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source: trunk/GSASII.py @ 1170

Last change on this file since 1170 was 1170, checked in by vondreele, 10 years ago
remove Rigid bodies from delete data list revise geometric correction for tilted detectors
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
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1	#!/usr/bin/env python
2	# -- coding: utf-8 --
3	#GSASII
4	########### SVN repository information ###################
5	# $Date: 2013-12-17 18:06:10 +0000 (Tue, 17 Dec 2013) $
6	# $Author: vondreele $
7	# $Revision: 1170 $
8	# $URL: trunk/GSASII.py $
9	# $Id: GSASII.py 1170 2013-12-17 18:06:10Z 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: 1170 $")
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
76	#wx inspector - use as needed
77	wxInspector = False
78
79	# print versions
80	print "Python module versions loaded:"
81	print "python: ",sys.version[:5]
82	print "wxpython: ",wx.__version__
83	print "matplotlib: ",mpl.__version__
84	print "numpy: ",np.__version__
85	print "scipy: ",sp.__version__
86	print "OpenGL: ",ogl.__version__
87	try:
88	import mkl
89	print "Max threads ",mkl.get_max_threads()
90	except:
91	pass
92	# print "MKL module not present"
93	__version__ = '0.2.0'
94	G2gd.__version__ = __version__
95	print "This is GSAS-II version: ",__version__,' revision '+str(GSASIIpath.GetVersionNumber())
96
97	# useful degree trig functions
98	sind = lambda x: math.sin(x*math.pi/180.)
99	cosd = lambda x: math.cos(x*math.pi/180.)
100	tand = lambda x: math.tan(x*math.pi/180.)
101	asind = lambda x: 180.*math.asin(x)/math.pi
102	acosd = lambda x: 180.*math.acos(x)/math.pi
103	atan2d = lambda x,y: 180.*math.atan2(y,x)/math.pi
104
105	def create(parent):
106	return GSASII(parent)
107
108	class GSASII(wx.Frame):
109	'''Define the main GSAS-II frame and its associated menu items
110	'''
111	def _Add_FileMenuItems(self, parent):
112	item = parent.Append(
113	help='Open a GSAS-II project file (*.gpx)', id=wx.ID_ANY,
114	kind=wx.ITEM_NORMAL,text='&Open project...')
115	self.Bind(wx.EVT_MENU, self.OnFileOpen, id=item.GetId())
116	item = parent.Append(
117	help='Save project under current name', id=wx.ID_ANY,
118	kind=wx.ITEM_NORMAL,text='&Save project')
119	self.Bind(wx.EVT_MENU, self.OnFileSave, id=item.GetId())
120	item = parent.Append(
121	help='Save current project to new file', id=wx.ID_ANY,
122	kind=wx.ITEM_NORMAL,text='Save project as...')
123	self.Bind(wx.EVT_MENU, self.OnFileSaveas, id=item.GetId())
124	item = parent.Append(
125	help='Create empty new project, saving current is optional', id=wx.ID_ANY,
126	kind=wx.ITEM_NORMAL,text='&New project')
127	self.Bind(wx.EVT_MENU, self.OnFileClose, id=item.GetId())
128	item = parent.Append(
129	help='Exit from GSAS-II', id=wx.ID_ANY,
130	kind=wx.ITEM_NORMAL,text='&Exit')
131	self.Bind(wx.EVT_MENU, self.OnFileExit, id=item.GetId())
132
133	def _Add_DataMenuItems(self,parent):
134	item = parent.Append(
135	help='',id=wx.ID_ANY,
136	kind=wx.ITEM_NORMAL,
137	text='Read image data...')
138	self.Bind(wx.EVT_MENU, self.OnImageRead, id=item.GetId())
139	item = parent.Append(
140	help='',id=wx.ID_ANY,
141	kind=wx.ITEM_NORMAL,
142	text='Read Powder Pattern Peaks...')
143	self.Bind(wx.EVT_MENU, self.OnReadPowderPeaks, id=item.GetId())
144	item = parent.Append(
145	help='',id=wx.ID_ANY,
146	kind=wx.ITEM_NORMAL,
147	text='Sum powder data')
148	self.Bind(wx.EVT_MENU, self.OnPwdrSum, id=item.GetId())
149	item = parent.Append(
150	help='',id=wx.ID_ANY,
151	kind=wx.ITEM_NORMAL,
152	text='Sum image data')
153	self.Bind(wx.EVT_MENU, self.OnImageSum, id=item.GetId())
154	item = parent.Append(
155	help='',id=wx.ID_ANY,
156	kind=wx.ITEM_NORMAL,
157	text='Add phase')
158	self.Bind(wx.EVT_MENU, self.OnAddPhase, id=item.GetId())
159	item = parent.Append(
160	help='',id=wx.ID_ANY,
161	kind=wx.ITEM_NORMAL,
162	text='Delete phase')
163	self.Bind(wx.EVT_MENU, self.OnDeletePhase, id=item.GetId())
164	item = parent.Append(
165	help='',id=wx.ID_ANY,
166	kind=wx.ITEM_NORMAL,
167	text='Rename data')
168	self.Bind(wx.EVT_MENU, self.OnRenameData, id=item.GetId())
169	item = parent.Append(
170	help='',id=wx.ID_ANY,
171	kind=wx.ITEM_NORMAL,
172	text='Delete data')
173	self.Bind(wx.EVT_MENU, self.OnDataDelete, id=item.GetId())
174
175	def _Add_CalculateMenuItems(self,parent):
176	item = parent.Append(help='Make new PDFs from selected powder patterns',
177	id=wx.ID_ANY, kind=wx.ITEM_NORMAL,text='Make new PDFs')
178	self.MakePDF.append(item)
179	# item.Enable(False)
180	self.Bind(wx.EVT_MENU, self.OnMakePDFs, id=item.GetId())
181
182	item = parent.Append(help='View least squares parameters',
183	id=wx.ID_ANY, kind=wx.ITEM_NORMAL,text='&View LS parms')
184	self.Bind(wx.EVT_MENU, self.ShowLSParms, id=item.GetId())
185
186	item = parent.Append(help='', id=wx.ID_ANY, kind=wx.ITEM_NORMAL,
187	text='&Refine')
188	if len(self.Refine): # extend state for new menus to match main (on mac)
189	state = self.Refine[0].IsEnabled()
190	else:
191	state = False
192	item.Enable(state)
193	self.Refine.append(item)
194	self.Bind(wx.EVT_MENU, self.OnRefine, id=item.GetId())
195
196	item = parent.Append(help='', id=wx.ID_ANY, kind=wx.ITEM_NORMAL,
197	text='Sequential refine')
198	if len(self.SeqRefine): # extend state for new menus to match main (on mac)
199	state = self.SeqRefine[0].IsEnabled()
200	else:
201	state = False
202	item.Enable(state)
203	self.SeqRefine.append(item)
204	self.Bind(wx.EVT_MENU, self.OnSeqRefine, id=item.GetId())
205
206	def _init_Imports(self):
207	'''import all the G2phase.py & G2sfact.py & G2pwd*.py files that
208	are found in the path
209	'''
210
211	self.ImportPhaseReaderlist = []
212	self._init_Import_routines('phase',self.ImportPhaseReaderlist,'Phase')
213	self.ImportSfactReaderlist = []
214	self._init_Import_routines('sfact',self.ImportSfactReaderlist,'Struct_Factor')
215	self.ImportPowderReaderlist = []
216	self._init_Import_routines('pwd',self.ImportPowderReaderlist,'Powder_Data')
217	self.ImportMenuId = {}
218
219	def _init_Import_routines(self,prefix,readerlist,errprefix):
220	'''import all the import readers matching the prefix
221	'''
222	#path2GSAS2 = os.path.dirname(os.path.realpath(__file__)) # location of this file
223	#pathlist = sys.path[:]
224	#if path2GSAS2 not in pathlist: pathlist.append(path2GSAS2)
225	#path2GSAS2 = os.path.join(
226	# os.path.dirname(os.path.realpath(__file__)), # location of this file
227	# 'imports')
228	pathlist = sys.path[:]
229	#if path2GSAS2 not in pathlist: pathlist.append(path2GSAS2)
230
231	filelist = []
232	for path in pathlist:
233	for filename in glob.iglob(os.path.join(
234	path,
235	"G2"+prefix+"*.py")):
236	filelist.append(filename)
237	#print 'debug: found',filename
238	filelist = sorted(list(set(filelist))) # remove duplicates
239	for filename in filelist:
240	path,rootname = os.path.split(filename)
241	pkg = os.path.splitext(rootname)[0]
242	try:
243	fp = None
244	fp, fppath,desc = imp.find_module(pkg,[path,])
245	pkg = imp.load_module(pkg,fp,fppath,desc)
246	for clss in inspect.getmembers(pkg): # find classes defined in package
247	if clss[0].startswith('_'): continue
248	if inspect.isclass(clss[1]):
249	# check if we have the required methods
250	for m in 'Reader','ExtensionValidator','ContentsValidator':
251	if not hasattr(clss[1],m): break
252	if not callable(getattr(clss[1],m)): break
253	else:
254	reader = clss[1]() # create an import instance
255	readerlist.append(reader)
256	except AttributeError:
257	print 'Import_'+errprefix+': Attribute Error'+str(filename)
258	pass
259	except ImportError:
260	print 'Import_'+errprefix+': Error importing file'+str(filename)
261	pass
262	if fp: fp.close()
263
264	def OnImportGeneric(self,reader,readerlist,label,multiple=False,usedRanIdList=[]):
265	'''Used to import Phases, powder dataset or single
266	crystal datasets (structure factor tables) using reader objects
267	subclassed from :class:`GSASIIIO.ImportPhase`, :class:`GSASIIIO.ImportStructFactor`
268	or :class:`GSASIIIO.ImportPowderData`. If a reader is specified, only
269	that will be attempted, but if no reader is specified, every one
270	that is potentially compatible (by file extension) will
271	be tried on the selected file(s).
272
273	:param readerobject reader: This will be a reference to
274	a particular object to be used to read a file or None,
275	if every appropriate reader should be used.
276
277	:param list readerlist: a list of reader objects appropriate for
278	the current read attempt. At present, this will be either
279	self.ImportPhaseReaderlist, self.ImportSfactReaderlist or
280	self.ImportPowderReaderlist (defined in _init_Imports from
281	the files found in the path), but in theory this list could
282	be tailored. Used only when reader is None.
283
284	:param str label: string to place on the open file dialog:
285	Open `label` input file
286
287	:param bool multiple: True if multiple files can be selected
288	in the file dialog. False is default. At present True is used
289	only for reading of powder data.
290
291	:param list usedRanIdList: an optional list of random Ids that
292	have been used and should not be reused
293
294	:returns: a list of reader objects (rd_list) that were able
295	to read the specified file(s). This list may be empty.
296	'''
297	self.lastimport = ''
298	self.zipfile = None
299	singlereader = True
300	if reader is None:
301	singlereader = False
302	multiple = False
303	#print "use all formats"
304	choices = "any file (.)\|."
305	choices += "\|zip archive (.zip)\|*.zip"
306	extdict = {}
307	# compile a list of allowed extensions
308	for rd in readerlist:
309	fmt = rd.formatName
310	for extn in rd.extensionlist:
311	if not extdict.get(extn): extdict[extn] = []
312	extdict[extn] += [fmt,]
313	for extn in sorted(extdict.keys(),cmp=lambda x,y: cmp(x.lower(), y.lower())):
314	fmt = ''
315	for f in extdict[extn]:
316	if fmt != "": fmt += ', '
317	fmt += f
318	choices += "\|" + fmt + " file (" + extn + ")\|" + extn
319	else:
320	readerlist = [reader,]
321	# compile a list of allowed extensions
322	choices = reader.formatName + " file ("
323	w = ""
324	for extn in reader.extensionlist:
325	if w != "": w += ";"
326	w += "*" + extn
327	choices += w + ")\|" + w
328	choices += "\|zip archive (.zip)\|*.zip"
329	if not reader.strictExtension:
330	choices += "\|any file (.)\|."
331	# get the file(s)
332	if multiple:
333	mode = style=wx.OPEN \| wx.CHANGE_DIR \| wx.MULTIPLE
334	else:
335	mode = style=wx.OPEN \| wx.CHANGE_DIR
336	dlg = wx.FileDialog(self, message="Choose "+label+" input file",
337	defaultFile="",wildcard=choices, style=mode)
338	try:
339	if dlg.ShowModal() == wx.ID_OK:
340	if multiple:
341	filelist = dlg.GetPaths()
342	if len(filelist) == 0: return []
343	else:
344	filename = dlg.GetPath()
345	filelist = [filename,]
346	os.chdir(dlg.GetDirectory()) # to get Mac/Linux to change directory!
347	else: # cancel was pressed
348	return []
349	finally:
350	dlg.Destroy()
351	rd_list = []
352	filelist1 = []
353	for filename in filelist:
354	# is this a zip file?
355	if os.path.splitext(filename)[1].lower() == '.zip':
356	extractedfiles = G2IO.ExtractFileFromZip(
357	filename,parent=self,
358	multipleselect=True)
359	if extractedfiles is None: continue # error or Cancel
360	if extractedfiles != filename:
361	self.zipfile = filename # save zip name
362	filelist1 += extractedfiles
363	continue
364	filelist1.append(filename)
365	filelist = filelist1
366	for filename in filelist:
367	# is this a zip file?
368	if os.path.splitext(filename)[1].lower() == '.zip':
369	extractedfile = G2IO.ExtractFileFromZip(filename,parent=self)
370	if extractedfile is None: continue # error or Cancel
371	if extractedfile != filename:
372	filename,self.zipfile = extractedfile,filename # now use the file that was created
373	# set what formats are compatible with this file
374	primaryReaders = []
375	secondaryReaders = []
376	for rd in readerlist:
377	flag = rd.ExtensionValidator(filename)
378	if flag is None:
379	secondaryReaders.append(rd)
380	elif flag:
381	primaryReaders.append(rd)
382	if len(secondaryReaders) + len(primaryReaders) == 0:
383	self.ErrorDialog('No Format','No matching format for file '+filename)
384	return []
385
386	fp = None
387	msg = ''
388	try:
389	fp = open(filename,'Ur')
390	if len(filelist) == 1:
391	# confirm we have the right file
392	rdmsg = 'File '+str(filename)+' begins:\n\n'
393	for i in range(3):
394	rdmsg += fp.readline()
395	rdmsg += '\n\nDo you want to read this file?'
396	if not all([ord(c) < 128 and ord(c) != 0 for c in rdmsg]): # show only if ASCII
397	rdmsg = 'File '+str(
398	filename)+' is a binary file. Do you want to read this file?'
399	result = wx.ID_NO
400	# it would be better to use something that
401	# would resize better, but this will do for now
402	dlg = wx.MessageDialog(
403	self, rdmsg,
404	'Is this the file you want?',
405	wx.YES_NO \| wx.ICON_QUESTION,
406	)
407	dlg.SetSize((700,300)) # does not resize on Mac
408	try:
409	result = dlg.ShowModal()
410	finally:
411	dlg.Destroy()
412	if result == wx.ID_NO: return []
413
414	self.lastimport = filename
415	# try the file first with Readers that specify the
416	# file's extension and later with ones that merely allow it
417	errorReport = ''
418	for rd in primaryReaders+secondaryReaders:
419	fp.seek(0) # rewind
420	rd.errors = "" # clear out any old errors
421	if not rd.ContentsValidator(fp): # rejected on cursory check
422	errorReport += "\n "+rd.formatName + ' validator error'
423	if rd.errors:
424	errorReport += ': '+rd.errors
425	continue
426	repeat = True
427	rdbuffer = {} # create temporary storage for file reader
428	block = 0
429	while repeat: # loop if the reader asks for another pass on the file
430	block += 1
431	repeat = False
432	fp.seek(0) # rewind
433	rd.objname = os.path.basename(filename)
434	flag = False
435	try:
436	flag = rd.Reader(filename,fp,self,
437	buffer=rdbuffer,
438	blocknum=block,
439	usedRanIdList=usedRanIdList,
440	)
441	except rd.ImportException as detail:
442	rd.errors += "\n Read exception: "+str(detail)
443	except Exception as detail:
444	rd.errors += "\n Unhandled read exception: "+str(detail)
445	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
446	if flag: # this read succeeded
447	rd_list.append(copy.deepcopy(rd)) # save the result before it is written over
448	if rd.repeat:
449	repeat = True
450	continue
451	errorReport += '\n'+rd.formatName + ' read error'
452	if rd.errors:
453	errorReport += ': '+rd.errors
454	if rd_list: # read succeeded, was there a warning or any errors?
455	if rd.warnings:
456	self.ErrorDialog('Read Warning','The '+ rd.formatName+
457	' reader reported a warning message:\n\n'+
458	rd.warnings)
459	break # success in reading, try no further
460	else:
461	if singlereader:
462	self.ErrorDialog('Read Error','The '+ rd.formatName+
463	' reader was not able to read file '+filename+msg+
464	'\n\nError message(s):\n'+errorReport
465	)
466	else:
467	self.ErrorDialog('Read Error','No reader was able to read file '+filename+msg+
468	'\n\nError messages:\n'+errorReport
469	)
470	except:
471	import traceback
472	print traceback.format_exc()
473	self.ErrorDialog('Open Error','Unexpected error trying to open or read file '+filename)
474	if fp: fp.close()
475	return rd_list
476
477	def _Add_ImportMenu_Phase(self,parent):
478	'''configure the Import Phase menus accord to the readers found in _init_Imports
479	'''
480	submenu = wx.Menu()
481	item = parent.AppendMenu(wx.ID_ANY, 'Phase',
482	submenu, help='Import phase data')
483	for reader in self.ImportPhaseReaderlist:
484	item = submenu.Append(wx.ID_ANY,help=reader.longFormatName,
485	kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file')
486	self.ImportMenuId[item.GetId()] = reader
487	self.Bind(wx.EVT_MENU, self.OnImportPhase, id=item.GetId())
488	item = submenu.Append(wx.ID_ANY,
489	help='Import phase data, use file to try to determine format',
490	kind=wx.ITEM_NORMAL,
491	text='guess format from file')
492	self.Bind(wx.EVT_MENU, self.OnImportPhase, id=item.GetId())
493
494	def OnImportPhase(self,event):
495	'''Called in response to an Import/Phase/... menu item
496	to read phase information.
497	dict self.ImportMenuId is used to look up the specific
498	reader item associated with the menu item, which will be
499	None for the last menu item, which is the "guess" option
500	where all appropriate formats will be tried.
501	'''
502	# look up which format was requested
503	reqrdr = self.ImportMenuId.get(event.GetId())
504	# make a list of used phase ranId's
505	phaseRIdList = []
506	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
507	if sub:
508	item, cookie = self.PatternTree.GetFirstChild(sub)
509	while item:
510	phaseName = self.PatternTree.GetItemText(item)
511	ranId = self.PatternTree.GetItemPyData(item).get('ranId')
512	if ranId: phaseRIdList.append(ranId)
513	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
514	rdlist = self.OnImportGeneric(reqrdr,
515	self.ImportPhaseReaderlist,
516	'phase',usedRanIdList=phaseRIdList)
517	if len(rdlist) == 0: return
518	# for now rdlist is only expected to have one element
519	# but this will allow multiple phases to be imported
520	self.CheckNotebook()
521	for rd in rdlist:
522	dlg = wx.TextEntryDialog( # allow editing of phase name
523	self, 'Enter the name for the new phase',
524	'Edit phase name', rd.Phase['General']['Name'],
525	style=wx.OK)
526	dlg.CenterOnParent()
527	if dlg.ShowModal() == wx.ID_OK:
528	rd.Phase['General']['Name'] = dlg.GetValue()
529	dlg.Destroy()
530	PhaseName = rd.Phase['General']['Name']
531	print 'Read phase '+str(PhaseName)+' from file '+str(self.lastimport)
532	if not G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
533	sub = self.PatternTree.AppendItem(parent=self.root,text='Phases')
534	else:
535	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
536	psub = self.PatternTree.AppendItem(parent=sub,text=PhaseName)
537	self.PatternTree.SetItemPyData(psub,rd.Phase)
538	self.PatternTree.Expand(self.root) # make sure phases are seen
539	self.PatternTree.Expand(sub)
540	self.PatternTree.Expand(psub)
541	if rd.Constraints:
542	sub = G2gd.GetPatternTreeItemId(self,self.root,'Constraints') # was created in CheckNotebook if needed
543	Constraints = self.PatternTree.GetItemPyData(sub)
544	# TODO: make sure that NEWVAR names are unique here?
545	for i in rd.Constraints:
546	if type(i) is dict:
547	#for j in i: print j,' --> ',i[j]
548	if '_Explain' not in Constraints: Constraints['_Explain'] = {}
549	Constraints['_Explain'].update(i)
550	continue
551	Constraints['Phase'].append(i)
552	return # success
553
554	def _Add_ImportMenu_Sfact(self,parent):
555	'''configure the Import Structure Factor menus accord to the readers found in _init_Imports
556	'''
557	submenu = wx.Menu()
558	item = parent.AppendMenu(wx.ID_ANY, 'Structure Factor',
559	submenu, help='Import Structure Factor data')
560	for reader in self.ImportSfactReaderlist:
561	item = submenu.Append(wx.ID_ANY,help=reader.longFormatName,
562	kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file')
563	self.ImportMenuId[item.GetId()] = reader
564	self.Bind(wx.EVT_MENU, self.OnImportSfact, id=item.GetId())
565	item = submenu.Append(wx.ID_ANY,
566	help='Import Structure Factor, use file to try to determine format',
567	kind=wx.ITEM_NORMAL,
568	text='guess format from file')
569	self.Bind(wx.EVT_MENU, self.OnImportSfact, id=item.GetId())
570
571	def OnImportSfact(self,event):
572	'''Called in response to an Import/Structure Factor/... menu item
573	to read single crystal datasets.
574	dict self.ImportMenuId is used to look up the specific
575	reader item associated with the menu item, which will be
576	None for the last menu item, which is the "guess" option
577	where all appropriate formats will be tried.
578	'''
579	# look up which format was requested
580	reqrdr = self.ImportMenuId.get(event.GetId())
581	rdlist = self.OnImportGeneric(reqrdr,self.ImportSfactReaderlist,
582	'Structure Factor')
583	if len(rdlist) == 0: return
584	self.CheckNotebook()
585	for rd in rdlist:
586	HistName = rd.objname
587	if len(rdlist) <= 2:
588	dlg = wx.TextEntryDialog( # allow editing of Structure Factor name
589	self, 'Enter the name for the new Structure Factor',
590	'Edit Structure Factor name', HistName,
591	style=wx.OK)
592	dlg.CenterOnParent()
593	if dlg.ShowModal() == wx.ID_OK:
594	HistName = dlg.GetValue()
595	dlg.Destroy()
596	print 'Read structure factor table '+str(HistName)+' from file '+str(self.lastimport)
597	if not rd.RefDict['FF']:
598	rd.RefDict['FF'] = [{} for i in range(len(rd.RefDict['RefList']))]
599	Id = self.PatternTree.AppendItem(parent=self.root,
600	text='HKLF '+HistName)
601	valuesdict = {
602	'wtFactor':1.0,
603	'Dummy':False,
604	'ranId':ran.randint(0,sys.maxint),
605	}
606	self.PatternTree.SetItemPyData(Id,[valuesdict,rd.RefDict])
607	Sub = self.PatternTree.AppendItem(Id,text='Instrument Parameters')
608	self.PatternTree.SetItemPyData(Sub,rd.Parameters)
609	self.PatternTree.SetItemPyData(
610	self.PatternTree.AppendItem(Id,text='HKL Plot Controls'),
611	rd.Controls)
612	self.PatternTree.SetItemPyData(
613	self.PatternTree.AppendItem(Id,text='Reflection List'),[]) #dummy entry for GUI use
614	self.PatternTree.SelectItem(Id)
615	self.PatternTree.Expand(Id)
616	self.Sngl = Id
617	return # success
618
619	def _Add_ImportMenu_powder(self,parent):
620	'''configure the Powder Data menus accord to the readers found in _init_Imports
621	'''
622	submenu = wx.Menu()
623	item = parent.AppendMenu(wx.ID_ANY, 'Powder Data',
624	submenu, help='Import Powder data')
625	for reader in self.ImportPowderReaderlist:
626	item = submenu.Append(wx.ID_ANY,help=reader.longFormatName,
627	kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file')
628	self.ImportMenuId[item.GetId()] = reader
629	self.Bind(wx.EVT_MENU, self.OnImportPowder, id=item.GetId())
630	item = submenu.Append(wx.ID_ANY,
631	help='Import powder data, use file to try to determine format',
632	kind=wx.ITEM_NORMAL,text='guess format from file')
633	self.Bind(wx.EVT_MENU, self.OnImportPowder, id=item.GetId())
634	submenu.AppendSeparator()
635	item = submenu.Append(wx.ID_ANY,
636	help='Create a powder data set entry that will be simulated',
637	kind=wx.ITEM_NORMAL,text='Simulate a dataset')
638	self.Bind(wx.EVT_MENU, self.OnDummyPowder, id=item.GetId())
639
640	def ReadPowderInstprm(self,instfile): #fix the write routine for [inst1,inst2] style
641	'''Read a GSAS-II (new) instrument parameter file
642
643	:param str instfile: name of instrument parameter file
644
645	'''
646	if os.path.splitext(instfile)[1].lower() != '.instprm': # invalid file
647	return None
648	if not os.path.exists(instfile): # no such file
649	return None
650	File = open(instfile,'r')
651	S = File.readline()
652	if not S.startswith('#GSAS-II'): # not a valid file
653	File.close()
654	return None
655	newItems = []
656	newVals = []
657	while S:
658	if S[0] == '#':
659	S = File.readline()
660	continue
661	[item,val] = S[:-1].split(':')
662	newItems.append(item)
663	try:
664	newVals.append(float(val))
665	except ValueError:
666	newVals.append(val)
667	S = File.readline()
668	File.close()
669	# add a second MT dict here. TOF parms? (BHT)
670	return G2IO.makeInstDict(newItems,newVals,len(newVals)*[False,]),{}
671
672	def ReadPowderIparm(self,instfile,bank,databanks,rd):
673	'''Read a GSAS (old) instrument parameter file
674
675	:param str instfile: name of instrument parameter file
676
677	:param int bank: the bank number read in the raw data file
678
679	:param int databanks: the number of banks in the raw data file.
680	If the number of banks in the data and instrument parameter files
681	agree, then the sets of banks are assumed to match up and bank
682	is used to select the instrument parameter file. If not, the user
683	is asked to make a selection.
684
685	:param obj rd: the raw data (histogram) data object. This
686	sets rd.instbank.
687
688	'''
689	if not os.path.exists(instfile): # no such file
690	return {}
691	fp = 0
692	try:
693	fp = open(instfile,'Ur')
694	Iparm = {}
695	for S in fp:
696	Iparm[S[:12]] = S[12:-1]
697	except IOError:
698	print('Error reading file:'+str(instfile))
699	if fp:
700	fp.close()
701
702	ibanks = int(Iparm.get('INS BANK ','1').strip())
703	hType = Iparm['INS HTYPE '].strip()
704	if ibanks == 1: # there is only one bank here, return it
705	rd.instbank = 1
706	return Iparm
707	if 'PNT' in hType:
708	rd.instbank = bank
709	elif ibanks != databanks:
710	# number of banks in data and prm file not not agree, need a
711	# choice from a human here
712	choices = []
713	for i in range(1,1+ibanks):
714	choices.append('Bank '+str(i))
715	bank = rd.BlockSelector(
716	choices, self,
717	title='Select an instrument parameter bank for '+
718	os.path.split(rd.powderentry[0])[1]+' BANK '+str(bank)+
719	'\nOr use Cancel to select from the default parameter sets',
720	header='Block Selector')
721	if bank is None: return {}
722	# pull out requested bank # bank from the data, and change the bank to 1
723	IparmS = {}
724	for key in Iparm:
725	if key[4:6] == " ":
726	IparmS[key] = Iparm[key]
727	elif int(key[4:6].strip()) == bank:
728	IparmS[key[:4]+' 1'+key[6:]] = Iparm[key]
729	rd.instbank = bank
730	return IparmS
731
732	def GetPowderIparm(self,rd, prevIparm, lastIparmfile, lastdatafile):
733	'''Open and read an instrument parameter file for a data file
734	Returns the list of parameters used in the data tree
735
736	:param obj rd: the raw data (histogram) data object.
737
738	:param str prevIparm: not used
739
740	:param str lastIparmfile: Name of last instrument parameter
741	file that was read, or a empty string.
742
743	:param str lastdatafile: Name of last data file that was read.
744
745	:returns: a list of two dicts, the first containing instrument parameters
746	and the second used for future TOF datasets (timemaps?)
747
748	'''
749	def SetPowderInstParms(Iparm, rd):
750	'''extracts values from instrument parameters in rd.instdict
751	or in array Iparm.
752	Create and return the contents of the instrument parameter tree entry.
753	'''
754	DataType = Iparm['INS HTYPE '].strip()[:3] # take 1st 3 chars
755	# override inst values with values read from data file
756	if rd.instdict.get('type'):
757	DataType = rd.instdict.get('type')
758	data = [DataType,]
759	instname = Iparm.get('INS 1INAME ')
760	if instname:
761	rd.Sample['InstrName'] = instname.strip()
762	if 'C' in DataType:
763	wave1 = None
764	wave2 = 0.0
765	if rd.instdict.get('wave'):
766	wl = rd.instdict.get('wave')
767	wave1 = wl[0]
768	if len(wl) > 1: wave2 = wl[1]
769	s = Iparm['INS 1 ICONS']
770	if not wave1:
771	wave1 = G2IO.sfloat(s[:10])
772	wave2 = G2IO.sfloat(s[10:20])
773	v = (wave1,wave2,
774	G2IO.sfloat(s[20:30]),G2IO.sfloat(s[55:65]),G2IO.sfloat(s[40:50])) #get lam1, lam2, zero, pola & ratio
775	if not v[1]:
776	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
777	v = (v[0],v[2],v[4])
778	codes = [0,0,0,0]
779	else:
780	names = ['Type','Lam1','Lam2','Zero','I(L2)/I(L1)','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
781	codes = [0,0,0,0,0,0]
782	data.extend(v)
783	v1 = Iparm['INS 1PRCF1 '].split()
784	v = Iparm['INS 1PRCF11'].split()
785	data.extend([float(v[0]),float(v[1]),float(v[2])]) #get GU, GV & GW - always here
786	azm = float(Iparm.get('INS 1DETAZM','0.0'))
787	v = Iparm['INS 1PRCF12'].split()
788	if v1[0] == 3:
789	data.extend([float(v[0]),float(v[1]),float(v[2])+float(v[3],azm)]) #get LX, LY, S+H/L & azimuth
790	else:
791	data.extend([0.0,0.0,0.002,azm]) #OK defaults if fxn #3 not 1st in iprm file
792	codes.extend([0,0,0,0,0,0,0])
793	return [G2IO.makeInstDict(names,data,codes),{}]
794	elif 'T' in DataType:
795	names = ['Type','2-theta','difC','difA','Zero','alpha','beta-0','beta-1',
796	'beta-q','sig-0','sig-1','sig-q','X','Y','Azimuth']
797	codes = [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
798	azm = 0.
799	if 'INS 1DETAZM' in Iparm:
800	azm = float(Iparm['INS 1DETAZM'])
801	s = Iparm['INS 1BNKPAR'].split()
802	data.extend([G2IO.sfloat(s[1]),]) #2-theta for bank
803	s = Iparm['INS 1 ICONS'].split()
804	data.extend([G2IO.sfloat(s[0]),G2IO.sfloat(s[1]),G2IO.sfloat(s[2])]) #difC, difA, Zero
805	s = Iparm['INS 1PRCF1 '].split()
806	pfType = int(s[0])
807	s = Iparm['INS 1PRCF11'].split()
808	if abs(pfType) == 1:
809	data.extend([G2IO.sfloat(s[1]),G2IO.sfloat(s[2]),G2IO.sfloat(s[3])])
810	s = Iparm['INS 1PRCF12'].split()
811	data.extend([0.0,0.0,G2IO.sfloat(s[1]),0.0,0.0,0.0,azm])
812	elif abs(pfType) in [3,4,5]:
813	data.extend([G2IO.sfloat(s[0]),G2IO.sfloat(s[1]),G2IO.sfloat(s[2])])
814	if abs(pfType) == 4:
815	data.extend([0.0,0.0,G2IO.sfloat(s[3]),0.0,0.0,0.0,azm])
816	else:
817	s = Iparm['INS 1PRCF12'].split()
818	data.extend([0.0,0.0,G2IO.sfloat(s[0]),0.0,0.0,0.0,azm])
819	Inst1 = G2IO.makeInstDict(names,data,codes)
820	Inst2 = {}
821	if pfType < 0:
822	Ipab = 'INS 1PAB'+str(-pfType)
823	Npab = int(Iparm[Ipab+' '].strip())
824	Inst2['Pdabc'] = []
825	for i in range(Npab):
826	k = Ipab+str(i+1).rjust(2)
827	s = Iparm[k].split()
828	Inst2['Pdabc'].append([float(t) for t in s])
829	Inst2['Pdabc'] = np.array(Inst2['Pdabc'])
830	Inst2['Pdabc'].T[3] += Inst2['Pdabc'].T[0]*Inst1['difC'][0] #turn 3rd col into TOF
831	if 'INS 1I ITYP' in Iparm:
832	s = Iparm['INS 1I ITYP'].split()
833	Ityp = int(s[0])
834	Tminmax = [float(s[1])1000.,float(s[2])1000.]
835	Itypes = ['Exponential','Maxwell/Exponential','','Maxwell/Chebyschev','']
836	if Ityp in [1,2,4]:
837	Inst2['Itype'] = Itypes[Ityp-1]
838	Inst2['Tminmax'] = Tminmax
839	Icoeff = []
840	Iesd = []
841	Icovar = []
842	for i in range(3):
843	s = Iparm['INS 1ICOFF'+str(i+1)].split()
844	Icoeff += [float(S) for S in s]
845	s = Iparm['INS 1IECOF'+str(i+1)].split()
846	Iesd += [float(S) for S in s]
847	for i in range(8):
848	s = Iparm['INS 1IECOR'+str(i+1)].split()
849	Icovar += [float(S) for S in s]
850	Inst2['Icoeff'] = Icoeff
851	Inst2['Iesd'] = Iesd
852	Inst2['Icovar'] = Icovar
853	return [Inst1,Inst2]
854
855	# stuff we might need from the reader
856	filename = rd.powderentry[0]
857	bank = rd.powderentry[2]
858	numbanks = rd.numbanks
859	# is there an instrument parameter file defined for the current data set?
860	if rd.instparm or (lastdatafile == filename and lastIparmfile):
861	if rd.instparm:
862	instfile = os.path.join(os.path.split(filename)[0],
863	rd.instparm)
864	else:
865	# for multiple reads of one data file, reuse the inst parm file
866	instfile = lastIparmfile
867	if os.path.exists(instfile):
868	#print 'debug: try read',instfile
869	instParmList = self.ReadPowderInstprm(instfile)
870	if instParmList is not None:
871	rd.instfile = instfile
872	rd.instmsg = 'GSAS-II file '+instfile
873	return instParmList
874	Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd)
875	if Iparm:
876	#print 'debug: success'
877	rd.instfile = instfile
878	rd.instmsg = instfile + ' bank ' + str(rd.instbank)
879	return SetPowderInstParms(Iparm,rd)
880	else:
881	self.ErrorDialog('Open Error','Error opening instrument parameter file '
882	+str(instfile)+' requested by file '+ filename)
883	# is there an instrument parameter file matching the current file
884	# with extension .inst or .prm? If so read it
885	basename = os.path.splitext(filename)[0]
886	for ext in '.instprm','.prm','.inst','.ins':
887	instfile = basename + ext
888	instParmList = self.ReadPowderInstprm(instfile)
889	if instParmList is not None:
890	rd.instfile = instfile
891	rd.instmsg = 'GSAS-II file '+instfile
892	return instParmList
893	Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd)
894	if Iparm:
895	#print 'debug: success'
896	rd.instfile = instfile
897	rd.instmsg = instfile + ' bank ' + str(rd.instbank)
898	return SetPowderInstParms(Iparm,rd)
899	else:
900	#print 'debug: open/read failed',instfile
901	pass # fail silently
902
903	# did we read the data file from a zip? If so, look there for a
904	# instrument parameter file
905	if self.zipfile:
906	for ext in '.instprm','.prm','.inst','.ins':
907	instfile = G2IO.ExtractFileFromZip(
908	self.zipfile,
909	selection=os.path.split(basename + ext)[1],
910	parent=self)
911	if instfile is not None and instfile != self.zipfile:
912	print 'debug:',instfile,'created from ',self.zipfile
913	instParmList = self.ReadPowderInstprm(instfile)
914	if instParmList is not None:
915	rd.instfile = instfile
916	rd.instmsg = 'GSAS-II file '+instfile
917	return instParmList
918	Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd)
919	if Iparm:
920	rd.instfile = instfile
921	rd.instmsg = instfile + ' bank ' + str(rd.instbank)
922	return SetPowderInstParms(Iparm,rd)
923	else:
924	#print 'debug: open/read for',instfile,'from',self.zipfile,'failed'
925	pass # fail silently
926
927	while True: # loop until we get a file that works or we get a cancel
928	instfile = ''
929	dlg = wx.FileDialog(
930	self,
931	'Choose inst. param file for "'
932	+rd.idstring
933	+'" (or Cancel for default)',
934	'.', '',
935	'GSAS iparm file (.prm,.inst,.ins)\|.prm;.inst;.ins\|'
936	'GSAS-II iparm file (.instprm)\|.instprm\|'
937	'All files (.)\|.',
938	wx.OPEN\|wx.CHANGE_DIR)
939	if os.path.exists(lastIparmfile):
940	dlg.SetFilename(lastIparmfile)
941	if dlg.ShowModal() == wx.ID_OK:
942	instfile = dlg.GetPath()
943	dlg.Destroy()
944	if not instfile: break
945	instParmList = self.ReadPowderInstprm(instfile)
946	if instParmList is not None:
947	rd.instfile = instfile
948	rd.instmsg = 'GSAS-II file '+instfile
949	return instParmList
950	Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd)
951	if Iparm:
952	#print 'debug: success with',instfile
953	rd.instfile = instfile
954	rd.instmsg = instfile + ' bank ' + str(rd.instbank)
955	return SetPowderInstParms(Iparm,rd)
956	else:
957	self.ErrorDialog('Read Error',
958	'Error opening/reading file '+str(instfile))
959
960	# still no success: offer user choice of defaults
961	while True: # loop until we get a choice
962	choices = []
963	head = 'Select from default instrument parameters for '+rd.idstring
964
965	for l in rd.defaultIparm_lbl:
966	choices.append('Defaults for '+l)
967	res = rd.BlockSelector(
968	choices,
969	ParentFrame=self,
970	title=head,
971	header='Select default inst parms',
972	useCancel=False)
973	if res is None: continue
974	rd.instfile = ''
975	rd.instmsg = 'default: '+rd.defaultIparm_lbl[res]
976	return SetPowderInstParms(rd.defaultIparms[res],rd)
977
978	def OnImportPowder(self,event):
979	'''Called in response to an Import/Powder Data/... menu item
980	to read a powder diffraction data set.
981	dict self.ImportMenuId is used to look up the specific
982	reader item associated with the menu item, which will be
983	None for the last menu item, which is the "guess" option
984	where all appropriate formats will be tried.
985
986	Also reads an instrument parameter file for each dataset.
987	'''
988	reqrdr = self.ImportMenuId.get(event.GetId()) # look up which format was requested
989	rdlist = self.OnImportGeneric(
990	reqrdr,self.ImportPowderReaderlist,'Powder Data',multiple=True)
991	if len(rdlist) == 0: return
992	self.CheckNotebook()
993	Iparm = None
994	lastIparmfile = ''
995	lastdatafile = ''
996	for rd in rdlist:
997	# get instrument parameters for each dataset
998	Iparm1,Iparm2 = self.GetPowderIparm(rd, Iparm, lastIparmfile, lastdatafile)
999	if rd.repeat_instparm:
1000	lastIparmfile = rd.instfile
1001	lastdatafile = rd.powderentry[0]
1002	print 'Read powder data '+str(rd.idstring)+ \
1003	' from file '+str(self.lastimport) + \
1004	' with parameters from '+str(rd.instmsg)
1005	# data are read, now store them in the tree
1006	Id = self.PatternTree.AppendItem(parent=self.root,
1007	text='PWDR '+rd.idstring)
1008	if 'T' in Iparm1['Type'][0]:
1009	if not rd.clockWd and rd.GSAS:
1010	rd.powderdata[0] *= 100. #put back the CW centideg correction
1011	cw = np.diff(rd.powderdata[0])
1012	rd.powderdata[0] = rd.powderdata[0][:-1]+cw/2.
1013	rd.powderdata[1] = rd.powderdata[1][:-1]/cw
1014	rd.powderdata[2] = rd.powderdata[2][:-1]cw*2 #1/var=w at this point
1015	if 'Itype' in Iparm2:
1016	Ibeg = np.searchsorted(rd.powderdata[0],Iparm2['Tminmax'][0])
1017	Ifin = np.searchsorted(rd.powderdata[0],Iparm2['Tminmax'][1])
1018	rd.powderdata[0] = rd.powderdata[0][Ibeg:Ifin]
1019	YI,WYI = G2pwd.calcIncident(Iparm2,rd.powderdata[0])
1020	rd.powderdata[1] = rd.powderdata[1][Ibeg:Ifin]/YI
1021	var = 1./rd.powderdata[2][Ibeg:Ifin]
1022	var += WYIrd.powderdata[1]*2
1023	var /= YI**2
1024	rd.powderdata[2] = 1./var
1025	rd.powderdata[3] = np.zeros_like(rd.powderdata[0])
1026	rd.powderdata[4] = np.zeros_like(rd.powderdata[0])
1027	rd.powderdata[5] = np.zeros_like(rd.powderdata[0])
1028	Tmin = min(rd.powderdata[0])
1029	Tmax = max(rd.powderdata[0])
1030	valuesdict = {
1031	'wtFactor':1.0,
1032	'Dummy':False,
1033	'ranId':ran.randint(0,sys.maxint),
1034	}
1035	rd.Sample['ranId'] = valuesdict['ranId'] # this should be removed someday
1036	self.PatternTree.SetItemPyData(Id,[valuesdict,rd.powderdata])
1037	self.PatternTree.SetItemPyData(
1038	self.PatternTree.AppendItem(Id,text='Comments'),
1039	rd.comments)
1040	self.PatternTree.SetItemPyData(
1041	self.PatternTree.AppendItem(Id,text='Limits'),
1042	[(Tmin,Tmax),[Tmin,Tmax]])
1043	self.PatternId = G2gd.GetPatternTreeItemId(self,Id,'Limits')
1044	self.PatternTree.SetItemPyData(
1045	self.PatternTree.AppendItem(Id,text='Background'),
1046	[['chebyschev',True,3,1.0,0.0,0.0],
1047	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
1048	self.PatternTree.SetItemPyData(
1049	self.PatternTree.AppendItem(Id,text='Instrument Parameters'),
1050	[Iparm1,Iparm2])
1051	self.PatternTree.SetItemPyData(
1052	self.PatternTree.AppendItem(Id,text='Sample Parameters'),
1053	rd.Sample)
1054	self.PatternTree.SetItemPyData(
1055	self.PatternTree.AppendItem(Id,text='Peak List')
1056	,[])
1057	self.PatternTree.SetItemPyData(
1058	self.PatternTree.AppendItem(Id,text='Index Peak List'),
1059	[])
1060	self.PatternTree.SetItemPyData(
1061	self.PatternTree.AppendItem(Id,text='Unit Cells List'),
1062	[])
1063	self.PatternTree.SetItemPyData(
1064	self.PatternTree.AppendItem(Id,text='Reflection Lists'),
1065	{})
1066	self.PatternTree.Expand(Id)
1067	self.PatternTree.SelectItem(Id)
1068	return # success
1069
1070	def OnDummyPowder(self,event):
1071	'''Called in response to Import/Powder Data/Simulate menu item
1072	to create a Dummy powder diffraction data set.
1073
1074	Reads an instrument parameter file and then gets input from the user
1075	'''
1076	rd = G2IO.ImportPowderData(
1077	extensionlist=tuple(),
1078	strictExtension=False,
1079	formatName = 'Simulate dataset',
1080	longFormatName = 'Compute a simulated pattern')
1081	rd.powderentry[0] = '' # no filename
1082	# #self.powderentry[1] = pos # bank offset (N/A here)
1083	rd.powderentry[2] = 1 # only one bank
1084	rd.comments.append('This is a dummy dataset for powder pattern simulation')
1085	self.CheckNotebook()
1086	Iparm = None
1087	lastIparmfile = ''
1088	lastdatafile = ''
1089	self.zipfile = None
1090	# get instrument parameters for
1091	Iparm1,Iparm2 = self.GetPowderIparm(rd, Iparm, lastIparmfile, lastdatafile)
1092	if 'T' in Iparm1['Type'][0]:
1093	print('TOF simulation not supported yet')
1094	return False
1095	else:
1096	# need to get name, 2theta start, end, step
1097	rd.idstring = ' CW'
1098	if 'X' in Iparm1['Type'][0]:
1099	rd.idstring = 'CW x-ray simulation'
1100	else:
1101	rd.idstring = 'CW neutron simulation'
1102	# base initial range on wavelength
1103	wave = Iparm1.get('Lam')
1104	if wave:
1105	wave = wave[0]
1106	else:
1107	wave = Iparm1.get('Lam1')
1108	if wave:
1109	wave = wave[0]
1110	N = 0
1111	while (N < 3): # insist on a dataset with a few points
1112	names = ('dataset name', 'start angle', 'end angle', 'step size')
1113	if not wave or wave < 1.0:
1114	inp = [rd.idstring, 10.,40.,0.005] # see names for what's what
1115	else:
1116	inp = [rd.idstring, 10.,80.,0.01] # see names for what's what
1117	dlg = G2gd.ScrolledMultiEditor(
1118	self,[inp] * len(inp),range(len(inp)),names,
1119	header='Enter simulation name and range',
1120	minvals=(None,0.001,0.001,0.0001),
1121	maxvals=(None,180.,180.,.1),
1122	sizevals=((225,-1),)
1123	)
1124	dlg.CenterOnParent()
1125	if dlg.ShowModal() == wx.ID_OK:
1126	if inp[1] > inp[2]:
1127	end,start,step = inp[1:]
1128	else:
1129	start,end,step = inp[1:]
1130	step = abs(step)
1131	else:
1132	return False
1133	N = int((end-start)/step)+1
1134	x = np.linspace(start,end,N,True)
1135	N = len(x)
1136	rd.powderdata = [
1137	np.array(x), # x-axis values
1138	np.zeros_like(x), # powder pattern intensities
1139	np.ones_like(x), # 1/sig(intensity)^2 values (weights)
1140	np.zeros_like(x), # calc. intensities (zero)
1141	np.zeros_like(x), # calc. background (zero)
1142	np.zeros_like(x), # obs-calc profiles
1143	]
1144	Tmin = rd.powderdata[0][0]
1145	Tmax = rd.powderdata[0][-1]
1146	# data are read, now store them in the tree
1147	Id = self.PatternTree.AppendItem(parent=self.root,
1148	text='PWDR '+inp[0])
1149	valuesdict = {
1150	'wtFactor':1.0,
1151	'Dummy':True,
1152	'ranId':ran.randint(0,sys.maxint),
1153	}
1154	self.PatternTree.SetItemPyData(Id,[valuesdict,rd.powderdata])
1155	self.PatternTree.SetItemPyData(
1156	self.PatternTree.AppendItem(Id,text='Comments'),
1157	rd.comments)
1158	self.PatternTree.SetItemPyData(
1159	self.PatternTree.AppendItem(Id,text='Limits'),
1160	[(Tmin,Tmax),[Tmin,Tmax]])
1161	self.PatternId = G2gd.GetPatternTreeItemId(self,Id,'Limits')
1162	self.PatternTree.SetItemPyData(
1163	self.PatternTree.AppendItem(Id,text='Background'),
1164	[['chebyschev',True,3,1.0,0.0,0.0],
1165	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
1166	self.PatternTree.SetItemPyData(
1167	self.PatternTree.AppendItem(Id,text='Instrument Parameters'),
1168	[Iparm1,Iparm2])
1169	self.PatternTree.SetItemPyData(
1170	self.PatternTree.AppendItem(Id,text='Sample Parameters'),
1171	rd.Sample)
1172	self.PatternTree.SetItemPyData(
1173	self.PatternTree.AppendItem(Id,text='Peak List')
1174	,[])
1175	self.PatternTree.SetItemPyData(
1176	self.PatternTree.AppendItem(Id,text='Index Peak List'),
1177	[])
1178	self.PatternTree.SetItemPyData(
1179	self.PatternTree.AppendItem(Id,text='Unit Cells List'),
1180	[])
1181	self.PatternTree.SetItemPyData(
1182	self.PatternTree.AppendItem(Id,text='Reflection Lists'),
1183	{})
1184	self.PatternTree.Expand(Id)
1185	self.PatternTree.SelectItem(Id)
1186	print('Added simulation powder data '+str(rd.idstring)+
1187	' with parameters from '+str(rd.instmsg))
1188	return # success
1189
1190	def _init_Exports(self,menu):
1191	'''Find exporter routines and add them into menus
1192	'''
1193	# set up the top-level menus
1194	projectmenu = wx.Menu()
1195	item = menu.AppendMenu(
1196	wx.ID_ANY, 'Entire project as',
1197	projectmenu, help='Export entire project')
1198
1199	phasemenu = wx.Menu()
1200	item = menu.AppendMenu(
1201	wx.ID_ANY, 'Phase as',
1202	phasemenu, help='Export phase or sometimes phases')
1203
1204	powdermenu = wx.Menu()
1205	item = menu.AppendMenu(
1206	wx.ID_ANY, 'Powder data as',
1207	powdermenu, help='Export powder diffraction histogram(s)')
1208
1209	singlemenu = wx.Menu()
1210	item = menu.AppendMenu(
1211	wx.ID_ANY, 'Single crystal data as',
1212	singlemenu, help='Export single crystal histogram(s)')
1213
1214	imagemenu = wx.Menu()
1215	item = menu.AppendMenu(
1216	wx.ID_ANY, 'Images as',
1217	imagemenu, help='Export powder image(s)')
1218
1219	mapmenu = wx.Menu()
1220	item = menu.AppendMenu(
1221	wx.ID_ANY, 'Maps as',
1222	mapmenu, help='Export density map(s)')
1223
1224	# pdfmenu = wx.Menu()
1225	# item = menu.AppendMenu(
1226	# wx.ID_ANY, 'PDFs as',
1227	# pdfmenu, help='Export pair distribution function(s)')
1228
1229	# find all the exporter files
1230	pathlist = sys.path
1231	filelist = []
1232	for path in pathlist:
1233	for filename in glob.iglob(os.path.join(
1234	path,
1235	"G2export*.py")):
1236	filelist.append(filename)
1237	filelist = sorted(list(set(filelist))) # remove duplicates
1238	exporterlist = []
1239	# go through the routines and import them, saving objects that
1240	# have export routines (method Exporter)
1241	for filename in filelist:
1242	path,rootname = os.path.split(filename)
1243	pkg = os.path.splitext(rootname)[0]
1244	try:
1245	fp = None
1246	fp, fppath,desc = imp.find_module(pkg,[path,])
1247	pkg = imp.load_module(pkg,fp,fppath,desc)
1248	for clss in inspect.getmembers(pkg): # find classes defined in package
1249	if clss[0].startswith('_'): continue
1250	if inspect.isclass(clss[1]):
1251	# check if we have the required methods
1252	for m in 'Exporter','loadParmDict':
1253	if not hasattr(clss[1],m): break
1254	if not callable(getattr(clss[1],m)): break
1255	else:
1256	exporter = clss[1](self) # create an export instance
1257	exporterlist.append(exporter)
1258	except AttributeError:
1259	print 'Import_'+errprefix+': Attribute Error'+str(filename)
1260	pass
1261	except ImportError:
1262	print 'Import_'+errprefix+': Error importing file'+str(filename)
1263	pass
1264	if fp: fp.close()
1265	# Add submenu item(s) for each Exporter by its self-declared type (can be more than one)
1266	for obj in exporterlist:
1267	#print 'exporter',obj
1268	for typ in obj.exporttype:
1269	if typ == "project":
1270	submenu = projectmenu
1271	elif typ == "phase":
1272	submenu = phasemenu
1273	elif typ == "powder":
1274	submenu = powdermenu
1275	elif typ == "single":
1276	submenu = singlemenu
1277	elif typ == "image":
1278	submenu = imagemenu
1279	elif typ == "map":
1280	submenu = mapmenu
1281	# elif typ == "pdf":
1282	# submenu = pdfmenu
1283	else:
1284	print("Error, unknown type in "+str(obj))
1285	break
1286	item = submenu.Append(
1287	wx.ID_ANY,
1288	help=obj.longFormatName,
1289	kind=wx.ITEM_NORMAL,
1290	text=obj.formatName)
1291	self.Bind(wx.EVT_MENU, obj.Exporter, id=item.GetId())
1292	self.ExportLookup[item.GetId()] = typ # lookup table for submenu item
1293	#code to debug an Exporter. much is hard-coded below, but code is reloaded before
1294	# each use allowing faster development
1295	# def DebugExport(event):
1296	# print 'start reload'
1297	# reload(G2IO)
1298	# import G2export_ASCIImap as dev
1299	# reload(dev)
1300	# dev.ExportMapASCII(self).Exporter(event)
1301	# item = menu.Append(
1302	# wx.ID_ANY,kind=wx.ITEM_NORMAL,
1303	# help="debug exporter",text="test Export")
1304	# self.Bind(wx.EVT_MENU, DebugExport, id=item.GetId())
1305	# #self.ExportLookup[item.GetId()] = 'image'
1306	# self.ExportLookup[item.GetId()] = 'map'
1307
1308	def _Add_ExportMenuItems(self,parent):
1309	item = parent.Append(
1310	help='Select PWDR item to enable',id=wx.ID_ANY,
1311	kind=wx.ITEM_NORMAL,
1312	text='Export Powder Patterns...')
1313	self.ExportPattern.append(item)
1314	item.Enable(False)
1315	self.Bind(wx.EVT_MENU, self.OnExportPatterns, id=item.GetId())
1316
1317	item = parent.Append(
1318	help='',id=wx.ID_ANY,
1319	kind=wx.ITEM_NORMAL,
1320	text='Export All Peak Lists...')
1321	self.ExportPeakList.append(item)
1322	item.Enable(True)
1323	self.Bind(wx.EVT_MENU, self.OnExportPeakList, id=item.GetId())
1324
1325	item = parent.Append(
1326	help='',id=wx.ID_ANY,
1327	kind=wx.ITEM_NORMAL,
1328	text='Export HKLs...')
1329	self.ExportHKL.append(item)
1330	self.Bind(wx.EVT_MENU, self.OnExportHKL, id=item.GetId())
1331
1332	item = parent.Append(
1333	help='Select PDF item to enable',
1334	id=wx.ID_ANY,
1335	kind=wx.ITEM_NORMAL,
1336	text='Export PDF...')
1337	self.ExportPDF.append(item)
1338	item.Enable(False)
1339	self.Bind(wx.EVT_MENU, self.OnExportPDF, id=item.GetId())
1340
1341	def FillMainMenu(self,menubar):
1342	'''Define contents of the main GSAS-II menu for the (main) data tree window
1343	in the mac, used also for the data item windows as well.
1344	'''
1345	File = wx.Menu(title='')
1346	menubar.Append(menu=File, title='&File')
1347	self._Add_FileMenuItems(File)
1348	Data = wx.Menu(title='')
1349	menubar.Append(menu=Data, title='Data')
1350	self._Add_DataMenuItems(Data)
1351	Calculate = wx.Menu(title='')
1352	menubar.Append(menu=Calculate, title='&Calculate')
1353	self._Add_CalculateMenuItems(Calculate)
1354	Import = wx.Menu(title='')
1355	menubar.Append(menu=Import, title='Import')
1356	self._Add_ImportMenu_Phase(Import)
1357	self._Add_ImportMenu_powder(Import)
1358	self._Add_ImportMenu_Sfact(Import)
1359	#======================================================================
1360	# Code to help develop/debug an importer, much is hard-coded below
1361	# but module is reloaded before each use, allowing faster testing
1362	# def DebugImport(event):
1363	# print 'start reload'
1364	# import G2phase_ISO as dev
1365	# reload(dev)
1366	# rd = dev.ISODISTORTPhaseReader()
1367	# self.ImportMenuId[event.GetId()] = rd
1368	# self.OnImportPhase(event)
1369	# or ----------------------------------------------------------------------
1370	#self.OnImportGeneric(rd,[],'test of ISODISTORTPhaseReader')
1371	# special debug code
1372	# or ----------------------------------------------------------------------
1373	# filename = '/Users/toby/projects/branton/subgroup_cif.txt'
1374	# fp = open(filename,'Ur')
1375	# if not rd.ContentsValidator(fp):
1376	# print 'not validated'
1377	# # make a list of used phase ranId's
1378	# phaseRIdList = []
1379	# sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
1380	# if sub:
1381	# item, cookie = self.PatternTree.GetFirstChild(sub)
1382	# while item:
1383	# phaseName = self.PatternTree.GetItemText(item)
1384	# ranId = self.PatternTree.GetItemPyData(item).get('ranId')
1385	# if ranId: phaseRIdList.append(ranId)
1386	# item, cookie = self.PatternTree.GetNextChild(sub, cookie)
1387	# if rd.Reader(filename,fp,usedRanIdList=phaseRIdList):
1388	# print 'read OK'
1389	# item = Import.Append(
1390	# wx.ID_ANY,kind=wx.ITEM_NORMAL,
1391	# help="debug importer",text="test importer")
1392	# self.Bind(wx.EVT_MENU, DebugImport, id=item.GetId())
1393	#======================================================================
1394	self.ExportMenu = wx.Menu(title='')
1395	menubar.Append(menu=self.ExportMenu, title='Export')
1396	self._init_Exports(self.ExportMenu)
1397	self._Add_ExportMenuItems(self.ExportMenu)
1398	HelpMenu=G2gd.MyHelp(self,helpType='Data tree',
1399	morehelpitems=[('&Tutorials','Tutorials')])
1400	menubar.Append(menu=HelpMenu,title='&Help')
1401
1402	def _init_ctrls(self, parent):
1403	wx.Frame.__init__(self, name='GSASII', parent=parent,
1404	size=wx.Size(400, 250),style=wx.DEFAULT_FRAME_STYLE, title='GSAS-II data tree')
1405	clientSize = wx.ClientDisplayRect()
1406	Size = self.GetSize()
1407	xPos = clientSize[2]-Size[0]
1408	self.SetPosition(wx.Point(xPos,clientSize[1]))
1409	self._init_Imports()
1410	#initialize Menu item objects (these contain lists of menu items that are enabled or disabled)
1411	self.MakePDF = []
1412	self.Refine = []
1413	self.SeqRefine = []
1414	self.ExportPattern = []
1415	self.ExportPeakList = []
1416	self.ExportHKL = []
1417	self.ExportPDF = []
1418	self.ExportPhase = []
1419	self.ExportCIF = []
1420	#
1421	self.GSASIIMenu = wx.MenuBar()
1422	self.FillMainMenu(self.GSASIIMenu)
1423	self.SetMenuBar(self.GSASIIMenu)
1424	self.Bind(wx.EVT_SIZE, self.OnSize)
1425	self.CreateStatusBar()
1426	self.mainPanel = wx.Panel(self,-1)
1427
1428	wxID_PATTERNTREE = wx.NewId()
1429	self.PatternTree = wx.TreeCtrl(id=wxID_PATTERNTREE,
1430	parent=self.mainPanel, pos=wx.Point(0, 0),style=wx.TR_DEFAULT_STYLE )
1431	self.PatternTree.Bind(wx.EVT_TREE_SEL_CHANGED,
1432	self.OnPatternTreeSelChanged, id=wxID_PATTERNTREE)
1433	self.PatternTree.Bind(wx.EVT_TREE_ITEM_COLLAPSED,
1434	self.OnPatternTreeItemCollapsed, id=wxID_PATTERNTREE)
1435	self.PatternTree.Bind(wx.EVT_TREE_ITEM_EXPANDED,
1436	self.OnPatternTreeItemExpanded, id=wxID_PATTERNTREE)
1437	self.PatternTree.Bind(wx.EVT_TREE_DELETE_ITEM,
1438	self.OnPatternTreeItemDelete, id=wxID_PATTERNTREE)
1439	self.PatternTree.Bind(wx.EVT_TREE_KEY_DOWN,
1440	self.OnPatternTreeKeyDown, id=wxID_PATTERNTREE)
1441	self.root = self.PatternTree.AddRoot('Loaded Data: ')
1442
1443	plotFrame = wx.Frame(None,-1,'GSASII Plots',size=wx.Size(700,600), \
1444	style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX)
1445	self.G2plotNB = G2plt.G2PlotNoteBook(plotFrame)
1446	plotFrame.Show()
1447
1448	self.dataDisplay = None
1449
1450	def __init__(self, parent):
1451	self.ExportLookup = {}
1452	self._init_ctrls(parent)
1453	self.Image = wx.Image(
1454	os.path.join(GSASIIpath.path2GSAS2,'gsas2.ico'),
1455	wx.BITMAP_TYPE_ICO)
1456	if "wxMSW" in wx.PlatformInfo:
1457	img = self.Image.Scale(16, 16).ConvertToBitmap()
1458	elif "wxGTK" in wx.PlatformInfo:
1459	img = self.Image.Scale(22, 22).ConvertToBitmap()
1460	else:
1461	img = self.Image.ConvertToBitmap()
1462	self.SetIcon(wx.IconFromBitmap(img))
1463	self.Bind(wx.EVT_CLOSE, self.ExitMain)
1464	# various defaults
1465	self.oldFocus = None
1466	self.GSASprojectfile = ''
1467	self.dirname = os.path.expanduser('~') #start in the users home directory by default; may be meaningless
1468	self.undofile = ''
1469	self.TreeItemDelete = False
1470	self.Offset = [0.0,0.0]
1471	self.delOffset = .02
1472	self.refOffset = -100.0
1473	self.refDelt = .01
1474	self.Weight = False
1475	self.IparmName = '' # to be removed when SelectPowderData & GetInstrumentFile is
1476	self.IfPlot = False
1477	self.PatternId = 0
1478	self.PickId = 0
1479	self.PeakTable = []
1480	self.LimitsTable = []
1481	self.HKL = []
1482	self.Lines = []
1483	self.itemPicked = None
1484	self.dataFrame = None
1485	self.Interpolate = 'nearest'
1486	self.ContourColor = 'Paired'
1487	self.VcovColor = 'RdYlGn'
1488	self.RamaColor = 'Blues'
1489	self.Projection = 'equal area'
1490	self.logPlot = False
1491	self.qPlot = False
1492	self.Contour = False
1493	self.Legend = False
1494	self.SinglePlot = False
1495	self.SubBack = False
1496	self.plotView = 0
1497	self.Image = 0
1498	self.oldImagefile = ''
1499	self.ImageZ = []
1500	self.Integrate = 0
1501	self.imageDefault = {}
1502	self.Sngl = 0
1503	self.ifGetRing = False
1504	self.MaskKey = '' #trigger for making image masks
1505	arg = sys.argv
1506	if len(arg) > 1:
1507	self.GSASprojectfile = os.path.splitext(arg[1])[0]+'.gpx'
1508	self.dirname = os.path.dirname(arg[1])
1509	if self.dirname: os.chdir(self.dirname)
1510	try:
1511	G2IO.ProjFileOpen(self)
1512	self.PatternTree.Expand(self.root)
1513	for item in self.Refine: item.Enable(True)
1514	for item in self.SeqRefine: item.Enable(True)
1515	except:
1516	print 'Error opening file',arg[1]
1517
1518	def OnSize(self,event):
1519	'Called when the main window is resized. Not sure why'
1520	w,h = self.GetClientSizeTuple()
1521	self.mainPanel.SetSize(wx.Size(w,h))
1522	self.PatternTree.SetSize(wx.Size(w,h))
1523
1524	def OnPatternTreeSelChanged(self, event):
1525	'''Called when a data tree item is selected'''
1526	if self.TreeItemDelete:
1527	self.TreeItemDelete = False
1528	else:
1529	pltNum = self.G2plotNB.nb.GetSelection()
1530	if pltNum >= 0: #to avoid the startup with no plot!
1531	pltPage = self.G2plotNB.nb.GetPage(pltNum)
1532	pltPlot = pltPage.figure
1533	item = event.GetItem()
1534	G2gd.MovePatternTreeToGrid(self,item)
1535	if self.oldFocus:
1536	self.oldFocus.SetFocus()
1537
1538	def OnPatternTreeItemCollapsed(self, event):
1539	'Called when a tree item is collapsed'
1540	event.Skip()
1541
1542	def OnPatternTreeItemExpanded(self, event):
1543	'Called when a tree item is expanded'
1544	event.Skip()
1545
1546	def OnPatternTreeItemDelete(self, event):
1547	'Called when a tree item is deleted -- not sure what this does'
1548	self.TreeItemDelete = True
1549
1550	def OnPatternTreeItemActivated(self, event):
1551	'Called when a tree item is activated'
1552	event.Skip()
1553
1554	def OnPatternTreeKeyDown(self,event):
1555	'Not sure what this does'
1556	key = event.GetKeyCode()
1557	item = self.PickId
1558	if type(item) is int: return # is this the toplevel in tree?
1559	if key == wx.WXK_UP:
1560	self.oldFocus = wx.Window.FindFocus()
1561	self.PatternTree.GetPrevSibling(item)
1562	elif key == wx.WXK_DOWN:
1563	self.oldFocus = wx.Window.FindFocus()
1564	self.PatternTree.GetNextSibling(item)
1565
1566	def OnReadPowderPeaks(self,event):
1567	'Bound to menu Data/Read Powder Peaks -- still needed?'
1568	Cuka = 1.54052
1569	self.CheckNotebook()
1570	dlg = wx.FileDialog(self, 'Choose file with peak list', '.', '',
1571	'peak files (.txt)\|.txt\|All files (.)\|.',wx.OPEN\|wx.CHANGE_DIR)
1572	try:
1573	if dlg.ShowModal() == wx.ID_OK:
1574	self.HKL = []
1575	self.powderfile = dlg.GetPath()
1576	comments,peaks = G2IO.GetPowderPeaks(self.powderfile)
1577	Id = self.PatternTree.AppendItem(parent=self.root,text='PKS '+os.path.basename(self.powderfile))
1578	data = ['PKS',Cuka,0.0]
1579	names = ['Type','Lam','Zero']
1580	codes = [0,0,0]
1581	inst = [G2IO.makeInstDict(names,data,codes),{}]
1582	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
1583	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),comments)
1584	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Index Peak List'),peaks)
1585	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
1586	self.PatternTree.Expand(Id)
1587	self.PatternTree.SelectItem(Id)
1588	os.chdir(dlg.GetDirectory()) # to get Mac/Linux to change directory!
1589	finally:
1590	dlg.Destroy()
1591
1592	def OnImageRead(self,event):
1593	'Called to read in an image in any known format'
1594	self.CheckNotebook()
1595	dlg = wx.FileDialog(
1596	self, 'Choose image files', '.', '',
1597	'Any image file (.edf;.tif;.tiff;.mar;.avg;.sum;.img;*.G2img)\|'
1598	'.edf;.tif;.tiff;.mar;.avg;.sum;.img;.G2img;.zip\|'
1599	'European detector file (.edf)\|.edf\|'
1600	'Any detector tif (.tif;.tiff)\|.tif;.tiff\|'
1601	'MAR file (.mar)\|.mar\|'
1602	'GE Image (.avg;.sum)\|.avg;.sum\|'
1603	'ADSC Image (.img)\|.img\|'
1604	'GSAS-II Image (.G2img)\|.G2img\|'
1605	'Zip archive (.zip)\|.zip\|'
1606	'All files (.)\|.',
1607	wx.OPEN \| wx.MULTIPLE\|wx.CHANGE_DIR)
1608	try:
1609	if dlg.ShowModal() == wx.ID_OK:
1610	imagefiles = dlg.GetPaths()
1611	imagefiles.sort()
1612	for imagefile in imagefiles:
1613	# if a zip file, open and extract
1614	if os.path.splitext(imagefile)[1].lower() == '.zip':
1615	extractedfile = G2IO.ExtractFileFromZip(imagefile,parent=self)
1616	if extractedfile is not None and extractedfile != imagefile:
1617	imagefile = extractedfile
1618	Comments,Data,Npix,Image = G2IO.GetImageData(self,imagefile)
1619	if Comments:
1620	Id = self.PatternTree.AppendItem(parent=self.root,text='IMG '+os.path.basename(imagefile))
1621	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),Comments)
1622	Imax = np.amax(Image)
1623	Imin = max(0.0,np.amin(Image)) #force positive
1624	if self.imageDefault:
1625	Data = copy.copy(self.imageDefault)
1626	Data['showLines'] = True
1627	Data['ring'] = []
1628	Data['rings'] = []
1629	Data['cutoff'] = 10
1630	Data['pixLimit'] = 20
1631	Data['edgemin'] = 100000000
1632	Data['calibdmin'] = 0.5
1633	Data['calibskip'] = 0
1634	Data['ellipses'] = []
1635	Data['calibrant'] = ''
1636	Data['GonioAngles'] = [0.,0.,0.]
1637	Data['DetDepth'] = 0.
1638	Data['DetDepthRef'] = False
1639	else:
1640	Data['type'] = 'PWDR'
1641	Data['color'] = 'Paired'
1642	Data['tilt'] = 0.0
1643	Data['rotation'] = 0.0
1644	Data['showLines'] = False
1645	Data['ring'] = []
1646	Data['rings'] = []
1647	Data['cutoff'] = 10
1648	Data['pixLimit'] = 20
1649	Data['calibdmin'] = 0.5
1650	Data['calibskip'] = 0
1651	Data['edgemin'] = 100000000
1652	Data['ellipses'] = []
1653	Data['GonioAngles'] = [0.,0.,0.]
1654	Data['DetDepth'] = 0.
1655	Data['DetDepthRef'] = False
1656	Data['calibrant'] = ''
1657	Data['IOtth'] = [2.0,5.0]
1658	Data['LRazimuth'] = [135,225]
1659	Data['azmthOff'] = 0.0
1660	Data['outChannels'] = 2500
1661	Data['outAzimuths'] = 1
1662	Data['centerAzm'] = False
1663	Data['fullIntegrate'] = False
1664	Data['setRings'] = False
1665	Data['background image'] = ['',1.0]
1666	Data['setDefault'] = False
1667	Data['range'] = [(Imin,Imax),[Imin,Imax]]
1668	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Image Controls'),Data)
1669	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(Imin,Imax),[Imin,Imax]]}
1670	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Masks'),Masks)
1671	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Stress/Strain'),
1672	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'strain':np.zeros((3,3))})
1673	self.PatternTree.SetItemPyData(Id,[Npix,imagefile])
1674	self.PickId = Id
1675	self.Image = Id
1676	os.chdir(dlg.GetDirectory()) # to get Mac/Linux to change directory!
1677	self.PatternTree.SelectItem(G2gd.GetPatternTreeItemId(self,Id,'Image Controls')) #show last one
1678	finally:
1679	path = dlg.GetDirectory() # to get Mac/Linux to change directory!
1680	os.chdir(path)
1681	dlg.Destroy()
1682
1683	def CheckNotebook(self):
1684	'''Make sure the data tree has the minimally expected controls.
1685	(BHT) correct?
1686	'''
1687	if not G2gd.GetPatternTreeItemId(self,self.root,'Notebook'):
1688	sub = self.PatternTree.AppendItem(parent=self.root,text='Notebook')
1689	self.PatternTree.SetItemPyData(sub,[''])
1690	if not G2gd.GetPatternTreeItemId(self,self.root,'Controls'):
1691	sub = self.PatternTree.AppendItem(parent=self.root,text='Controls')
1692	self.PatternTree.SetItemPyData(sub,copy.copy(G2obj.DefaultControls))
1693	if not G2gd.GetPatternTreeItemId(self,self.root,'Covariance'):
1694	sub = self.PatternTree.AppendItem(parent=self.root,text='Covariance')
1695	self.PatternTree.SetItemPyData(sub,{})
1696	if not G2gd.GetPatternTreeItemId(self,self.root,'Constraints'):
1697	sub = self.PatternTree.AppendItem(parent=self.root,text='Constraints')
1698	self.PatternTree.SetItemPyData(sub,{'Hist':[],'HAP':[],'Phase':[]})
1699	if not G2gd.GetPatternTreeItemId(self,self.root,'Restraints'):
1700	sub = self.PatternTree.AppendItem(parent=self.root,text='Restraints')
1701	self.PatternTree.SetItemPyData(sub,{})
1702	if not G2gd.GetPatternTreeItemId(self,self.root,'Rigid bodies'):
1703	sub = self.PatternTree.AppendItem(parent=self.root,text='Rigid bodies')
1704	self.PatternTree.SetItemPyData(sub,{'Vector':{'AtInfo':{}},
1705	'Residue':{'AtInfo':{}},'RBIds':{'Vector':[],'Residue':[]}})
1706
1707	class CopyDialog(wx.Dialog):
1708	'''Creates a dialog for copying control settings between
1709	data tree items'''
1710	def __init__(self,parent,title,text,data):
1711	wx.Dialog.__init__(self,parent,-1,title,
1712	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1713	self.data = data
1714	panel = wx.Panel(self)
1715	mainSizer = wx.BoxSizer(wx.VERTICAL)
1716	topLabl = wx.StaticText(panel,-1,text)
1717	mainSizer.Add((10,10),1)
1718	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.LEFT,10)
1719	mainSizer.Add((10,10),1)
1720	ncols = len(data)/40+1
1721	dataGridSizer = wx.FlexGridSizer(rows=len(data),cols=ncols,hgap=2,vgap=2)
1722	for id,item in enumerate(self.data):
1723	ckbox = wx.CheckBox(panel,id,item[1])
1724	ckbox.Bind(wx.EVT_CHECKBOX,self.OnCopyChange)
1725	dataGridSizer.Add(ckbox,0,wx.LEFT,10)
1726	mainSizer.Add(dataGridSizer,0,wx.EXPAND)
1727	OkBtn = wx.Button(panel,-1,"Ok")
1728	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1729	cancelBtn = wx.Button(panel,-1,"Cancel")
1730	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1731	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1732	btnSizer.Add((20,20),1)
1733	btnSizer.Add(OkBtn)
1734	btnSizer.Add((20,20),1)
1735	btnSizer.Add(cancelBtn)
1736	btnSizer.Add((20,20),1)
1737
1738	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1739	panel.SetSizer(mainSizer)
1740	panel.Fit()
1741	self.Fit()
1742
1743	def OnCopyChange(self,event):
1744	id = event.GetId()
1745	self.data[id][0] = self.FindWindowById(id).GetValue()
1746
1747	def OnOk(self,event):
1748	parent = self.GetParent()
1749	parent.Raise()
1750	self.EndModal(wx.ID_OK)
1751
1752	def OnCancel(self,event):
1753	parent = self.GetParent()
1754	parent.Raise()
1755	self.EndModal(wx.ID_CANCEL)
1756
1757	def GetData(self):
1758	return self.data
1759
1760	class SumDialog(wx.Dialog):
1761	'Allows user to supply scale factor(s) when summing data'
1762	def __init__(self,parent,title,text,dataType,data):
1763	wx.Dialog.__init__(self,parent,-1,title,
1764	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1765	self.data = data
1766	panel = wx.Panel(self)
1767	mainSizer = wx.BoxSizer(wx.VERTICAL)
1768	topLabl = wx.StaticText(panel,-1,text)
1769	mainSizer.Add((10,10),1)
1770	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.LEFT,10)
1771	mainSizer.Add((10,10),1)
1772	dataGridSizer = wx.FlexGridSizer(rows=len(data),cols=2,hgap=2,vgap=2)
1773	for id,item in enumerate(self.data[:-1]):
1774	name = wx.TextCtrl(panel,-1,item[1],size=wx.Size(200,20))
1775	name.SetEditable(False)
1776	scale = wx.TextCtrl(panel,id,'%.3f'%(item[0]),style=wx.TE_PROCESS_ENTER)
1777	scale.Bind(wx.EVT_TEXT_ENTER,self.OnScaleChange)
1778	scale.Bind(wx.EVT_KILL_FOCUS,self.OnScaleChange)
1779	dataGridSizer.Add(scale,0,wx.LEFT,10)
1780	dataGridSizer.Add(name,0,wx.RIGHT,10)
1781	if dataType:
1782	dataGridSizer.Add(wx.StaticText(panel,-1,'Sum result name: '+dataType),0, \
1783	wx.LEFT\|wx.TOP\|wx.ALIGN_CENTER_VERTICAL,10)
1784	self.name = wx.TextCtrl(panel,-1,self.data[-1],size=wx.Size(200,20),style=wx.TE_PROCESS_ENTER)
1785	self.name.Bind(wx.EVT_TEXT_ENTER,self.OnNameChange)
1786	self.name.Bind(wx.EVT_KILL_FOCUS,self.OnNameChange)
1787	dataGridSizer.Add(self.name,0,wx.RIGHT\|wx.TOP,10)
1788	mainSizer.Add(dataGridSizer,0,wx.EXPAND)
1789	OkBtn = wx.Button(panel,-1,"Ok")
1790	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1791	cancelBtn = wx.Button(panel,-1,"Cancel")
1792	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1793	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1794	btnSizer.Add((20,20),1)
1795	btnSizer.Add(OkBtn)
1796	btnSizer.Add((20,20),1)
1797	btnSizer.Add(cancelBtn)
1798	btnSizer.Add((20,20),1)
1799
1800	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1801	panel.SetSizer(mainSizer)
1802	panel.Fit()
1803	self.Fit()
1804
1805	def OnScaleChange(self,event):
1806	id = event.GetId()
1807	value = self.FindWindowById(id).GetValue()
1808	try:
1809	self.data[id][0] = float(value)
1810	self.FindWindowById(id).SetValue('%.3f'%(self.data[id][0]))
1811	except ValueError:
1812	if value and '-' not in value[0]:
1813	print 'bad input - numbers only'
1814	self.FindWindowById(id).SetValue('0.000')
1815
1816	def OnNameChange(self,event):
1817	self.data[-1] = self.name.GetValue()
1818
1819	def OnOk(self,event):
1820	parent = self.GetParent()
1821	parent.Raise()
1822	self.EndModal(wx.ID_OK)
1823
1824	def OnCancel(self,event):
1825	parent = self.GetParent()
1826	parent.Raise()
1827	self.EndModal(wx.ID_CANCEL)
1828
1829	def GetData(self):
1830	return self.data
1831
1832	def OnPwdrSum(self,event):
1833	'Sum together powder data(?)'
1834	TextList = []
1835	DataList = []
1836	SumList = []
1837	Names = []
1838	Inst = None
1839	SumItemList = []
1840	Comments = ['Sum equals: \n']
1841	if self.PatternTree.GetCount():
1842	item, cookie = self.PatternTree.GetFirstChild(self.root)
1843	while item:
1844	name = self.PatternTree.GetItemText(item)
1845	Names.append(name)
1846	if 'PWDR' in name:
1847	TextList.append([0.0,name])
1848	DataList.append(self.PatternTree.GetItemPyData(item)[1]) # (x,y,w,yc,yb,yd)
1849	if not Inst:
1850	Inst = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,item, 'Instrument Parameters'))
1851	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
1852	if len(TextList) < 2:
1853	self.ErrorDialog('Not enough data to sum','There must be more than one "PWDR" pattern')
1854	return
1855	TextList.append('default_sum_name')
1856	dlg = self.SumDialog(self,'Sum data','Enter scale for each pattern in summation','PWDR',TextList)
1857	try:
1858	if dlg.ShowModal() == wx.ID_OK:
1859	lenX = 0
1860	Xminmax = [0,0]
1861	Xsum = []
1862	Ysum = []
1863	Vsum = []
1864	result = dlg.GetData()
1865	for i,item in enumerate(result[:-1]):
1866	scale,name = item
1867	data = DataList[i]
1868	if scale:
1869	Comments.append("%10.3f %s" % (scale,' * '+name))
1870	x,y,w,yc,yb,yd = data #numpy arrays!
1871	v = 1./w
1872	if lenX:
1873	if lenX != len(x):
1874	self.ErrorDialog('Data length error','Data to be summed must have same number of points'+ \
1875	'\nExpected:'+str(lenX)+ \
1876	'\nFound: '+str(len(x))+'\nfor '+name)
1877	return
1878	else:
1879	lenX = len(x)
1880	if Xminmax[1]:
1881	if Xminmax != [x[0],x[-1]]:
1882	self.ErrorDialog('Data range error','Data to be summed must span same range'+ \
1883	'\nExpected:'+str(Xminmax[0])+' '+str(Xminmax[1])+ \
1884	'\nFound: '+str(x[0])+' '+str(x[-1])+'\nfor '+name)
1885	return
1886	else:
1887	for j,yi in enumerate(y):
1888	Ysum[j] += scale*yi
1889	Vsum[j] += abs(scale)*v[j]
1890	else:
1891	Xminmax = [x[0],x[-1]]
1892	YCsum = YBsum = YDsum = [0.0 for i in range(lenX)]
1893	for j,yi in enumerate(y):
1894	Xsum.append(x[j])
1895	Ysum.append(scale*yi)
1896	Vsum.append(abs(scale*v[j]))
1897	Wsum = 1./np.array(Vsum)
1898	outname = 'PWDR '+result[-1]
1899	Id = 0
1900	if outname in Names:
1901	dlg2 = wx.MessageDialog(self,'Overwrite data?','Duplicate data name',wx.OK\|wx.CANCEL)
1902	try:
1903	if dlg2.ShowModal() == wx.ID_OK:
1904	Id = G2gd.GetPatternTreeItemId(self,self.root,name)
1905	self.PatternTree.Delete(Id)
1906	finally:
1907	dlg2.Destroy()
1908	Id = self.PatternTree.AppendItem(parent=self.root,text=outname)
1909	if Id:
1910	Sample = G2pdG.SetDefaultSample()
1911	valuesdict = {
1912	'wtFactor':1.0,
1913	'Dummy':False,
1914	'ranId':ran.randint(0,sys.maxint),
1915	}
1916	self.PatternTree.SetItemPyData(Id,[valuesdict,[np.array(Xsum),np.array(Ysum),np.array(Wsum),
1917	np.array(YCsum),np.array(YBsum),np.array(YDsum)]])
1918	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),Comments)
1919	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
1920	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',True,3,1.0,0.0,0.0],
1921	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
1922	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Instrument Parameters'),Inst)
1923	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1924	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Peak List'),[])
1925	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Index Peak List'),[])
1926	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
1927	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
1928	self.PatternTree.SelectItem(Id)
1929	self.PatternTree.Expand(Id)
1930	finally:
1931	dlg.Destroy()
1932
1933	def OnImageSum(self,event):
1934	'Sum together image data(?)'
1935	TextList = []
1936	DataList = []
1937	SumList = []
1938	Names = []
1939	Inst = []
1940	SumItemList = []
1941	Comments = ['Sum equals: \n']
1942	if self.PatternTree.GetCount():
1943	item, cookie = self.PatternTree.GetFirstChild(self.root)
1944	while item:
1945	name = self.PatternTree.GetItemText(item)
1946	Names.append(name)
1947	if 'IMG' in name:
1948	TextList.append([0.0,name])
1949	DataList.append(self.PatternTree.GetItemPyData(item)) #Size,Image
1950	Data = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,item,'Image Controls'))
1951	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
1952	if len(TextList) < 2:
1953	self.ErrorDialog('Not enough data to sum','There must be more than one "IMG" pattern')
1954	return
1955	TextList.append('default_sum_name')
1956	dlg = self.SumDialog(self,'Sum data','Enter scale for each image in summation','IMG',TextList)
1957	try:
1958	if dlg.ShowModal() == wx.ID_OK:
1959	imSize = 0
1960	result = dlg.GetData()
1961	First = True
1962	Found = False
1963	for i,item in enumerate(result[:-1]):
1964	scale,name = item
1965	data = DataList[i]
1966	if scale:
1967	Found = True
1968	Comments.append("%10.3f %s" % (scale,' * '+name))
1969	Npix,imagefile = data
1970	image = G2IO.GetImageData(self,imagefile,imageOnly=True)
1971	if First:
1972	newImage = np.zeros_like(image)
1973	First = False
1974	if imSize:
1975	if imSize != Npix:
1976	self.ErrorDialog('Image size error','Images to be summed must be same size'+ \
1977	'\nExpected:'+str(imSize)+ \
1978	'\nFound: '+str(Npix)+'\nfor '+name)
1979	return
1980	newImage = newImage+scale*image
1981	else:
1982	imSize = Npix
1983	newImage = newImage+scale*image
1984	del(image)
1985	if not Found:
1986	self.ErrorDialog('Image sum error','No nonzero image multipliers found')
1987	return
1988
1989	newImage = np.asfarray(newImage,dtype=np.float32)
1990	outname = 'IMG '+result[-1]
1991	Id = 0
1992	if outname in Names:
1993	dlg2 = wx.MessageDialog(self,'Overwrite data?','Duplicate data name',wx.OK\|wx.CANCEL)
1994	try:
1995	if dlg2.ShowModal() == wx.ID_OK:
1996	Id = G2gd.GetPatternTreeItemId(self,self.root,name)
1997	finally:
1998	dlg2.Destroy()
1999	else:
2000	Id = self.PatternTree.AppendItem(parent=self.root,text=outname)
2001	if Id:
2002	dlg = wx.FileDialog(self, 'Choose sum image filename', '.', '',
2003	'G2img files (.G2img)\|.G2img',
2004	wx.SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2005	if dlg.ShowModal() == wx.ID_OK:
2006	newimagefile = dlg.GetPath()
2007	newimagefile = G2IO.FileDlgFixExt(dlg,newimagefile)
2008	G2IO.PutG2Image(newimagefile,Comments,Data,Npix,newImage)
2009	Imax = np.amax(newImage)
2010	Imin = np.amin(newImage)
2011	newImage = []
2012	self.PatternTree.SetItemPyData(Id,[imSize,newimagefile])
2013	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),Comments)
2014	del(newImage)
2015	if self.imageDefault:
2016	Data = copy.copy(self.imageDefault)
2017	Data['showLines'] = True
2018	Data['ring'] = []
2019	Data['rings'] = []
2020	Data['cutoff'] = 10
2021	Data['pixLimit'] = 20
2022	Data['ellipses'] = []
2023	Data['calibrant'] = ''
2024	Data['range'] = [(Imin,Imax),[Imin,Imax]]
2025	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Image Controls'),Data)
2026	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(Imin,Imax),[Imin,Imax]]}
2027	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Masks'),Masks)
2028	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Stress/Strain'),{})
2029	self.PatternTree.SelectItem(Id)
2030	self.PatternTree.Expand(Id)
2031	self.PickId = G2gd.GetPatternTreeItemId(self,self.root,outname)
2032	self.Image = self.PickId
2033	finally:
2034	dlg.Destroy()
2035
2036	def OnAddPhase(self,event):
2037	'Add a new, empty phase to the tree. Called by Data/Add Phase menu'
2038	if not G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
2039	sub = self.PatternTree.AppendItem(parent=self.root,text='Phases')
2040	else:
2041	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
2042	PhaseName = ''
2043	dlg = wx.TextEntryDialog(None,'Enter a name for this phase','Phase Name Entry','New phase',
2044	style=wx.OK)
2045	if dlg.ShowModal() == wx.ID_OK:
2046	PhaseName = dlg.GetValue()
2047	dlg.Destroy()
2048	sub = self.PatternTree.AppendItem(parent=sub,text=PhaseName)
2049	E,SGData = G2spc.SpcGroup('P 1')
2050	self.PatternTree.SetItemPyData(sub,G2IO.SetNewPhase(Name=PhaseName,SGData=SGData))
2051
2052	def OnDeletePhase(self,event):
2053	'Delete a phase from the tree. Called by Data/Delete Phase menu'
2054	#Hmm, also need to delete this phase from Reflection Lists for each PWDR histogram
2055	if self.dataFrame:
2056	self.dataFrame.Clear()
2057	TextList = []
2058	DelList = []
2059	DelItemList = []
2060	if G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
2061	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
2062	else:
2063	return
2064	if sub:
2065	item, cookie = self.PatternTree.GetFirstChild(sub)
2066	while item:
2067	TextList.append(self.PatternTree.GetItemText(item))
2068	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
2069	dlg = wx.MultiChoiceDialog(self, 'Which phase to delete?', 'Delete phase', TextList, wx.CHOICEDLG_STYLE)
2070	try:
2071	if dlg.ShowModal() == wx.ID_OK:
2072	result = dlg.GetSelections()
2073	for i in result: DelList.append([i,TextList[i]])
2074	item, cookie = self.PatternTree.GetFirstChild(sub)
2075	i = 0
2076	while item:
2077	if [i,self.PatternTree.GetItemText(item)] in DelList: DelItemList.append(item)
2078	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
2079	i += 1
2080	for item in DelItemList:
2081	name = self.PatternTree.GetItemText(item)
2082	self.PatternTree.Delete(item)
2083	self.G2plotNB.Delete(name)
2084	item, cookie = self.PatternTree.GetFirstChild(self.root)
2085	while item:
2086	name = self.PatternTree.GetItemText(item)
2087	if 'PWDR' in name:
2088	Id = G2gd.GetPatternTreeItemId(self,item, 'Reflection Lists')
2089	refList = self.PatternTree.GetItemPyData(Id)
2090	for i,item in DelList:
2091	del(refList[item])
2092	self.PatternTree.SetItemPyData(Id,refList)
2093	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2094	finally:
2095	dlg.Destroy()
2096
2097	def OnRenameData(self,event):
2098	'Renames an existing phase. Called by Data/Rename Phase menu'
2099	name = self.PatternTree.GetItemText(self.PickId)
2100	if 'PWDR' in name or 'HKLF' in name or 'IMG' in name:
2101	dataType = name[:name.index(' ')+1] #includes the ' '
2102	dlg = wx.TextEntryDialog(self,'Data name: '+dataType,'Change data name',
2103	defaultValue=name[name.index(' ')+1:])
2104	try:
2105	if dlg.ShowModal() == wx.ID_OK:
2106	self.PatternTree.SetItemText(self.PickId,dataType+dlg.GetValue())
2107	finally:
2108	dlg.Destroy()
2109
2110	def GetFileList(self,fileType,skip=None): #potentially useful?
2111	'Appears unused. Note routine of same name in GSASIIpwdGUI'
2112	fileList = []
2113	Source = ''
2114	id, cookie = self.PatternTree.GetFirstChild(self.root)
2115	while id:
2116	name = self.PatternTree.GetItemText(id)
2117	if fileType in name:
2118	if id == skip:
2119	Source = name
2120	else:
2121	fileList.append([False,name,id])
2122	id, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2123	if skip:
2124	return fileList,Source
2125	else:
2126	return fileList
2127
2128	def OnDataDelete(self, event):
2129	'''Delete one or more histograms from data tree. Called by the
2130	Data/DeleteData menu
2131	'''
2132	TextList = ['All Data']
2133	DelList = []
2134	DelItemList = []
2135	ifPWDR = False
2136	ifIMG = False
2137	ifHKLF = False
2138	ifPDF = False
2139	if self.PatternTree.GetCount():
2140	item, cookie = self.PatternTree.GetFirstChild(self.root)
2141	while item:
2142	name = self.PatternTree.GetItemText(item)
2143	if name not in ['Notebook','Controls','Covariance','Constraints',
2144	'Restraints','Phases','Rigid bodies']:
2145	if 'PWDR' in name: ifPWDR = True
2146	if 'IMG' in name: ifIMG = True
2147	if 'HKLF' in name: ifHKLF = True
2148	if 'PDF' in name: ifPDF = True
2149	TextList.append(name)
2150	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2151	if ifPWDR: TextList.insert(1,'All PWDR')
2152	if ifIMG: TextList.insert(1,'All IMG')
2153	if ifHKLF: TextList.insert(1,'All HKLF')
2154	if ifPDF: TextList.insert(1,'All PDF')
2155	dlg = wx.MultiChoiceDialog(self, 'Which data to delete?', 'Delete data', TextList, wx.CHOICEDLG_STYLE)
2156	try:
2157	if dlg.ShowModal() == wx.ID_OK:
2158	result = dlg.GetSelections()
2159	for i in result: DelList.append(TextList[i])
2160	if 'All Data' in DelList:
2161	DelList = [item for item in TextList if item[:3] != 'All']
2162	elif 'All PWDR' in DelList:
2163	DelList = [item for item in TextList if item[:4] == 'PWDR']
2164	elif 'All IMG' in DelList:
2165	DelList = [item for item in TextList if item[:3] == 'IMG']
2166	elif 'All HKLF' in DelList:
2167	DelList = [item for item in TextList if item[:4] == 'HKLF']
2168	elif 'All PDF' in DelList:
2169	DelList = [item for item in TextList if item[:3] == 'PDF']
2170	item, cookie = self.PatternTree.GetFirstChild(self.root)
2171	while item:
2172	if self.PatternTree.GetItemText(item) in DelList: DelItemList.append(item)
2173	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2174	for item in DelItemList:
2175	self.PatternTree.Delete(item)
2176	self.PickId = 0
2177	wx.CallAfter(G2plt.PlotPatterns,self,True) #so plot gets updated
2178	finally:
2179	dlg.Destroy()
2180
2181	def OnFileOpen(self, event, filename=None):
2182	'''Reads in a GSAS-II .gpx project file in response to the
2183	File/Open Project menu button
2184	'''
2185	result = wx.ID_OK
2186	Id = 0
2187	if self.PatternTree.GetChildrenCount(self.root,False):
2188	if self.dataFrame:
2189	self.dataFrame.Clear()
2190	dlg = wx.MessageDialog(
2191	self,
2192	'Do you want to overwrite the current project? '
2193	'Any unsaved changes will be lost. Press OK to continue.',
2194	'Overwrite?', wx.OK \| wx.CANCEL)
2195	try:
2196	result = dlg.ShowModal()
2197	if result == wx.ID_OK:
2198	self.PatternTree.DeleteChildren(self.root)
2199	self.GSASprojectfile = ''
2200	if self.HKL: self.HKL = []
2201	if self.G2plotNB.plotList:
2202	self.G2plotNB.clear()
2203	finally:
2204	dlg.Destroy()
2205	if result != wx.ID_OK: return
2206
2207	if not filename:
2208	if self.dataDisplay: self.dataDisplay.Destroy()
2209	dlg = wx.FileDialog(self, 'Choose GSAS-II project file', '.', '',
2210	'GSAS-II project file (.gpx)\|.gpx',wx.OPEN\|wx.CHANGE_DIR)
2211	try:
2212	if dlg.ShowModal() != wx.ID_OK: return
2213	self.GSASprojectfile = dlg.GetPath()
2214	self.GSASprojectfile = G2IO.FileDlgFixExt(dlg,self.GSASprojectfile)
2215	self.dirname = dlg.GetDirectory()
2216	finally:
2217	dlg.Destroy()
2218	else:
2219	self.GSASprojectfile = os.path.splitext(filename)[0]+'.gpx'
2220	self.dirname = os.path.split(filename)[0]
2221
2222	G2IO.ProjFileOpen(self)
2223	self.PatternTree.SetItemText(self.root,'Loaded Data: '+self.GSASprojectfile)
2224	self.PatternTree.Expand(self.root)
2225	self.HKL = []
2226	item, cookie = self.PatternTree.GetFirstChild(self.root)
2227	while item and not Id:
2228	name = self.PatternTree.GetItemText(item)
2229	if name[:4] in ['PWDR','HKLF','IMG ','PDF ']:
2230	Id = item
2231	elif name == 'Controls':
2232	data = self.PatternTree.GetItemPyData(item)
2233	if data:
2234	for item in self.Refine: item.Enable(True)
2235	for item in self.SeqRefine: item.Enable(True)
2236	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2237	if Id:
2238	self.PatternTree.SelectItem(Id)
2239	self.CheckNotebook()
2240	os.chdir(self.dirname) # to get Mac/Linux to change directory!
2241
2242	def OnFileClose(self, event):
2243	'''Clears the data tree in response to the
2244	File/New Project menu button. User is given option to save
2245	the project.
2246	'''
2247	if self.dataFrame:
2248	self.dataFrame.Clear()
2249	self.dataFrame.SetLabel('GSAS-II data display')
2250	dlg = wx.MessageDialog(self, 'Save current project?', ' ', wx.YES \| wx.NO \| wx.CANCEL)
2251	try:
2252	result = dlg.ShowModal()
2253	if result == wx.ID_OK:
2254	self.OnFileSaveMenu(event)
2255	if result != wx.ID_CANCEL:
2256	self.GSASprojectfile = ''
2257	self.PatternTree.SetItemText(self.root,'Loaded Data: ')
2258	self.PatternTree.DeleteChildren(self.root)
2259	if self.HKL: self.HKL = []
2260	if self.G2plotNB.plotList:
2261	self.G2plotNB.clear()
2262	finally:
2263	dlg.Destroy()
2264
2265	def OnFileSave(self, event):
2266	'''Save the current project in response to the
2267	File/Save Project menu button
2268	'''
2269
2270	if self.GSASprojectfile:
2271	self.PatternTree.SetItemText(self.root,'Loaded Data: '+self.GSASprojectfile)
2272	G2IO.ProjFileSave(self)
2273	else:
2274	self.OnFileSaveas(event)
2275
2276	def OnFileSaveas(self, event):
2277	'''Save the current project in response to the
2278	File/Save as menu button
2279	'''
2280	dlg = wx.FileDialog(self, 'Choose GSAS-II project file name', '.', '',
2281	'GSAS-II project file (.gpx)\|.gpx',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2282	try:
2283	if dlg.ShowModal() == wx.ID_OK:
2284	self.GSASprojectfile = dlg.GetPath()
2285	self.GSASprojectfile = G2IO.FileDlgFixExt(dlg,self.GSASprojectfile)
2286	self.PatternTree.SetItemText(self.root,'Saving project as'+self.GSASprojectfile)
2287	self.SetTitle("GSAS-II data tree: "+os.path.split(self.GSASprojectfile)[1])
2288	G2IO.ProjFileSave(self)
2289	os.chdir(dlg.GetDirectory()) # to get Mac/Linux to change directory!
2290	finally:
2291	dlg.Destroy()
2292
2293	def ExitMain(self, event):
2294	'''Called if the main window is closed'''
2295	if self.undofile:
2296	os.remove(self.undofile)
2297	sys.exit()
2298
2299	def OnFileExit(self, event):
2300	'''Called in response to the File/Quit menu button'''
2301	if self.dataFrame:
2302	self.dataFrame.Clear()
2303	self.dataFrame.Destroy()
2304	self.Close()
2305
2306	def OnExportPatterns(self,event):
2307	names = ['All']
2308	exports = []
2309	item, cookie = self.PatternTree.GetFirstChild(self.root)
2310	while item:
2311	name = self.PatternTree.GetItemText(item)
2312	if 'PWDR' in name:
2313	names.append(name)
2314	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2315	if names:
2316	dlg = wx.MultiChoiceDialog(self,'Select','Powder patterns to export',names)
2317	if dlg.ShowModal() == wx.ID_OK:
2318	sel = dlg.GetSelections()
2319	if sel[0] == 0:
2320	exports = names[1:]
2321	else:
2322	for x in sel:
2323	exports.append(names[x])
2324	dlg.Destroy()
2325	if exports:
2326	dlg = wx.FileDialog(self, 'Choose output powder file name', '.', '',
2327	'GSAS fxye file (.fxye)\|.fxye\|xye file (.xye)\|.xye',
2328	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2329	try:
2330	if dlg.ShowModal() == wx.ID_OK:
2331	powderfile = dlg.GetPath()
2332	powderfile = G2IO.FileDlgFixExt(dlg,powderfile)
2333	if 'fxye' in powderfile:
2334	G2IO.powderFxyeSave(self,exports,powderfile)
2335	else: #just xye
2336	G2IO.powderXyeSave(self,exports,powderfile)
2337	finally:
2338	dlg.Destroy()
2339
2340	def OnExportPeakList(self,event):
2341	dlg = wx.FileDialog(self, 'Choose output peak list file name', '.', '',
2342	'(.)\|.',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2343	try:
2344	if dlg.ShowModal() == wx.ID_OK:
2345	self.peaklistfile = dlg.GetPath()
2346	self.peaklistfile = G2IO.FileDlgFixExt(dlg,self.peaklistfile)
2347	file = open(self.peaklistfile,'w')
2348	item, cookie = self.PatternTree.GetFirstChild(self.root)
2349	while item:
2350	name = self.PatternTree.GetItemText(item)
2351	if 'PWDR' in name:
2352	item2, cookie2 = self.PatternTree.GetFirstChild(item)
2353	while item2:
2354	name2 = self.PatternTree.GetItemText(item2)
2355	if name2 == 'Peak List':
2356	peaks = self.PatternTree.GetItemPyData(item2)
2357	file.write("%s \n" % (name+' Peak List'))
2358	for peak in peaks:
2359	file.write("%10.5f %12.2f %10.3f %10.3f \n" % \
2360	(peak[0],peak[2],peak[4],peak[6]))
2361	item2, cookie2 = self.PatternTree.GetNextChild(item, cookie2)
2362	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2363	file.close()
2364	finally:
2365	dlg.Destroy()
2366
2367	def OnExportHKL(self,event):
2368	dlg = wx.FileDialog(self, 'Choose output reflection list file name', '.', '',
2369	'(.)\|.',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2370	try:
2371	if dlg.ShowModal() == wx.ID_OK:
2372	self.peaklistfile = dlg.GetPath()
2373	self.peaklistfile = G2IO.FileDlgFixExt(dlg,self.peaklistfile)
2374	file = open(self.peaklistfile,'w')
2375	item, cookie = self.PatternTree.GetFirstChild(self.root)
2376	while item:
2377	name = self.PatternTree.GetItemText(item)
2378	if 'PWDR' in name:
2379	item2, cookie2 = self.PatternTree.GetFirstChild(item)
2380	while item2:
2381	name2 = self.PatternTree.GetItemText(item2)
2382	if name2 == 'Reflection Lists':
2383	data = self.PatternTree.GetItemPyData(item2)
2384	phases = data.keys()
2385	for phase in phases:
2386	peaks = data[phase]
2387	file.write("%s %s %s \n" % (name,phase,' Reflection List'))
2388	file.write('%s \n'%(' h k l m d-space 2-theta wid F**2'))
2389	for peak in peaks:
2390	FWHM = G2pwd.getgamFW(peak[7],peak[6])/50. #to get delta-2-theta in deg.
2391	file.write(" %3d %3d %3d %3d %10.5f %10.5f %10.5f %10.3f \n" % \
2392	(int(peak[0]),int(peak[1]),int(peak[2]),int(peak[3]),peak[4],peak[5],FWHM,peak[8]))
2393	item2, cookie2 = self.PatternTree.GetNextChild(item, cookie2)
2394	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2395	file.close()
2396	finally:
2397	dlg.Destroy()
2398
2399	def OnExportPDF(self,event):
2400	#need S(Q) and G(R) to be saved here - probably best from selection?
2401	names = ['All']
2402	exports = []
2403	item, cookie = self.PatternTree.GetFirstChild(self.root)
2404	while item:
2405	name = self.PatternTree.GetItemText(item)
2406	if 'PDF' in name:
2407	names.append(name)
2408	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2409	if names:
2410	dlg = wx.MultiChoiceDialog(self,'Select','PDF patterns to export',names)
2411	if dlg.ShowModal() == wx.ID_OK:
2412	sel = dlg.GetSelections()
2413	if sel[0] == 0:
2414	exports = names[1:]
2415	else:
2416	for x in sel:
2417	exports.append(names[x])
2418	dlg.Destroy()
2419	if exports:
2420	G2IO.PDFSave(self,exports)
2421
2422	def OnMakePDFs(self,event):
2423	'''Calculates PDFs
2424	'''
2425	tth2q = lambda t,w:4.0math.pisind(t/2.0)/w
2426	TextList = ['All PWDR']
2427	PDFlist = []
2428	Names = []
2429	if self.PatternTree.GetCount():
2430	id, cookie = self.PatternTree.GetFirstChild(self.root)
2431	while id:
2432	name = self.PatternTree.GetItemText(id)
2433	Names.append(name)
2434	if 'PWDR' in name:
2435	TextList.append(name)
2436	id, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2437	if len(TextList) == 1:
2438	self.ErrorDialog('Nothing to make PDFs for','There must be at least one "PWDR" pattern')
2439	return
2440	dlg = wx.MultiChoiceDialog(self,'Make PDF controls','Make PDF controls for:',TextList, wx.CHOICEDLG_STYLE)
2441	try:
2442	if dlg.ShowModal() == wx.ID_OK:
2443	result = dlg.GetSelections()
2444	for i in result: PDFlist.append(TextList[i])
2445	if 0 in result:
2446	PDFlist = [item for item in TextList if item[:4] == 'PWDR']
2447	for item in PDFlist:
2448	PWDRname = item[4:]
2449	Id = self.PatternTree.AppendItem(parent=self.root,text='PDF '+PWDRname)
2450	Data = {
2451	'Sample':{'Name':item,'Mult':1.0,'Add':0.0},
2452	'Sample Bkg.':{'Name':'','Mult':-1.0,'Add':0.0},
2453	'Container':{'Name':'','Mult':-1.0,'Add':0.0},
2454	'Container Bkg.':{'Name':'','Mult':-1.0,'Add':0.0},'ElList':{},
2455	'Geometry':'Cylinder','Diam':1.0,'Pack':0.50,'Form Vol':10.0,
2456	'DetType':'Image plate','ObliqCoeff':0.2,'Ruland':0.025,'QScaleLim':[0,100],
2457	'Lorch':True,}
2458	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='PDF Controls'),Data)
2459	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='I(Q)'+PWDRname),[])
2460	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='S(Q)'+PWDRname),[])
2461	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='F(Q)'+PWDRname),[])
2462	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='G(R)'+PWDRname),[])
2463	for item in self.ExportPDF: item.Enable(True)
2464	finally:
2465	dlg.Destroy()
2466
2467	def GetPWDRdatafromTree(self,PWDRname):
2468	''' Returns powder data from GSASII tree
2469
2470	:param str PWDRname: a powder histogram name as obtained from
2471	:meth:`GSASIIstruct.GetHistogramNames`
2472
2473	:returns: PWDRdata = powder data dictionary with
2474	Powder data arrays, Limits, Instrument Parameters,
2475	Sample Parameters
2476	'''
2477	PWDRdata = {}
2478	try:
2479	PWDRdata.update(self.PatternTree.GetItemPyData(PWDRname)[0]) #wtFactor + ?
2480	except ValueError:
2481	PWDRdata['wtFactor'] = 1.0
2482	PWDRdata['Data'] = self.PatternTree.GetItemPyData(PWDRname)[1] #powder data arrays
2483	PWDRdata['Limits'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Limits'))
2484	PWDRdata['Background'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Background'))
2485	PWDRdata['Instrument Parameters'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Instrument Parameters'))
2486	PWDRdata['Sample Parameters'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Sample Parameters'))
2487	PWDRdata['Reflection Lists'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Reflection Lists'))
2488	if 'ranId' not in PWDRdata: # patch, add a random Id
2489	PWDRdata['ranId'] = ran.randint(0,sys.maxint)
2490	if 'ranId' not in PWDRdata['Sample Parameters']: # I hope this becomes obsolete at some point
2491	PWDRdata['Sample Parameters']['ranId'] = PWDRdata['ranId']
2492	return PWDRdata
2493
2494	def GetHKLFdatafromTree(self,HKLFname):
2495	''' Returns single crystal data from GSASII tree
2496
2497	:param str HKLFname: a single crystal histogram name as obtained
2498	from
2499	:meth:`GSASIIstruct.GetHistogramNames`
2500
2501	:returns: HKLFdata = single crystal data list of reflections
2502
2503	'''
2504	HKLFdata = {}
2505	HKLFdata.update(self.PatternTree.GetItemPyData(HKLFname)[0]) #wtFactor + ?
2506	# try:
2507	# HKLFdata.update(self.PatternTree.GetItemPyData(HKLFname)[0]) #wtFactor + ?
2508	# except ValueError:
2509	# HKLFdata['wtFactor'] = 1.0
2510	HKLFdata['Data'] = self.PatternTree.GetItemPyData(HKLFname)[1]
2511	HKLFdata['Instrument Parameters'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,HKLFname,'Instrument Parameters'))
2512	return HKLFdata
2513
2514	def GetPhaseData(self):
2515	'''Returns a dict with defined phases.
2516	Note routine :func:`GSASIIstrIO.GetPhaseData` also exists to
2517	get same info from GPX file.
2518	'''
2519	phaseData = {}
2520	if G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
2521	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
2522	else:
2523	print 'no phases found in GetPhaseData'
2524	sub = None
2525	if sub:
2526	item, cookie = self.PatternTree.GetFirstChild(sub)
2527	while item:
2528	phaseName = self.PatternTree.GetItemText(item)
2529	phaseData[phaseName] = self.PatternTree.GetItemPyData(item)
2530	if 'ranId' not in phaseData[phaseName]:
2531	phaseData[phaseName]['ranId'] = ran.randint(0,sys.maxint)
2532	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
2533	return phaseData
2534
2535	def GetPhaseNames(self):
2536	'''Returns a list of defined phases.
2537	Note routine :func:`GSASIIstrIO.GetPhaseNames` also exists to
2538	get same info from GPX file.
2539	'''
2540	phaseNames = []
2541	if G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
2542	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
2543	else:
2544	print 'no phases found in GetPhaseNames'
2545	sub = None
2546	if sub:
2547	item, cookie = self.PatternTree.GetFirstChild(sub)
2548	while item:
2549	phase = self.PatternTree.GetItemText(item)
2550	phaseNames.append(phase)
2551	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
2552	return phaseNames
2553
2554	def GetHistogramNames(self,hType):
2555	""" Returns a list of histogram names found in the GSASII data tree
2556	Note routine :func:`GSASIIstrIO.GetHistogramNames` also exists to
2557	get same info from GPX file.
2558
2559	:param str hType: list of histogram types
2560	:return: list of histogram names
2561
2562	"""
2563	HistogramNames = []
2564	if self.PatternTree.GetCount():
2565	item, cookie = self.PatternTree.GetFirstChild(self.root)
2566	while item:
2567	name = self.PatternTree.GetItemText(item)
2568	if name[:4] in hType:
2569	HistogramNames.append(name)
2570	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2571
2572	return HistogramNames
2573
2574
2575	def GetUsedHistogramsAndPhasesfromTree(self):
2576	''' Returns all histograms that are found in any phase
2577	and any phase that uses a histogram.
2578	This also assigns numbers to used phases and histograms by the
2579	order they appear in the file.
2580	Note routine :func:`GSASIIstrIO.GetUsedHistogramsAndPhasesfromTree` also exists to
2581	get same info from GPX file.
2582
2583	:returns: (Histograms,Phases)
2584
2585	* Histograms = dictionary of histograms as {name:data,...}
2586	* Phases = dictionary of phases that use histograms
2587	'''
2588	Histograms = {}
2589	Phases = {}
2590	phaseNames = self.GetPhaseNames()
2591	phaseData = self.GetPhaseData()
2592	histoList = self.GetHistogramNames(['PWDR','HKLF'])
2593
2594	for phase in phaseData:
2595	Phase = phaseData[phase]
2596	pId = phaseNames.index(phase)
2597	Phase['pId'] = pId
2598	if Phase['Histograms']:
2599	if phase not in Phases:
2600	Phases[phase] = Phase
2601	for hist in Phase['Histograms']:
2602	if 'Use' not in Phase['Histograms'][hist]: #patch: add Use flag as True
2603	Phase['Histograms'][hist]['Use'] = True
2604	if hist not in Histograms and Phase['Histograms'][hist]['Use']:
2605	item = G2gd.GetPatternTreeItemId(self,self.root,hist)
2606	if item:
2607	if 'PWDR' in hist[:4]:
2608	Histograms[hist] = self.GetPWDRdatafromTree(item)
2609	elif 'HKLF' in hist[:4]:
2610	Histograms[hist] = self.GetHKLFdatafromTree(item)
2611	hId = histoList.index(hist)
2612	Histograms[hist]['hId'] = hId
2613	else: # would happen if a referenced histogram were renamed or deleted
2614	print('For phase "'+str(phase)+
2615	'" unresolved reference to histogram "'+str(hist)+'"')
2616	#G2obj.IndexAllIds(Histograms=Histograms,Phases=Phases)
2617	G2obj.IndexAllIds(Histograms=Histograms,Phases=phaseData)
2618	return Histograms,Phases
2619
2620	def MakeLSParmDict(self):
2621	'''Load all parameters used for computation from the tree into a
2622	dict of paired values [value, refine flag]. Note that this is
2623	different than the parmDict used in the refinement, which only has
2624	values.
2625
2626	:returns: (parmDict,varyList) where:
2627
2628	* parmDict is a dict with values and refinement flags
2629	for each parameter and
2630	* varyList is a list of variables (refined parameters).
2631	'''
2632	parmDict = {}
2633	Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree()
2634	for phase in Phases:
2635	if 'pId' not in Phases[phase]:
2636	self.ErrorDialog('View parameter error','You must run least squares at least once')
2637	raise Exception,'No pId for phase '+str(phase)
2638	rigidbodyDict = self.PatternTree.GetItemPyData(
2639	G2gd.GetPatternTreeItemId(self,self.root,'Rigid bodies'))
2640	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
2641	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
2642	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtable,BLtable = G2stIO.GetPhaseData(Phases,RestraintDict=None,rbIds=rbIds,Print=False)
2643	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(Phases,Histograms,Print=False)
2644	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
2645	varyList = rbVary+phaseVary+hapVary+histVary
2646	parmDict.update(rbDict)
2647	parmDict.update(phaseDict)
2648	parmDict.update(hapDict)
2649	parmDict.update(histDict)
2650	for parm in parmDict:
2651	if parm.split(':')[-1] in ['Azimuth','Gonio. radius','Lam1','Lam2',
2652	'Omega','Chi','Phi','nDebye','nPeaks']:
2653	parmDict[parm] = [parmDict[parm],'-']
2654	elif parm.split(':')[-2] in ['Ax','Ay','Az','SHmodel','SHord']:
2655	parmDict[parm] = [parmDict[parm],'-']
2656	elif parm in varyList:
2657	parmDict[parm] = [parmDict[parm],'T']
2658	else:
2659	parmDict[parm] = [parmDict[parm],'F']
2660	return parmDict,varyList
2661
2662	def ShowLSParms(self,event):
2663	'''Displays a window showing all parameters in the refinement.
2664	Called from the Calculate/View LS Parms menu.
2665	'''
2666	parmDict,varyList = self.MakeLSParmDict()
2667	parmValDict = {}
2668	for i in parmDict:
2669	parmValDict[i] = parmDict[i][0]
2670
2671	reqVaryList = tuple(varyList) # save requested variables
2672	try:
2673	# process constraints
2674	sub = G2gd.GetPatternTreeItemId(self,self.root,'Constraints')
2675	Constraints = self.PatternTree.GetItemPyData(sub)
2676	constList = []
2677	for item in Constraints:
2678	if item.startswith('_'): continue
2679	constList += Constraints[item]
2680	G2mv.InitVars()
2681	constrDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
2682	groups,parmlist = G2mv.GroupConstraints(constrDict)
2683	G2mv.GenerateConstraints(groups,parmlist,varyList,constrDict,fixedList)
2684	G2mv.Map2Dict(parmValDict,varyList)
2685	except:
2686	pass
2687	dlg = G2gd.ShowLSParms(self,'Least Squares Parameters',parmValDict,varyList,reqVaryList)
2688	dlg.ShowModal()
2689	dlg.Destroy()
2690
2691	def OnRefine(self,event):
2692	'''Perform a refinement.
2693	Called from the Calculate/Refine menu.
2694	'''
2695	self.OnFileSave(event)
2696	# check that constraints are OK here
2697	errmsg, warnmsg = G2stIO.CheckConstraints(self.GSASprojectfile)
2698	if errmsg:
2699	print('Error in constraints:\n'+errmsg+
2700	'\nRefinement not possible')
2701	self.ErrorDialog('Constraint Error',
2702	'Error in constraints:\n'+errmsg+
2703	'\nRefinement not possible')
2704	return
2705	if warnmsg:
2706	print('Conflict between refinment flag settings and constraints:\n'+
2707	warnmsg+'\nRefinement not possible')
2708	self.ErrorDialog('Refinement Flag Error',
2709	'Conflict between refinment flag settings and constraints:\n'+
2710	warnmsg+
2711	'\nRefinement not possible')
2712	return
2713	#works - but it'd be better if it could restore plots
2714	dlg = wx.ProgressDialog('Residual','All data Rw =',101.0,
2715	style = wx.PD_ELAPSED_TIME\|wx.PD_AUTO_HIDE\|wx.PD_CAN_ABORT)
2716	screenSize = wx.ClientDisplayRect()
2717	Size = dlg.GetSize()
2718	Size = (int(Size[0]*1.2),Size[1]) # increase size a bit along x
2719	dlg.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5))
2720	dlg.SetSize(Size)
2721	Rw = 100.00
2722	try:
2723	Rw = G2stMn.Refine(self.GSASprojectfile,dlg)
2724	finally:
2725	dlg.Destroy()
2726	oldId = self.PatternTree.GetSelection()
2727	oldName = self.PatternTree.GetItemText(oldId)
2728	parentId = self.PatternTree.GetItemParent(oldId)
2729	parentName = ''
2730	if parentId:
2731	parentName = self.PatternTree.GetItemText(parentId)
2732	dlg = wx.MessageDialog(self,'Load new result?','Refinement results, Rw =%.3f'%(Rw),wx.OK\|wx.CANCEL)
2733	try:
2734	if dlg.ShowModal() == wx.ID_OK:
2735	Id = 0
2736	self.PatternTree.DeleteChildren(self.root)
2737	if self.HKL: self.HKL = []
2738	if self.G2plotNB.plotList:
2739	self.G2plotNB.clear()
2740	G2IO.ProjFileOpen(self)
2741	item, cookie = self.PatternTree.GetFirstChild(self.root)
2742	while item and not Id:
2743	name = self.PatternTree.GetItemText(item)
2744	if name[:4] in ['PWDR','HKLF']:
2745	Id = item
2746	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2747	if parentName:
2748	parentId = G2gd.GetPatternTreeItemId(self, self.root, parentName)
2749	if parentId:
2750	itemId = G2gd.GetPatternTreeItemId(self, parentId, oldName)
2751	else:
2752	itemId = G2gd.GetPatternTreeItemId(self, self.root, oldName)
2753	self.PatternTree.SelectItem(itemId)
2754	elif Id:
2755	self.PatternTree.SelectItem(Id)
2756	finally:
2757	dlg.Destroy()
2758
2759	def OnSeqRefine(self,event):
2760	'''Perform a sequential refinement.
2761	Called from the Calculate/Sequential refine menu.
2762	'''
2763	Id = G2gd.GetPatternTreeItemId(self,self.root,'Sequential results')
2764	if not Id:
2765	Id = self.PatternTree.AppendItem(self.root,text='Sequential results')
2766	self.PatternTree.SetItemPyData(Id,{})
2767	self.OnFileSave(event)
2768	# check that constraints are OK here
2769	errmsg, warnmsg = G2stIO.CheckConstraints(self.GSASprojectfile)
2770	if errmsg:
2771	print('Error in constraints:\n'+errmsg+
2772	'\nRefinement not possible')
2773	self.ErrorDialog('Constraint Error',
2774	'Error in constraints:\n'+errmsg+
2775	'\nRefinement not possible')
2776	return
2777	if warnmsg:
2778	print('Conflict between refinment flag settings and constraints:\n'+
2779	warnmsg+'\nRefinement not possible')
2780	self.ErrorDialog('Refinement Flag Error',
2781	'Conflict between refinment flag settings and constraints:\n'+
2782	warnmsg+'\nRefinement not possible')
2783	return
2784	dlg = wx.ProgressDialog('Residual for histogram 0','Powder profile Rwp =',101.0,
2785	style = wx.PD_ELAPSED_TIME\|wx.PD_AUTO_HIDE\|wx.PD_CAN_ABORT)
2786	screenSize = wx.ClientDisplayRect()
2787	Size = dlg.GetSize()
2788	Size = (int(Size[0]*1.2),Size[1]) # increase size a bit along x
2789	dlg.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5))
2790	dlg.SetSize(Size)
2791	try:
2792	G2stMn.SeqRefine(self.GSASprojectfile,dlg)
2793	finally:
2794	dlg.Destroy()
2795	dlg = wx.MessageDialog(self,'Load new result?','Refinement results',wx.OK\|wx.CANCEL)
2796	try:
2797	if dlg.ShowModal() == wx.ID_OK:
2798	Id = 0
2799	self.PatternTree.DeleteChildren(self.root)
2800	if self.HKL: self.HKL = []
2801	if self.G2plotNB.plotList:
2802	self.G2plotNB.clear()
2803	G2IO.ProjFileOpen(self)
2804	item, cookie = self.PatternTree.GetFirstChild(self.root)
2805	while item and not Id:
2806	name = self.PatternTree.GetItemText(item)
2807	if name[:4] in ['PWDR','HKLF']:
2808	Id = item
2809	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2810	if Id:
2811	self.PatternTree.SelectItem(Id)
2812	finally:
2813	dlg.Destroy()
2814
2815	def ErrorDialog(self,title,message,parent=None, wtype=wx.OK):
2816	'Display an error message'
2817	result = None
2818	if parent is None:
2819	dlg = wx.MessageDialog(self, message, title, wtype)
2820	else:
2821	dlg = wx.MessageDialog(parent, message, title, wtype)
2822	dlg.CenterOnParent() # not working on Mac
2823	try:
2824	result = dlg.ShowModal()
2825	finally:
2826	dlg.Destroy()
2827	return result
2828
2829	class GSASIImain(wx.App):
2830	'''Defines a wxApp for GSAS-II
2831
2832	Creates a wx frame (self.main) which contains the display of the
2833	data tree.
2834	'''
2835	def OnInit(self):
2836	'''Called automatically when the app is created.'''
2837	self.main = GSASII(None)
2838	self.main.Show()
2839	self.SetTopWindow(self.main)
2840	return True
2841	def MacOpenFile(self, filename):
2842	'''Called on Mac every time a file is dropped on the app when it is running,
2843	treat this like a File/Open project menu action.
2844	Should be ignored on other platforms
2845	'''
2846	self.main.OnFileOpen(None,filename)
2847
2848	def main():
2849	'''Start up the GSAS-II application'''
2850	#application = GSASIImain() # don't redirect output, someday we
2851	# may want to do this if we can
2852	application = GSASIImain(0)
2853	if wxInspector:
2854	import wx.lib.inspection as wxeye
2855	wxeye.InspectionTool().Show()
2856
2857	#application.main.OnRefine(None)
2858	application.MainLoop()
2859
2860	if __name__ == '__main__':
2861	main() # start the GUI

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