:
1669	print 'Import_'+errprefix+': Error importing file'+str(filename)
1670	pass
1671	if fp: fp.close()
1672	# Add submenu item(s) for each Exporter by its self-declared type (can be more than one)
1673	for obj in exporterlist:
1674	#print 'exporter',obj
1675	for typ in obj.exporttype:
1676	if typ == "project":
1677	submenu = projectmenu
1678	elif typ == "phase":
1679	submenu = phasemenu
1680	elif typ == "powder":
1681	submenu = powdermenu
1682	elif typ == "single":
1683	submenu = singlemenu
1684	elif typ == "image":
1685	submenu = imagemenu
1686	elif typ == "map":
1687	submenu = mapmenu
1688	# elif typ == "pdf":
1689	# submenu = pdfmenu
1690	else:
1691	print("Error, unknown type in "+str(obj))
1692	break
1693	item = submenu.Append(
1694	wx.ID_ANY,
1695	help=obj.longFormatName,
1696	kind=wx.ITEM_NORMAL,
1697	text=obj.formatName)
1698	self.Bind(wx.EVT_MENU, obj.Exporter, id=item.GetId())
1699	self.ExportLookup[item.GetId()] = typ # lookup table for submenu item
1700
1701	#code to debug an Exporter. hard-coded the routine below, to allow a reload before use
1702	# def DebugExport(event):
1703	# print 'start reload'
1704	# reload(G2IO)
1705	# import G2export_pwdr as dev
1706	# reload(dev)
1707	# dev.ExportPowderFXYE(self).Exporter(event)
1708	# item = menu.Append(
1709	# wx.ID_ANY,kind=wx.ITEM_NORMAL,
1710	# help="debug exporter",text="test Export FXYE")
1711	# self.Bind(wx.EVT_MENU, DebugExport, id=item.GetId())
1712	# # #self.ExportLookup[item.GetId()] = 'image'
1713	# self.ExportLookup[item.GetId()] = 'powder'
1714
1715	def _Add_ExportMenuItems(self,parent):
1716	# item = parent.Append(
1717	# help='Select PWDR item to enable',id=wx.ID_ANY,
1718	# kind=wx.ITEM_NORMAL,
1719	# text='Export Powder Patterns...')
1720	# self.ExportPattern.append(item)
1721	# item.Enable(False)
1722	# self.Bind(wx.EVT_MENU, self.OnExportPatterns, id=item.GetId())
1723
1724	item = parent.Append(
1725	help='',id=wx.ID_ANY,
1726	kind=wx.ITEM_NORMAL,
1727	text='Export All Peak Lists...')
1728	self.ExportPeakList.append(item)
1729	item.Enable(True)
1730	self.Bind(wx.EVT_MENU, self.OnExportPeakList, id=item.GetId())
1731
1732	item = parent.Append(
1733	help='',id=wx.ID_ANY,
1734	kind=wx.ITEM_NORMAL,
1735	text='Export HKLs...')
1736	self.ExportHKL.append(item)
1737	self.Bind(wx.EVT_MENU, self.OnExportHKL, id=item.GetId())
1738
1739	item = parent.Append(
1740	help='Select PDF item to enable',
1741	id=wx.ID_ANY,
1742	kind=wx.ITEM_NORMAL,
1743	text='Export PDF...')
1744	self.ExportPDF.append(item)
1745	item.Enable(False)
1746	self.Bind(wx.EVT_MENU, self.OnExportPDF, id=item.GetId())
1747
1748	def FillMainMenu(self,menubar):
1749	'''Define contents of the main GSAS-II menu for the (main) data tree window
1750	in the mac, used also for the data item windows as well.
1751	'''
1752	File = wx.Menu(title='')
1753	menubar.Append(menu=File, title='&File')
1754	self._Add_FileMenuItems(File)
1755	Data = wx.Menu(title='')
1756	menubar.Append(menu=Data, title='Data')
1757	self._Add_DataMenuItems(Data)
1758	Calculate = wx.Menu(title='')
1759	menubar.Append(menu=Calculate, title='&Calculate')
1760	self._Add_CalculateMenuItems(Calculate)
1761	Import = wx.Menu(title='')
1762	menubar.Append(menu=Import, title='Import')
1763	self._Add_ImportMenu_Phase(Import)
1764	self._Add_ImportMenu_powder(Import)
1765	self._Add_ImportMenu_Sfact(Import)
1766	self._Add_ImportMenu_smallangle(Import)
1767	#======================================================================
1768	# Code to help develop/debug an importer, much is hard-coded below
1769	# but module is reloaded before each use, allowing faster testing
1770	# def DebugImport(event):
1771	# print 'start reload'
1772	# import G2phase_ISO as dev
1773	# reload(dev)
1774	# rd = dev.ISODISTORTPhaseReader()
1775	# self.ImportMenuId[event.GetId()] = rd
1776	# self.OnImportPhase(event)
1777	# or ----------------------------------------------------------------------
1778	#self.OnImportGeneric(rd,[],'test of ISODISTORTPhaseReader')
1779	# special debug code
1780	# or ----------------------------------------------------------------------
1781	# filename = '/Users/toby/projects/branton/subgroup_cif.txt'
1782	# fp = open(filename,'Ur')
1783	# if not rd.ContentsValidator(fp):
1784	# print 'not validated'
1785	# # make a list of used phase ranId's
1786	# phaseRIdList = []
1787	# sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
1788	# if sub:
1789	# item, cookie = self.PatternTree.GetFirstChild(sub)
1790	# while item:
1791	# phaseName = self.PatternTree.GetItemText(item)
1792	# ranId = self.PatternTree.GetItemPyData(item).get('ranId')
1793	# if ranId: phaseRIdList.append(ranId)
1794	# item, cookie = self.PatternTree.GetNextChild(sub, cookie)
1795	# if rd.Reader(filename,fp,usedRanIdList=phaseRIdList):
1796	# print 'read OK'
1797	# item = Import.Append(
1798	# wx.ID_ANY,kind=wx.ITEM_NORMAL,
1799	# help="debug importer",text="test importer")
1800	# self.Bind(wx.EVT_MENU, DebugImport, id=item.GetId())
1801	#======================================================================
1802	self.ExportMenu = wx.Menu(title='')
1803	menubar.Append(menu=self.ExportMenu, title='Export')
1804	self._init_Exports(self.ExportMenu)
1805	self._Add_ExportMenuItems(self.ExportMenu)
1806	HelpMenu=G2gd.MyHelp(self,helpType='Data tree',
1807	morehelpitems=[('&Tutorials','Tutorials')])
1808	menubar.Append(menu=HelpMenu,title='&Help')
1809
1810	def _init_ctrls(self, parent):
1811	wx.Frame.__init__(self, name='GSASII', parent=parent,
1812	size=wx.Size(400, 250),style=wx.DEFAULT_FRAME_STYLE, title='GSAS-II data tree')
1813	clientSize = wx.ClientDisplayRect()
1814	Size = self.GetSize()
1815	xPos = clientSize[2]-Size[0]
1816	self.SetPosition(wx.Point(xPos,clientSize[1]))
1817	self._init_Imports()
1818	#initialize Menu item objects (these contain lists of menu items that are enabled or disabled)
1819	self.MakePDF = []
1820	self.Refine = []
1821	self.SeqRefine = [] # pointer(s) to Sequential Refinement menu objects
1822	#self.ExportPattern = []
1823	self.ExportPeakList = []
1824	self.ExportHKL = []
1825	self.ExportPDF = []
1826	self.ExportPhase = []
1827	self.ExportCIF = []
1828	#
1829	self.GSASIIMenu = wx.MenuBar()
1830	self.FillMainMenu(self.GSASIIMenu)
1831	self.SetMenuBar(self.GSASIIMenu)
1832	self.Bind(wx.EVT_SIZE, self.OnSize)
1833	self.CreateStatusBar()
1834	self.mainPanel = wx.Panel(self,-1)
1835
1836	wxID_PATTERNTREE = wx.NewId()
1837	self.PatternTree = wx.TreeCtrl(id=wxID_PATTERNTREE,
1838	parent=self.mainPanel, pos=wx.Point(0, 0),style=wx.TR_DEFAULT_STYLE )
1839	self.PatternTree.Bind(wx.EVT_TREE_SEL_CHANGED,
1840	self.OnPatternTreeSelChanged, id=wxID_PATTERNTREE)
1841	self.PatternTree.Bind(wx.EVT_TREE_ITEM_COLLAPSED,
1842	self.OnPatternTreeItemCollapsed, id=wxID_PATTERNTREE)
1843	self.PatternTree.Bind(wx.EVT_TREE_ITEM_EXPANDED,
1844	self.OnPatternTreeItemExpanded, id=wxID_PATTERNTREE)
1845	self.PatternTree.Bind(wx.EVT_TREE_DELETE_ITEM,
1846	self.OnPatternTreeItemDelete, id=wxID_PATTERNTREE)
1847	self.PatternTree.Bind(wx.EVT_TREE_KEY_DOWN,
1848	self.OnPatternTreeKeyDown, id=wxID_PATTERNTREE)
1849	self.root = self.PatternTree.AddRoot('Loaded Data: ')
1850
1851	plotFrame = wx.Frame(None,-1,'GSASII Plots',size=wx.Size(700,600), \
1852	style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX)
1853	self.G2plotNB = G2plt.G2PlotNoteBook(plotFrame)
1854	plotFrame.Show()
1855
1856	self.dataDisplay = None
1857
1858	def __init__(self, parent):
1859	self.ExportLookup = {}
1860	self._init_ctrls(parent)
1861	self.Image = wx.Image(
1862	os.path.join(GSASIIpath.path2GSAS2,'gsas2.ico'),
1863	wx.BITMAP_TYPE_ICO)
1864	if "wxMSW" in wx.PlatformInfo:
1865	img = self.Image.Scale(16, 16).ConvertToBitmap()
1866	elif "wxGTK" in wx.PlatformInfo:
1867	img = self.Image.Scale(22, 22).ConvertToBitmap()
1868	else:
1869	img = self.Image.ConvertToBitmap()
1870	self.SetIcon(wx.IconFromBitmap(img))
1871	self.Bind(wx.EVT_CLOSE, self.ExitMain)
1872	# various defaults
1873	self.oldFocus = None
1874	self.GSASprojectfile = ''
1875	self.dirname = os.path.expanduser('~') #start in the users home directory by default; may be meaningless
1876	self.exportDir = None # the last directory used for exports, if any.
1877	self.undofile = ''
1878	self.TreeItemDelete = False
1879	self.Offset = [0.0,0.0]
1880	self.delOffset = .02
1881	self.refOffset = -100.0
1882	self.refDelt = .01
1883	self.Weight = False
1884	self.IparmName = '' # to be removed when SelectPowderData & GetInstrumentFile is
1885	self.IfPlot = False
1886	self.PatternId = 0
1887	self.PickId = 0
1888	self.PeakTable = []
1889	self.LimitsTable = []
1890	self.HKL = []
1891	self.Lines = []
1892	self.itemPicked = None
1893	self.dataFrame = None
1894	self.Interpolate = 'nearest'
1895	self.ContourColor = 'Paired'
1896	self.VcovColor = 'RdYlGn'
1897	self.RamaColor = 'Blues'
1898	self.Projection = 'equal area'
1899	self.logPlot = False
1900	self.qPlot = False
1901	self.sqPlot = False
1902	self.ErrorBars = False
1903	self.Contour = False
1904	self.Legend = False
1905	self.SinglePlot = False
1906	self.SubBack = False
1907	self.plotView = 0
1908	self.Image = 0
1909	self.oldImagefile = ''
1910	self.ImageZ = []
1911	self.Integrate = 0
1912	self.imageDefault = {}
1913	self.Sngl = False
1914	self.ifGetRing = False
1915	self.MaskKey = '' #trigger for making image masks
1916	self.StrainKey = '' #ditto for new strain d-zeros
1917	self.EnablePlot = True
1918	self.Tutorials = False #used for changing default directory
1919	arg = sys.argv
1920	if len(arg) > 1:
1921	self.GSASprojectfile = os.path.splitext(arg[1])[0]+'.gpx'
1922	self.dirname = os.path.dirname(arg[1])
1923	if self.dirname: os.chdir(self.dirname)
1924	try:
1925	G2IO.ProjFileOpen(self)
1926	self.PatternTree.Expand(self.root)
1927	for item in self.Refine: item.Enable(True)
1928	self.EnableSeqRefineMenu()
1929
1930	except:
1931	print 'Error opening file',arg[1]
1932
1933	def OnSize(self,event):
1934	'Called when the main window is resized. Not sure why'
1935	w,h = self.GetClientSizeTuple()
1936	self.mainPanel.SetSize(wx.Size(w,h))
1937	self.PatternTree.SetSize(wx.Size(w,h))
1938
1939	def OnPatternTreeSelChanged(self, event):
1940	'''Called when a data tree item is selected'''
1941	if self.TreeItemDelete:
1942	self.TreeItemDelete = False
1943	else:
1944	pltNum = self.G2plotNB.nb.GetSelection()
1945	if pltNum >= 0: #to avoid the startup with no plot!
1946	pltPage = self.G2plotNB.nb.GetPage(pltNum)
1947	pltPlot = pltPage.figure
1948	item = event.GetItem()
1949	G2gd.MovePatternTreeToGrid(self,item)
1950	if self.oldFocus:
1951	self.oldFocus.SetFocus()
1952
1953	def OnPatternTreeItemCollapsed(self, event):
1954	'Called when a tree item is collapsed'
1955	event.Skip()
1956
1957	def OnPatternTreeItemExpanded(self, event):
1958	'Called when a tree item is expanded'
1959	event.Skip()
1960
1961	def OnPatternTreeItemDelete(self, event):
1962	'Called when a tree item is deleted -- not sure what this does'
1963	self.TreeItemDelete = True
1964
1965	def OnPatternTreeItemActivated(self, event):
1966	'Called when a tree item is activated'
1967	event.Skip()
1968
1969	def OnPatternTreeKeyDown(self,event):
1970	'Not sure what this does'
1971	key = event.GetKeyCode()
1972	item = self.PickId
1973	if type(item) is int: return # is this the toplevel in tree?
1974	if key == wx.WXK_UP:
1975	self.oldFocus = wx.Window.FindFocus()
1976	self.PatternTree.GetPrevSibling(item)
1977	elif key == wx.WXK_DOWN:
1978	self.oldFocus = wx.Window.FindFocus()
1979	self.PatternTree.GetNextSibling(item)
1980
1981	def OnReadPowderPeaks(self,event):
1982	'Bound to menu Data/Read Powder Peaks -- still needed?'
1983	Cuka = 1.54052
1984	self.CheckNotebook()
1985	dlg = wx.FileDialog(self, 'Choose file with peak list', '.', '',
1986	'peak files (.txt)\|.txt\|All files (.)\|.',wx.OPEN\|wx.CHANGE_DIR)
1987	try:
1988	if dlg.ShowModal() == wx.ID_OK:
1989	self.HKL = []
1990	self.powderfile = dlg.GetPath()
1991	comments,peaks = G2IO.GetPowderPeaks(self.powderfile)
1992	Id = self.PatternTree.AppendItem(parent=self.root,text='PKS '+os.path.basename(self.powderfile))
1993	data = ['PKS',Cuka,0.0]
1994	names = ['Type','Lam','Zero']
1995	codes = [0,0,0]
1996	inst = [G2IO.makeInstDict(names,data,codes),{}]
1997	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
1998	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),comments)
1999	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Index Peak List'),peaks)
2000	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
2001	self.PatternTree.Expand(Id)
2002	self.PatternTree.SelectItem(Id)
2003	os.chdir(dlg.GetDirectory()) # to get Mac/Linux to change directory!
2004	finally:
2005	dlg.Destroy()
2006
2007	def OnImageRead(self,event):
2008	'Called to read in an image in any known format'
2009	self.CheckNotebook()
2010	dlg = wx.FileDialog(
2011	self, 'Choose image files', '.', '',
2012	'Any supported image file (.edf;.tif;.tiff;.mar;.avg;.sum;.img;.G2img;.png)\|'
2013	'.edf;.tif;.tiff;.mar;.avg;.sum;.img;.G2img;.png;*.zip\|'
2014	'European detector file (.edf)\|.edf\|'
2015	'Any detector tif (.tif;.tiff)\|.tif;.tiff\|'
2016	'MAR file (.mar)\|.mar\|'
2017	'GE Image (.avg;.sum)\|.avg;.sum\|'
2018	'ADSC Image (.img)\|.img\|'
2019	'GSAS-II Image (.G2img)\|.G2img\|'
2020	'Portable Network Graphics image (.png)\|.png\|'
2021	'Zip archive (.zip)\|.zip\|'
2022	'All files (.)\|.',
2023	wx.OPEN \| wx.MULTIPLE\|wx.CHANGE_DIR)
2024	try:
2025	if dlg.ShowModal() == wx.ID_OK:
2026	imagefiles = dlg.GetPaths()
2027	imagefiles.sort()
2028	for imagefile in imagefiles:
2029	# if a zip file, open and extract
2030	if os.path.splitext(imagefile)[1].lower() == '.zip':
2031	extractedfile = G2IO.ExtractFileFromZip(imagefile,parent=self)
2032	if extractedfile is not None and extractedfile != imagefile:
2033	imagefile = extractedfile
2034	Comments,Data,Npix,Image = G2IO.GetImageData(self,imagefile)
2035	if Comments:
2036	Id = self.PatternTree.AppendItem(parent=self.root,text='IMG '+os.path.basename(imagefile))
2037	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),Comments)
2038	Imax = np.amax(Image)
2039	Imin = max(0.0,np.amin(Image)) #force positive
2040	if self.imageDefault:
2041	Data = copy.copy(self.imageDefault)
2042	Data['showLines'] = True
2043	Data['ring'] = []
2044	Data['rings'] = []
2045	Data['cutoff'] = 10
2046	Data['pixLimit'] = 20
2047	Data['edgemin'] = 100000000
2048	Data['calibdmin'] = 0.5
2049	Data['calibskip'] = 0
2050	Data['ellipses'] = []
2051	Data['calibrant'] = ''
2052	Data['GonioAngles'] = [0.,0.,0.]
2053	Data['DetDepth'] = 0.
2054	Data['DetDepthRef'] = False
2055	else:
2056	Data['type'] = 'PWDR'
2057	Data['color'] = 'Paired'
2058	Data['tilt'] = 0.0
2059	Data['rotation'] = 0.0
2060	Data['showLines'] = False
2061	Data['ring'] = []
2062	Data['rings'] = []
2063	Data['cutoff'] = 10
2064	Data['pixLimit'] = 20
2065	Data['calibdmin'] = 0.5
2066	Data['calibskip'] = 0
2067	Data['edgemin'] = 100000000
2068	Data['ellipses'] = []
2069	Data['GonioAngles'] = [0.,0.,0.]
2070	Data['DetDepth'] = 0.
2071	Data['DetDepthRef'] = False
2072	Data['calibrant'] = ''
2073	Data['IOtth'] = [2.0,5.0]
2074	Data['LRazimuth'] = [135,225]
2075	Data['azmthOff'] = 0.0
2076	Data['outChannels'] = 2500
2077	Data['outAzimuths'] = 1
2078	Data['centerAzm'] = False
2079	Data['fullIntegrate'] = False
2080	Data['setRings'] = False
2081	Data['background image'] = ['',-1.0]
2082	Data['dark image'] = ['',-1.0]
2083	Data['setDefault'] = False
2084	Data['range'] = [(Imin,Imax),[Imin,Imax]]
2085	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Image Controls'),Data)
2086	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(Imin,Imax),[Imin,Imax]]}
2087	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Masks'),Masks)
2088	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Stress/Strain'),
2089	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'strain':np.zeros((3,3))})
2090	self.PatternTree.SetItemPyData(Id,[Npix,imagefile])
2091	self.PickId = Id
2092	self.Image = Id
2093	os.chdir(dlg.GetDirectory()) # to get Mac/Linux to change directory!
2094	self.PatternTree.SelectItem(G2gd.GetPatternTreeItemId(self,Id,'Image Controls')) #show last one
2095	finally:
2096	path = dlg.GetDirectory() # to get Mac/Linux to change directory!
2097	os.chdir(path)
2098	dlg.Destroy()
2099
2100	def CheckNotebook(self):
2101	'''Make sure the data tree has the minimally expected controls.
2102	(BHT) correct?
2103	'''
2104	if not G2gd.GetPatternTreeItemId(self,self.root,'Notebook'):
2105	sub = self.PatternTree.AppendItem(parent=self.root,text='Notebook')
2106	self.PatternTree.SetItemPyData(sub,[''])
2107	if not G2gd.GetPatternTreeItemId(self,self.root,'Controls'):
2108	sub = self.PatternTree.AppendItem(parent=self.root,text='Controls')
2109	self.PatternTree.SetItemPyData(sub,copy.copy(G2obj.DefaultControls))
2110	if not G2gd.GetPatternTreeItemId(self,self.root,'Covariance'):
2111	sub = self.PatternTree.AppendItem(parent=self.root,text='Covariance')
2112	self.PatternTree.SetItemPyData(sub,{})
2113	if not G2gd.GetPatternTreeItemId(self,self.root,'Constraints'):
2114	sub = self.PatternTree.AppendItem(parent=self.root,text='Constraints')
2115	self.PatternTree.SetItemPyData(sub,{'Hist':[],'HAP':[],'Phase':[]})
2116	if not G2gd.GetPatternTreeItemId(self,self.root,'Restraints'):
2117	sub = self.PatternTree.AppendItem(parent=self.root,text='Restraints')
2118	self.PatternTree.SetItemPyData(sub,{})
2119	if not G2gd.GetPatternTreeItemId(self,self.root,'Rigid bodies'):
2120	sub = self.PatternTree.AppendItem(parent=self.root,text='Rigid bodies')
2121	self.PatternTree.SetItemPyData(sub,{'Vector':{'AtInfo':{}},
2122	'Residue':{'AtInfo':{}},'RBIds':{'Vector':[],'Residue':[]}})
2123
2124	class CopyDialog(wx.Dialog):
2125	'''Creates a dialog for copying control settings between
2126	data tree items'''
2127	def __init__(self,parent,title,text,data):
2128	wx.Dialog.__init__(self,parent,-1,title,
2129	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
2130	self.data = data
2131	panel = wx.Panel(self)
2132	mainSizer = wx.BoxSizer(wx.VERTICAL)
2133	topLabl = wx.StaticText(panel,-1,text)
2134	mainSizer.Add((10,10),1)
2135	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.LEFT,10)
2136	mainSizer.Add((10,10),1)
2137	ncols = len(data)/40+1
2138	dataGridSizer = wx.FlexGridSizer(rows=len(data),cols=ncols,hgap=2,vgap=2)
2139	for id,item in enumerate(self.data):
2140	ckbox = wx.CheckBox(panel,id,item[1])
2141	ckbox.Bind(wx.EVT_CHECKBOX,self.OnCopyChange)
2142	dataGridSizer.Add(ckbox,0,wx.LEFT,10)
2143	mainSizer.Add(dataGridSizer,0,wx.EXPAND)
2144	OkBtn = wx.Button(panel,-1,"Ok")
2145	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
2146	cancelBtn = wx.Button(panel,-1,"Cancel")
2147	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
2148	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
2149	btnSizer.Add((20,20),1)
2150	btnSizer.Add(OkBtn)
2151	btnSizer.Add((20,20),1)
2152	btnSizer.Add(cancelBtn)
2153	btnSizer.Add((20,20),1)
2154
2155	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
2156	panel.SetSizer(mainSizer)
2157	panel.Fit()
2158	self.Fit()
2159
2160	def OnCopyChange(self,event):
2161	id = event.GetId()
2162	self.data[id][0] = self.FindWindowById(id).GetValue()
2163
2164	def OnOk(self,event):
2165	parent = self.GetParent()
2166	parent.Raise()
2167	self.EndModal(wx.ID_OK)
2168
2169	def OnCancel(self,event):
2170	parent = self.GetParent()
2171	parent.Raise()
2172	self.EndModal(wx.ID_CANCEL)
2173
2174	def GetData(self):
2175	return self.data
2176
2177	class SumDialog(wx.Dialog):
2178	'Allows user to supply scale factor(s) when summing data'
2179	def __init__(self,parent,title,text,dataType,data):
2180	wx.Dialog.__init__(self,parent,-1,title,
2181	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
2182	self.data = data
2183	panel = wx.Panel(self)
2184	mainSizer = wx.BoxSizer(wx.VERTICAL)
2185	topLabl = wx.StaticText(panel,-1,text)
2186	mainSizer.Add((10,10),1)
2187	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.LEFT,10)
2188	mainSizer.Add((10,10),1)
2189	dataGridSizer = wx.FlexGridSizer(rows=len(data),cols=2,hgap=2,vgap=2)
2190	for id,item in enumerate(self.data[:-1]):
2191	name = wx.TextCtrl(panel,-1,item[1],size=wx.Size(200,20))
2192	name.SetEditable(False)
2193	scale = wx.TextCtrl(panel,id,'%.3f'%(item[0]),style=wx.TE_PROCESS_ENTER)
2194	scale.Bind(wx.EVT_TEXT_ENTER,self.OnScaleChange)
2195	scale.Bind(wx.EVT_KILL_FOCUS,self.OnScaleChange)
2196	dataGridSizer.Add(scale,0,wx.LEFT,10)
2197	dataGridSizer.Add(name,0,wx.RIGHT,10)
2198	if dataType:
2199	dataGridSizer.Add(wx.StaticText(panel,-1,'Sum result name: '+dataType),0, \
2200	wx.LEFT\|wx.TOP\|wx.ALIGN_CENTER_VERTICAL,10)
2201	self.name = wx.TextCtrl(panel,-1,self.data[-1],size=wx.Size(200,20),style=wx.TE_PROCESS_ENTER)
2202	self.name.Bind(wx.EVT_TEXT_ENTER,self.OnNameChange)
2203	self.name.Bind(wx.EVT_KILL_FOCUS,self.OnNameChange)
2204	dataGridSizer.Add(self.name,0,wx.RIGHT\|wx.TOP,10)
2205	mainSizer.Add(dataGridSizer,0,wx.EXPAND)
2206	OkBtn = wx.Button(panel,-1,"Ok")
2207	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
2208	cancelBtn = wx.Button(panel,-1,"Cancel")
2209	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
2210	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
2211	btnSizer.Add((20,20),1)
2212	btnSizer.Add(OkBtn)
2213	btnSizer.Add((20,20),1)
2214	btnSizer.Add(cancelBtn)
2215	btnSizer.Add((20,20),1)
2216
2217	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
2218	panel.SetSizer(mainSizer)
2219	panel.Fit()
2220	self.Fit()
2221
2222	def OnScaleChange(self,event):
2223	id = event.GetId()
2224	value = self.FindWindowById(id).GetValue()
2225	try:
2226	self.data[id][0] = float(value)
2227	self.FindWindowById(id).SetValue('%.3f'%(self.data[id][0]))
2228	except ValueError:
2229	if value and '-' not in value[0]:
2230	print 'bad input - numbers only'
2231	self.FindWindowById(id).SetValue('0.000')
2232
2233	def OnNameChange(self,event):
2234	self.data[-1] = self.name.GetValue()
2235
2236	def OnOk(self,event):
2237	parent = self.GetParent()
2238	parent.Raise()
2239	self.EndModal(wx.ID_OK)
2240
2241	def OnCancel(self,event):
2242	parent = self.GetParent()
2243	parent.Raise()
2244	self.EndModal(wx.ID_CANCEL)
2245
2246	def GetData(self):
2247	return self.data
2248
2249	def OnPwdrSum(self,event):
2250	'Sum together powder data(?)'
2251	TextList = []
2252	DataList = []
2253	SumList = []
2254	Names = []
2255	Inst = None
2256	SumItemList = []
2257	Comments = ['Sum equals: \n']
2258	if self.PatternTree.GetCount():
2259	item, cookie = self.PatternTree.GetFirstChild(self.root)
2260	while item:
2261	name = self.PatternTree.GetItemText(item)
2262	Names.append(name)
2263	if 'PWDR' in name:
2264	TextList.append([0.0,name])
2265	DataList.append(self.PatternTree.GetItemPyData(item)[1]) # (x,y,w,yc,yb,yd)
2266	if not Inst:
2267	Inst = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,item, 'Instrument Parameters'))
2268	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2269	if len(TextList) < 2:
2270	self.ErrorDialog('Not enough data to sum','There must be more than one "PWDR" pattern')
2271	return
2272	TextList.append('default_sum_name')
2273	dlg = self.SumDialog(self,'Sum data','Enter scale for each pattern in summation','PWDR',TextList)
2274	try:
2275	if dlg.ShowModal() == wx.ID_OK:
2276	lenX = 0
2277	Xminmax = [0,0]
2278	Xsum = []
2279	Ysum = []
2280	Vsum = []
2281	result = dlg.GetData()
2282	for i,item in enumerate(result[:-1]):
2283	scale,name = item
2284	data = DataList[i]
2285	if scale:
2286	Comments.append("%10.3f %s" % (scale,' * '+name))
2287	x,y,w,yc,yb,yd = data #numpy arrays!
2288	v = 1./w
2289	if lenX:
2290	if lenX != len(x):
2291	self.ErrorDialog('Data length error','Data to be summed must have same number of points'+ \
2292	'\nExpected:'+str(lenX)+ \
2293	'\nFound: '+str(len(x))+'\nfor '+name)
2294	return
2295	else:
2296	lenX = len(x)
2297	if Xminmax[1]:
2298	if Xminmax != [x[0],x[-1]]:
2299	self.ErrorDialog('Data range error','Data to be summed must span same range'+ \
2300	'\nExpected:'+str(Xminmax[0])+' '+str(Xminmax[1])+ \
2301	'\nFound: '+str(x[0])+' '+str(x[-1])+'\nfor '+name)
2302	return
2303	else:
2304	for j,yi in enumerate(y):
2305	Ysum[j] += scale*yi
2306	Vsum[j] += abs(scale)*v[j]
2307	else:
2308	Xminmax = [x[0],x[-1]]
2309	YCsum = YBsum = YDsum = [0.0 for i in range(lenX)]
2310	for j,yi in enumerate(y):
2311	Xsum.append(x[j])
2312	Ysum.append(scale*yi)
2313	Vsum.append(abs(scale*v[j]))
2314	Wsum = 1./np.array(Vsum)
2315	outname = 'PWDR '+result[-1]
2316	Id = 0
2317	if outname in Names:
2318	dlg2 = wx.MessageDialog(self,'Overwrite data?','Duplicate data name',wx.OK\|wx.CANCEL)
2319	try:
2320	if dlg2.ShowModal() == wx.ID_OK:
2321	Id = G2gd.GetPatternTreeItemId(self,self.root,name)
2322	self.PatternTree.Delete(Id)
2323	finally:
2324	dlg2.Destroy()
2325	Id = self.PatternTree.AppendItem(parent=self.root,text=outname)
2326	if Id:
2327	Sample = G2pdG.SetDefaultSample()
2328	valuesdict = {
2329	'wtFactor':1.0,
2330	'Dummy':False,
2331	'ranId':ran.randint(0,sys.maxint),
2332	}
2333	self.PatternTree.SetItemPyData(Id,[valuesdict,[np.array(Xsum),np.array(Ysum),np.array(Wsum),
2334	np.array(YCsum),np.array(YBsum),np.array(YDsum)]])
2335	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),Comments)
2336	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
2337	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',True,3,1.0,0.0,0.0],
2338	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
2339	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Instrument Parameters'),Inst)
2340	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
2341	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Peak List'),[])
2342	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Index Peak List'),[])
2343	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
2344	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
2345	self.PatternTree.SelectItem(Id)
2346	self.PatternTree.Expand(Id)
2347	finally:
2348	dlg.Destroy()
2349
2350	def OnImageSum(self,event):
2351	'Sum together image data(?)'
2352	TextList = []
2353	DataList = []
2354	SumList = []
2355	Names = []
2356	Inst = []
2357	SumItemList = []
2358	Comments = ['Sum equals: \n']
2359	if self.PatternTree.GetCount():
2360	item, cookie = self.PatternTree.GetFirstChild(self.root)
2361	while item:
2362	name = self.PatternTree.GetItemText(item)
2363	Names.append(name)
2364	if 'IMG' in name:
2365	TextList.append([0.0,name])
2366	DataList.append(self.PatternTree.GetItemPyData(item)) #Size,Image
2367	Data = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,item,'Image Controls'))
2368	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2369	if len(TextList) < 2:
2370	self.ErrorDialog('Not enough data to sum','There must be more than one "IMG" pattern')
2371	return
2372	TextList.append('default_sum_name')
2373	dlg = self.SumDialog(self,'Sum data','Enter scale for each image in summation','IMG',TextList)
2374	try:
2375	if dlg.ShowModal() == wx.ID_OK:
2376	imSize = 0
2377	result = dlg.GetData()
2378	First = True
2379	Found = False
2380	for i,item in enumerate(result[:-1]):
2381	scale,name = item
2382	data = DataList[i]
2383	if scale:
2384	Found = True
2385	Comments.append("%10.3f %s" % (scale,' * '+name))
2386	Npix,imagefile = data
2387	image = G2IO.GetImageData(self,imagefile,imageOnly=True)
2388	if First:
2389	newImage = np.zeros_like(image)
2390	First = False
2391	if imSize:
2392	if imSize != Npix:
2393	self.ErrorDialog('Image size error','Images to be summed must be same size'+ \
2394	'\nExpected:'+str(imSize)+ \
2395	'\nFound: '+str(Npix)+'\nfor '+name)
2396	return
2397	newImage = newImage+scale*image
2398	else:
2399	imSize = Npix
2400	newImage = newImage+scale*image
2401	del(image)
2402	if not Found:
2403	self.ErrorDialog('Image sum error','No nonzero image multipliers found')
2404	return
2405
2406	newImage = np.asfarray(newImage,dtype=np.float32)
2407	outname = 'IMG '+result[-1]
2408	Id = 0
2409	if outname in Names:
2410	dlg2 = wx.MessageDialog(self,'Overwrite data?','Duplicate data name',wx.OK\|wx.CANCEL)
2411	try:
2412	if dlg2.ShowModal() == wx.ID_OK:
2413	Id = G2gd.GetPatternTreeItemId(self,self.root,name)
2414	finally:
2415	dlg2.Destroy()
2416	else:
2417	Id = self.PatternTree.AppendItem(parent=self.root,text=outname)
2418	if Id:
2419	dlg = wx.FileDialog(self, 'Choose sum image filename', '.', '',
2420	'G2img files (.G2img)\|.G2img',
2421	wx.SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2422	if dlg.ShowModal() == wx.ID_OK:
2423	newimagefile = dlg.GetPath()
2424	newimagefile = G2IO.FileDlgFixExt(dlg,newimagefile)
2425	G2IO.PutG2Image(newimagefile,Comments,Data,Npix,newImage)
2426	Imax = np.amax(newImage)
2427	Imin = np.amin(newImage)
2428	newImage = []
2429	self.PatternTree.SetItemPyData(Id,[imSize,newimagefile])
2430	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),Comments)
2431	del(newImage)
2432	if self.imageDefault:
2433	Data = copy.copy(self.imageDefault)
2434	Data['showLines'] = True
2435	Data['ring'] = []
2436	Data['rings'] = []
2437	Data['cutoff'] = 10
2438	Data['pixLimit'] = 20
2439	Data['ellipses'] = []
2440	Data['calibrant'] = ''
2441	Data['range'] = [(Imin,Imax),[Imin,Imax]]
2442	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Image Controls'),Data)
2443	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(Imin,Imax),[Imin,Imax]]}
2444	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Masks'),Masks)
2445	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Stress/Strain'),{})
2446	self.PatternTree.SelectItem(Id)
2447	self.PatternTree.Expand(Id)
2448	self.PickId = G2gd.GetPatternTreeItemId(self,self.root,outname)
2449	self.Image = self.PickId
2450	finally:
2451	dlg.Destroy()
2452
2453	def OnAddPhase(self,event):
2454	'Add a new, empty phase to the tree. Called by Data/Add Phase menu'
2455	if not G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
2456	sub = self.PatternTree.AppendItem(parent=self.root,text='Phases')
2457	else:
2458	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
2459	PhaseName = ''
2460	dlg = wx.TextEntryDialog(None,'Enter a name for this phase','Phase Name Entry','New phase',
2461	style=wx.OK)
2462	if dlg.ShowModal() == wx.ID_OK:
2463	PhaseName = dlg.GetValue()
2464	dlg.Destroy()
2465	sub = self.PatternTree.AppendItem(parent=sub,text=PhaseName)
2466	E,SGData = G2spc.SpcGroup('P 1')
2467	self.PatternTree.SetItemPyData(sub,G2IO.SetNewPhase(Name=PhaseName,SGData=SGData))
2468
2469	def OnDeletePhase(self,event):
2470	'Delete a phase from the tree. Called by Data/Delete Phase menu'
2471	#Hmm, also need to delete this phase from Reflection Lists for each PWDR histogram
2472	if self.dataFrame:
2473	self.dataFrame.Clear()
2474	TextList = []
2475	DelList = []
2476	DelItemList = []
2477	if G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
2478	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
2479	else:
2480	return
2481	if sub:
2482	item, cookie = self.PatternTree.GetFirstChild(sub)
2483	while item:
2484	TextList.append(self.PatternTree.GetItemText(item))
2485	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
2486	dlg = wx.MultiChoiceDialog(self, 'Which phase to delete?', 'Delete phase', TextList, wx.CHOICEDLG_STYLE)
2487	try:
2488	if dlg.ShowModal() == wx.ID_OK:
2489	result = dlg.GetSelections()
2490	for i in result: DelList.append([i,TextList[i]])
2491	item, cookie = self.PatternTree.GetFirstChild(sub)
2492	i = 0
2493	while item:
2494	if [i,self.PatternTree.GetItemText(item)] in DelList: DelItemList.append(item)
2495	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
2496	i += 1
2497	for item in DelItemList:
2498	name = self.PatternTree.GetItemText(item)
2499	self.PatternTree.Delete(item)
2500	self.G2plotNB.Delete(name)
2501	item, cookie = self.PatternTree.GetFirstChild(self.root)
2502	while item:
2503	name = self.PatternTree.GetItemText(item)
2504	if 'PWDR' in name:
2505	Id = G2gd.GetPatternTreeItemId(self,item, 'Reflection Lists')
2506	refList = self.PatternTree.GetItemPyData(Id)
2507	for i,item in DelList:
2508	del(refList[item])
2509	self.PatternTree.SetItemPyData(Id,refList)
2510	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2511	finally:
2512	dlg.Destroy()
2513
2514	def OnRenameData(self,event):
2515	'Renames an existing phase. Called by Data/Rename Phase menu'
2516	name = self.PatternTree.GetItemText(self.PickId)
2517	if 'PWDR' in name or 'HKLF' in name or 'IMG' in name:
2518	dataType = name[:name.index(' ')+1] #includes the ' '
2519	dlg = wx.TextEntryDialog(self,'Data name: '+dataType,'Change data name',
2520	defaultValue=name[name.index(' ')+1:])
2521	try:
2522	if dlg.ShowModal() == wx.ID_OK:
2523	self.PatternTree.SetItemText(self.PickId,dataType+dlg.GetValue())
2524	finally:
2525	dlg.Destroy()
2526
2527	def GetFileList(self,fileType,skip=None): #potentially useful?
2528	'Appears unused. Note routine of same name in GSASIIpwdGUI'
2529	fileList = []
2530	Source = ''
2531	id, cookie = self.PatternTree.GetFirstChild(self.root)
2532	while id:
2533	name = self.PatternTree.GetItemText(id)
2534	if fileType in name:
2535	if id == skip:
2536	Source = name
2537	else:
2538	fileList.append([False,name,id])
2539	id, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2540	if skip:
2541	return fileList,Source
2542	else:
2543	return fileList
2544
2545	def OnDataDelete(self, event):
2546	'''Delete one or more histograms from data tree. Called by the
2547	Data/DeleteData menu
2548	'''
2549	TextList = ['All Data']
2550	DelList = []
2551	DelItemList = []
2552	ifPWDR = False
2553	ifSASD = False
2554	ifIMG = False
2555	ifHKLF = False
2556	ifPDF = False
2557	if self.PatternTree.GetCount():
2558	item, cookie = self.PatternTree.GetFirstChild(self.root)
2559	while item:
2560	name = self.PatternTree.GetItemText(item)
2561	if name not in ['Notebook','Controls','Covariance','Constraints',
2562	'Restraints','Phases','Rigid bodies']:
2563	if 'PWDR' in name: ifPWDR = True
2564	if 'SASD' in name: ifSASD = True
2565	if 'IMG' in name: ifIMG = True
2566	if 'HKLF' in name: ifHKLF = True
2567	if 'PDF' in name: ifPDF = True
2568	TextList.append(name)
2569	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2570	if ifPWDR: TextList.insert(1,'All PWDR')
2571	if ifSASD: TextList.insert(1,'All SASD')
2572	if ifIMG: TextList.insert(1,'All IMG')
2573	if ifHKLF: TextList.insert(1,'All HKLF')
2574	if ifPDF: TextList.insert(1,'All PDF')
2575	dlg = wx.MultiChoiceDialog(self, 'Which data to delete?', 'Delete data', TextList, wx.CHOICEDLG_STYLE)
2576	try:
2577	if dlg.ShowModal() == wx.ID_OK:
2578	result = dlg.GetSelections()
2579	for i in result: DelList.append(TextList[i])
2580	if 'All Data' in DelList:
2581	DelList = [item for item in TextList if item[:3] != 'All']
2582	elif 'All PWDR' in DelList:
2583	DelList = [item for item in TextList if item[:4] == 'PWDR']
2584	elif 'All SASD' in DelList:
2585	DelList = [item for item in TextList if item[:4] == 'SASD']
2586	elif 'All IMG' in DelList:
2587	DelList = [item for item in TextList if item[:3] == 'IMG']
2588	elif 'All HKLF' in DelList:
2589	DelList = [item for item in TextList if item[:4] == 'HKLF']
2590	elif 'All PDF' in DelList:
2591	DelList = [item for item in TextList if item[:3] == 'PDF']
2592	item, cookie = self.PatternTree.GetFirstChild(self.root)
2593	while item:
2594	if self.PatternTree.GetItemText(item) in DelList: DelItemList.append(item)
2595	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2596	for item in DelItemList:
2597	self.PatternTree.Delete(item)
2598	self.PickId = 0
2599	wx.CallAfter(G2plt.PlotPatterns,self,True) #so plot gets updated
2600	finally:
2601	dlg.Destroy()
2602
2603	def OnFileOpen(self, event, filename=None):
2604	'''Reads in a GSAS-II .gpx project file in response to the
2605	File/Open Project menu button
2606	'''
2607	result = wx.ID_OK
2608	Id = 0
2609	self.EnablePlot = False
2610	if self.PatternTree.GetChildrenCount(self.root,False):
2611	if self.dataFrame:
2612	self.dataFrame.Clear()
2613	dlg = wx.MessageDialog(
2614	self,
2615	'Do you want to overwrite the current project? '
2616	'Any unsaved changes will be lost. Press OK to continue.',
2617	'Overwrite?', wx.OK \| wx.CANCEL)
2618	try:
2619	result = dlg.ShowModal()
2620	if result == wx.ID_OK:
2621	self.PatternTree.DeleteChildren(self.root)
2622	self.GSASprojectfile = ''
2623	if self.HKL: self.HKL = []
2624	if self.G2plotNB.plotList:
2625	self.G2plotNB.clear()
2626	finally:
2627	dlg.Destroy()
2628	if result != wx.ID_OK: return
2629
2630	if not filename:
2631	if self.dataDisplay: self.dataDisplay.Destroy()
2632	dlg = wx.FileDialog(self, 'Choose GSAS-II project file', '.', '',
2633	'GSAS-II project file (.gpx)\|.gpx',wx.OPEN\|wx.CHANGE_DIR)
2634	try:
2635	if dlg.ShowModal() != wx.ID_OK: return
2636	self.GSASprojectfile = dlg.GetPath()
2637	self.GSASprojectfile = G2IO.FileDlgFixExt(dlg,self.GSASprojectfile)
2638	self.dirname = dlg.GetDirectory()
2639	finally:
2640	dlg.Destroy()
2641	else:
2642	self.GSASprojectfile = os.path.splitext(filename)[0]+'.gpx'
2643	self.dirname = os.path.split(filename)[0]
2644
2645	G2IO.ProjFileOpen(self)
2646	self.PatternTree.SetItemText(self.root,'Loaded Data: '+self.GSASprojectfile)
2647	self.PatternTree.Expand(self.root)
2648	self.HKL = []
2649	item, cookie = self.PatternTree.GetFirstChild(self.root)
2650	while item and not Id:
2651	name = self.PatternTree.GetItemText(item)
2652	if name[:4] in ['PWDR','HKLF','IMG ','PDF ','SASD',]:
2653	Id = item
2654	elif name == 'Controls':
2655	data = self.PatternTree.GetItemPyData(item)
2656	if data:
2657	for item in self.Refine: item.Enable(True)
2658	self.EnableSeqRefineMenu()
2659	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2660	if Id:
2661	self.EnablePlot = True
2662	self.PatternTree.SelectItem(Id)
2663	self.CheckNotebook()
2664	os.chdir(self.dirname) # to get Mac/Linux to change directory!
2665
2666	def OnFileClose(self, event):
2667	'''Clears the data tree in response to the
2668	File/New Project menu button. User is given option to save
2669	the project.
2670	'''
2671	if self.dataFrame:
2672	self.dataFrame.Clear()
2673	self.dataFrame.SetLabel('GSAS-II data display')
2674	dlg = wx.MessageDialog(self, 'Save current project?', ' ', wx.YES \| wx.NO \| wx.CANCEL)
2675	try:
2676	result = dlg.ShowModal()
2677	if result == wx.ID_OK:
2678	self.OnFileSaveMenu(event)
2679	if result != wx.ID_CANCEL:
2680	self.GSASprojectfile = ''
2681	self.PatternTree.SetItemText(self.root,'Loaded Data: ')
2682	self.PatternTree.DeleteChildren(self.root)
2683	if self.HKL: self.HKL = []
2684	if self.G2plotNB.plotList:
2685	self.G2plotNB.clear()
2686	finally:
2687	dlg.Destroy()
2688
2689	def OnFileSave(self, event):
2690	'''Save the current project in response to the
2691	File/Save Project menu button
2692	'''
2693
2694	if self.GSASprojectfile:
2695	self.PatternTree.SetItemText(self.root,'Loaded Data: '+self.GSASprojectfile)
2696	G2IO.ProjFileSave(self)
2697	else:
2698	self.OnFileSaveas(event)
2699
2700	def OnFileSaveas(self, event):
2701	'''Save the current project in response to the
2702	File/Save as menu button
2703	'''
2704	dlg = wx.FileDialog(self, 'Choose GSAS-II project file name', '.', '',
2705	'GSAS-II project file (.gpx)\|.gpx',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2706	try:
2707	if dlg.ShowModal() == wx.ID_OK:
2708	self.GSASprojectfile = dlg.GetPath()
2709	self.GSASprojectfile = G2IO.FileDlgFixExt(dlg,self.GSASprojectfile)
2710	self.PatternTree.SetItemText(self.root,'Saving project as'+self.GSASprojectfile)
2711	self.SetTitle("GSAS-II data tree: "+os.path.split(self.GSASprojectfile)[1])
2712	G2IO.ProjFileSave(self)
2713	os.chdir(dlg.GetDirectory()) # to get Mac/Linux to change directory!
2714	finally:
2715	dlg.Destroy()
2716
2717	def ExitMain(self, event):
2718	'''Called if the main window is closed'''
2719	if self.undofile:
2720	os.remove(self.undofile)
2721	sys.exit()
2722
2723	def OnFileExit(self, event):
2724	'''Called in response to the File/Quit menu button'''
2725	if self.dataFrame:
2726	self.dataFrame.Clear()
2727	self.dataFrame.Destroy()
2728	self.Close()
2729
2730	# def OnExportPatterns(self,event):
2731	# names = ['All']
2732	# exports = []
2733	# item, cookie = self.PatternTree.GetFirstChild(self.root)
2734	# while item:
2735	# name = self.PatternTree.GetItemText(item)
2736	# if 'PWDR' in name:
2737	# names.append(name)
2738	# item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2739	# if names:
2740	# dlg = wx.MultiChoiceDialog(self,'Select','Powder patterns to export',names)
2741	# if dlg.ShowModal() == wx.ID_OK:
2742	# sel = dlg.GetSelections()
2743	# if sel[0] == 0:
2744	# exports = names[1:]
2745	# else:
2746	# for x in sel:
2747	# exports.append(names[x])
2748	# dlg.Destroy()
2749	# if exports:
2750	# dlg = wx.FileDialog(self, 'Choose output powder file name', '.', '',
2751	# 'GSAS fxye file (.fxye)\|.fxye\|xye file (.xye)\|.xye',
2752	# wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2753	# try:
2754	# if dlg.ShowModal() == wx.ID_OK:
2755	# powderfile = dlg.GetPath()
2756	# powderfile = G2IO.FileDlgFixExt(dlg,powderfile)
2757	# if 'fxye' in powderfile:
2758	# G2IO.powderFxyeSave(self,exports,powderfile)
2759	# else: #just xye
2760	# G2IO.powderXyeSave(self,exports,powderfile)
2761	# finally:
2762	# dlg.Destroy()
2763
2764	def OnExportPeakList(self,event):
2765	dlg = wx.FileDialog(self, 'Choose output peak list file name', '.', '',
2766	'(.)\|.',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2767	try:
2768	if dlg.ShowModal() == wx.ID_OK:
2769	self.peaklistfile = dlg.GetPath()
2770	self.peaklistfile = G2IO.FileDlgFixExt(dlg,self.peaklistfile)
2771	file = open(self.peaklistfile,'w')
2772	item, cookie = self.PatternTree.GetFirstChild(self.root)
2773	while item:
2774	name = self.PatternTree.GetItemText(item)
2775	if 'PWDR' in name:
2776	item2, cookie2 = self.PatternTree.GetFirstChild(item)
2777	while item2:
2778	name2 = self.PatternTree.GetItemText(item2)
2779	if name2 == 'Peak List':
2780	peaks = self.PatternTree.GetItemPyData(item2)
2781	file.write("%s \n" % (name+' Peak List'))
2782	for peak in peaks:
2783	file.write("%10.5f %12.2f %10.3f %10.3f \n" % \
2784	(peak[0],peak[2],peak[4],peak[6]))
2785	item2, cookie2 = self.PatternTree.GetNextChild(item, cookie2)
2786	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2787	file.close()
2788	finally:
2789	dlg.Destroy()
2790
2791	def OnExportHKL(self,event):
2792	dlg = wx.FileDialog(self, 'Choose output reflection list file name', '.', '',
2793	'(.)\|.',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2794	try:
2795	if dlg.ShowModal() == wx.ID_OK:
2796	self.peaklistfile = dlg.GetPath()
2797	self.peaklistfile = G2IO.FileDlgFixExt(dlg,self.peaklistfile)
2798	file = open(self.peaklistfile,'w')
2799	item, cookie = self.PatternTree.GetFirstChild(self.root)
2800	while item:
2801	name = self.PatternTree.GetItemText(item)
2802	if 'PWDR' in name:
2803	item2, cookie2 = self.PatternTree.GetFirstChild(item)
2804	while item2:
2805	name2 = self.PatternTree.GetItemText(item2)
2806	if name2 == 'Reflection Lists':
2807	data = self.PatternTree.GetItemPyData(item2)
2808	phases = data.keys()
2809	for phase in phases:
2810	peaks = data[phase]
2811	file.write("%s %s %s \n" % (name,phase,' Reflection List'))
2812	file.write('%s \n'%(' h k l m d-space 2-theta wid F**2'))
2813	for peak in peaks:
2814	FWHM = G2pwd.getgamFW(peak[7],peak[6])/50. #to get delta-2-theta in deg.
2815	file.write(" %3d %3d %3d %3d %10.5f %10.5f %10.5f %10.3f \n" % \
2816	(int(peak[0]),int(peak[1]),int(peak[2]),int(peak[3]),peak[4],peak[5],FWHM,peak[8]))
2817	item2, cookie2 = self.PatternTree.GetNextChild(item, cookie2)
2818	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2819	file.close()
2820	finally:
2821	dlg.Destroy()
2822
2823	def OnExportPDF(self,event):
2824	#need S(Q) and G(R) to be saved here - probably best from selection?
2825	names = ['All']
2826	exports = []
2827	item, cookie = self.PatternTree.GetFirstChild(self.root)
2828	while item:
2829	name = self.PatternTree.GetItemText(item)
2830	if 'PDF' in name:
2831	names.append(name)
2832	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2833	if names:
2834	dlg = wx.MultiChoiceDialog(self,'Select','PDF patterns to export',names)
2835	if dlg.ShowModal() == wx.ID_OK:
2836	sel = dlg.GetSelections()
2837	if sel[0] == 0:
2838	exports = names[1:]
2839	else:
2840	for x in sel:
2841	exports.append(names[x])
2842	dlg.Destroy()
2843	if exports:
2844	G2IO.PDFSave(self,exports)
2845
2846	def OnMakePDFs(self,event):
2847	'''Calculates PDFs
2848	'''
2849	tth2q = lambda t,w:4.0math.pisind(t/2.0)/w
2850	TextList = ['All PWDR']
2851	PDFlist = []
2852	Names = []
2853	if self.PatternTree.GetCount():
2854	id, cookie = self.PatternTree.GetFirstChild(self.root)
2855	while id:
2856	name = self.PatternTree.GetItemText(id)
2857	Names.append(name)
2858	if 'PWDR' in name:
2859	TextList.append(name)
2860	id, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2861	if len(TextList) == 1:
2862	self.ErrorDialog('Nothing to make PDFs for','There must be at least one "PWDR" pattern')
2863	return
2864	dlg = wx.MultiChoiceDialog(self,'Make PDF controls','Make PDF controls for:',TextList, wx.CHOICEDLG_STYLE)
2865	try:
2866	if dlg.ShowModal() == wx.ID_OK:
2867	result = dlg.GetSelections()
2868	for i in result: PDFlist.append(TextList[i])
2869	if 0 in result:
2870	PDFlist = [item for item in TextList if item[:4] == 'PWDR']
2871	for item in PDFlist:
2872	PWDRname = item[4:]
2873	Id = self.PatternTree.AppendItem(parent=self.root,text='PDF '+PWDRname)
2874	Data = {
2875	'Sample':{'Name':item,'Mult':1.0,'Add':0.0},
2876	'Sample Bkg.':{'Name':'','Mult':-1.0,'Add':0.0},
2877	'Container':{'Name':'','Mult':-1.0,'Add':0.0},
2878	'Container Bkg.':{'Name':'','Mult':-1.0,'Add':0.0},'ElList':{},
2879	'Geometry':'Cylinder','Diam':1.0,'Pack':0.50,'Form Vol':10.0,
2880	'DetType':'Image plate','ObliqCoeff':0.2,'Ruland':0.025,'QScaleLim':[0,100],
2881	'Lorch':True,}
2882	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='PDF Controls'),Data)
2883	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='I(Q)'+PWDRname),[])
2884	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='S(Q)'+PWDRname),[])
2885	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='F(Q)'+PWDRname),[])
2886	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='G(R)'+PWDRname),[])
2887	for item in self.ExportPDF: item.Enable(True)
2888	finally:
2889	dlg.Destroy()
2890
2891	def GetPWDRdatafromTree(self,PWDRname):
2892	''' Returns powder data from GSASII tree
2893
2894	:param str PWDRname: a powder histogram name as obtained from
2895	:meth:`GSASIIstruct.GetHistogramNames`
2896
2897	:returns: PWDRdata = powder data dictionary with
2898	Powder data arrays, Limits, Instrument Parameters,
2899	Sample Parameters
2900	'''
2901	PWDRdata = {}
2902	try:
2903	PWDRdata.update(self.PatternTree.GetItemPyData(PWDRname)[0]) #wtFactor + ?
2904	except ValueError:
2905	PWDRdata['wtFactor'] = 1.0
2906	PWDRdata['Data'] = self.PatternTree.GetItemPyData(PWDRname)[1] #powder data arrays
2907	PWDRdata['Limits'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Limits'))
2908	PWDRdata['Background'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Background'))
2909	PWDRdata['Instrument Parameters'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Instrument Parameters'))
2910	PWDRdata['Sample Parameters'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Sample Parameters'))
2911	PWDRdata['Reflection Lists'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Reflection Lists'))
2912	if 'ranId' not in PWDRdata: # patch, add a random Id
2913	PWDRdata['ranId'] = ran.randint(0,sys.maxint)
2914	if 'ranId' not in PWDRdata['Sample Parameters']: # I hope this becomes obsolete at some point
2915	PWDRdata['Sample Parameters']['ranId'] = PWDRdata['ranId']
2916	return PWDRdata
2917
2918	def GetHKLFdatafromTree(self,HKLFname):
2919	''' Returns single crystal data from GSASII tree
2920
2921	:param str HKLFname: a single crystal histogram name as obtained
2922	from
2923	:meth:`GSASIIstruct.GetHistogramNames`
2924
2925	:returns: HKLFdata = single crystal data list of reflections
2926
2927	'''
2928	HKLFdata = {}
2929	HKLFdata.update(self.PatternTree.GetItemPyData(HKLFname)[0]) #wtFactor + ?
2930	# try:
2931	# HKLFdata.update(self.PatternTree.GetItemPyData(HKLFname)[0]) #wtFactor + ?
2932	# except ValueError:
2933	# HKLFdata['wtFactor'] = 1.0
2934	HKLFdata['Data'] = self.PatternTree.GetItemPyData(HKLFname)[1]
2935	HKLFdata['Instrument Parameters'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,HKLFname,'Instrument Parameters'))
2936	return HKLFdata
2937
2938	def GetPhaseData(self):
2939	'''Returns a dict with defined phases.
2940	Note routine :func:`GSASIIstrIO.GetPhaseData` also exists to
2941	get same info from GPX file.
2942	'''
2943	phaseData = {}
2944	if G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
2945	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
2946	else:
2947	print 'no phases found in GetPhaseData'
2948	sub = None
2949	if sub:
2950	item, cookie = self.PatternTree.GetFirstChild(sub)
2951	while item:
2952	phaseName = self.PatternTree.GetItemText(item)
2953	phaseData[phaseName] = self.PatternTree.GetItemPyData(item)
2954	if 'ranId' not in phaseData[phaseName]:
2955	phaseData[phaseName]['ranId'] = ran.randint(0,sys.maxint)
2956	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
2957	return phaseData
2958
2959	def GetPhaseInfofromTree(self):
2960	'''Get the phase names and their rId values,
2961	also the histograms used in each phase.
2962
2963	:returns: (phaseRIdList, usedHistograms) where
2964
2965	* phaseRIdList is a list of random Id values for each phase
2966	* usedHistograms is a dict where the keys are the phase names
2967	and the values for each key are a list of the histogram names
2968	used in each phase.
2969	'''
2970	phaseRIdList = []
2971	usedHistograms = {}
2972	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
2973	if sub:
2974	item, cookie = self.PatternTree.GetFirstChild(sub)
2975	while item:
2976	phaseName = self.PatternTree.GetItemText(item)
2977	ranId = self.PatternTree.GetItemPyData(item).get('ranId')
2978	if ranId: phaseRIdList.append(ranId)
2979	data = self.PatternTree.GetItemPyData(item)
2980	UseList = data['Histograms']
2981	usedHistograms[phaseName] = UseList.keys()
2982	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
2983	return phaseRIdList,usedHistograms
2984
2985	def GetPhaseNames(self):
2986	'''Returns a list of defined phases.
2987	Note routine :func:`GSASIIstrIO.GetPhaseNames` also exists to
2988	get same info from GPX file.
2989	'''
2990	phaseNames = []
2991	if G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
2992	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
2993	else:
2994	print 'no phases found in GetPhaseNames'
2995	sub = None
2996	if sub:
2997	item, cookie = self.PatternTree.GetFirstChild(sub)
2998	while item:
2999	phase = self.PatternTree.GetItemText(item)
3000	phaseNames.append(phase)
3001	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
3002	return phaseNames
3003
3004	def GetHistogramNames(self,hType):
3005	""" Returns a list of histogram names found in the GSASII data tree
3006	Note routine :func:`GSASIIstrIO.GetHistogramNames` also exists to
3007	get same info from GPX file.
3008
3009	:param str hType: list of histogram types
3010	:return: list of histogram names
3011
3012	"""
3013	HistogramNames = []
3014	if self.PatternTree.GetCount():
3015	item, cookie = self.PatternTree.GetFirstChild(self.root)
3016	while item:
3017	name = self.PatternTree.GetItemText(item)
3018	if name[:4] in hType:
3019	HistogramNames.append(name)
3020	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
3021
3022	return HistogramNames
3023
3024
3025	def GetUsedHistogramsAndPhasesfromTree(self):
3026	''' Returns all histograms that are found in any phase
3027	and any phase that uses a histogram.
3028	This also assigns numbers to used phases and histograms by the
3029	order they appear in the file.
3030	Note routine :func:`GSASIIstrIO.GetUsedHistogramsAndPhasesfromTree` also exists to
3031	get same info from GPX file.
3032
3033	:returns: (Histograms,Phases)
3034
3035	* Histograms = dictionary of histograms as {name:data,...}
3036	* Phases = dictionary of phases that use histograms
3037	'''
3038	Histograms = {}
3039	Phases = {}
3040	phaseNames = self.GetPhaseNames()
3041	phaseData = self.GetPhaseData()
3042	histoList = self.GetHistogramNames(['PWDR','HKLF'])
3043
3044	for phase in phaseData:
3045	Phase = phaseData[phase]
3046	pId = phaseNames.index(phase)
3047	Phase['pId'] = pId
3048	if Phase['Histograms']:
3049	if phase not in Phases:
3050	Phases[phase] = Phase
3051	for hist in Phase['Histograms']:
3052	if 'Use' not in Phase['Histograms'][hist]: #patch: add Use flag as True
3053	Phase['Histograms'][hist]['Use'] = True
3054	if hist not in Histograms and Phase['Histograms'][hist]['Use']:
3055	item = G2gd.GetPatternTreeItemId(self,self.root,hist)
3056	if item:
3057	if 'PWDR' in hist[:4]:
3058	Histograms[hist] = self.GetPWDRdatafromTree(item)
3059	elif 'HKLF' in hist[:4]:
3060	Histograms[hist] = self.GetHKLFdatafromTree(item)
3061	hId = histoList.index(hist)
3062	Histograms[hist]['hId'] = hId
3063	else: # would happen if a referenced histogram were renamed or deleted
3064	print('For phase "'+str(phase)+
3065	'" unresolved reference to histogram "'+str(hist)+'"')
3066	#G2obj.IndexAllIds(Histograms=Histograms,Phases=Phases)
3067	G2obj.IndexAllIds(Histograms=Histograms,Phases=phaseData)
3068	return Histograms,Phases
3069
3070	def MakeLSParmDict(self):
3071	'''Load all parameters used for computation from the tree into a
3072	dict of paired values [value, refine flag]. Note that this is
3073	different than the parmDict used in the refinement, which only has
3074	values.
3075
3076	Note that similar things are done in
3077	:meth:`GSASIIIO.ExportBaseclass.loadParmDict` (from the tree) and
3078	:func:`GSASIIstrMain.Refine` and :func:`GSASIIstrMain.SeqRefine` (from
3079	a GPX file).
3080
3081	:returns: (parmDict,varyList) where:
3082
3083	* parmDict is a dict with values and refinement flags
3084	for each parameter and
3085	* varyList is a list of variables (refined parameters).
3086	'''
3087	parmDict = {}
3088	Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree()
3089	for phase in Phases:
3090	if 'pId' not in Phases[phase]:
3091	self.ErrorDialog('View parameter error','You must run least squares at least once')
3092	raise Exception,'No pId for phase '+str(phase)
3093	rigidbodyDict = self.PatternTree.GetItemPyData(
3094	G2gd.GetPatternTreeItemId(self,self.root,'Rigid bodies'))
3095	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
3096	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
3097	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtable,BLtable = G2stIO.GetPhaseData(Phases,RestraintDict=None,rbIds=rbIds,Print=False)
3098	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(Phases,Histograms,Print=False)
3099	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
3100	varyList = rbVary+phaseVary+hapVary+histVary
3101	parmDict.update(rbDict)
3102	parmDict.update(phaseDict)
3103	parmDict.update(hapDict)
3104	parmDict.update(histDict)
3105	for parm in parmDict:
3106	if parm.split(':')[-1] in ['Azimuth','Gonio. radius','Lam1','Lam2',
3107	'Omega','Chi','Phi','nDebye','nPeaks']:
3108	parmDict[parm] = [parmDict[parm],'-']
3109	elif parm.split(':')[-2] in ['Ax','Ay','Az','SHmodel','SHord']:
3110	parmDict[parm] = [parmDict[parm],'-']
3111	elif parm in varyList:
3112	parmDict[parm] = [parmDict[parm],'T']
3113	else:
3114	parmDict[parm] = [parmDict[parm],'F']
3115	# for i in parmDict: print i,'\t',parmDict[i]
3116	# fl = open('parmDict.dat','wb')
3117	# import cPickle
3118	# cPickle.dump(parmDict,fl,1)
3119	# fl.close()
3120	return parmDict,varyList
3121
3122	def ShowLSParms(self,event):
3123	'''Displays a window showing all parameters in the refinement.
3124	Called from the Calculate/View LS Parms menu.
3125	'''
3126	parmDict,varyList = self.MakeLSParmDict()
3127	parmValDict = {}
3128	for i in parmDict:
3129	parmValDict[i] = parmDict[i][0]
3130
3131	reqVaryList = tuple(varyList) # save requested variables
3132	try:
3133	# process constraints
3134	sub = G2gd.GetPatternTreeItemId(self,self.root,'Constraints')
3135	Constraints = self.PatternTree.GetItemPyData(sub)
3136	constList = []
3137	for item in Constraints:
3138	if item.startswith('_'): continue
3139	constList += Constraints[item]
3140	G2mv.InitVars()
3141	constrDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
3142	groups,parmlist = G2mv.GroupConstraints(constrDict)
3143	G2mv.GenerateConstraints(groups,parmlist,varyList,constrDict,fixedList,parmValDict)
3144	G2mv.Map2Dict(parmValDict,varyList)
3145	except:
3146	pass
3147	dlg = G2gd.ShowLSParms(self,'Least Squares Parameters',parmValDict,varyList,reqVaryList)
3148	dlg.ShowModal()
3149	dlg.Destroy()
3150
3151	def OnRefine(self,event):
3152	'''Perform a refinement.
3153	Called from the Calculate/Refine menu.
3154	'''
3155	Id = G2gd.GetPatternTreeItemId(self,self.root,'Sequential results')
3156	if Id:
3157	dlg = wx.MessageDialog(
3158	self,
3159	'Your last refinement was sequential. Continue with "Refine", removing previous sequential results?',
3160	'Remove sequential results?',wx.OK\|wx.CANCEL)
3161	if dlg.ShowModal() == wx.ID_OK:
3162	self.PatternTree.Delete(Id)
3163	dlg.Destroy()
3164	else:
3165	dlg.Destroy()
3166	return
3167
3168	self.OnFileSave(event)
3169	# check that constraints are OK here
3170	errmsg, warnmsg = G2stIO.CheckConstraints(self.GSASprojectfile)
3171	if errmsg:
3172	print('Error in constraints:\n'+errmsg+
3173	'\nRefinement not possible')
3174	self.ErrorDialog('Constraint Error',
3175	'Error in constraints:\n'+errmsg+
3176	'\nRefinement not possible')
3177	return
3178	if warnmsg:
3179	print('Conflict between refinment flag settings and constraints:\n'+
3180	warnmsg+'\nRefinement not possible')
3181	self.ErrorDialog('Refinement Flag Error',
3182	'Conflict between refinment flag settings and constraints:\n'+
3183	warnmsg+
3184	'\nRefinement not possible')
3185	return
3186	#works - but it'd be better if it could restore plots
3187	dlg = wx.ProgressDialog('Residual','All data Rw =',101.0,
3188	style = wx.PD_ELAPSED_TIME\|wx.PD_AUTO_HIDE\|wx.PD_CAN_ABORT)
3189	screenSize = wx.ClientDisplayRect()
3190	Size = dlg.GetSize()
3191	Size = (int(Size[0]*1.2),Size[1]) # increase size a bit along x
3192	dlg.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5))
3193	dlg.SetSize(Size)
3194	Rw = 100.00
3195	try:
3196	Rw = G2stMn.Refine(self.GSASprojectfile,dlg)
3197	finally:
3198	dlg.Destroy()
3199	oldId = self.PatternTree.GetSelection() #retain current selection
3200	oldName = self.PatternTree.GetItemText(oldId)
3201	parentId = self.PatternTree.GetItemParent(oldId)
3202	parentName = ''
3203	if parentId:
3204	parentName = self.PatternTree.GetItemText(parentId) #find the current data tree name
3205	dlg = wx.MessageDialog(self,'Load new result?','Refinement results, Rw =%.3f'%(Rw),wx.OK\|wx.CANCEL)
3206	try:
3207	if dlg.ShowModal() == wx.ID_OK:
3208	Id = 0
3209	self.PatternTree.DeleteChildren(self.root)
3210	if self.HKL: self.HKL = []
3211	if self.G2plotNB.plotList:
3212	self.G2plotNB.clear()
3213	G2IO.ProjFileOpen(self)
3214	item, cookie = self.PatternTree.GetFirstChild(self.root)
3215	while item and not Id:
3216	name = self.PatternTree.GetItemText(item)
3217	if name[:4] in ['PWDR','HKLF']:
3218	Id = item
3219	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
3220	if parentName:
3221	parentId = G2gd.GetPatternTreeItemId(self, self.root, parentName)
3222	if parentId:
3223	itemId = G2gd.GetPatternTreeItemId(self, parentId, oldName)
3224	else:
3225	itemId = G2gd.GetPatternTreeItemId(self, self.root, oldName)
3226	self.PatternTree.SelectItem(itemId)
3227	elif Id:
3228	self.PatternTree.SelectItem(Id)
3229	finally:
3230	dlg.Destroy()
3231
3232	def OnSeqRefine(self,event):
3233	'''Perform a sequential refinement.
3234	Called from the Calculate/Sequential refine menu.
3235	'''
3236	Id = G2gd.GetPatternTreeItemId(self,self.root,'Sequential results')
3237	if not Id:
3238	Id = self.PatternTree.AppendItem(self.root,text='Sequential results')
3239	self.PatternTree.SetItemPyData(Id,{})
3240	self.OnFileSave(event)
3241	# check that constraints are OK here
3242	errmsg, warnmsg = G2stIO.CheckConstraints(self.GSASprojectfile)
3243	if errmsg:
3244	print('Error in constraints:\n'+errmsg+
3245	'\nRefinement not possible')
3246	self.ErrorDialog('Constraint Error',
3247	'Error in constraints:\n'+errmsg+
3248	'\nRefinement not possible')
3249	return
3250	if warnmsg:
3251	print('Conflict between refinment flag settings and constraints:\n'+
3252	warnmsg+'\nRefinement not possible')
3253	self.ErrorDialog('Refinement Flag Error',
3254	'Conflict between refinment flag settings and constraints:\n'+
3255	warnmsg+'\nRefinement not possible')
3256	return
3257	dlg = wx.ProgressDialog('Residual for histogram 0','Powder profile Rwp =',101.0,
3258	style = wx.PD_ELAPSED_TIME\|wx.PD_AUTO_HIDE\|wx.PD_CAN_ABORT)
3259	screenSize = wx.ClientDisplayRect()
3260	Size = dlg.GetSize()
3261	Size = (int(Size[0]*1.2),Size[1]) # increase size a bit along x
3262	dlg.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5))
3263	dlg.SetSize(Size)
3264	try:
3265	G2stMn.SeqRefine(self.GSASprojectfile,dlg)
3266	finally:
3267	dlg.Destroy()
3268	dlg = wx.MessageDialog(self,'Load new result?','Refinement results',wx.OK\|wx.CANCEL)
3269	try:
3270	if dlg.ShowModal() == wx.ID_OK:
3271	Id = 0
3272	self.PatternTree.DeleteChildren(self.root)
3273	if self.HKL: self.HKL = []
3274	if self.G2plotNB.plotList:
3275	self.G2plotNB.clear()
3276	G2IO.ProjFileOpen(self)
3277	Id = G2gd.GetPatternTreeItemId(self,self.root,'Sequential results')
3278	self.PatternTree.SelectItem(Id)
3279
3280	finally:
3281	dlg.Destroy()
3282
3283	def ErrorDialog(self,title,message,parent=None, wtype=wx.OK):
3284	'Display an error message'
3285	result = None
3286	if parent is None:
3287	dlg = wx.MessageDialog(self, message, title, wtype)
3288	else:
3289	dlg = wx.MessageDialog(parent, message, title, wtype)
3290	dlg.CenterOnParent() # not working on Mac
3291	try:
3292	result = dlg.ShowModal()
3293	finally:
3294	dlg.Destroy()
3295	return result
3296
3297	class GSASIImain(wx.App):
3298	'''Defines a wxApp for GSAS-II
3299
3300	Creates a wx frame (self.main) which contains the display of the
3301	data tree.
3302	'''
3303	def OnInit(self):
3304	'''Called automatically when the app is created.'''
3305	if '2.7' not in sys.version[:5]:
3306	dlg = wx.MessageDialog(None,
3307	'GSAS-II requires Python 2.7.x\n Yours is '+sys.version[:5],
3308	'Python version error', wx.OK)
3309	try:
3310	result = dlg.ShowModal()
3311	finally:
3312	dlg.Destroy()
3313	sys.exit()
3314	self.main = GSASII(None)
3315	self.main.Show()
3316	self.SetTopWindow(self.main)
3317	return True
3318	def MacOpenFile(self, filename):
3319	'''Called on Mac every time a file is dropped on the app when it is running,
3320	treat this like a File/Open project menu action.
3321	Should be ignored on other platforms
3322	'''
3323	self.main.OnFileOpen(None,filename)
3324
3325	def main():
3326	'''Start up the GSAS-II application'''
3327	#application = GSASIImain() # don't redirect output, someday we
3328	# may want to do this if we can
3329	application = GSASIImain(0)
3330	if wxInspector:
3331	import wx.lib.inspection as wxeye
3332	wxeye.InspectionTool().Show()
3333
3334	#application.main.OnRefine(None)
3335	application.MainLoop()
3336
3337	if __name__ == '__main__':
3338	main() # start the GUI

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