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source: trunk/GSASII.py @ 1147

Last change on this file since 1147 was 1147, checked in by toby, 12 years ago
Complete initial ISODISPLACE implementation; mod. phase initialization; change atom pointer init.; rework parameter display window
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
File size: 129.0 KB

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1	#!/usr/bin/env python
2	# -- coding: utf-8 --
3	#GSASII
4	########### SVN repository information ###################
5	# $Date: 2013-11-22 22:24:29 +0000 (Fri, 22 Nov 2013) $
6	# $Author: toby $
7	# $Revision: 1147 $
8	# $URL: trunk/GSASII.py $
9	# $Id: GSASII.py 1147 2013-11-22 22:24:29Z toby $
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: 1147 $")
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	if reader is None:
300	multiple = False
301	#print "use all formats"
302	choices = "any file (.)\|."
303	choices += "\|zip archive (.zip)\|*.zip"
304	extdict = {}
305	# compile a list of allowed extensions
306	for rd in readerlist:
307	fmt = rd.formatName
308	for extn in rd.extensionlist:
309	if not extdict.get(extn): extdict[extn] = []
310	extdict[extn] += [fmt,]
311	for extn in sorted(extdict.keys(),cmp=lambda x,y: cmp(x.lower(), y.lower())):
312	fmt = ''
313	for f in extdict[extn]:
314	if fmt != "": fmt += ', '
315	fmt += f
316	choices += "\|" + fmt + " file (" + extn + ")\|" + extn
317	else:
318	readerlist = [reader,]
319	# compile a list of allowed extensions
320	choices = reader.formatName + " file ("
321	w = ""
322	for extn in reader.extensionlist:
323	if w != "": w += ";"
324	w += "*" + extn
325	choices += w + ")\|" + w
326	choices += "\|zip archive (.zip)\|*.zip"
327	if not reader.strictExtension:
328	choices += "\|any file (.)\|."
329	# get the file(s)
330	if multiple:
331	mode = style=wx.OPEN \| wx.CHANGE_DIR \| wx.MULTIPLE
332	else:
333	mode = style=wx.OPEN \| wx.CHANGE_DIR
334	dlg = wx.FileDialog(self, message="Choose "+label+" input file",
335	defaultFile="",wildcard=choices, style=mode)
336	try:
337	if dlg.ShowModal() == wx.ID_OK:
338	if multiple:
339	filelist = dlg.GetPaths()
340	if len(filelist) == 0: return []
341	else:
342	filename = dlg.GetPath()
343	filelist = [filename,]
344	os.chdir(dlg.GetDirectory()) # to get Mac/Linux to change directory!
345	else: # cancel was pressed
346	return []
347	finally:
348	dlg.Destroy()
349	rd_list = []
350	filelist1 = []
351	for filename in filelist:
352	# is this a zip file?
353	if os.path.splitext(filename)[1].lower() == '.zip':
354	extractedfiles = G2IO.ExtractFileFromZip(
355	filename,parent=self,
356	multipleselect=True)
357	if extractedfiles is None: continue # error or Cancel
358	if extractedfiles != filename:
359	self.zipfile = filename # save zip name
360	filelist1 += extractedfiles
361	continue
362	filelist1.append(filename)
363	filelist = filelist1
364	for filename in filelist:
365	# is this a zip file?
366	if os.path.splitext(filename)[1].lower() == '.zip':
367	extractedfile = G2IO.ExtractFileFromZip(filename,parent=self)
368	if extractedfile is None: continue # error or Cancel
369	if extractedfile != filename:
370	filename,self.zipfile = extractedfile,filename # now use the file that was created
371	# set what formats are compatible with this file
372	primaryReaders = []
373	secondaryReaders = []
374	for r in readerlist:
375	flag = r.ExtensionValidator(filename)
376	if flag is None:
377	secondaryReaders.append(r)
378	elif flag:
379	primaryReaders.append(r)
380	if len(secondaryReaders) + len(primaryReaders) == 0:
381	self.ErrorDialog('No Format','No matching format for file '+filename)
382	return []
383
384	fp = None
385	msg = ''
386	try:
387	fp = open(filename,'Ur')
388	if len(filelist) == 1:
389	# confirm we have the right file
390	rdmsg = 'File '+str(filename)+' begins:\n\n'
391	for i in range(3):
392	rdmsg += fp.readline()
393	rdmsg += '\n\nDo you want to read this file?'
394	if not all([ord(c) < 128 and ord(c) != 0 for c in rdmsg]): # show only if ASCII
395	rdmsg = 'File '+str(
396	filename)+' is a binary file. Do you want to read this file?'
397	result = wx.ID_NO
398	# it would be better to use something that
399	# would resize better, but this will do for now
400	dlg = wx.MessageDialog(
401	self, rdmsg,
402	'Is this the file you want?',
403	wx.YES_NO \| wx.ICON_QUESTION,
404	)
405	dlg.SetSize((700,300)) # does not resize on Mac
406	try:
407	result = dlg.ShowModal()
408	finally:
409	dlg.Destroy()
410	if result == wx.ID_NO: return []
411
412	self.lastimport = filename
413	# try the file first with Readers that specify the
414	# files extension and later with ones that allow it
415	flag = False
416	for rd in primaryReaders+secondaryReaders:
417	try:
418	fp.seek(0) # rewind
419	if not rd.ContentsValidator(fp): continue # rejected on cursory check
420	repeat = True
421	rdbuffer = {} # create temporary storage for file reader
422	block = 0
423	while repeat:
424	block += 1
425	repeat = False
426	fp.seek(0) # rewind
427	rd.objname = os.path.basename(filename)
428	flag = rd.Reader(filename,fp,self,
429	buffer=rdbuffer,
430	blocknum=block,
431	usedRanIdList=usedRanIdList,
432	)
433	if flag:
434	rd_list.append(copy.deepcopy(rd)) # success
435	if rd.repeat: repeat = True
436	except:
437	import traceback
438	print traceback.format_exc()
439	msg += '\nError reading file '+filename+' with format '+ rd.formatName
440	#self.ErrorDialog('Read Error',
441	# 'Error reading file '+filename
442	# +' with format '+ rd.formatName)
443	continue
444	if flag:
445	if rd.warnings:
446	self.ErrorDialog('Read Warning','The '+ rd.formatName+
447	' reader reported a warning message:\n\n'+
448	rd.warnings)
449	break # success reading
450	else:
451	if reader:
452	self.ErrorDialog('Read Error','The '+ rd.formatName+
453	' reader was not able to read file '+filename+msg)
454	else:
455	self.ErrorDialog('Read Error','No reader is able to read file '+filename+msg)
456	except:
457	import traceback
458	print traceback.format_exc()
459	self.ErrorDialog('Open Error','Error on open of file '+filename)
460	if fp: fp.close()
461	return rd_list
462
463	def _Add_ImportMenu_Phase(self,parent):
464	'''configure the Import Phase menus accord to the readers found in _init_Imports
465	'''
466	submenu = wx.Menu()
467	item = parent.AppendMenu(wx.ID_ANY, 'Phase',
468	submenu, help='Import phase data')
469	for reader in self.ImportPhaseReaderlist:
470	item = submenu.Append(wx.ID_ANY,help=reader.longFormatName,
471	kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file')
472	self.ImportMenuId[item.GetId()] = reader
473	self.Bind(wx.EVT_MENU, self.OnImportPhase, id=item.GetId())
474	item = submenu.Append(wx.ID_ANY,
475	help='Import phase data, use file to try to determine format',
476	kind=wx.ITEM_NORMAL,
477	text='guess format from file')
478	self.Bind(wx.EVT_MENU, self.OnImportPhase, id=item.GetId())
479
480	def OnImportPhase(self,event):
481	'''Called in response to an Import/Phase/... menu item
482	to read phase information.
483	dict self.ImportMenuId is used to look up the specific
484	reader item associated with the menu item, which will be
485	None for the last menu item, which is the "guess" option
486	where all appropriate formats will be tried.
487	'''
488	# look up which format was requested
489	reqrdr = self.ImportMenuId.get(event.GetId())
490	# make a list of used phase ranId's
491	phaseRIdList = []
492	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
493	if sub:
494	item, cookie = self.PatternTree.GetFirstChild(sub)
495	while item:
496	phaseName = self.PatternTree.GetItemText(item)
497	ranId = self.PatternTree.GetItemPyData(item).get('ranId')
498	if ranId: phaseRIdList.append(ranId)
499	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
500	rdlist = self.OnImportGeneric(reqrdr,
501	self.ImportPhaseReaderlist,
502	'phase',usedRanIdList=phaseRIdList)
503	if len(rdlist) == 0: return
504	# for now rdlist is only expected to have one element
505	# but this will allow multiple phases to be imported
506	self.CheckNotebook()
507	for rd in rdlist:
508	dlg = wx.TextEntryDialog( # allow editing of phase name
509	self, 'Enter the name for the new phase',
510	'Edit phase name', rd.Phase['General']['Name'],
511	style=wx.OK)
512	dlg.CenterOnParent()
513	if dlg.ShowModal() == wx.ID_OK:
514	rd.Phase['General']['Name'] = dlg.GetValue()
515	dlg.Destroy()
516	PhaseName = rd.Phase['General']['Name']
517	print 'Read phase '+str(PhaseName)+' from file '+str(self.lastimport)
518	if not G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
519	sub = self.PatternTree.AppendItem(parent=self.root,text='Phases')
520	else:
521	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
522	psub = self.PatternTree.AppendItem(parent=sub,text=PhaseName)
523	self.PatternTree.SetItemPyData(psub,rd.Phase)
524	self.PatternTree.Expand(self.root) # make sure phases are seen
525	self.PatternTree.Expand(sub)
526	self.PatternTree.Expand(psub)
527	if rd.Constraints:
528	sub = G2gd.GetPatternTreeItemId(self,self.root,'Constraints') # was created in CheckNotebook if needed
529	Constraints = self.PatternTree.GetItemPyData(sub)
530	# TODO: make sure that NEWVAR names are unique here?
531	for i in rd.Constraints:
532	if type(i) is dict:
533	#for j in i: print j,' --> ',i[j]
534	if '_Explain' not in Constraints: Constraints['_Explain'] = {}
535	Constraints['_Explain'].update(i)
536	continue
537	Constraints['Phase'].append(i)
538	return # success
539
540	def _Add_ImportMenu_Sfact(self,parent):
541	'''configure the Import Structure Factor menus accord to the readers found in _init_Imports
542	'''
543	submenu = wx.Menu()
544	item = parent.AppendMenu(wx.ID_ANY, 'Structure Factor',
545	submenu, help='Import Structure Factor data')
546	for reader in self.ImportSfactReaderlist:
547	item = submenu.Append(wx.ID_ANY,help=reader.longFormatName,
548	kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file')
549	self.ImportMenuId[item.GetId()] = reader
550	self.Bind(wx.EVT_MENU, self.OnImportSfact, id=item.GetId())
551	item = submenu.Append(wx.ID_ANY,
552	help='Import Structure Factor, use file to try to determine format',
553	kind=wx.ITEM_NORMAL,
554	text='guess format from file')
555	self.Bind(wx.EVT_MENU, self.OnImportSfact, id=item.GetId())
556
557	def OnImportSfact(self,event):
558	'''Called in response to an Import/Structure Factor/... menu item
559	to read single crystal datasets.
560	dict self.ImportMenuId is used to look up the specific
561	reader item associated with the menu item, which will be
562	None for the last menu item, which is the "guess" option
563	where all appropriate formats will be tried.
564	'''
565	# look up which format was requested
566	reqrdr = self.ImportMenuId.get(event.GetId())
567	rdlist = self.OnImportGeneric(reqrdr,self.ImportSfactReaderlist,
568	'Structure Factor')
569	if len(rdlist) == 0: return
570	self.CheckNotebook()
571	for rd in rdlist:
572	HistName = rd.objname
573	if len(rdlist) <= 2:
574	dlg = wx.TextEntryDialog( # allow editing of Structure Factor name
575	self, 'Enter the name for the new Structure Factor',
576	'Edit Structure Factor name', HistName,
577	style=wx.OK)
578	dlg.CenterOnParent()
579	if dlg.ShowModal() == wx.ID_OK:
580	HistName = dlg.GetValue()
581	dlg.Destroy()
582	print 'Read structure factor table '+str(HistName)+' from file '+str(self.lastimport)
583	Id = self.PatternTree.AppendItem(parent=self.root,
584	text='HKLF '+HistName)
585	valuesdict = {
586	'wtFactor':1.0,
587	'Dummy':False,
588	'ranId':ran.randint(0,sys.maxint),
589	}
590	self.PatternTree.SetItemPyData(Id,[valuesdict,rd.RefDict])
591	Sub = self.PatternTree.AppendItem(Id,text='Instrument Parameters')
592	self.PatternTree.SetItemPyData(Sub,rd.Parameters)
593	self.PatternTree.SetItemPyData(
594	self.PatternTree.AppendItem(Id,text='HKL Plot Controls'),
595	rd.Controls)
596	self.PatternTree.SetItemPyData(
597	self.PatternTree.AppendItem(Id,text='Reflection List'),[]) #dummy entry for GUI use
598	self.PatternTree.SelectItem(Id)
599	self.PatternTree.Expand(Id)
600	self.Sngl = Id
601	return # success
602
603	def _Add_ImportMenu_powder(self,parent):
604	'''configure the Powder Data menus accord to the readers found in _init_Imports
605	'''
606	submenu = wx.Menu()
607	item = parent.AppendMenu(wx.ID_ANY, 'Powder Data',
608	submenu, help='Import Powder data')
609	for reader in self.ImportPowderReaderlist:
610	item = submenu.Append(wx.ID_ANY,help=reader.longFormatName,
611	kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file')
612	self.ImportMenuId[item.GetId()] = reader
613	self.Bind(wx.EVT_MENU, self.OnImportPowder, id=item.GetId())
614	item = submenu.Append(wx.ID_ANY,
615	help='Import powder data, use file to try to determine format',
616	kind=wx.ITEM_NORMAL,text='guess format from file')
617	self.Bind(wx.EVT_MENU, self.OnImportPowder, id=item.GetId())
618	submenu.AppendSeparator()
619	item = submenu.Append(wx.ID_ANY,
620	help='Create a powder data set entry that will be simulated',
621	kind=wx.ITEM_NORMAL,text='Simulate a dataset')
622	self.Bind(wx.EVT_MENU, self.OnDummyPowder, id=item.GetId())
623
624	def ReadPowderInstprm(self,instfile): #fix the write routine for [inst1,inst2] style
625	'''Read a GSAS-II (new) instrument parameter file
626
627	:param str instfile: name of instrument parameter file
628
629	'''
630	if os.path.splitext(instfile)[1].lower() != '.instprm': # invalid file
631	return None
632	if not os.path.exists(instfile): # no such file
633	return None
634	File = open(instfile,'r')
635	S = File.readline()
636	if not S.startswith('#GSAS-II'): # not a valid file
637	File.close()
638	return None
639	newItems = []
640	newVals = []
641	while S:
642	if S[0] == '#':
643	S = File.readline()
644	continue
645	[item,val] = S[:-1].split(':')
646	newItems.append(item)
647	try:
648	newVals.append(float(val))
649	except ValueError:
650	newVals.append(val)
651	S = File.readline()
652	File.close()
653	# add a second MT dict here. TOF parms? (BHT)
654	return G2IO.makeInstDict(newItems,newVals,len(newVals)*[False,]),{}
655
656	def ReadPowderIparm(self,instfile,bank,databanks,rd):
657	'''Read a GSAS (old) instrument parameter file
658
659	:param str instfile: name of instrument parameter file
660
661	:param int bank: the bank number read in the raw data file
662
663	:param int databanks: the number of banks in the raw data file.
664	If the number of banks in the data and instrument parameter files
665	agree, then the sets of banks are assumed to match up and bank
666	is used to select the instrument parameter file. If not, the user
667	is asked to make a selection.
668
669	:param obj rd: the raw data (histogram) data object. This
670	sets rd.instbank.
671
672	'''
673	if not os.path.exists(instfile): # no such file
674	return {}
675	fp = 0
676	try:
677	fp = open(instfile,'Ur')
678	Iparm = {}
679	for S in fp:
680	Iparm[S[:12]] = S[12:-1]
681	except IOError:
682	print('Error reading file:'+str(instfile))
683	if fp:
684	fp.close()
685
686	ibanks = int(Iparm.get('INS BANK ','1').strip())
687	hType = Iparm['INS HTYPE '].strip()
688	if ibanks == 1: # there is only one bank here, return it
689	rd.instbank = 1
690	return Iparm
691	if 'PNT' in hType:
692	rd.instbank = bank
693	elif ibanks != databanks:
694	# number of banks in data and prm file not not agree, need a
695	# choice from a human here
696	choices = []
697	for i in range(1,1+ibanks):
698	choices.append('Bank '+str(i))
699	bank = rd.BlockSelector(
700	choices, self,
701	title='Select an instrument parameter bank for '+
702	os.path.split(rd.powderentry[0])[1]+' BANK '+str(bank)+
703	'\nOr use Cancel to select from the default parameter sets',
704	header='Block Selector')
705	if bank is None: return {}
706	# pull out requested bank # bank from the data, and change the bank to 1
707	IparmS = {}
708	for key in Iparm:
709	if key[4:6] == " ":
710	IparmS[key] = Iparm[key]
711	elif int(key[4:6].strip()) == bank:
712	IparmS[key[:4]+' 1'+key[6:]] = Iparm[key]
713	rd.instbank = bank
714	return IparmS
715
716	def GetPowderIparm(self,rd, prevIparm, lastIparmfile, lastdatafile):
717	'''Open and read an instrument parameter file for a data file
718	Returns the list of parameters used in the data tree
719
720	:param obj rd: the raw data (histogram) data object.
721
722	:param str prevIparm: not used
723
724	:param str lastIparmfile: Name of last instrument parameter
725	file that was read, or a empty string.
726
727	:param str lastdatafile: Name of last data file that was read.
728
729	:returns: a list of two dicts, the first containing instrument parameters
730	and the second used for future TOF datasets (timemaps?)
731
732	'''
733	def SetPowderInstParms(Iparm, rd):
734	'''extracts values from instrument parameters in rd.instdict
735	or in array Iparm.
736	Create and return the contents of the instrument parameter tree entry.
737	'''
738	DataType = Iparm['INS HTYPE '].strip()[:3] # take 1st 3 chars
739	# override inst values with values read from data file
740	if rd.instdict.get('type'):
741	DataType = rd.instdict.get('type')
742	data = [DataType,]
743	instname = Iparm.get('INS 1INAME ')
744	if instname:
745	rd.Sample['InstrName'] = instname.strip()
746	if 'C' in DataType:
747	wave1 = None
748	wave2 = 0.0
749	if rd.instdict.get('wave'):
750	wl = rd.instdict.get('wave')
751	wave1 = wl[0]
752	if len(wl) > 1: wave2 = wl[1]
753	s = Iparm['INS 1 ICONS']
754	if not wave1:
755	wave1 = G2IO.sfloat(s[:10])
756	wave2 = G2IO.sfloat(s[10:20])
757	v = (wave1,wave2,
758	G2IO.sfloat(s[20:30]),G2IO.sfloat(s[55:65]),G2IO.sfloat(s[40:50])) #get lam1, lam2, zero, pola & ratio
759	if not v[1]:
760	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
761	v = (v[0],v[2],v[4])
762	codes = [0,0,0,0]
763	else:
764	names = ['Type','Lam1','Lam2','Zero','I(L2)/I(L1)','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
765	codes = [0,0,0,0,0,0]
766	data.extend(v)
767	v1 = Iparm['INS 1PRCF1 '].split()
768	v = Iparm['INS 1PRCF11'].split()
769	data.extend([float(v[0]),float(v[1]),float(v[2])]) #get GU, GV & GW - always here
770	azm = float(Iparm.get('INS 1DETAZM','0.0'))
771	v = Iparm['INS 1PRCF12'].split()
772	if v1[0] == 3:
773	data.extend([float(v[0]),float(v[1]),float(v[2])+float(v[3],azm)]) #get LX, LY, S+H/L & azimuth
774	else:
775	data.extend([0.0,0.0,0.002,azm]) #OK defaults if fxn #3 not 1st in iprm file
776	codes.extend([0,0,0,0,0,0,0])
777	return [G2IO.makeInstDict(names,data,codes),{}]
778	elif 'T' in DataType:
779	names = ['Type','2-theta','difC','difA','Zero','alpha','beta-0','beta-1',
780	'beta-q','sig-0','sig-1','sig-q','X','Y','Azimuth']
781	codes = [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
782	azm = 0.
783	if 'INS 1DETAZM' in Iparm:
784	azm = float(Iparm['INS 1DETAZM'])
785	s = Iparm['INS 1BNKPAR'].split()
786	data.extend([G2IO.sfloat(s[1]),]) #2-theta for bank
787	s = Iparm['INS 1 ICONS'].split()
788	data.extend([G2IO.sfloat(s[0]),G2IO.sfloat(s[1]),G2IO.sfloat(s[2])]) #difC, difA, Zero
789	s = Iparm['INS 1PRCF1 '].split()
790	pfType = int(s[0])
791	s = Iparm['INS 1PRCF11'].split()
792	if abs(pfType) == 1:
793	data.extend([G2IO.sfloat(s[1]),G2IO.sfloat(s[2]),G2IO.sfloat(s[3])])
794	s = Iparm['INS 1PRCF12'].split()
795	data.extend([0.0,0.0,G2IO.sfloat(s[1]),0.0,0.0,0.0,azm])
796	elif abs(pfType) in [3,4,5]:
797	data.extend([G2IO.sfloat(s[0]),G2IO.sfloat(s[1]),G2IO.sfloat(s[2])])
798	if abs(pfType) == 4:
799	data.extend([0.0,0.0,G2IO.sfloat(s[3]),0.0,0.0,0.0,azm])
800	else:
801	s = Iparm['INS 1PRCF12'].split()
802	data.extend([0.0,0.0,G2IO.sfloat(s[0]),0.0,0.0,0.0,azm])
803	Inst1 = G2IO.makeInstDict(names,data,codes)
804	Inst2 = {}
805	if pfType < 0:
806	Ipab = 'INS 1PAB'+str(-pfType)
807	Npab = int(Iparm[Ipab+' '].strip())
808	Inst2['Pdabc'] = []
809	for i in range(Npab):
810	k = Ipab+str(i+1).rjust(2)
811	s = Iparm[k].split()
812	Inst2['Pdabc'].append([float(t) for t in s])
813	Inst2['Pdabc'] = np.array(Inst2['Pdabc'])
814	Inst2['Pdabc'].T[3] += Inst2['Pdabc'].T[0]*Inst1['difC'][0] #turn 3rd col into TOF
815	if 'INS 1I ITYP' in Iparm:
816	s = Iparm['INS 1I ITYP'].split()
817	Ityp = int(s[0])
818	Tminmax = [float(s[1])1000.,float(s[2])1000.]
819	Itypes = ['Exponential','Maxwell/Exponential','','Maxwell/Chebyschev','']
820	if Ityp in [1,2,4]:
821	Inst2['Itype'] = Itypes[Ityp-1]
822	Inst2['Tminmax'] = Tminmax
823	Icoeff = []
824	Iesd = []
825	Icovar = []
826	for i in range(3):
827	s = Iparm['INS 1ICOFF'+str(i+1)].split()
828	Icoeff += [float(S) for S in s]
829	s = Iparm['INS 1IECOF'+str(i+1)].split()
830	Iesd += [float(S) for S in s]
831	for i in range(8):
832	s = Iparm['INS 1IECOR'+str(i+1)].split()
833	Icovar += [float(S) for S in s]
834	Inst2['Icoeff'] = Icoeff
835	Inst2['Iesd'] = Iesd
836	Inst2['Icovar'] = Icovar
837	return [Inst1,Inst2]
838
839	# stuff we might need from the reader
840	filename = rd.powderentry[0]
841	bank = rd.powderentry[2]
842	numbanks = rd.numbanks
843	# is there an instrument parameter file defined for the current data set?
844	if rd.instparm or (lastdatafile == filename and lastIparmfile):
845	if rd.instparm:
846	instfile = os.path.join(os.path.split(filename)[0],
847	rd.instparm)
848	else:
849	# for multiple reads of one data file, reuse the inst parm file
850	instfile = lastIparmfile
851	if os.path.exists(instfile):
852	#print 'debug: try read',instfile
853	instParmList = self.ReadPowderInstprm(instfile)
854	if instParmList is not None:
855	rd.instfile = instfile
856	rd.instmsg = 'GSAS-II file '+instfile
857	return instParmList
858	Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd)
859	if Iparm:
860	#print 'debug: success'
861	rd.instfile = instfile
862	rd.instmsg = instfile + ' bank ' + str(rd.instbank)
863	return SetPowderInstParms(Iparm,rd)
864	else:
865	self.ErrorDialog('Open Error','Error opening instrument parameter file '
866	+str(instfile)+' requested by file '+ filename)
867	# is there an instrument parameter file matching the current file
868	# with extension .inst or .prm? If so read it
869	basename = os.path.splitext(filename)[0]
870	for ext in '.instprm','.prm','.inst','.ins':
871	instfile = basename + ext
872	instParmList = self.ReadPowderInstprm(instfile)
873	if instParmList is not None:
874	rd.instfile = instfile
875	rd.instmsg = 'GSAS-II file '+instfile
876	return instParmList
877	Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd)
878	if Iparm:
879	#print 'debug: success'
880	rd.instfile = instfile
881	rd.instmsg = instfile + ' bank ' + str(rd.instbank)
882	return SetPowderInstParms(Iparm,rd)
883	else:
884	#print 'debug: open/read failed',instfile
885	pass # fail silently
886
887	# did we read the data file from a zip? If so, look there for a
888	# instrument parameter file
889	if self.zipfile:
890	for ext in '.instprm','.prm','.inst','.ins':
891	instfile = G2IO.ExtractFileFromZip(
892	self.zipfile,
893	selection=os.path.split(basename + ext)[1],
894	parent=self)
895	if instfile is not None and instfile != self.zipfile:
896	print 'debug:',instfile,'created from ',self.zipfile
897	instParmList = self.ReadPowderInstprm(instfile)
898	if instParmList is not None:
899	rd.instfile = instfile
900	rd.instmsg = 'GSAS-II file '+instfile
901	return instParmList
902	Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd)
903	if Iparm:
904	rd.instfile = instfile
905	rd.instmsg = instfile + ' bank ' + str(rd.instbank)
906	return SetPowderInstParms(Iparm,rd)
907	else:
908	#print 'debug: open/read for',instfile,'from',self.zipfile,'failed'
909	pass # fail silently
910
911	while True: # loop until we get a file that works or we get a cancel
912	instfile = ''
913	dlg = wx.FileDialog(
914	self,
915	'Choose inst. param file for "'
916	+rd.idstring
917	+'" (or Cancel for default)',
918	'.', '',
919	'GSAS iparm file (.prm,.inst,.ins)\|.prm;.inst;.ins\|'
920	'GSAS-II iparm file (.instprm)\|.instprm\|'
921	'All files (.)\|.',
922	wx.OPEN\|wx.CHANGE_DIR)
923	if os.path.exists(lastIparmfile):
924	dlg.SetFilename(lastIparmfile)
925	if dlg.ShowModal() == wx.ID_OK:
926	instfile = dlg.GetPath()
927	dlg.Destroy()
928	if not instfile: break
929	instParmList = self.ReadPowderInstprm(instfile)
930	if instParmList is not None:
931	rd.instfile = instfile
932	rd.instmsg = 'GSAS-II file '+instfile
933	return instParmList
934	Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd)
935	if Iparm:
936	#print 'debug: success with',instfile
937	rd.instfile = instfile
938	rd.instmsg = instfile + ' bank ' + str(rd.instbank)
939	return SetPowderInstParms(Iparm,rd)
940	else:
941	self.ErrorDialog('Read Error',
942	'Error opening/reading file '+str(instfile))
943
944	# still no success: offer user choice of defaults
945	while True: # loop until we get a choice
946	choices = []
947	head = 'Select from default instrument parameters for '+rd.idstring
948
949	for l in rd.defaultIparm_lbl:
950	choices.append('Defaults for '+l)
951	res = rd.BlockSelector(
952	choices,
953	ParentFrame=self,
954	title=head,
955	header='Select default inst parms',
956	useCancel=False)
957	if res is None: continue
958	rd.instfile = ''
959	rd.instmsg = 'default: '+rd.defaultIparm_lbl[res]
960	return SetPowderInstParms(rd.defaultIparms[res],rd)
961
962	def OnImportPowder(self,event):
963	'''Called in response to an Import/Powder Data/... menu item
964	to read a powder diffraction data set.
965	dict self.ImportMenuId is used to look up the specific
966	reader item associated with the menu item, which will be
967	None for the last menu item, which is the "guess" option
968	where all appropriate formats will be tried.
969
970	Also reads an instrument parameter file for each dataset.
971	'''
972	reqrdr = self.ImportMenuId.get(event.GetId()) # look up which format was requested
973	rdlist = self.OnImportGeneric(
974	reqrdr,self.ImportPowderReaderlist,'Powder Data',multiple=True)
975	if len(rdlist) == 0: return
976	self.CheckNotebook()
977	Iparm = None
978	lastIparmfile = ''
979	lastdatafile = ''
980	for rd in rdlist:
981	# get instrument parameters for each dataset
982	Iparm1,Iparm2 = self.GetPowderIparm(rd, Iparm, lastIparmfile, lastdatafile)
983	if rd.repeat_instparm:
984	lastIparmfile = rd.instfile
985	lastdatafile = rd.powderentry[0]
986	print 'Read powder data '+str(rd.idstring)+ \
987	' from file '+str(self.lastimport) + \
988	' with parameters from '+str(rd.instmsg)
989	# data are read, now store them in the tree
990	Id = self.PatternTree.AppendItem(parent=self.root,
991	text='PWDR '+rd.idstring)
992	if 'T' in Iparm1['Type'][0]:
993	if not rd.clockWd and rd.GSAS:
994	rd.powderdata[0] *= 100. #put back the CW centideg correction
995	cw = np.diff(rd.powderdata[0])
996	rd.powderdata[0] = rd.powderdata[0][:-1]+cw/2.
997	rd.powderdata[1] = rd.powderdata[1][:-1]/cw
998	rd.powderdata[2] = rd.powderdata[2][:-1]cw*2 #1/var=w at this point
999	if 'Itype' in Iparm2:
1000	Ibeg = np.searchsorted(rd.powderdata[0],Iparm2['Tminmax'][0])
1001	Ifin = np.searchsorted(rd.powderdata[0],Iparm2['Tminmax'][1])
1002	rd.powderdata[0] = rd.powderdata[0][Ibeg:Ifin]
1003	YI,WYI = G2pwd.calcIncident(Iparm2,rd.powderdata[0])
1004	rd.powderdata[1] = rd.powderdata[1][Ibeg:Ifin]/YI
1005	var = 1./rd.powderdata[2][Ibeg:Ifin]
1006	var += WYIrd.powderdata[1]*2
1007	var /= YI**2
1008	rd.powderdata[2] = 1./var
1009	rd.powderdata[3] = np.zeros_like(rd.powderdata[0])
1010	rd.powderdata[4] = np.zeros_like(rd.powderdata[0])
1011	rd.powderdata[5] = np.zeros_like(rd.powderdata[0])
1012	Tmin = min(rd.powderdata[0])
1013	Tmax = max(rd.powderdata[0])
1014	valuesdict = {
1015	'wtFactor':1.0,
1016	'Dummy':False,
1017	'ranId':ran.randint(0,sys.maxint),
1018	}
1019	rd.Sample['ranId'] = valuesdict['ranId'] # this should be removed someday
1020	self.PatternTree.SetItemPyData(Id,[valuesdict,rd.powderdata])
1021	self.PatternTree.SetItemPyData(
1022	self.PatternTree.AppendItem(Id,text='Comments'),
1023	rd.comments)
1024	self.PatternTree.SetItemPyData(
1025	self.PatternTree.AppendItem(Id,text='Limits'),
1026	[(Tmin,Tmax),[Tmin,Tmax]])
1027	self.PatternId = G2gd.GetPatternTreeItemId(self,Id,'Limits')
1028	self.PatternTree.SetItemPyData(
1029	self.PatternTree.AppendItem(Id,text='Background'),
1030	[['chebyschev',True,3,1.0,0.0,0.0],
1031	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
1032	self.PatternTree.SetItemPyData(
1033	self.PatternTree.AppendItem(Id,text='Instrument Parameters'),
1034	[Iparm1,Iparm2])
1035	self.PatternTree.SetItemPyData(
1036	self.PatternTree.AppendItem(Id,text='Sample Parameters'),
1037	rd.Sample)
1038	self.PatternTree.SetItemPyData(
1039	self.PatternTree.AppendItem(Id,text='Peak List')
1040	,[])
1041	self.PatternTree.SetItemPyData(
1042	self.PatternTree.AppendItem(Id,text='Index Peak List'),
1043	[])
1044	self.PatternTree.SetItemPyData(
1045	self.PatternTree.AppendItem(Id,text='Unit Cells List'),
1046	[])
1047	self.PatternTree.SetItemPyData(
1048	self.PatternTree.AppendItem(Id,text='Reflection Lists'),
1049	{})
1050	self.PatternTree.Expand(Id)
1051	self.PatternTree.SelectItem(Id)
1052	return # success
1053
1054	def OnDummyPowder(self,event):
1055	'''Called in response to Import/Powder Data/Simulate menu item
1056	to create a Dummy powder diffraction data set.
1057
1058	Reads an instrument parameter file and then gets input from the user
1059	'''
1060	rd = G2IO.ImportPowderData(
1061	extensionlist=tuple(),
1062	strictExtension=False,
1063	formatName = 'Simulate dataset',
1064	longFormatName = 'Compute a simulated pattern')
1065	rd.powderentry[0] = '' # no filename
1066	# #self.powderentry[1] = pos # bank offset (N/A here)
1067	rd.powderentry[2] = 1 # only one bank
1068	rd.comments.append('This is a dummy dataset for powder pattern simulation')
1069	self.CheckNotebook()
1070	Iparm = None
1071	lastIparmfile = ''
1072	lastdatafile = ''
1073	self.zipfile = None
1074	# get instrument parameters for
1075	Iparm1,Iparm2 = self.GetPowderIparm(rd, Iparm, lastIparmfile, lastdatafile)
1076	if 'T' in Iparm1['Type'][0]:
1077	print('TOF simulation not supported yet')
1078	return False
1079	else:
1080	# need to get name, 2theta start, end, step
1081	rd.idstring = ' CW'
1082	if 'X' in Iparm1['Type'][0]:
1083	rd.idstring = 'CW x-ray simulation'
1084	else:
1085	rd.idstring = 'CW neutron simulation'
1086	# base initial range on wavelength
1087	wave = Iparm1.get('Lam')
1088	if wave:
1089	wave = wave[0]
1090	else:
1091	wave = Iparm1.get('Lam1')
1092	if wave:
1093	wave = wave[0]
1094	N = 0
1095	while (N < 3): # insist on a dataset with a few points
1096	names = ('dataset name', 'start angle', 'end angle', 'step size')
1097	if not wave or wave < 1.0:
1098	inp = [rd.idstring, 10.,40.,0.005] # see names for what's what
1099	else:
1100	inp = [rd.idstring, 10.,80.,0.01] # see names for what's what
1101	dlg = G2gd.ScrolledMultiEditor(
1102	self,[inp] * len(inp),range(len(inp)),names,
1103	header='Enter simulation name and range',
1104	minvals=(None,0.001,0.001,0.0001),
1105	maxvals=(None,180.,180.,.1),
1106	sizevals=((225,-1),)
1107	)
1108	dlg.CenterOnParent()
1109	if dlg.ShowModal() == wx.ID_OK:
1110	if inp[1] > inp[2]:
1111	end,start,step = inp[1:]
1112	else:
1113	start,end,step = inp[1:]
1114	step = abs(step)
1115	else:
1116	return False
1117	N = int((end-start)/step)+1
1118	x = np.linspace(start,end,N,True)
1119	N = len(x)
1120	rd.powderdata = [
1121	np.array(x), # x-axis values
1122	np.zeros_like(x), # powder pattern intensities
1123	np.ones_like(x), # 1/sig(intensity)^2 values (weights)
1124	np.zeros_like(x), # calc. intensities (zero)
1125	np.zeros_like(x), # calc. background (zero)
1126	np.zeros_like(x), # obs-calc profiles
1127	]
1128	Tmin = rd.powderdata[0][0]
1129	Tmax = rd.powderdata[0][-1]
1130	# data are read, now store them in the tree
1131	Id = self.PatternTree.AppendItem(parent=self.root,
1132	text='PWDR '+inp[0])
1133	valuesdict = {
1134	'wtFactor':1.0,
1135	'Dummy':True,
1136	'ranId':ran.randint(0,sys.maxint),
1137	}
1138	self.PatternTree.SetItemPyData(Id,[valuesdict,rd.powderdata])
1139	self.PatternTree.SetItemPyData(
1140	self.PatternTree.AppendItem(Id,text='Comments'),
1141	rd.comments)
1142	self.PatternTree.SetItemPyData(
1143	self.PatternTree.AppendItem(Id,text='Limits'),
1144	[(Tmin,Tmax),[Tmin,Tmax]])
1145	self.PatternId = G2gd.GetPatternTreeItemId(self,Id,'Limits')
1146	self.PatternTree.SetItemPyData(
1147	self.PatternTree.AppendItem(Id,text='Background'),
1148	[['chebyschev',True,3,1.0,0.0,0.0],
1149	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
1150	self.PatternTree.SetItemPyData(
1151	self.PatternTree.AppendItem(Id,text='Instrument Parameters'),
1152	[Iparm1,Iparm2])
1153	self.PatternTree.SetItemPyData(
1154	self.PatternTree.AppendItem(Id,text='Sample Parameters'),
1155	rd.Sample)
1156	self.PatternTree.SetItemPyData(
1157	self.PatternTree.AppendItem(Id,text='Peak List')
1158	,[])
1159	self.PatternTree.SetItemPyData(
1160	self.PatternTree.AppendItem(Id,text='Index Peak List'),
1161	[])
1162	self.PatternTree.SetItemPyData(
1163	self.PatternTree.AppendItem(Id,text='Unit Cells List'),
1164	[])
1165	self.PatternTree.SetItemPyData(
1166	self.PatternTree.AppendItem(Id,text='Reflection Lists'),
1167	{})
1168	self.PatternTree.Expand(Id)
1169	self.PatternTree.SelectItem(Id)
1170	print('Added simulation powder data '+str(rd.idstring)+
1171	' with parameters from '+str(rd.instmsg))
1172	return # success
1173
1174	def _init_Exports(self,menu):
1175	'''Find exporter routines and add them into menus
1176	'''
1177	# set up the top-level menus
1178	projectmenu = wx.Menu()
1179	item = menu.AppendMenu(
1180	wx.ID_ANY, 'Entire project as',
1181	projectmenu, help='Export entire project')
1182
1183	phasemenu = wx.Menu()
1184	item = menu.AppendMenu(
1185	wx.ID_ANY, 'Phase as',
1186	phasemenu, help='Export phase or sometimes phases')
1187
1188	powdermenu = wx.Menu()
1189	item = menu.AppendMenu(
1190	wx.ID_ANY, 'Powder data as',
1191	powdermenu, help='Export powder diffraction histogram(s)')
1192
1193	singlemenu = wx.Menu()
1194	item = menu.AppendMenu(
1195	wx.ID_ANY, 'Single crystal data as',
1196	singlemenu, help='Export single crystal histogram(s)')
1197
1198	imagemenu = wx.Menu()
1199	item = menu.AppendMenu(
1200	wx.ID_ANY, 'Images as',
1201	imagemenu, help='Export powder image(s)')
1202
1203	mapmenu = wx.Menu()
1204	item = menu.AppendMenu(
1205	wx.ID_ANY, 'Maps as',
1206	mapmenu, help='Export density map(s)')
1207
1208	# pdfmenu = wx.Menu()
1209	# item = menu.AppendMenu(
1210	# wx.ID_ANY, 'PDFs as',
1211	# pdfmenu, help='Export pair distribution function(s)')
1212
1213	# find all the exporter files
1214	pathlist = sys.path
1215	filelist = []
1216	for path in pathlist:
1217	for filename in glob.iglob(os.path.join(
1218	path,
1219	"G2export*.py")):
1220	filelist.append(filename)
1221	filelist = sorted(list(set(filelist))) # remove duplicates
1222	exporterlist = []
1223	# go through the routines and import them, saving objects that
1224	# have export routines (method Exporter)
1225	for filename in filelist:
1226	path,rootname = os.path.split(filename)
1227	pkg = os.path.splitext(rootname)[0]
1228	try:
1229	fp = None
1230	fp, fppath,desc = imp.find_module(pkg,[path,])
1231	pkg = imp.load_module(pkg,fp,fppath,desc)
1232	for clss in inspect.getmembers(pkg): # find classes defined in package
1233	if clss[0].startswith('_'): continue
1234	if inspect.isclass(clss[1]):
1235	# check if we have the required methods
1236	for m in 'Exporter','loadParmDict':
1237	if not hasattr(clss[1],m): break
1238	if not callable(getattr(clss[1],m)): break
1239	else:
1240	exporter = clss[1](self) # create an export instance
1241	exporterlist.append(exporter)
1242	except AttributeError:
1243	print 'Import_'+errprefix+': Attribute Error'+str(filename)
1244	pass
1245	except ImportError:
1246	print 'Import_'+errprefix+': Error importing file'+str(filename)
1247	pass
1248	if fp: fp.close()
1249	# Add submenu item(s) for each Exporter by its self-declared type (can be more than one)
1250	for obj in exporterlist:
1251	#print 'exporter',obj
1252	for typ in obj.exporttype:
1253	if typ == "project":
1254	submenu = projectmenu
1255	elif typ == "phase":
1256	submenu = phasemenu
1257	elif typ == "powder":
1258	submenu = powdermenu
1259	elif typ == "single":
1260	submenu = singlemenu
1261	elif typ == "image":
1262	submenu = imagemenu
1263	elif typ == "map":
1264	submenu = mapmenu
1265	# elif typ == "pdf":
1266	# submenu = pdfmenu
1267	else:
1268	print("Error, unknown type in "+str(obj))
1269	break
1270	item = submenu.Append(
1271	wx.ID_ANY,
1272	help=obj.longFormatName,
1273	kind=wx.ITEM_NORMAL,
1274	text=obj.formatName)
1275	self.Bind(wx.EVT_MENU, obj.Exporter, id=item.GetId())
1276	self.ExportLookup[item.GetId()] = typ # lookup table for submenu item
1277	#code to debug an Exporter. much is hard-coded below, but code is reloaded before
1278	# each use allowing faster development
1279	# def DebugExport(event):
1280	# print 'start reload'
1281	# reload(G2IO)
1282	# import G2export_ASCIImap as dev
1283	# reload(dev)
1284	# dev.ExportMapASCII(self).Exporter(event)
1285	# item = menu.Append(
1286	# wx.ID_ANY,kind=wx.ITEM_NORMAL,
1287	# help="debug exporter",text="test Export")
1288	# self.Bind(wx.EVT_MENU, DebugExport, id=item.GetId())
1289	# #self.ExportLookup[item.GetId()] = 'image'
1290	# self.ExportLookup[item.GetId()] = 'map'
1291
1292	def _Add_ExportMenuItems(self,parent):
1293	item = parent.Append(
1294	help='Select PWDR item to enable',id=wx.ID_ANY,
1295	kind=wx.ITEM_NORMAL,
1296	text='Export Powder Patterns...')
1297	self.ExportPattern.append(item)
1298	item.Enable(False)
1299	self.Bind(wx.EVT_MENU, self.OnExportPatterns, id=item.GetId())
1300
1301	item = parent.Append(
1302	help='',id=wx.ID_ANY,
1303	kind=wx.ITEM_NORMAL,
1304	text='Export All Peak Lists...')
1305	self.ExportPeakList.append(item)
1306	item.Enable(True)
1307	self.Bind(wx.EVT_MENU, self.OnExportPeakList, id=item.GetId())
1308
1309	item = parent.Append(
1310	help='',id=wx.ID_ANY,
1311	kind=wx.ITEM_NORMAL,
1312	text='Export HKLs...')
1313	self.ExportHKL.append(item)
1314	self.Bind(wx.EVT_MENU, self.OnExportHKL, id=item.GetId())
1315
1316	item = parent.Append(
1317	help='Select PDF item to enable',
1318	id=wx.ID_ANY,
1319	kind=wx.ITEM_NORMAL,
1320	text='Export PDF...')
1321	self.ExportPDF.append(item)
1322	item.Enable(False)
1323	self.Bind(wx.EVT_MENU, self.OnExportPDF, id=item.GetId())
1324
1325	def FillMainMenu(self,menubar):
1326	'''Define contents of the main GSAS-II menu for the (main) data tree window
1327	in the mac, used also for the data item windows as well.
1328	'''
1329	File = wx.Menu(title='')
1330	menubar.Append(menu=File, title='&File')
1331	self._Add_FileMenuItems(File)
1332	Data = wx.Menu(title='')
1333	menubar.Append(menu=Data, title='Data')
1334	self._Add_DataMenuItems(Data)
1335	Calculate = wx.Menu(title='')
1336	menubar.Append(menu=Calculate, title='&Calculate')
1337	self._Add_CalculateMenuItems(Calculate)
1338	Import = wx.Menu(title='')
1339	menubar.Append(menu=Import, title='Import')
1340	self._Add_ImportMenu_Phase(Import)
1341	self._Add_ImportMenu_powder(Import)
1342	self._Add_ImportMenu_Sfact(Import)
1343	#======================================================================
1344	# Code to help develop/debug an importer, much is hard-coded below
1345	# but module is reloaded before each use, allowing faster testing
1346	# def DebugImport(event):
1347	# print 'start reload'
1348	# import G2phase_ISO as dev
1349	# reload(dev)
1350	# rd = dev.ISODISTORTPhaseReader()
1351	# self.ImportMenuId[event.GetId()] = rd
1352	# self.OnImportPhase(event)
1353	# or ----------------------------------------------------------------------
1354	#self.OnImportGeneric(rd,[],'test of ISODISTORTPhaseReader')
1355	# special debug code
1356	# or ----------------------------------------------------------------------
1357	# filename = '/Users/toby/projects/branton/subgroup_cif.txt'
1358	# fp = open(filename,'Ur')
1359	# if not rd.ContentsValidator(fp):
1360	# print 'not validated'
1361	# # make a list of used phase ranId's
1362	# phaseRIdList = []
1363	# sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
1364	# if sub:
1365	# item, cookie = self.PatternTree.GetFirstChild(sub)
1366	# while item:
1367	# phaseName = self.PatternTree.GetItemText(item)
1368	# ranId = self.PatternTree.GetItemPyData(item).get('ranId')
1369	# if ranId: phaseRIdList.append(ranId)
1370	# item, cookie = self.PatternTree.GetNextChild(sub, cookie)
1371	# if rd.Reader(filename,fp,usedRanIdList=phaseRIdList):
1372	# print 'read OK'
1373	# item = Import.Append(
1374	# wx.ID_ANY,kind=wx.ITEM_NORMAL,
1375	# help="debug importer",text="test importer")
1376	# self.Bind(wx.EVT_MENU, DebugImport, id=item.GetId())
1377	#======================================================================
1378	self.ExportMenu = wx.Menu(title='')
1379	menubar.Append(menu=self.ExportMenu, title='Export')
1380	self._init_Exports(self.ExportMenu)
1381	self._Add_ExportMenuItems(self.ExportMenu)
1382	HelpMenu=G2gd.MyHelp(self,helpType='Data tree',
1383	morehelpitems=[('&Tutorials','Tutorials')])
1384	menubar.Append(menu=HelpMenu,title='&Help')
1385
1386	def _init_ctrls(self, parent):
1387	wx.Frame.__init__(self, name='GSASII', parent=parent,
1388	size=wx.Size(400, 250),style=wx.DEFAULT_FRAME_STYLE, title='GSAS-II data tree')
1389	clientSize = wx.ClientDisplayRect()
1390	Size = self.GetSize()
1391	xPos = clientSize[2]-Size[0]
1392	self.SetPosition(wx.Point(xPos,clientSize[1]))
1393	self._init_Imports()
1394	#initialize Menu item objects (these contain lists of menu items that are enabled or disabled)
1395	self.MakePDF = []
1396	self.Refine = []
1397	self.SeqRefine = []
1398	self.ExportPattern = []
1399	self.ExportPeakList = []
1400	self.ExportHKL = []
1401	self.ExportPDF = []
1402	self.ExportPhase = []
1403	self.ExportCIF = []
1404	#
1405	self.GSASIIMenu = wx.MenuBar()
1406	self.FillMainMenu(self.GSASIIMenu)
1407	self.SetMenuBar(self.GSASIIMenu)
1408	self.Bind(wx.EVT_SIZE, self.OnSize)
1409	self.CreateStatusBar()
1410	self.mainPanel = wx.Panel(self,-1)
1411
1412	wxID_PATTERNTREE = wx.NewId()
1413	self.PatternTree = wx.TreeCtrl(id=wxID_PATTERNTREE,
1414	parent=self.mainPanel, pos=wx.Point(0, 0),style=wx.TR_DEFAULT_STYLE )
1415	self.PatternTree.Bind(wx.EVT_TREE_SEL_CHANGED,
1416	self.OnPatternTreeSelChanged, id=wxID_PATTERNTREE)
1417	self.PatternTree.Bind(wx.EVT_TREE_ITEM_COLLAPSED,
1418	self.OnPatternTreeItemCollapsed, id=wxID_PATTERNTREE)
1419	self.PatternTree.Bind(wx.EVT_TREE_ITEM_EXPANDED,
1420	self.OnPatternTreeItemExpanded, id=wxID_PATTERNTREE)
1421	self.PatternTree.Bind(wx.EVT_TREE_DELETE_ITEM,
1422	self.OnPatternTreeItemDelete, id=wxID_PATTERNTREE)
1423	self.PatternTree.Bind(wx.EVT_TREE_KEY_DOWN,
1424	self.OnPatternTreeKeyDown, id=wxID_PATTERNTREE)
1425	self.root = self.PatternTree.AddRoot('Loaded Data: ')
1426
1427	plotFrame = wx.Frame(None,-1,'GSASII Plots',size=wx.Size(700,600), \
1428	style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX)
1429	self.G2plotNB = G2plt.G2PlotNoteBook(plotFrame)
1430	plotFrame.Show()
1431
1432	self.dataDisplay = None
1433
1434	def __init__(self, parent):
1435	self.ExportLookup = {}
1436	self._init_ctrls(parent)
1437	self.Image = wx.Image(
1438	os.path.join(GSASIIpath.path2GSAS2,'gsas2.ico'),
1439	wx.BITMAP_TYPE_ICO)
1440	if "wxMSW" in wx.PlatformInfo:
1441	img = self.Image.Scale(16, 16).ConvertToBitmap()
1442	elif "wxGTK" in wx.PlatformInfo:
1443	img = self.Image.Scale(22, 22).ConvertToBitmap()
1444	else:
1445	img = self.Image.ConvertToBitmap()
1446	self.SetIcon(wx.IconFromBitmap(img))
1447	self.Bind(wx.EVT_CLOSE, self.ExitMain)
1448	# various defaults
1449	self.oldFocus = None
1450	self.GSASprojectfile = ''
1451	self.dirname = os.path.expanduser('~') #start in the users home directory by default; may be meaningless
1452	self.undofile = ''
1453	self.TreeItemDelete = False
1454	self.Offset = [0.0,0.0]
1455	self.delOffset = .02
1456	self.refOffset = -100.0
1457	self.refDelt = .01
1458	self.Weight = False
1459	self.IparmName = '' # to be removed when SelectPowderData & GetInstrumentFile is
1460	self.IfPlot = False
1461	self.PatternId = 0
1462	self.PickId = 0
1463	self.PeakTable = []
1464	self.LimitsTable = []
1465	self.HKL = []
1466	self.Lines = []
1467	self.itemPicked = None
1468	self.dataFrame = None
1469	self.Interpolate = 'nearest'
1470	self.ContourColor = 'Paired'
1471	self.VcovColor = 'RdYlGn'
1472	self.RamaColor = 'Blues'
1473	self.Projection = 'equal area'
1474	self.logPlot = False
1475	self.qPlot = False
1476	self.Contour = False
1477	self.Legend = False
1478	self.SinglePlot = False
1479	self.SubBack = False
1480	self.plotView = 0
1481	self.Image = 0
1482	self.oldImagefile = ''
1483	self.ImageZ = []
1484	self.Integrate = 0
1485	self.imageDefault = {}
1486	self.Sngl = 0
1487	self.ifGetRing = False
1488	self.MaskKey = '' #trigger for making image masks
1489	arg = sys.argv
1490	if len(arg) > 1:
1491	self.GSASprojectfile = os.path.splitext(arg[1])[0]+'.gpx'
1492	self.dirname = os.path.dirname(arg[1])
1493	if self.dirname: os.chdir(self.dirname)
1494	try:
1495	G2IO.ProjFileOpen(self)
1496	self.PatternTree.Expand(self.root)
1497	for item in self.Refine: item.Enable(True)
1498	for item in self.SeqRefine: item.Enable(True)
1499	except:
1500	print 'Error opening file',arg[1]
1501
1502	def OnSize(self,event):
1503	'Called when the main window is resized. Not sure why'
1504	w,h = self.GetClientSizeTuple()
1505	self.mainPanel.SetSize(wx.Size(w,h))
1506	self.PatternTree.SetSize(wx.Size(w,h))
1507
1508	def OnPatternTreeSelChanged(self, event):
1509	'''Called when a data tree item is selected'''
1510	if self.TreeItemDelete:
1511	self.TreeItemDelete = False
1512	else:
1513	pltNum = self.G2plotNB.nb.GetSelection()
1514	if pltNum >= 0: #to avoid the startup with no plot!
1515	pltPage = self.G2plotNB.nb.GetPage(pltNum)
1516	pltPlot = pltPage.figure
1517	item = event.GetItem()
1518	G2gd.MovePatternTreeToGrid(self,item)
1519	if self.oldFocus:
1520	self.oldFocus.SetFocus()
1521
1522	def OnPatternTreeItemCollapsed(self, event):
1523	'Called when a tree item is collapsed'
1524	event.Skip()
1525
1526	def OnPatternTreeItemExpanded(self, event):
1527	'Called when a tree item is expanded'
1528	event.Skip()
1529
1530	def OnPatternTreeItemDelete(self, event):
1531	'Called when a tree item is deleted -- not sure what this does'
1532	self.TreeItemDelete = True
1533
1534	def OnPatternTreeItemActivated(self, event):
1535	'Called when a tree item is activated'
1536	event.Skip()
1537
1538	def OnPatternTreeKeyDown(self,event):
1539	'Not sure what this does'
1540	key = event.GetKeyCode()
1541	item = self.PickId
1542	if type(item) is int: return # is this the toplevel in tree?
1543	if key == wx.WXK_UP:
1544	self.oldFocus = wx.Window.FindFocus()
1545	self.PatternTree.GetPrevSibling(item)
1546	elif key == wx.WXK_DOWN:
1547	self.oldFocus = wx.Window.FindFocus()
1548	self.PatternTree.GetNextSibling(item)
1549
1550	def OnReadPowderPeaks(self,event):
1551	'Bound to menu Data/Read Powder Peaks -- still needed?'
1552	Cuka = 1.54052
1553	self.CheckNotebook()
1554	dlg = wx.FileDialog(self, 'Choose file with peak list', '.', '',
1555	'peak files (.txt)\|.txt\|All files (.)\|.',wx.OPEN\|wx.CHANGE_DIR)
1556	try:
1557	if dlg.ShowModal() == wx.ID_OK:
1558	self.HKL = []
1559	self.powderfile = dlg.GetPath()
1560	comments,peaks = G2IO.GetPowderPeaks(self.powderfile)
1561	Id = self.PatternTree.AppendItem(parent=self.root,text='PKS '+os.path.basename(self.powderfile))
1562	data = ['PKS',Cuka,0.0]
1563	names = ['Type','Lam','Zero']
1564	codes = [0,0,0]
1565	inst = [G2IO.makeInstDict(names,data,codes),{}]
1566	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
1567	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),comments)
1568	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Index Peak List'),peaks)
1569	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
1570	self.PatternTree.Expand(Id)
1571	self.PatternTree.SelectItem(Id)
1572	os.chdir(dlg.GetDirectory()) # to get Mac/Linux to change directory!
1573	finally:
1574	dlg.Destroy()
1575
1576	def OnImageRead(self,event):
1577	'Called to read in an image in any known format'
1578	self.CheckNotebook()
1579	dlg = wx.FileDialog(
1580	self, 'Choose image files', '.', '',
1581	'Any image file (.edf;.tif;.tiff;.mar;.avg;.sum;.img;*.G2img)\|'
1582	'.edf;.tif;.tiff;.mar;.avg;.sum;.img;.G2img;.zip\|'
1583	'European detector file (.edf)\|.edf\|'
1584	'Any detector tif (.tif;.tiff)\|.tif;.tiff\|'
1585	'MAR file (.mar)\|.mar\|'
1586	'GE Image (.avg;.sum)\|.avg;.sum\|'
1587	'ADSC Image (.img)\|.img\|'
1588	'GSAS-II Image (.G2img)\|.G2img\|'
1589	'Zip archive (.zip)\|.zip\|'
1590	'All files (.)\|.',
1591	wx.OPEN \| wx.MULTIPLE\|wx.CHANGE_DIR)
1592	try:
1593	if dlg.ShowModal() == wx.ID_OK:
1594	imagefiles = dlg.GetPaths()
1595	imagefiles.sort()
1596	for imagefile in imagefiles:
1597	# if a zip file, open and extract
1598	if os.path.splitext(imagefile)[1].lower() == '.zip':
1599	extractedfile = G2IO.ExtractFileFromZip(imagefile,parent=self)
1600	if extractedfile is not None and extractedfile != imagefile:
1601	imagefile = extractedfile
1602	Comments,Data,Npix,Image = G2IO.GetImageData(self,imagefile)
1603	if Comments:
1604	Id = self.PatternTree.AppendItem(parent=self.root,text='IMG '+os.path.basename(imagefile))
1605	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),Comments)
1606	Imax = np.amax(Image)
1607	Imin = max(0.0,np.amin(Image)) #force positive
1608	if self.imageDefault:
1609	Data = copy.copy(self.imageDefault)
1610	Data['showLines'] = True
1611	Data['ring'] = []
1612	Data['rings'] = []
1613	Data['cutoff'] = 10
1614	Data['pixLimit'] = 20
1615	Data['edgemin'] = 100000000
1616	Data['calibdmin'] = 0.5
1617	Data['calibskip'] = 0
1618	Data['ellipses'] = []
1619	Data['calibrant'] = ''
1620	Data['GonioAngles'] = [0.,0.,0.]
1621	Data['DetDepth'] = 0.
1622	Data['DetDepthRef'] = False
1623	else:
1624	Data['type'] = 'PWDR'
1625	Data['color'] = 'Paired'
1626	Data['tilt'] = 0.0
1627	Data['rotation'] = 0.0
1628	Data['showLines'] = False
1629	Data['ring'] = []
1630	Data['rings'] = []
1631	Data['cutoff'] = 10
1632	Data['pixLimit'] = 20
1633	Data['calibdmin'] = 0.5
1634	Data['calibskip'] = 0
1635	Data['edgemin'] = 100000000
1636	Data['ellipses'] = []
1637	Data['GonioAngles'] = [0.,0.,0.]
1638	Data['DetDepth'] = 0.
1639	Data['DetDepthRef'] = False
1640	Data['calibrant'] = ''
1641	Data['IOtth'] = [2.0,5.0]
1642	Data['LRazimuth'] = [135,225]
1643	Data['azmthOff'] = 0.0
1644	Data['outChannels'] = 2500
1645	Data['outAzimuths'] = 1
1646	Data['centerAzm'] = False
1647	Data['fullIntegrate'] = False
1648	Data['setRings'] = False
1649	Data['background image'] = ['',1.0]
1650	Data['setDefault'] = False
1651	Data['range'] = [(Imin,Imax),[Imin,Imax]]
1652	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Image Controls'),Data)
1653	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(Imin,Imax),[Imin,Imax]]}
1654	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Masks'),Masks)
1655	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Stress/Strain'),
1656	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'strain':np.zeros((3,3))})
1657	self.PatternTree.SetItemPyData(Id,[Npix,imagefile])
1658	self.PickId = Id
1659	self.Image = Id
1660	os.chdir(dlg.GetDirectory()) # to get Mac/Linux to change directory!
1661	self.PatternTree.SelectItem(G2gd.GetPatternTreeItemId(self,Id,'Image Controls')) #show last one
1662	finally:
1663	path = dlg.GetDirectory() # to get Mac/Linux to change directory!
1664	os.chdir(path)
1665	dlg.Destroy()
1666
1667	def CheckNotebook(self):
1668	'''Make sure the data tree has the minimally expected controls.
1669	(BHT) correct?
1670	'''
1671	if not G2gd.GetPatternTreeItemId(self,self.root,'Notebook'):
1672	sub = self.PatternTree.AppendItem(parent=self.root,text='Notebook')
1673	self.PatternTree.SetItemPyData(sub,[''])
1674	if not G2gd.GetPatternTreeItemId(self,self.root,'Controls'):
1675	sub = self.PatternTree.AppendItem(parent=self.root,text='Controls')
1676	self.PatternTree.SetItemPyData(sub,copy.copy(G2obj.DefaultControls))
1677	if not G2gd.GetPatternTreeItemId(self,self.root,'Covariance'):
1678	sub = self.PatternTree.AppendItem(parent=self.root,text='Covariance')
1679	self.PatternTree.SetItemPyData(sub,{})
1680	if not G2gd.GetPatternTreeItemId(self,self.root,'Constraints'):
1681	sub = self.PatternTree.AppendItem(parent=self.root,text='Constraints')
1682	self.PatternTree.SetItemPyData(sub,{'Hist':[],'HAP':[],'Phase':[]})
1683	if not G2gd.GetPatternTreeItemId(self,self.root,'Restraints'):
1684	sub = self.PatternTree.AppendItem(parent=self.root,text='Restraints')
1685	self.PatternTree.SetItemPyData(sub,{})
1686	if not G2gd.GetPatternTreeItemId(self,self.root,'Rigid bodies'):
1687	sub = self.PatternTree.AppendItem(parent=self.root,text='Rigid bodies')
1688	self.PatternTree.SetItemPyData(sub,{'Vector':{'AtInfo':{}},
1689	'Residue':{'AtInfo':{}},'RBIds':{'Vector':[],'Residue':[]}})
1690
1691	class CopyDialog(wx.Dialog):
1692	'''Creates a dialog for copying control settings between
1693	data tree items'''
1694	def __init__(self,parent,title,text,data):
1695	wx.Dialog.__init__(self,parent,-1,title,
1696	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1697	self.data = data
1698	panel = wx.Panel(self)
1699	mainSizer = wx.BoxSizer(wx.VERTICAL)
1700	topLabl = wx.StaticText(panel,-1,text)
1701	mainSizer.Add((10,10),1)
1702	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.LEFT,10)
1703	mainSizer.Add((10,10),1)
1704	ncols = len(data)/40+1
1705	dataGridSizer = wx.FlexGridSizer(rows=len(data),cols=ncols,hgap=2,vgap=2)
1706	for id,item in enumerate(self.data):
1707	ckbox = wx.CheckBox(panel,id,item[1])
1708	ckbox.Bind(wx.EVT_CHECKBOX,self.OnCopyChange)
1709	dataGridSizer.Add(ckbox,0,wx.LEFT,10)
1710	mainSizer.Add(dataGridSizer,0,wx.EXPAND)
1711	OkBtn = wx.Button(panel,-1,"Ok")
1712	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1713	cancelBtn = wx.Button(panel,-1,"Cancel")
1714	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1715	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1716	btnSizer.Add((20,20),1)
1717	btnSizer.Add(OkBtn)
1718	btnSizer.Add((20,20),1)
1719	btnSizer.Add(cancelBtn)
1720	btnSizer.Add((20,20),1)
1721
1722	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1723	panel.SetSizer(mainSizer)
1724	panel.Fit()
1725	self.Fit()
1726
1727	def OnCopyChange(self,event):
1728	id = event.GetId()
1729	self.data[id][0] = self.FindWindowById(id).GetValue()
1730
1731	def OnOk(self,event):
1732	parent = self.GetParent()
1733	parent.Raise()
1734	self.EndModal(wx.ID_OK)
1735
1736	def OnCancel(self,event):
1737	parent = self.GetParent()
1738	parent.Raise()
1739	self.EndModal(wx.ID_CANCEL)
1740
1741	def GetData(self):
1742	return self.data
1743
1744	class SumDialog(wx.Dialog):
1745	'Allows user to supply scale factor(s) when summing data'
1746	def __init__(self,parent,title,text,dataType,data):
1747	wx.Dialog.__init__(self,parent,-1,title,
1748	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1749	self.data = data
1750	panel = wx.Panel(self)
1751	mainSizer = wx.BoxSizer(wx.VERTICAL)
1752	topLabl = wx.StaticText(panel,-1,text)
1753	mainSizer.Add((10,10),1)
1754	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.LEFT,10)
1755	mainSizer.Add((10,10),1)
1756	dataGridSizer = wx.FlexGridSizer(rows=len(data),cols=2,hgap=2,vgap=2)
1757	for id,item in enumerate(self.data[:-1]):
1758	name = wx.TextCtrl(panel,-1,item[1],size=wx.Size(200,20))
1759	name.SetEditable(False)
1760	scale = wx.TextCtrl(panel,id,'%.3f'%(item[0]),style=wx.TE_PROCESS_ENTER)
1761	scale.Bind(wx.EVT_TEXT_ENTER,self.OnScaleChange)
1762	scale.Bind(wx.EVT_KILL_FOCUS,self.OnScaleChange)
1763	dataGridSizer.Add(scale,0,wx.LEFT,10)
1764	dataGridSizer.Add(name,0,wx.RIGHT,10)
1765	if dataType:
1766	dataGridSizer.Add(wx.StaticText(panel,-1,'Sum result name: '+dataType),0, \
1767	wx.LEFT\|wx.TOP\|wx.ALIGN_CENTER_VERTICAL,10)
1768	self.name = wx.TextCtrl(panel,-1,self.data[-1],size=wx.Size(200,20),style=wx.TE_PROCESS_ENTER)
1769	self.name.Bind(wx.EVT_TEXT_ENTER,self.OnNameChange)
1770	self.name.Bind(wx.EVT_KILL_FOCUS,self.OnNameChange)
1771	dataGridSizer.Add(self.name,0,wx.RIGHT\|wx.TOP,10)
1772	mainSizer.Add(dataGridSizer,0,wx.EXPAND)
1773	OkBtn = wx.Button(panel,-1,"Ok")
1774	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1775	cancelBtn = wx.Button(panel,-1,"Cancel")
1776	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1777	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1778	btnSizer.Add((20,20),1)
1779	btnSizer.Add(OkBtn)
1780	btnSizer.Add((20,20),1)
1781	btnSizer.Add(cancelBtn)
1782	btnSizer.Add((20,20),1)
1783
1784	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1785	panel.SetSizer(mainSizer)
1786	panel.Fit()
1787	self.Fit()
1788
1789	def OnScaleChange(self,event):
1790	id = event.GetId()
1791	value = self.FindWindowById(id).GetValue()
1792	try:
1793	self.data[id][0] = float(value)
1794	self.FindWindowById(id).SetValue('%.3f'%(self.data[id][0]))
1795	except ValueError:
1796	if value and '-' not in value[0]:
1797	print 'bad input - numbers only'
1798	self.FindWindowById(id).SetValue('0.000')
1799
1800	def OnNameChange(self,event):
1801	self.data[-1] = self.name.GetValue()
1802
1803	def OnOk(self,event):
1804	parent = self.GetParent()
1805	parent.Raise()
1806	self.EndModal(wx.ID_OK)
1807
1808	def OnCancel(self,event):
1809	parent = self.GetParent()
1810	parent.Raise()
1811	self.EndModal(wx.ID_CANCEL)
1812
1813	def GetData(self):
1814	return self.data
1815
1816	def OnPwdrSum(self,event):
1817	'Sum together powder data(?)'
1818	TextList = []
1819	DataList = []
1820	SumList = []
1821	Names = []
1822	Inst = None
1823	SumItemList = []
1824	Comments = ['Sum equals: \n']
1825	if self.PatternTree.GetCount():
1826	item, cookie = self.PatternTree.GetFirstChild(self.root)
1827	while item:
1828	name = self.PatternTree.GetItemText(item)
1829	Names.append(name)
1830	if 'PWDR' in name:
1831	TextList.append([0.0,name])
1832	DataList.append(self.PatternTree.GetItemPyData(item)[1]) # (x,y,w,yc,yb,yd)
1833	if not Inst:
1834	Inst = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,item, 'Instrument Parameters'))
1835	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
1836	if len(TextList) < 2:
1837	self.ErrorDialog('Not enough data to sum','There must be more than one "PWDR" pattern')
1838	return
1839	TextList.append('default_sum_name')
1840	dlg = self.SumDialog(self,'Sum data','Enter scale for each pattern in summation','PWDR',TextList)
1841	try:
1842	if dlg.ShowModal() == wx.ID_OK:
1843	lenX = 0
1844	Xminmax = [0,0]
1845	Xsum = []
1846	Ysum = []
1847	Vsum = []
1848	result = dlg.GetData()
1849	for i,item in enumerate(result[:-1]):
1850	scale,name = item
1851	data = DataList[i]
1852	if scale:
1853	Comments.append("%10.3f %s" % (scale,' * '+name))
1854	x,y,w,yc,yb,yd = data #numpy arrays!
1855	v = 1./w
1856	if lenX:
1857	if lenX != len(x):
1858	self.ErrorDialog('Data length error','Data to be summed must have same number of points'+ \
1859	'\nExpected:'+str(lenX)+ \
1860	'\nFound: '+str(len(x))+'\nfor '+name)
1861	return
1862	else:
1863	lenX = len(x)
1864	if Xminmax[1]:
1865	if Xminmax != [x[0],x[-1]]:
1866	self.ErrorDialog('Data range error','Data to be summed must span same range'+ \
1867	'\nExpected:'+str(Xminmax[0])+' '+str(Xminmax[1])+ \
1868	'\nFound: '+str(x[0])+' '+str(x[-1])+'\nfor '+name)
1869	return
1870	else:
1871	for j,yi in enumerate(y):
1872	Ysum[j] += scale*yi
1873	Vsum[j] += abs(scale)*v[j]
1874	else:
1875	Xminmax = [x[0],x[-1]]
1876	YCsum = YBsum = YDsum = [0.0 for i in range(lenX)]
1877	for j,yi in enumerate(y):
1878	Xsum.append(x[j])
1879	Ysum.append(scale*yi)
1880	Vsum.append(abs(scale*v[j]))
1881	Wsum = 1./np.array(Vsum)
1882	outname = 'PWDR '+result[-1]
1883	Id = 0
1884	if outname in Names:
1885	dlg2 = wx.MessageDialog(self,'Overwrite data?','Duplicate data name',wx.OK\|wx.CANCEL)
1886	try:
1887	if dlg2.ShowModal() == wx.ID_OK:
1888	Id = G2gd.GetPatternTreeItemId(self,self.root,name)
1889	self.PatternTree.Delete(Id)
1890	finally:
1891	dlg2.Destroy()
1892	Id = self.PatternTree.AppendItem(parent=self.root,text=outname)
1893	if Id:
1894	Sample = G2pdG.SetDefaultSample()
1895	valuesdict = {
1896	'wtFactor':1.0,
1897	'Dummy':False,
1898	'ranId':ran.randint(0,sys.maxint),
1899	}
1900	self.PatternTree.SetItemPyData(Id,[valuesdict,[np.array(Xsum),np.array(Ysum),np.array(Wsum),
1901	np.array(YCsum),np.array(YBsum),np.array(YDsum)]])
1902	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),Comments)
1903	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
1904	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',True,3,1.0,0.0,0.0],
1905	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
1906	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Instrument Parameters'),Inst)
1907	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
1908	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Peak List'),[])
1909	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Index Peak List'),[])
1910	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
1911	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
1912	self.PatternTree.SelectItem(Id)
1913	self.PatternTree.Expand(Id)
1914	finally:
1915	dlg.Destroy()
1916
1917	def OnImageSum(self,event):
1918	'Sum together image data(?)'
1919	TextList = []
1920	DataList = []
1921	SumList = []
1922	Names = []
1923	Inst = []
1924	SumItemList = []
1925	Comments = ['Sum equals: \n']
1926	if self.PatternTree.GetCount():
1927	item, cookie = self.PatternTree.GetFirstChild(self.root)
1928	while item:
1929	name = self.PatternTree.GetItemText(item)
1930	Names.append(name)
1931	if 'IMG' in name:
1932	TextList.append([0.0,name])
1933	DataList.append(self.PatternTree.GetItemPyData(item)) #Size,Image
1934	Data = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,item,'Image Controls'))
1935	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
1936	if len(TextList) < 2:
1937	self.ErrorDialog('Not enough data to sum','There must be more than one "IMG" pattern')
1938	return
1939	TextList.append('default_sum_name')
1940	dlg = self.SumDialog(self,'Sum data','Enter scale for each image in summation','IMG',TextList)
1941	try:
1942	if dlg.ShowModal() == wx.ID_OK:
1943	imSize = 0
1944	result = dlg.GetData()
1945	First = True
1946	Found = False
1947	for i,item in enumerate(result[:-1]):
1948	scale,name = item
1949	data = DataList[i]
1950	if scale:
1951	Found = True
1952	Comments.append("%10.3f %s" % (scale,' * '+name))
1953	Npix,imagefile = data
1954	image = G2IO.GetImageData(self,imagefile,imageOnly=True)
1955	if First:
1956	newImage = np.zeros_like(image)
1957	First = False
1958	if imSize:
1959	if imSize != Npix:
1960	self.ErrorDialog('Image size error','Images to be summed must be same size'+ \
1961	'\nExpected:'+str(imSize)+ \
1962	'\nFound: '+str(Npix)+'\nfor '+name)
1963	return
1964	newImage = newImage+scale*image
1965	else:
1966	imSize = Npix
1967	newImage = newImage+scale*image
1968	del(image)
1969	if not Found:
1970	self.ErrorDialog('Image sum error','No nonzero image multipliers found')
1971	return
1972
1973	newImage = np.asfarray(newImage,dtype=np.float32)
1974	outname = 'IMG '+result[-1]
1975	Id = 0
1976	if outname in Names:
1977	dlg2 = wx.MessageDialog(self,'Overwrite data?','Duplicate data name',wx.OK\|wx.CANCEL)
1978	try:
1979	if dlg2.ShowModal() == wx.ID_OK:
1980	Id = G2gd.GetPatternTreeItemId(self,self.root,name)
1981	finally:
1982	dlg2.Destroy()
1983	else:
1984	Id = self.PatternTree.AppendItem(parent=self.root,text=outname)
1985	if Id:
1986	dlg = wx.FileDialog(self, 'Choose sum image filename', '.', '',
1987	'G2img files (.G2img)\|.G2img',
1988	wx.SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
1989	if dlg.ShowModal() == wx.ID_OK:
1990	newimagefile = dlg.GetPath()
1991	newimagefile = G2IO.FileDlgFixExt(dlg,newimagefile)
1992	G2IO.PutG2Image(newimagefile,Comments,Data,Npix,newImage)
1993	Imax = np.amax(newImage)
1994	Imin = np.amin(newImage)
1995	newImage = []
1996	self.PatternTree.SetItemPyData(Id,[imSize,newimagefile])
1997	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),Comments)
1998	del(newImage)
1999	if self.imageDefault:
2000	Data = copy.copy(self.imageDefault)
2001	Data['showLines'] = True
2002	Data['ring'] = []
2003	Data['rings'] = []
2004	Data['cutoff'] = 10
2005	Data['pixLimit'] = 20
2006	Data['ellipses'] = []
2007	Data['calibrant'] = ''
2008	Data['range'] = [(Imin,Imax),[Imin,Imax]]
2009	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Image Controls'),Data)
2010	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(Imin,Imax),[Imin,Imax]]}
2011	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Masks'),Masks)
2012	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Stress/Strain'),{})
2013	self.PatternTree.SelectItem(Id)
2014	self.PatternTree.Expand(Id)
2015	self.PickId = G2gd.GetPatternTreeItemId(self,self.root,outname)
2016	self.Image = self.PickId
2017	finally:
2018	dlg.Destroy()
2019
2020	def OnAddPhase(self,event):
2021	'Add a new, empty phase to the tree. Called by Data/Add Phase menu'
2022	if not G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
2023	sub = self.PatternTree.AppendItem(parent=self.root,text='Phases')
2024	else:
2025	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
2026	PhaseName = ''
2027	dlg = wx.TextEntryDialog(None,'Enter a name for this phase','Phase Name Entry','New phase',
2028	style=wx.OK)
2029	if dlg.ShowModal() == wx.ID_OK:
2030	PhaseName = dlg.GetValue()
2031	dlg.Destroy()
2032	sub = self.PatternTree.AppendItem(parent=sub,text=PhaseName)
2033	E,SGData = G2spc.SpcGroup('P 1')
2034	self.PatternTree.SetItemPyData(sub,G2IO.SetNewPhase(Name=PhaseName,SGData=SGData))
2035
2036	def OnDeletePhase(self,event):
2037	'Delete a phase from the tree. Called by Data/Delete Phase menu'
2038	#Hmm, also need to delete this phase from Reflection Lists for each PWDR histogram
2039	if self.dataFrame:
2040	self.dataFrame.Clear()
2041	TextList = []
2042	DelList = []
2043	DelItemList = []
2044	if G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
2045	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
2046	else:
2047	return
2048	if sub:
2049	item, cookie = self.PatternTree.GetFirstChild(sub)
2050	while item:
2051	TextList.append(self.PatternTree.GetItemText(item))
2052	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
2053	dlg = wx.MultiChoiceDialog(self, 'Which phase to delete?', 'Delete phase', TextList, wx.CHOICEDLG_STYLE)
2054	try:
2055	if dlg.ShowModal() == wx.ID_OK:
2056	result = dlg.GetSelections()
2057	for i in result: DelList.append([i,TextList[i]])
2058	item, cookie = self.PatternTree.GetFirstChild(sub)
2059	i = 0
2060	while item:
2061	if [i,self.PatternTree.GetItemText(item)] in DelList: DelItemList.append(item)
2062	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
2063	i += 1
2064	for item in DelItemList:
2065	name = self.PatternTree.GetItemText(item)
2066	self.PatternTree.Delete(item)
2067	self.G2plotNB.Delete(name)
2068	item, cookie = self.PatternTree.GetFirstChild(self.root)
2069	while item:
2070	name = self.PatternTree.GetItemText(item)
2071	if 'PWDR' in name:
2072	Id = G2gd.GetPatternTreeItemId(self,item, 'Reflection Lists')
2073	refList = self.PatternTree.GetItemPyData(Id)
2074	for i,item in DelList:
2075	del(refList[item])
2076	self.PatternTree.SetItemPyData(Id,refList)
2077	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2078	finally:
2079	dlg.Destroy()
2080
2081	def OnRenameData(self,event):
2082	'Renames an existing phase. Called by Data/Rename Phase menu'
2083	name = self.PatternTree.GetItemText(self.PickId)
2084	if 'PWDR' in name or 'HKLF' in name or 'IMG' in name:
2085	dataType = name[:name.index(' ')+1] #includes the ' '
2086	dlg = wx.TextEntryDialog(self,'Data name: '+dataType,'Change data name',
2087	defaultValue=name[name.index(' ')+1:])
2088	try:
2089	if dlg.ShowModal() == wx.ID_OK:
2090	self.PatternTree.SetItemText(self.PickId,dataType+dlg.GetValue())
2091	finally:
2092	dlg.Destroy()
2093
2094	def GetFileList(self,fileType,skip=None): #potentially useful?
2095	'Appears unused. Note routine of same name in GSASIIpwdGUI'
2096	fileList = []
2097	Source = ''
2098	id, cookie = self.PatternTree.GetFirstChild(self.root)
2099	while id:
2100	name = self.PatternTree.GetItemText(id)
2101	if fileType in name:
2102	if id == skip:
2103	Source = name
2104	else:
2105	fileList.append([False,name,id])
2106	id, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2107	if skip:
2108	return fileList,Source
2109	else:
2110	return fileList
2111
2112	def OnDataDelete(self, event):
2113	'''Delete one or more histograms from data tree. Called by the
2114	Data/DeleteData menu
2115	'''
2116	TextList = ['All Data']
2117	DelList = []
2118	DelItemList = []
2119	ifPWDR = False
2120	ifIMG = False
2121	ifHKLF = False
2122	ifPDF = False
2123	if self.PatternTree.GetCount():
2124	item, cookie = self.PatternTree.GetFirstChild(self.root)
2125	while item:
2126	name = self.PatternTree.GetItemText(item)
2127	if name not in ['Notebook','Controls','Covariance','Constraints','Restraints','Phases']:
2128	if 'PWDR' in name: ifPWDR = True
2129	if 'IMG' in name: ifIMG = True
2130	if 'HKLF' in name: ifHKLF = True
2131	if 'PDF' in name: ifPDF = True
2132	TextList.append(name)
2133	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2134	if ifPWDR: TextList.insert(1,'All PWDR')
2135	if ifIMG: TextList.insert(1,'All IMG')
2136	if ifHKLF: TextList.insert(1,'All HKLF')
2137	if ifPDF: TextList.insert(1,'All PDF')
2138	dlg = wx.MultiChoiceDialog(self, 'Which data to delete?', 'Delete data', TextList, wx.CHOICEDLG_STYLE)
2139	try:
2140	if dlg.ShowModal() == wx.ID_OK:
2141	result = dlg.GetSelections()
2142	for i in result: DelList.append(TextList[i])
2143	if 'All Data' in DelList:
2144	DelList = [item for item in TextList if item[:3] != 'All']
2145	elif 'All PWDR' in DelList:
2146	DelList = [item for item in TextList if item[:4] == 'PWDR']
2147	elif 'All IMG' in DelList:
2148	DelList = [item for item in TextList if item[:3] == 'IMG']
2149	elif 'All HKLF' in DelList:
2150	DelList = [item for item in TextList if item[:4] == 'HKLF']
2151	elif 'All PDF' in DelList:
2152	DelList = [item for item in TextList if item[:3] == 'PDF']
2153	item, cookie = self.PatternTree.GetFirstChild(self.root)
2154	while item:
2155	if self.PatternTree.GetItemText(item) in DelList: DelItemList.append(item)
2156	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2157	for item in DelItemList:
2158	self.PatternTree.Delete(item)
2159	self.PickId = 0
2160	wx.CallAfter(G2plt.PlotPatterns,self,True) #so plot gets updated
2161	finally:
2162	dlg.Destroy()
2163
2164	def OnFileOpen(self, event, filename=None):
2165	'''Reads in a GSAS-II .gpx project file in response to the
2166	File/Open Project menu button
2167	'''
2168	result = wx.ID_OK
2169	Id = 0
2170	if self.PatternTree.GetChildrenCount(self.root,False):
2171	if self.dataFrame:
2172	self.dataFrame.Clear()
2173	dlg = wx.MessageDialog(
2174	self,
2175	'Do you want to overwrite the current project? '
2176	'Any unsaved changes will be lost. Press OK to continue.',
2177	'Overwrite?', wx.OK \| wx.CANCEL)
2178	try:
2179	result = dlg.ShowModal()
2180	if result == wx.ID_OK:
2181	self.PatternTree.DeleteChildren(self.root)
2182	self.GSASprojectfile = ''
2183	if self.HKL: self.HKL = []
2184	if self.G2plotNB.plotList:
2185	self.G2plotNB.clear()
2186	finally:
2187	dlg.Destroy()
2188	if result != wx.ID_OK: return
2189
2190	if not filename:
2191	if self.dataDisplay: self.dataDisplay.Destroy()
2192	dlg = wx.FileDialog(self, 'Choose GSAS-II project file', '.', '',
2193	'GSAS-II project file (.gpx)\|.gpx',wx.OPEN\|wx.CHANGE_DIR)
2194	try:
2195	if dlg.ShowModal() != wx.ID_OK: return
2196	self.GSASprojectfile = dlg.GetPath()
2197	self.GSASprojectfile = G2IO.FileDlgFixExt(dlg,self.GSASprojectfile)
2198	self.dirname = dlg.GetDirectory()
2199	finally:
2200	dlg.Destroy()
2201	else:
2202	self.GSASprojectfile = os.path.splitext(filename)[0]+'.gpx'
2203	self.dirname = os.path.split(filename)[0]
2204
2205	G2IO.ProjFileOpen(self)
2206	self.PatternTree.SetItemText(self.root,'Loaded Data: '+self.GSASprojectfile)
2207	self.PatternTree.Expand(self.root)
2208	self.HKL = []
2209	item, cookie = self.PatternTree.GetFirstChild(self.root)
2210	while item and not Id:
2211	name = self.PatternTree.GetItemText(item)
2212	if name[:4] in ['PWDR','HKLF','IMG ','PDF ']:
2213	Id = item
2214	elif name == 'Controls':
2215	data = self.PatternTree.GetItemPyData(item)
2216	if data:
2217	for item in self.Refine: item.Enable(True)
2218	for item in self.SeqRefine: item.Enable(True)
2219	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2220	if Id:
2221	self.PatternTree.SelectItem(Id)
2222	self.CheckNotebook()
2223	os.chdir(self.dirname) # to get Mac/Linux to change directory!
2224
2225	def OnFileClose(self, event):
2226	'''Clears the data tree in response to the
2227	File/New Project menu button. User is given option to save
2228	the project.
2229	'''
2230	if self.dataFrame:
2231	self.dataFrame.Clear()
2232	self.dataFrame.SetLabel('GSAS-II data display')
2233	dlg = wx.MessageDialog(self, 'Save current project?', ' ', wx.YES \| wx.NO \| wx.CANCEL)
2234	try:
2235	result = dlg.ShowModal()
2236	if result == wx.ID_OK:
2237	self.OnFileSaveMenu(event)
2238	if result != wx.ID_CANCEL:
2239	self.GSASprojectfile = ''
2240	self.PatternTree.SetItemText(self.root,'Loaded Data: ')
2241	self.PatternTree.DeleteChildren(self.root)
2242	if self.HKL: self.HKL = []
2243	if self.G2plotNB.plotList:
2244	self.G2plotNB.clear()
2245	finally:
2246	dlg.Destroy()
2247
2248	def OnFileSave(self, event):
2249	'''Save the current project in response to the
2250	File/Save Project menu button
2251	'''
2252
2253	if self.GSASprojectfile:
2254	self.PatternTree.SetItemText(self.root,'Loaded Data: '+self.GSASprojectfile)
2255	G2IO.ProjFileSave(self)
2256	else:
2257	self.OnFileSaveas(event)
2258
2259	def OnFileSaveas(self, event):
2260	'''Save the current project in response to the
2261	File/Save as menu button
2262	'''
2263	dlg = wx.FileDialog(self, 'Choose GSAS-II project file name', '.', '',
2264	'GSAS-II project file (.gpx)\|.gpx',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2265	try:
2266	if dlg.ShowModal() == wx.ID_OK:
2267	self.GSASprojectfile = dlg.GetPath()
2268	self.GSASprojectfile = G2IO.FileDlgFixExt(dlg,self.GSASprojectfile)
2269	self.PatternTree.SetItemText(self.root,'Saving project as'+self.GSASprojectfile)
2270	self.SetTitle("GSAS-II data tree: "+os.path.split(self.GSASprojectfile)[1])
2271	G2IO.ProjFileSave(self)
2272	os.chdir(dlg.GetDirectory()) # to get Mac/Linux to change directory!
2273	finally:
2274	dlg.Destroy()
2275
2276	def ExitMain(self, event):
2277	'''Called if the main window is closed'''
2278	if self.undofile:
2279	os.remove(self.undofile)
2280	sys.exit()
2281
2282	def OnFileExit(self, event):
2283	'''Called in response to the File/Quit menu button'''
2284	if self.dataFrame:
2285	self.dataFrame.Clear()
2286	self.dataFrame.Destroy()
2287	self.Close()
2288
2289	def OnExportPatterns(self,event):
2290	names = ['All']
2291	exports = []
2292	item, cookie = self.PatternTree.GetFirstChild(self.root)
2293	while item:
2294	name = self.PatternTree.GetItemText(item)
2295	if 'PWDR' in name:
2296	names.append(name)
2297	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2298	if names:
2299	dlg = wx.MultiChoiceDialog(self,'Select','Powder patterns to export',names)
2300	if dlg.ShowModal() == wx.ID_OK:
2301	sel = dlg.GetSelections()
2302	if sel[0] == 0:
2303	exports = names[1:]
2304	else:
2305	for x in sel:
2306	exports.append(names[x])
2307	dlg.Destroy()
2308	if exports:
2309	dlg = wx.FileDialog(self, 'Choose output powder file name', '.', '',
2310	'GSAS fxye file (.fxye)\|.fxye\|xye file (.xye)\|.xye',
2311	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2312	try:
2313	if dlg.ShowModal() == wx.ID_OK:
2314	powderfile = dlg.GetPath()
2315	powderfile = G2IO.FileDlgFixExt(dlg,powderfile)
2316	if 'fxye' in powderfile:
2317	G2IO.powderFxyeSave(self,exports,powderfile)
2318	else: #just xye
2319	G2IO.powderXyeSave(self,exports,powderfile)
2320	finally:
2321	dlg.Destroy()
2322
2323	def OnExportPeakList(self,event):
2324	dlg = wx.FileDialog(self, 'Choose output peak list file name', '.', '',
2325	'(.)\|.',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2326	try:
2327	if dlg.ShowModal() == wx.ID_OK:
2328	self.peaklistfile = dlg.GetPath()
2329	self.peaklistfile = G2IO.FileDlgFixExt(dlg,self.peaklistfile)
2330	file = open(self.peaklistfile,'w')
2331	item, cookie = self.PatternTree.GetFirstChild(self.root)
2332	while item:
2333	name = self.PatternTree.GetItemText(item)
2334	if 'PWDR' in name:
2335	item2, cookie2 = self.PatternTree.GetFirstChild(item)
2336	while item2:
2337	name2 = self.PatternTree.GetItemText(item2)
2338	if name2 == 'Peak List':
2339	peaks = self.PatternTree.GetItemPyData(item2)
2340	file.write("%s \n" % (name+' Peak List'))
2341	for peak in peaks:
2342	file.write("%10.5f %12.2f %10.3f %10.3f \n" % \
2343	(peak[0],peak[2],peak[4],peak[6]))
2344	item2, cookie2 = self.PatternTree.GetNextChild(item, cookie2)
2345	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2346	file.close()
2347	finally:
2348	dlg.Destroy()
2349
2350	def OnExportHKL(self,event):
2351	dlg = wx.FileDialog(self, 'Choose output reflection list file name', '.', '',
2352	'(.)\|.',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2353	try:
2354	if dlg.ShowModal() == wx.ID_OK:
2355	self.peaklistfile = dlg.GetPath()
2356	self.peaklistfile = G2IO.FileDlgFixExt(dlg,self.peaklistfile)
2357	file = open(self.peaklistfile,'w')
2358	item, cookie = self.PatternTree.GetFirstChild(self.root)
2359	while item:
2360	name = self.PatternTree.GetItemText(item)
2361	if 'PWDR' in name:
2362	item2, cookie2 = self.PatternTree.GetFirstChild(item)
2363	while item2:
2364	name2 = self.PatternTree.GetItemText(item2)
2365	if name2 == 'Reflection Lists':
2366	data = self.PatternTree.GetItemPyData(item2)
2367	phases = data.keys()
2368	for phase in phases:
2369	peaks = data[phase]
2370	file.write("%s %s %s \n" % (name,phase,' Reflection List'))
2371	file.write('%s \n'%(' h k l m d-space 2-theta wid F**2'))
2372	for peak in peaks:
2373	FWHM = G2pwd.getgamFW(peak[7],peak[6])/50. #to get delta-2-theta in deg.
2374	file.write(" %3d %3d %3d %3d %10.5f %10.5f %10.5f %10.3f \n" % \
2375	(int(peak[0]),int(peak[1]),int(peak[2]),int(peak[3]),peak[4],peak[5],FWHM,peak[8]))
2376	item2, cookie2 = self.PatternTree.GetNextChild(item, cookie2)
2377	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2378	file.close()
2379	finally:
2380	dlg.Destroy()
2381
2382	def OnExportPDF(self,event):
2383	#need S(Q) and G(R) to be saved here - probably best from selection?
2384	names = ['All']
2385	exports = []
2386	item, cookie = self.PatternTree.GetFirstChild(self.root)
2387	while item:
2388	name = self.PatternTree.GetItemText(item)
2389	if 'PDF' in name:
2390	names.append(name)
2391	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2392	if names:
2393	dlg = wx.MultiChoiceDialog(self,'Select','PDF patterns to export',names)
2394	if dlg.ShowModal() == wx.ID_OK:
2395	sel = dlg.GetSelections()
2396	if sel[0] == 0:
2397	exports = names[1:]
2398	else:
2399	for x in sel:
2400	exports.append(names[x])
2401	dlg.Destroy()
2402	if exports:
2403	G2IO.PDFSave(self,exports)
2404
2405	def OnMakePDFs(self,event):
2406	'''Calculates PDFs
2407	'''
2408	tth2q = lambda t,w:4.0math.pisind(t/2.0)/w
2409	TextList = ['All PWDR']
2410	PDFlist = []
2411	Names = []
2412	if self.PatternTree.GetCount():
2413	id, cookie = self.PatternTree.GetFirstChild(self.root)
2414	while id:
2415	name = self.PatternTree.GetItemText(id)
2416	Names.append(name)
2417	if 'PWDR' in name:
2418	TextList.append(name)
2419	id, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2420	if len(TextList) == 1:
2421	self.ErrorDialog('Nothing to make PDFs for','There must be at least one "PWDR" pattern')
2422	return
2423	dlg = wx.MultiChoiceDialog(self,'Make PDF controls','Make PDF controls for:',TextList, wx.CHOICEDLG_STYLE)
2424	try:
2425	if dlg.ShowModal() == wx.ID_OK:
2426	result = dlg.GetSelections()
2427	for i in result: PDFlist.append(TextList[i])
2428	if 0 in result:
2429	PDFlist = [item for item in TextList if item[:4] == 'PWDR']
2430	for item in PDFlist:
2431	PWDRname = item[4:]
2432	Id = self.PatternTree.AppendItem(parent=self.root,text='PDF '+PWDRname)
2433	Data = {
2434	'Sample':{'Name':item,'Mult':1.0,'Add':0.0},
2435	'Sample Bkg.':{'Name':'','Mult':-1.0,'Add':0.0},
2436	'Container':{'Name':'','Mult':-1.0,'Add':0.0},
2437	'Container Bkg.':{'Name':'','Mult':-1.0,'Add':0.0},'ElList':{},
2438	'Geometry':'Cylinder','Diam':1.0,'Pack':0.50,'Form Vol':10.0,
2439	'DetType':'Image plate','ObliqCoeff':0.2,'Ruland':0.025,'QScaleLim':[0,100],
2440	'Lorch':True,}
2441	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='PDF Controls'),Data)
2442	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='I(Q)'+PWDRname),[])
2443	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='S(Q)'+PWDRname),[])
2444	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='F(Q)'+PWDRname),[])
2445	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='G(R)'+PWDRname),[])
2446	for item in self.ExportPDF: item.Enable(True)
2447	finally:
2448	dlg.Destroy()
2449
2450	def GetPWDRdatafromTree(self,PWDRname):
2451	''' Returns powder data from GSASII tree
2452
2453	:param str PWDRname: a powder histogram name as obtained from
2454	:meth:`GSASIIstruct.GetHistogramNames`
2455
2456	:returns: PWDRdata = powder data dictionary with
2457	Powder data arrays, Limits, Instrument Parameters,
2458	Sample Parameters
2459	'''
2460	PWDRdata = {}
2461	try:
2462	PWDRdata.update(self.PatternTree.GetItemPyData(PWDRname)[0]) #wtFactor + ?
2463	except ValueError:
2464	PWDRdata['wtFactor'] = 1.0
2465	PWDRdata['Data'] = self.PatternTree.GetItemPyData(PWDRname)[1] #powder data arrays
2466	PWDRdata['Limits'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Limits'))
2467	PWDRdata['Background'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Background'))
2468	PWDRdata['Instrument Parameters'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Instrument Parameters'))
2469	PWDRdata['Sample Parameters'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Sample Parameters'))
2470	PWDRdata['Reflection Lists'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Reflection Lists'))
2471	if 'ranId' not in PWDRdata: # patch, add a random Id
2472	PWDRdata['ranId'] = ran.randint(0,sys.maxint)
2473	if 'ranId' not in PWDRdata['Sample Parameters']: # I hope this becomes obsolete at some point
2474	PWDRdata['Sample Parameters']['ranId'] = PWDRdata['ranId']
2475	return PWDRdata
2476
2477	def GetHKLFdatafromTree(self,HKLFname):
2478	''' Returns single crystal data from GSASII tree
2479
2480	:param str HKLFname: a single crystal histogram name as obtained
2481	from
2482	:meth:`GSASIIstruct.GetHistogramNames`
2483
2484	:returns: HKLFdata = single crystal data list of reflections
2485
2486	'''
2487	HKLFdata = {}
2488	HKLFdata.update(self.PatternTree.GetItemPyData(HKLFname)[0]) #wtFactor + ?
2489	# try:
2490	# HKLFdata.update(self.PatternTree.GetItemPyData(HKLFname)[0]) #wtFactor + ?
2491	# except ValueError:
2492	# HKLFdata['wtFactor'] = 1.0
2493	HKLFdata['Data'] = self.PatternTree.GetItemPyData(HKLFname)[1]
2494	HKLFdata['Instrument Parameters'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,HKLFname,'Instrument Parameters'))
2495	return HKLFdata
2496
2497	def GetPhaseData(self):
2498	'''Returns a dict with defined phases.
2499	Note routine :func:`GSASIIstrIO.GetPhaseData` also exists to
2500	get same info from GPX file.
2501	'''
2502	phaseData = {}
2503	if G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
2504	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
2505	else:
2506	print 'no phases found in GetPhaseData'
2507	sub = None
2508	if sub:
2509	item, cookie = self.PatternTree.GetFirstChild(sub)
2510	while item:
2511	phaseName = self.PatternTree.GetItemText(item)
2512	phaseData[phaseName] = self.PatternTree.GetItemPyData(item)
2513	if 'ranId' not in phaseData[phaseName]:
2514	phaseData[phaseName]['ranId'] = ran.randint(0,sys.maxint)
2515	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
2516	return phaseData
2517
2518	def GetPhaseNames(self):
2519	'''Returns a list of defined phases.
2520	Note routine :func:`GSASIIstrIO.GetPhaseNames` also exists to
2521	get same info from GPX file.
2522	'''
2523	phaseNames = []
2524	if G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
2525	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
2526	else:
2527	print 'no phases found in GetPhaseNames'
2528	sub = None
2529	if sub:
2530	item, cookie = self.PatternTree.GetFirstChild(sub)
2531	while item:
2532	phase = self.PatternTree.GetItemText(item)
2533	phaseNames.append(phase)
2534	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
2535	return phaseNames
2536
2537	def GetHistogramNames(self,hType):
2538	""" Returns a list of histogram names found in the GSASII data tree
2539	Note routine :func:`GSASIIstrIO.GetHistogramNames` also exists to
2540	get same info from GPX file.
2541
2542	:param str hType: list of histogram types
2543	:return: list of histogram names
2544
2545	"""
2546	HistogramNames = []
2547	if self.PatternTree.GetCount():
2548	item, cookie = self.PatternTree.GetFirstChild(self.root)
2549	while item:
2550	name = self.PatternTree.GetItemText(item)
2551	if name[:4] in hType:
2552	HistogramNames.append(name)
2553	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2554
2555	return HistogramNames
2556
2557
2558	def GetUsedHistogramsAndPhasesfromTree(self):
2559	''' Returns all histograms that are found in any phase
2560	and any phase that uses a histogram.
2561	This also assigns numbers to used phases and histograms by the
2562	order they appear in the file.
2563	Note routine :func:`GSASIIstrIO.GetUsedHistogramsAndPhasesfromTree` also exists to
2564	get same info from GPX file.
2565
2566	:returns: (Histograms,Phases)
2567
2568	* Histograms = dictionary of histograms as {name:data,...}
2569	* Phases = dictionary of phases that use histograms
2570	'''
2571	Histograms = {}
2572	Phases = {}
2573	phaseNames = self.GetPhaseNames()
2574	phaseData = self.GetPhaseData()
2575	histoList = self.GetHistogramNames(['PWDR','HKLF'])
2576
2577	for phase in phaseData:
2578	Phase = phaseData[phase]
2579	pId = phaseNames.index(phase)
2580	Phase['pId'] = pId
2581	if Phase['Histograms']:
2582	if phase not in Phases:
2583	Phases[phase] = Phase
2584	for hist in Phase['Histograms']:
2585	if 'Use' not in Phase['Histograms'][hist]: #patch: add Use flag as True
2586	Phase['Histograms'][hist]['Use'] = True
2587	if hist not in Histograms and Phase['Histograms'][hist]['Use']:
2588	item = G2gd.GetPatternTreeItemId(self,self.root,hist)
2589	if item:
2590	if 'PWDR' in hist[:4]:
2591	Histograms[hist] = self.GetPWDRdatafromTree(item)
2592	elif 'HKLF' in hist[:4]:
2593	Histograms[hist] = self.GetHKLFdatafromTree(item)
2594	hId = histoList.index(hist)
2595	Histograms[hist]['hId'] = hId
2596	else: # would happen if a referenced histogram were renamed or deleted
2597	print('For phase "'+str(phase)+
2598	'" unresolved reference to histogram "'+str(hist)+'"')
2599	#G2obj.IndexAllIds(Histograms=Histograms,Phases=Phases)
2600	G2obj.IndexAllIds(Histograms=Histograms,Phases=phaseData)
2601	return Histograms,Phases
2602
2603	def MakeLSParmDict(self):
2604	'''Load all parameters used for computation from the tree into a
2605	dict
2606
2607	:returns: (parmDict,varyList) where:
2608
2609	* parmDict is a dict with values and refinement flags
2610	for each parameter and
2611	* varyList is a list of variables (refined parameters).
2612	'''
2613	parmDict = {}
2614	Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree()
2615	for phase in Phases:
2616	if 'pId' not in Phases[phase]:
2617	self.ErrorDialog('View parameter error','You must run least squares at least once')
2618	raise Exception,'No pId for phase '+str(phase)
2619	rigidbodyDict = self.PatternTree.GetItemPyData(
2620	G2gd.GetPatternTreeItemId(self,self.root,'Rigid bodies'))
2621	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
2622	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
2623	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtable,BLtable = G2stIO.GetPhaseData(Phases,RestraintDict=None,rbIds=rbIds,Print=False)
2624	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(Phases,Histograms,Print=False)
2625	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
2626	varyList = rbVary+phaseVary+hapVary+histVary
2627	parmDict.update(rbDict)
2628	parmDict.update(phaseDict)
2629	parmDict.update(hapDict)
2630	parmDict.update(histDict)
2631	for parm in parmDict:
2632	if parm.split(':')[-1] in ['Azimuth','Gonio. radius','Lam1','Lam2',
2633	'Omega','Chi','Phi','nDebye','nPeaks']:
2634	parmDict[parm] = [parmDict[parm],'-']
2635	elif parm.split(':')[-2] in ['Ax','Ay','Az','SHmodel','SHord']:
2636	parmDict[parm] = [parmDict[parm],'-']
2637	elif parm in varyList:
2638	parmDict[parm] = [parmDict[parm],'T']
2639	else:
2640	parmDict[parm] = [parmDict[parm],'F']
2641	return parmDict,varyList
2642
2643	def ShowLSParms(self,event):
2644	'''Displays a window showing all parameters in the refinement.
2645	Called from the Calculate/View LS Parms menu.
2646	'''
2647	parmDict,varyList = self.MakeLSParmDict()
2648	dlg = G2gd.ShowLSParms(self,'Least Squares Parameters',parmDict,varyList)
2649	dlg.ShowModal()
2650	dlg.Destroy()
2651
2652	def OnRefine(self,event):
2653	'''Perform a refinement.
2654	Called from the Calculate/Refine menu.
2655	'''
2656	self.OnFileSave(event)
2657	# check that constraints are OK here
2658	errmsg, warnmsg = G2stIO.CheckConstraints(self.GSASprojectfile)
2659	if errmsg:
2660	print('Error in constraints:\n'+errmsg+
2661	'\nRefinement not possible')
2662	self.ErrorDialog('Constraint Error',
2663	'Error in constraints:\n'+errmsg+
2664	'\nRefinement not possible')
2665	return
2666	if warnmsg:
2667	print('Conflict between refinment flag settings and constraints:\n'+
2668	warnmsg+'\nRefinement not possible')
2669	self.ErrorDialog('Refinement Flag Error',
2670	'Conflict between refinment flag settings and constraints:\n'+
2671	warnmsg+
2672	'\nRefinement not possible')
2673	return
2674	#works - but it'd be better if it could restore plots
2675	dlg = wx.ProgressDialog('Residual','All data Rw =',101.0,
2676	style = wx.PD_ELAPSED_TIME\|wx.PD_AUTO_HIDE\|wx.PD_CAN_ABORT)
2677	screenSize = wx.ClientDisplayRect()
2678	Size = dlg.GetSize()
2679	Size = (int(Size[0]*1.2),Size[1]) # increase size a bit along x
2680	dlg.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5))
2681	dlg.SetSize(Size)
2682	Rw = 100.00
2683	try:
2684	Rw = G2stMn.Refine(self.GSASprojectfile,dlg)
2685	finally:
2686	dlg.Destroy()
2687	oldId = self.PatternTree.GetSelection()
2688	oldName = self.PatternTree.GetItemText(oldId)
2689	parentId = self.PatternTree.GetItemParent(oldId)
2690	parentName = ''
2691	if parentId:
2692	parentName = self.PatternTree.GetItemText(parentId)
2693	dlg = wx.MessageDialog(self,'Load new result?','Refinement results, Rw =%.3f'%(Rw),wx.OK\|wx.CANCEL)
2694	try:
2695	if dlg.ShowModal() == wx.ID_OK:
2696	Id = 0
2697	self.PatternTree.DeleteChildren(self.root)
2698	if self.HKL: self.HKL = []
2699	if self.G2plotNB.plotList:
2700	self.G2plotNB.clear()
2701	G2IO.ProjFileOpen(self)
2702	item, cookie = self.PatternTree.GetFirstChild(self.root)
2703	while item and not Id:
2704	name = self.PatternTree.GetItemText(item)
2705	if name[:4] in ['PWDR','HKLF']:
2706	Id = item
2707	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2708	if parentName:
2709	parentId = G2gd.GetPatternTreeItemId(self, self.root, parentName)
2710	if parentId:
2711	itemId = G2gd.GetPatternTreeItemId(self, parentId, oldName)
2712	else:
2713	itemId = G2gd.GetPatternTreeItemId(self, self.root, oldName)
2714	self.PatternTree.SelectItem(itemId)
2715	elif Id:
2716	self.PatternTree.SelectItem(Id)
2717	finally:
2718	dlg.Destroy()
2719
2720	def OnSeqRefine(self,event):
2721	'''Perform a sequential refinement.
2722	Called from the Calculate/Sequential refine menu.
2723	'''
2724	Id = G2gd.GetPatternTreeItemId(self,self.root,'Sequential results')
2725	if not Id:
2726	Id = self.PatternTree.AppendItem(self.root,text='Sequential results')
2727	self.PatternTree.SetItemPyData(Id,{})
2728	self.OnFileSave(event)
2729	# check that constraints are OK here
2730	errmsg, warnmsg = G2stIO.CheckConstraints(self.GSASprojectfile)
2731	if errmsg:
2732	print('Error in constraints:\n'+errmsg+
2733	'\nRefinement not possible')
2734	self.ErrorDialog('Constraint Error',
2735	'Error in constraints:\n'+errmsg+
2736	'\nRefinement not possible')
2737	return
2738	if warnmsg:
2739	print('Conflict between refinment flag settings and constraints:\n'+
2740	warnmsg+'\nRefinement not possible')
2741	self.ErrorDialog('Refinement Flag Error',
2742	'Conflict between refinment flag settings and constraints:\n'+
2743	warnmsg+'\nRefinement not possible')
2744	return
2745	dlg = wx.ProgressDialog('Residual for histogram 0','Powder profile Rwp =',101.0,
2746	style = wx.PD_ELAPSED_TIME\|wx.PD_AUTO_HIDE\|wx.PD_CAN_ABORT)
2747	screenSize = wx.ClientDisplayRect()
2748	Size = dlg.GetSize()
2749	Size = (int(Size[0]*1.2),Size[1]) # increase size a bit along x
2750	dlg.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5))
2751	dlg.SetSize(Size)
2752	try:
2753	G2stMn.SeqRefine(self.GSASprojectfile,dlg)
2754	finally:
2755	dlg.Destroy()
2756	dlg = wx.MessageDialog(self,'Load new result?','Refinement results',wx.OK\|wx.CANCEL)
2757	try:
2758	if dlg.ShowModal() == wx.ID_OK:
2759	Id = 0
2760	self.PatternTree.DeleteChildren(self.root)
2761	if self.HKL: self.HKL = []
2762	if self.G2plotNB.plotList:
2763	self.G2plotNB.clear()
2764	G2IO.ProjFileOpen(self)
2765	item, cookie = self.PatternTree.GetFirstChild(self.root)
2766	while item and not Id:
2767	name = self.PatternTree.GetItemText(item)
2768	if name[:4] in ['PWDR','HKLF']:
2769	Id = item
2770	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
2771	if Id:
2772	self.PatternTree.SelectItem(Id)
2773	finally:
2774	dlg.Destroy()
2775
2776	def ErrorDialog(self,title,message,parent=None, wtype=wx.OK):
2777	'Display an error message'
2778	result = None
2779	if parent is None:
2780	dlg = wx.MessageDialog(self, message, title, wtype)
2781	else:
2782	dlg = wx.MessageDialog(parent, message, title, wtype)
2783	dlg.CenterOnParent() # not working on Mac
2784	try:
2785	result = dlg.ShowModal()
2786	finally:
2787	dlg.Destroy()
2788	return result
2789
2790	class GSASIImain(wx.App):
2791	'''Defines a wxApp for GSAS-II
2792
2793	Creates a wx frame (self.main) which contains the display of the
2794	data tree.
2795	'''
2796	def OnInit(self):
2797	'''Called automatically when the app is created.'''
2798	self.main = GSASII(None)
2799	self.main.Show()
2800	self.SetTopWindow(self.main)
2801	return True
2802	def MacOpenFile(self, filename):
2803	'''Called on Mac every time a file is dropped on the app when it is running,
2804	treat this like a File/Open project menu action.
2805	Should be ignored on other platforms
2806	'''
2807	self.main.OnFileOpen(None,filename)
2808
2809	def main():
2810	'''Start up the GSAS-II application'''
2811	#application = GSASIImain() # don't redirect output, someday we
2812	# may want to do this if we can
2813	application = GSASIImain(0)
2814	if wxInspector:
2815	import wx.lib.inspection as wxeye
2816	wxeye.InspectionTool().Show()
2817
2818	#application.main.OnRefine(None)
2819	application.MainLoop()
2820
2821	if __name__ == '__main__':
2822	main() # start the GUI

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