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source: trunk/GSASII.py @ 481

Last change on this file since 481 was 481, checked in by vondreele, 10 years ago
fix the up/down arrow behavior on the tree - used to skip
Property svn:keywords set to `Date Author Revision URL Id`
File size: 90.5 KB

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1	#!/usr/bin/env python
2	# -- coding: utf-8 --
3	#GSASII
4	########### SVN repository information ###################
5	# $Date: 2012-02-10 21:10:46 +0000 (Fri, 10 Feb 2012) $
6	# $Author: vondreele $
7	# $Revision: 481 $
8	# $URL: trunk/GSASII.py $
9	# $Id: GSASII.py 481 2012-02-10 21:10:46Z vondreele $
10	########### SVN repository information ###################
11
12	import os
13	import os.path as ospath
14	import sys
15	import math
16	import cPickle
17	import time
18	import copy
19	import glob
20	import imp
21	import inspect
22	import numpy as np
23	import scipy as sp
24	import wx
25	import matplotlib as mpl
26	import wx.lib.inspection as wxeye
27
28	# load the GSAS routines
29	import GSASIIpath
30	import GSASIIIO as G2IO
31	import GSASIIgrid as G2gd
32	import GSASIIplot as G2plt
33	import GSASIIpwdGUI as G2pdG
34	import GSASIIspc as G2spc
35	import GSASIIstruct as G2str
36	import GSASIImapvars as G2mv
37	import GSASIIsolve as G2sol
38	import OpenGL as ogl
39
40	#wx inspector - use as needed
41	wxInspector = False
42
43	# print versions
44	print "Available python module versions for GSASII:"
45	print "python: ",sys.version[:5]
46	print "wxpython: ",wx.__version__
47	print "matplotlib: ",mpl.__version__
48	print "numpy: ",np.__version__
49	print "scipy: ",sp.__version__
50	print "OpenGL: ",ogl.__version__
51	try:
52	import mkl
53	print "Max threads ",mkl.get_max_threads()
54	except:
55	print "MKL module not present"
56	__version__ = '0.1.5'
57	G2gd.__version__ = __version__
58	print "This is GSAS-II version: ",__version__
59
60	# useful degree trig functions
61	sind = lambda x: math.sin(x*math.pi/180.)
62	cosd = lambda x: math.cos(x*math.pi/180.)
63	tand = lambda x: math.tan(x*math.pi/180.)
64	asind = lambda x: 180.*math.asin(x)/math.pi
65	acosd = lambda x: 180.*math.acos(x)/math.pi
66	atan2d = lambda x,y: 180.*math.atan2(y,x)/math.pi
67
68	def create(parent):
69	return GSASII(parent)
70
71	[wxID_PATTERNTREE,
72	] = [wx.NewId() for _init_ctrls in range(1)]
73
74	[wxID_FILECLOSE, wxID_FILEEXIT, wxID_FILEOPEN, wxID_FILESAVE, wxID_FILESAVEAS,
75	wxID_REFINE, wxID_SOLVE, wxID_MAKEPDFS, wxID_VIEWLSPARMS, wxID_SEQREFINE,
76	] = [wx.NewId() for _init_coll_File_Items in range(10)]
77
78	[wxID_PWDRREAD,wxID_SNGLREAD,wxID_ADDPHASE,wxID_DELETEPHASE,
79	wxID_DATADELETE,wxID_READPEAKS,wxID_PWDSUM,wxID_IMGREAD,
80	wxID_IMSUM, wxID_DATARENAME,
81	] = [wx.NewId() for _init_coll_Data_Items in range(10)]
82
83	[wxID_IMPORT, wxID_IMPORTPATTERN, wxID_IMPORTHKL
84	#, wxID_IMPORTPHASE,
85	#wxID_IMPORTCIF, wxID_IMPORTPDB,
86	] = [wx.NewId() for _init_coll_Import_Items in range(3)]
87
88	[wxID_EXPORT, wxID_EXPORTPATTERN, wxID_EXPORTHKL, wxID_EXPORTPHASE,
89	wxID_EXPORTCIF, wxID_EXPORTPEAKLIST, wxID_EXPORTPDF,
90	] = [wx.NewId() for _init_coll_Export_Items in range(7)]
91
92	def FileDlgFixExt(dlg,file): #this is needed to fix a problem in linux wx.FileDialog
93	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
94	if ext not in file:
95	file += ext
96	return file
97
98	class GSASII(wx.Frame):
99
100	def _init_coll_GSASIIMenu_Menus(self, parent):
101	parent.Append(menu=self.File, title='File')
102	parent.Append(menu=self.Data, title='Data')
103	parent.Append(menu=self.Calculate, title='Calculate')
104	parent.Append(menu=self.Import, title='Import')
105	parent.Append(menu=self.Export, title='Export')
106	parent.Append(menu=G2gd.MyHelp(self,helpType='Data tree'),title='&Help' )
107
108	def _init_coll_File_Items(self, parent):
109	parent.Append(help='Open a gsasii project file (*.gpx)', id=wxID_FILEOPEN,
110	kind=wx.ITEM_NORMAL,text='Open project...')
111	parent.Append(help='Save project to old file', id=wxID_FILESAVE,
112	kind=wx.ITEM_NORMAL,text='Save project')
113	parent.Append(help='Save project to new file', id=wxID_FILESAVEAS,
114	kind=wx.ITEM_NORMAL,text='Save As...')
115	parent.Append(help='Close project, saving is optional', id=wxID_FILECLOSE,
116	kind=wx.ITEM_NORMAL,text='Close project')
117	parent.Append(help='Exit from gsasii', id=wxID_FILEEXIT, kind=wx.ITEM_NORMAL,
118	text='Exit')
119	self.Bind(wx.EVT_MENU, self.OnFileOpen, id=wxID_FILEOPEN)
120	self.Bind(wx.EVT_MENU, self.OnFileSave, id=wxID_FILESAVE)
121	self.Bind(wx.EVT_MENU, self.OnFileSaveas, id=wxID_FILESAVEAS)
122	self.Bind(wx.EVT_MENU, self.OnFileClose, id=wxID_FILECLOSE)
123	self.Bind(wx.EVT_MENU, self.OnFileExit, id=wxID_FILEEXIT)
124
125	def _init_coll_Data_Items(self,parent):
126	parent.Append(help='', id=wxID_PWDRREAD, kind=wx.ITEM_NORMAL,
127	text='Read powder data...')
128	parent.Append(help='',id=wxID_IMGREAD, kind=wx.ITEM_NORMAL,
129	text='Read image data...')
130	parent.Append(help='',id=wxID_READPEAKS, kind=wx.ITEM_NORMAL,
131	text='Read Powder Pattern Peaks...')
132	parent.Append(help='', id=wxID_SNGLREAD, kind=wx.ITEM_NORMAL,
133	text='Read single crystal data...')
134	parent.Append(help='', id=wxID_PWDSUM, kind=wx.ITEM_NORMAL,
135	text='Sum powder data')
136	parent.Append(help='',id=wxID_IMSUM, kind=wx.ITEM_NORMAL,
137	text='Sum image data')
138	parent.Append(help='', id=wxID_ADDPHASE, kind=wx.ITEM_NORMAL,
139	text='Add phase')
140	parent.Append(help='', id=wxID_DELETEPHASE, kind=wx.ITEM_NORMAL,
141	text='Delete phase')
142	parent.Append(help='', id=wxID_DATARENAME, kind=wx.ITEM_NORMAL,
143	text='Rename data')
144	parent.Append(help='', id=wxID_DATADELETE, kind=wx.ITEM_NORMAL,
145	text='Delete data')
146	self.Bind(wx.EVT_MENU, self.OnPwdrRead, id=wxID_PWDRREAD)
147	self.Bind(wx.EVT_MENU, self.OnPwdrSum, id=wxID_PWDSUM)
148	self.Bind(wx.EVT_MENU, self.OnReadPowderPeaks, id=wxID_READPEAKS)
149	self.Bind(wx.EVT_MENU, self.OnImageRead, id=wxID_IMGREAD)
150	self.Bind(wx.EVT_MENU, self.OnImageSum, id=wxID_IMSUM)
151	self.Bind(wx.EVT_MENU, self.OnSnglRead, id=wxID_SNGLREAD)
152	self.Bind(wx.EVT_MENU, self.OnAddPhase, id=wxID_ADDPHASE)
153	self.Bind(wx.EVT_MENU, self.OnDeletePhase, id=wxID_DELETEPHASE)
154	self.Bind(wx.EVT_MENU, self.OnRenameData, id=wxID_DATARENAME)
155	self.Bind(wx.EVT_MENU, self.OnDataDelete, id=wxID_DATADELETE)
156
157	def _init_coll_Calculate_Items(self,parent):
158	self.MakePDF = parent.Append(help='Make new PDFs from selected powder patterns',
159	id=wxID_MAKEPDFS, kind=wx.ITEM_NORMAL,text='Make new PDFs')
160	self.Bind(wx.EVT_MENU, self.OnMakePDFs, id=wxID_MAKEPDFS)
161	self.ViewLSParms = parent.Append(help='View least squares parameters',
162	id=wxID_VIEWLSPARMS, kind=wx.ITEM_NORMAL,text='View LS parms')
163	self.Bind(wx.EVT_MENU, self.OnViewLSParms, id=wxID_VIEWLSPARMS)
164	self.Refine = parent.Append(help='', id=wxID_REFINE, kind=wx.ITEM_NORMAL,
165	text='Refine')
166	self.Refine.Enable(False)
167	self.Bind(wx.EVT_MENU, self.OnRefine, id=wxID_REFINE)
168	self.SeqRefine = parent.Append(help='', id=wxID_SEQREFINE, kind=wx.ITEM_NORMAL,
169	text='Sequental refine')
170	self.SeqRefine.Enable(False)
171	self.Bind(wx.EVT_MENU, self.OnSeqRefine, id=wxID_SEQREFINE)
172	self.Solve = parent.Append(help='', id=wxID_SOLVE, kind=wx.ITEM_NORMAL,
173	text='Solve')
174	self.Solve.Enable(False)
175	self.Bind(wx.EVT_MENU, self.OnSolve, id=wxID_SOLVE)
176
177	def _init_Import_Phase(self,parent):
178	'''import all the G2importphase*.py files that are found in the
179	path and configure the Import Phase menus accordingly
180	'''
181
182	path2GSAS2 = os.path.dirname(os.path.realpath(__file__)) # location of this file
183	pathlist = sys.path[:]
184	if path2GSAS2 not in pathlist: pathlist.append(path2GSAS2)
185	filelist = []
186	for path in pathlist:
187	for filename in glob.iglob(os.path.join(path, "G2importphase*.py")):
188	filelist.append(filename)
189	#print 'found',filename
190	filelist = sorted(list(set(filelist))) # remove duplicates
191	self.ImportPhaseReaderlist = []
192	for filename in filelist:
193	path,rootname = os.path.split(filename)
194	pkg = os.path.splitext(rootname)[0]
195	try:
196	fp = None
197	fp, fppath,desc = imp.find_module(pkg,[path,])
198	pkg = imp.load_module(pkg,fp,fppath,desc)
199	for clss in inspect.getmembers(pkg): # find classes defined in package
200	if clss[0].startswith('_'): continue
201	if inspect.isclass(clss[1]):
202	# check if we have the required methods
203	for m in 'Reader','ExtensionValidator','ContentsValidator':
204	if not hasattr(clss[1],m): break
205	if not callable(getattr(clss[1],m)): break
206	else:
207	reader = clss[1]() # create a phase import instance
208	self.ImportPhaseReaderlist.append(reader)
209	except AttributeError:
210	print 'Import_Phase: Attribute Error',filename
211	pass
212	except ImportError:
213	print 'Import_Phase: Error importing file',filename
214	pass
215	finally:
216	if fp: fp.close()
217	item = parent.Append(wx.ID_ANY, help='Import phase data',
218	kind=wx.ITEM_NORMAL,text='Import Phase (generic)...')
219	self.Bind(wx.EVT_MENU, self.OnImportPhaseGeneric, id=item.GetId())
220	submenu = wx.Menu()
221	item = parent.AppendMenu(wx.ID_ANY, 'Import Phase (specific)',
222	submenu,
223	help='Import phase data')
224	self.PhaseImportMenuId = {}
225	for reader in self.ImportPhaseReaderlist:
226	item = submenu.Append(wx.ID_ANY,
227	help='Import specific format phase data',
228	kind=wx.ITEM_NORMAL,
229	text='Import Phase '+reader.formatName+'...')
230	self.PhaseImportMenuId[item.GetId()] = reader
231	self.Bind(wx.EVT_MENU, self.OnImportPhaseGeneric, id=item.GetId())
232
233	def OnImportPhaseGeneric(self,event):
234	# find out which format was requested
235	reader = self.PhaseImportMenuId.get(event.GetId())
236	if reader is None:
237	#print "use all formats"
238	readerlist = self.ImportPhaseReaderlist
239	choices = "any file (.)\|."
240	extdict = {}
241	# compile a list of allowed extensions
242	for rd in readerlist:
243	fmt = rd.formatName
244	for extn in rd.extensionlist:
245	if not extdict.get(extn): extdict[extn] = []
246	extdict[extn] += [fmt,]
247	for extn in sorted(extdict.keys(),
248	cmp=lambda x,y: cmp(x.lower(), y.lower())):
249	fmt = ''
250	for f in extdict[extn]:
251	if fmt != "": fmt += ', '
252	fmt += f
253	choices += "\|" + fmt + " file (" + extn + ")\|" + extn
254	else:
255	readerlist = [reader,]
256	# compile a list of allowed extensions
257	choices = reader.formatName + " file ("
258	w = ""
259	for extn in reader.extensionlist:
260	if w != "": w += ";"
261	w += "*" + extn
262	choices += w + ")\|" + w
263	if not reader.strictExtension:
264	choices += "\|any file (.)\|."
265	# get the file
266	dlg = wx.FileDialog(
267	self, message="Choose phase input file",
268	#defaultDir=os.getcwd(),
269	defaultFile="",
270	wildcard=choices,
271	style=wx.OPEN \| wx.CHANGE_DIR
272	)
273	try:
274	if dlg.ShowModal() == wx.ID_OK:
275	file = dlg.GetPath()
276	else: # cancel was pressed
277	return
278	finally:
279	dlg.Destroy()
280	# set what formats are compatible with this file
281	primaryReaders = []
282	secondaryReaders = []
283	for reader in readerlist:
284	flag = reader.ExtensionValidator(file)
285	if flag is None:
286	secondaryReaders.append(reader)
287	elif flag:
288	primaryReaders.append(reader)
289	if len(secondaryReaders) + len(primaryReaders) == 0:
290	self.ErrorDialog('No matching format for file '+file,'No Format')
291	return
292
293	fp = None
294	try:
295	fp = open(file,'r')
296	# try the file first with Readers that specify the
297	# files extension and later with ones that allow it
298	for rd in primaryReaders+secondaryReaders:
299	if not rd.ContentsValidator(fp):
300	continue # rejected on cursory check
301	#flag = rd.Reader(file,fp,self)
302	try:
303	flag = rd.Reader(file,fp,self)
304	except:
305	self.ErrorDialog('Error reading file '+file
306	+' with format '+ rd.formatName,
307	'Read Error')
308	continue
309	if not flag: continue
310	dlg = wx.TextEntryDialog( # allow editing of phase name
311	self, 'Enter the name for the new phase',
312	'Edit phase name', rd.Phase['General']['Name'],
313	style=wx.OK)
314	#dlg.SetValue("Python is the best!")
315	dlg.CenterOnParent()
316	if dlg.ShowModal() == wx.ID_OK:
317	rd.Phase['General']['Name'] = dlg.GetValue()
318	dlg.Destroy()
319	PhaseName = rd.Phase['General']['Name']
320	if not G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
321	sub = self.PatternTree.AppendItem(parent=self.root,text='Phases')
322	else:
323	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
324	psub = self.PatternTree.AppendItem(parent=sub,text=PhaseName)
325	self.PatternTree.SetItemPyData(psub,rd.Phase)
326	self.PatternTree.Expand(self.root) # make sure phases are seen
327	self.PatternTree.Expand(sub)
328	self.PatternTree.Expand(psub)
329	return # success
330	except:
331	self.ErrorDialog('Error on open of file '+file,'Open Error')
332	finally:
333	if fp: fp.close()
334
335	return
336
337
338	def _init_coll_Import_Items(self,parent):
339	# self.ImportPhase = parent.Append(help='Import phase data from GSAS EXP file',
340	# id=wxID_IMPORTPHASE, kind=wx.ITEM_NORMAL,text='Import GSAS EXP Phase...')
341	# self.ImportPDB = parent.Append(help='Import phase data from PDB file',
342	# id=wxID_IMPORTPDB, kind=wx.ITEM_NORMAL,text='Import PDB Phase...')
343	# self.ImportCIF = parent.Append(help='Import phase data from cif file',id=wxID_IMPORTCIF, kind=wx.ITEM_NORMAL,
344	# text='Import CIF Phase...')
345	self.ImportPattern = parent.Append(help='',id=wxID_IMPORTPATTERN, kind=wx.ITEM_NORMAL,
346	text='Import Powder Pattern...')
347	self.ImportHKL = parent.Append(help='',id=wxID_IMPORTHKL, kind=wx.ITEM_NORMAL,
348	text='Import HKLs...')
349	# self.Bind(wx.EVT_MENU, self.OnImportPhase, id=wxID_IMPORTPHASE)
350	# self.Bind(wx.EVT_MENU, self.OnImportPDB, id=wxID_IMPORTPDB)
351	# self.Bind(wx.EVT_MENU, self.OnImportCIF, id=wxID_IMPORTCIF)
352	self.Bind(wx.EVT_MENU, self.OnImportPattern, id=wxID_IMPORTPATTERN)
353	self.Bind(wx.EVT_MENU, self.OnImportHKL, id=wxID_IMPORTHKL)
354
355	def _init_coll_Export_Items(self,parent):
356	self.ExportPattern = parent.Append(help='Select PWDR item to enable',id=wxID_EXPORTPATTERN, kind=wx.ITEM_NORMAL,
357	text='Export Powder Patterns...')
358	self.ExportPeakList = parent.Append(help='',id=wxID_EXPORTPEAKLIST, kind=wx.ITEM_NORMAL,
359	text='Export All Peak Lists...')
360	self.ExportHKL = parent.Append(help='',id=wxID_EXPORTHKL, kind=wx.ITEM_NORMAL,
361	text='Export HKLs...')
362	self.ExportPDF = parent.Append(help='Select PDF item to enable',id=wxID_EXPORTPDF, kind=wx.ITEM_NORMAL,
363	text='Export PDF...')
364	self.ExportPhase = parent.Append(help='',id=wxID_EXPORTPHASE, kind=wx.ITEM_NORMAL,
365	text='Export Phase...')
366	self.ExportCIF = parent.Append(help='',id=wxID_EXPORTCIF, kind=wx.ITEM_NORMAL,
367	text='Export CIF...')
368	self.ExportPattern.Enable(False)
369	self.ExportPeakList.Enable(True)
370	self.ExportHKL.Enable(False)
371	self.ExportPDF.Enable(False)
372	self.ExportPhase.Enable(False)
373	self.ExportCIF.Enable(False)
374	self.Bind(wx.EVT_MENU, self.OnExportPatterns, id=wxID_EXPORTPATTERN)
375	self.Bind(wx.EVT_MENU, self.OnExportPeakList, id=wxID_EXPORTPEAKLIST)
376	self.Bind(wx.EVT_MENU, self.OnExportHKL, id=wxID_EXPORTHKL)
377	self.Bind(wx.EVT_MENU, self.OnExportPDF, id=wxID_EXPORTPDF)
378	self.Bind(wx.EVT_MENU, self.OnExportPhase, id=wxID_EXPORTPHASE)
379	self.Bind(wx.EVT_MENU, self.OnExportCIF, id=wxID_EXPORTCIF)
380
381	def _init_utils(self):
382	self.GSASIIMenu = wx.MenuBar()
383	self.File = wx.Menu(title='')
384	self.Data = wx.Menu(title='')
385	self.Calculate = wx.Menu(title='')
386	self.Import = wx.Menu(title='')
387	self.Export = wx.Menu(title='')
388
389	self._init_coll_GSASIIMenu_Menus(self.GSASIIMenu)
390	self._init_coll_File_Items(self.File)
391	self._init_coll_Data_Items(self.Data)
392	self._init_coll_Calculate_Items(self.Calculate)
393	self._init_Import_Phase(self.Import)
394	self._init_coll_Import_Items(self.Import)
395	self._init_coll_Export_Items(self.Export)
396
397	def _init_ctrls(self, parent):
398	wx.Frame.__init__(self, name='GSASII', parent=parent,
399	size=wx.Size(300, 250),style=wx.DEFAULT_FRAME_STYLE, title='GSAS-II data tree')
400	clientSize = wx.ClientDisplayRect()
401	Size = self.GetSize()
402	xPos = clientSize[2]-Size[0]
403	self.SetPosition(wx.Point(xPos,clientSize[1]))
404	self._init_utils()
405	self.SetMenuBar(self.GSASIIMenu)
406	self.Bind(wx.EVT_SIZE, self.OnSize)
407	self.CreateStatusBar()
408	self.mainPanel = wx.Panel(self,-1)
409
410	self.PatternTree = wx.TreeCtrl(id=wxID_PATTERNTREE,
411	parent=self.mainPanel, pos=wx.Point(0, 0),style=wx.TR_DEFAULT_STYLE )
412	self.PatternTree.Bind(wx.EVT_TREE_SEL_CHANGED,
413	self.OnPatternTreeSelChanged, id=wxID_PATTERNTREE)
414	self.PatternTree.Bind(wx.EVT_TREE_ITEM_COLLAPSED,
415	self.OnPatternTreeItemCollapsed, id=wxID_PATTERNTREE)
416	self.PatternTree.Bind(wx.EVT_TREE_ITEM_EXPANDED,
417	self.OnPatternTreeItemExpanded, id=wxID_PATTERNTREE)
418	self.PatternTree.Bind(wx.EVT_TREE_DELETE_ITEM,
419	self.OnPatternTreeItemDelete, id=wxID_PATTERNTREE)
420	self.PatternTree.Bind(wx.EVT_TREE_KEY_DOWN,
421	self.OnPatternTreeKeyDown, id=wxID_PATTERNTREE)
422	self.root = self.PatternTree.AddRoot('Loaded Data: ')
423
424	plotFrame = wx.Frame(None,-1,'GSASII Plots',size=wx.Size(700,600), \
425	style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX)
426	self.G2plotNB = G2plt.G2PlotNoteBook(plotFrame)
427	plotFrame.Show()
428
429	self.dataDisplay = None
430
431	def __init__(self, parent):
432	self._init_ctrls(parent)
433	self.Bind(wx.EVT_CLOSE, self.ExitMain)
434	# various defaults
435	self.oldFocus = None
436	self.GSASprojectfile = ''
437	self.dirname = ospath.expanduser('~') #start in the users home directory by default; may be meaningless
438	self.undofile = ''
439	self.TreeItemDelete = False
440	self.Offset = [0.0,0.0]
441	self.delOffset = .02
442	self.refOffset = -100.0
443	self.refDelt = .01
444	self.Weight = False
445	self.IparmName = ''
446	self.IfPlot = False
447	self.PatternId = 0
448	self.PickId = 0
449	self.PeakTable = []
450	self.LimitsTable = []
451	self.HKL = []
452	self.Lines = []
453	self.itemPicked = None
454	self.dataFrame = None
455	self.Interpolate = 'nearest'
456	self.ContourColor = 'Paired'
457	self.VcovColor = 'RdYlGn'
458	self.Projection = 'equal area'
459	self.logPlot = False
460	self.qPlot = False
461	self.Contour = False
462	self.Legend = False
463	self.SinglePlot = False
464	self.plotView = 0
465	self.Image = 0
466	self.oldImagefile = ''
467	self.Integrate = 0
468	self.Pwdr = False
469	self.imageDefault = {}
470	self.Sngl = 0
471	self.ifGetRing = False
472	self.setPoly = False
473	arg = sys.argv
474	if len(arg) > 1:
475	self.GSASprojectfile = arg[1]
476	self.dirname = ospath.dirname(arg[1])
477	os.chdir(self.dirname)
478	G2IO.ProjFileOpen(self)
479	self.PatternTree.Expand(self.root)
480	self.Refine.Enable(True)
481	self.SeqRefine.Enable(True)
482	self.Solve.Enable(True)
483
484	def OnSize(self,event):
485	w,h = self.GetClientSizeTuple()
486	self.mainPanel.SetSize(wx.Size(w,h))
487	self.PatternTree.SetSize(wx.Size(w,h))
488
489	def OnPatternTreeSelChanged(self, event):
490	if self.TreeItemDelete:
491	self.TreeItemDelete = False
492	else:
493	pltNum = self.G2plotNB.nb.GetSelection()
494	if pltNum >= 0: #to avoid the startup with no plot!
495	pltPage = self.G2plotNB.nb.GetPage(pltNum)
496	pltPlot = pltPage.figure
497	item = event.GetItem()
498	G2gd.MovePatternTreeToGrid(self,item)
499	if self.oldFocus:
500	self.oldFocus.SetFocus()
501
502	def OnPatternTreeItemCollapsed(self, event):
503	event.Skip()
504
505	def OnPatternTreeItemExpanded(self, event):
506	event.Skip()
507
508	def OnPatternTreeItemDelete(self, event):
509	self.TreeItemDelete = True
510
511	def OnPatternTreeItemActivated(self, event):
512	event.Skip()
513
514	def OnPatternTreeKeyDown(self,event):
515	key = event.GetKeyCode()
516	item = self.PickId
517	if type(item) is int: return # is this the toplevel in tree?
518	if key == wx.WXK_UP:
519	self.oldFocus = wx.Window.FindFocus()
520	self.PatternTree.GetPrevSibling(item)
521	elif key == wx.WXK_DOWN:
522	self.oldFocus = wx.Window.FindFocus()
523	self.PatternTree.GetNextSibling(item)
524
525	def OnPwdrRead(self, event):
526	self.CheckNotebook()
527	dlg = wx.FileDialog(self, 'Choose files', '.', '',
528	'GSAS fxye files (.fxye)\|.fxye\|GSAS fxy files (.fxy)\|.fxy\|Topas xye files (.xye)\|.xye\|All files (.)\|.',
529	wx.OPEN \| wx.MULTIPLE \| wx.CHANGE_DIR)
530	try:
531	if dlg.ShowModal() == wx.ID_OK:
532	filenames = dlg.GetPaths()
533	filenames.sort()
534	for filename in filenames:
535	Data,Iparm,Comments,Temperature = G2IO.SelectPowderData(self, filename) #Data: list of tuples (filename,Pos,Bank)
536	if not Data: #if Data rejected by user - go to next one
537	continue
538	DataType = Iparm['INS HTYPE '] #expect only 4 char string
539	DataType = DataType.strip()[0:3] #just 1st 3 chars
540	wx.BeginBusyCursor()
541	Sample = G2pdG.SetDefaultSample()
542	Sample['Temperature'] = Temperature
543	try:
544	for Item in Data:
545	vals = Item[2].split() #split up the BANK record
546	Id = self.PatternTree.AppendItem(parent=self.root,text='PWDR '+ospath.basename(Item[0])+': '+vals[0]+vals[1])
547	data = G2IO.GetPowderData(filename,Item[1],Item[2],DataType)
548	self.PatternTree.SetItemPyData(Id,[Item,data])
549	'''
550	Each tree item data is a list with:
551	Item: the (filename,Pos,Bank) tuple
552	data: (x,y,w,yc,yb,yd) list of np.arrays from GetPowderData
553	'''
554
555	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),Comments)
556	Tmin = min(data[0])
557	Tmax = max(data[0])
558	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Limits'),[(Tmin,Tmax),[Tmin,Tmax]])
559	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
560	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
561
562	data = [DataType,]
563	if 'C' in DataType:
564	s = Iparm['INS 1 ICONS']
565	v = (G2IO.sfloat(s[:10]),G2IO.sfloat(s[10:20]),G2IO.sfloat(s[20:30]),G2IO.sfloat(s[55:65]),G2IO.sfloat(s[40:50])) #get lam1, lam2, zero, pola & ratio
566	if not v[1]:
567	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
568	v = (v[0],v[2],v[4])
569	codes = [0,0,0,0]
570	else:
571	names = ['Type','Lam1','Lam2','Zero','I(L2)/I(L1)','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
572	codes = [0,0,0,0,0,0]
573	data.extend(v)
574	v1 = Iparm['INS 1PRCF1 '].split()
575	v = Iparm['INS 1PRCF11'].split()
576	data.extend([float(v[0]),float(v[1]),float(v[2])]) #get GU, GV & GW - always here
577	try:
578	azm = float(Iparm['INS 1DETAZM'])
579	except KeyError: #not in this Iparm file
580	azm = 0.0
581	v = Iparm['INS 1PRCF12'].split()
582	if v1[0] == 3:
583	data.extend([float(v[0]),float(v[1]),float(v[2])+float(v[3],azm)]) #get LX, LY, S+H/L & azimuth
584	else:
585	data.extend([0.0,0.0,0.002,azm]) #OK defaults if fxn #3 not 1st in iprm file
586	codes.extend([0,0,0,0,0,0,0])
587	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Instrument Parameters'),[tuple(data),data,codes,names])
588	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
589	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Peak List'),[])
590	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Index Peak List'),[])
591	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
592	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
593	self.PatternId = G2gd.GetPatternTreeItemId(self,Id,'Limits')
594	finally:
595	wx.EndBusyCursor()
596	self.PatternTree.Expand(Id)
597	self.PatternTree.SelectItem(Id)
598
599	finally:
600	dlg.Destroy()
601
602	def OnReadPowderPeaks(self,event):
603	Cuka = 1.54052
604	self.CheckNotebook()
605	dlg = wx.FileDialog(self, 'Choose file with peak list', '.', '',
606	'peak files (.txt)\|.txt\|All files (.)\|.',wx.OPEN\|wx.CHANGE_DIR)
607	try:
608	if dlg.ShowModal() == wx.ID_OK:
609	self.HKL = []
610	self.powderfile = dlg.GetPath()
611	comments,peaks = G2IO.GetPowderPeaks(self.powderfile)
612	Id = self.PatternTree.AppendItem(parent=self.root,text='PKS '+ospath.basename(self.powderfile))
613	data = ['PKS',Cuka,0.0]
614	names = ['Type','Lam','Zero']
615	codes = [0,0]
616	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Instrument Parameters'),[tuple(data),data,codes,names])
617	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),comments)
618	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Index Peak List'),peaks)
619	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
620	self.PatternTree.Expand(Id)
621	self.PatternTree.SelectItem(Id)
622	finally:
623	dlg.Destroy()
624
625	def OnImageRead(self,event):
626	self.CheckNotebook()
627	dlg = wx.FileDialog(self, 'Choose image files', '.', '',\
628	'Any image file (.tif;.tiff;.mar;.avg;.sum;.img;.G2img)\
629	\|.tif;.tiff;.mar;.avg;.sum;.img;.G2img\|\
630	Any detector tif (.tif;.tiff)\|.tif;.tiff\|\
631	MAR file (.mar)\|.mar\|\
632	GE Image (.avg;.sum)\|.avg;.sum\|\
633	ADSC Image (.img)\|.img\|\
634	GSAS-II Image (.G2img)\|.G2img\|\
635	All files (.)\|.',
636	wx.OPEN \| wx.MULTIPLE\|wx.CHANGE_DIR)
637	try:
638	if dlg.ShowModal() == wx.ID_OK:
639	imagefiles = dlg.GetPaths()
640	imagefiles.sort()
641	for imagefile in imagefiles:
642	Comments,Data,Npix,Image = G2IO.GetImageData(self,imagefile)
643	if Comments:
644	Id = self.PatternTree.AppendItem(parent=self.root,text='IMG '+ospath.basename(imagefile))
645	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),Comments)
646	Imax = np.amax(Image)
647	Imin = max(0.0,np.amin(Image)) #force positive
648	if self.imageDefault:
649	Data = copy.copy(self.imageDefault)
650	Data['showLines'] = True
651	Data['ring'] = []
652	Data['rings'] = []
653	Data['cutoff'] = 10
654	Data['pixLimit'] = 20
655	Data['edgemin'] = 100000000
656	Data['calibdmin'] = 0.5
657	Data['calibskip'] = 0
658	Data['ellipses'] = []
659	Data['calibrant'] = ''
660	else:
661	Data['type'] = 'PWDR'
662	Data['color'] = 'binary'
663	Data['tilt'] = 0.0
664	Data['rotation'] = 0.0
665	Data['showLines'] = False
666	Data['ring'] = []
667	Data['rings'] = []
668	Data['cutoff'] = 10
669	Data['pixLimit'] = 20
670	Data['calibdmin'] = 0.5
671	Data['calibskip'] = 0
672	Data['edgemin'] = 100000000
673	Data['ellipses'] = []
674	Data['calibrant'] = ''
675	Data['IOtth'] = [2.0,5.0]
676	Data['LRazimuth'] = [-135,-45]
677	Data['azmthOff'] = 0.0
678	Data['outChannels'] = 2500
679	Data['outAzimuths'] = 1
680	Data['fullIntegrate'] = False
681	Data['setRings'] = False
682	Data['background image'] = ['',1.0]
683	Data['setDefault'] = False
684	Data['range'] = [(Imin,Imax),[Imin,Imax]]
685	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Image Controls'),Data)
686	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Thresholds':[(Imin,Imax),[Imin,Imax]]}
687	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Masks'),Masks)
688	self.PatternTree.SetItemPyData(Id,[Npix,imagefile])
689	self.PickId = Id
690	self.Image = Id
691	self.PatternTree.SelectItem(G2gd.GetPatternTreeItemId(self,Id,'Image Controls')) #show last one
692	finally:
693	dlg.Destroy()
694
695	def OnSnglRead(self,event):
696	self.CheckNotebook()
697	dlg = wx.FileDialog(self, 'Choose file', '.', '',
698	'hkl files (.hkl)\|.hkl\|All files (.)\|.',
699	wx.OPEN\|wx.CHANGE_DIR)
700	try:
701	if dlg.ShowModal() == wx.ID_OK:
702	filename = dlg.GetPath()
703	wx.BeginBusyCursor()
704	try:
705	Data = {}
706	names = ['Type','Lam']
707	HKLref,HKLmin,HKLmax,FoMax,ifFc = G2IO.GetHKLData(filename)
708	Id = self.PatternTree.AppendItem(parent=self.root,text='HKLF '+ospath.basename(filename))
709	self.PatternTree.SetItemPyData(Id,HKLref)
710	Sub = self.PatternTree.AppendItem(Id,text='Instrument Parameters')
711	data = ['SXC',1.5428,]
712	self.PatternTree.SetItemPyData(Sub,[tuple(data),data,names])
713	Data['Type'] = 'Fosq'
714	Data['ifFc'] = ifFc
715	Data['HKLmax'] = HKLmax
716	Data['HKLmin'] = HKLmin
717	Data['FoMax'] = FoMax
718	Data['Zone'] = '001'
719	Data['Layer'] = 0
720	Data['Scale'] = 1.0
721	Data['log-lin'] = 'lin'
722	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='HKL Plot Controls'),Data)
723	self.PatternTree.SelectItem(Id)
724	self.PatternTree.Expand(Id)
725	self.Sngl = Id
726	finally:
727	wx.EndBusyCursor()
728	finally:
729	dlg.Destroy()
730
731	def CheckNotebook(self):
732	if not G2gd.GetPatternTreeItemId(self,self.root,'Notebook'):
733	sub = self.PatternTree.AppendItem(parent=self.root,text='Notebook')
734	self.PatternTree.SetItemPyData(sub,[''])
735	if not G2gd.GetPatternTreeItemId(self,self.root,'Controls'):
736	sub = self.PatternTree.AppendItem(parent=self.root,text='Controls')
737	self.PatternTree.SetItemPyData(sub,{})
738	if not G2gd.GetPatternTreeItemId(self,self.root,'Covariance'):
739	sub = self.PatternTree.AppendItem(parent=self.root,text='Covariance')
740	self.PatternTree.SetItemPyData(sub,{})
741	if not G2gd.GetPatternTreeItemId(self,self.root,'Constraints'):
742	sub = self.PatternTree.AppendItem(parent=self.root,text='Constraints')
743	self.PatternTree.SetItemPyData(sub,{'Hist':[],'HAP':[],'Phase':[]})
744	if not G2gd.GetPatternTreeItemId(self,self.root,'Restraints'):
745	sub = self.PatternTree.AppendItem(parent=self.root,text='Restraints')
746	self.PatternTree.SetItemPyData(sub,{})
747
748
749	class CopyDialog(wx.Dialog):
750	def __init__(self,parent,title,text,data):
751	wx.Dialog.__init__(self,parent,-1,title,
752	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
753	self.data = data
754	panel = wx.Panel(self)
755	mainSizer = wx.BoxSizer(wx.VERTICAL)
756	topLabl = wx.StaticText(panel,-1,text)
757	mainSizer.Add((10,10),1)
758	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.LEFT,10)
759	mainSizer.Add((10,10),1)
760	ncols = len(data)/40+1
761	dataGridSizer = wx.FlexGridSizer(rows=len(data),cols=ncols,hgap=2,vgap=2)
762	for id,item in enumerate(self.data):
763	ckbox = wx.CheckBox(panel,id,item[1])
764	ckbox.Bind(wx.EVT_CHECKBOX,self.OnCopyChange)
765	dataGridSizer.Add(ckbox,0,wx.LEFT,10)
766	mainSizer.Add(dataGridSizer,0,wx.EXPAND)
767	OkBtn = wx.Button(panel,-1,"Ok")
768	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
769	cancelBtn = wx.Button(panel,-1,"Cancel")
770	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
771	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
772	btnSizer.Add((20,20),1)
773	btnSizer.Add(OkBtn)
774	btnSizer.Add((20,20),1)
775	btnSizer.Add(cancelBtn)
776	btnSizer.Add((20,20),1)
777
778	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
779	panel.SetSizer(mainSizer)
780	panel.Fit()
781	self.Fit()
782
783	def OnCopyChange(self,event):
784	id = event.GetId()
785	self.data[id][0] = self.FindWindowById(id).GetValue()
786
787	def OnOk(self,event):
788	parent = self.GetParent()
789	parent.Raise()
790	self.EndModal(wx.ID_OK)
791	self.Destroy()
792
793	def OnCancel(self,event):
794	parent = self.GetParent()
795	parent.Raise()
796	self.EndModal(wx.ID_CANCEL)
797	self.Destroy()
798
799	def GetData(self):
800	return self.data
801
802	class SumDialog(wx.Dialog):
803	def __init__(self,parent,title,text,dataType,data):
804	wx.Dialog.__init__(self,parent,-1,title,
805	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
806	self.data = data
807	panel = wx.Panel(self)
808	mainSizer = wx.BoxSizer(wx.VERTICAL)
809	topLabl = wx.StaticText(panel,-1,text)
810	mainSizer.Add((10,10),1)
811	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.LEFT,10)
812	mainSizer.Add((10,10),1)
813	dataGridSizer = wx.FlexGridSizer(rows=len(data),cols=2,hgap=2,vgap=2)
814	for id,item in enumerate(self.data[:-1]):
815	name = wx.TextCtrl(panel,-1,item[1],size=wx.Size(200,20))
816	name.SetEditable(False)
817	scale = wx.TextCtrl(panel,id,'%.3f'%(item[0]),style=wx.TE_PROCESS_ENTER)
818	scale.Bind(wx.EVT_TEXT_ENTER,self.OnScaleChange)
819	scale.Bind(wx.EVT_KILL_FOCUS,self.OnScaleChange)
820	dataGridSizer.Add(scale,0,wx.LEFT,10)
821	dataGridSizer.Add(name,0,wx.RIGHT,10)
822	if dataType:
823	dataGridSizer.Add(wx.StaticText(panel,-1,'Sum result name: '+dataType),0, \
824	wx.LEFT\|wx.TOP\|wx.ALIGN_CENTER_VERTICAL,10)
825	self.name = wx.TextCtrl(panel,-1,self.data[-1],size=wx.Size(200,20),style=wx.TE_PROCESS_ENTER)
826	self.name.Bind(wx.EVT_TEXT_ENTER,self.OnNameChange)
827	self.name.Bind(wx.EVT_KILL_FOCUS,self.OnNameChange)
828	dataGridSizer.Add(self.name,0,wx.RIGHT\|wx.TOP,10)
829	mainSizer.Add(dataGridSizer,0,wx.EXPAND)
830	OkBtn = wx.Button(panel,-1,"Ok")
831	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
832	cancelBtn = wx.Button(panel,-1,"Cancel")
833	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
834	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
835	btnSizer.Add((20,20),1)
836	btnSizer.Add(OkBtn)
837	btnSizer.Add((20,20),1)
838	btnSizer.Add(cancelBtn)
839	btnSizer.Add((20,20),1)
840
841	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
842	panel.SetSizer(mainSizer)
843	panel.Fit()
844	self.Fit()
845
846	def OnNameChange(self,event):
847	self.data[-1] = self.name.GetValue()
848
849	def OnScaleChange(self,event):
850	id = event.GetId()
851	value = self.FindWindowById(id).GetValue()
852	try:
853	self.data[id][0] = float(value)
854	self.FindWindowById(id).SetValue('%.3f'%(self.data[id][0]))
855	except ValueError:
856	if value and '-' not in value[0]:
857	print 'bad input - numbers only'
858	self.FindWindowById(id).SetValue('0.000')
859
860	def OnOk(self,event):
861	parent = self.GetParent()
862	parent.Raise()
863	self.EndModal(wx.ID_OK)
864	self.Destroy()
865
866	def OnCancel(self,event):
867	parent = self.GetParent()
868	parent.Raise()
869	self.EndModal(wx.ID_CANCEL)
870	self.Destroy()
871
872	def GetData(self):
873	return self.data
874
875	def OnPwdrSum(self,event):
876	TextList = []
877	DataList = []
878	SumList = []
879	Names = []
880	Inst = []
881	SumItemList = []
882	Comments = ['Sum equals: \n']
883	if self.PatternTree.GetCount():
884	item, cookie = self.PatternTree.GetFirstChild(self.root)
885	while item:
886	name = self.PatternTree.GetItemText(item)
887	Names.append(name)
888	if 'PWDR' in name:
889	TextList.append([0.0,name])
890	DataList.append(self.PatternTree.GetItemPyData(item)[1]) # (x,y,w,yc,yb,yd)
891	if not Inst:
892	Inst = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,item, 'Instrument Parameters'))
893	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
894	if len(TextList) < 2:
895	self.ErrorDialog('Not enough data to sum','There must be more than one "PWDR" pattern')
896	return
897	TextList.append('default_sum_name')
898	dlg = self.SumDialog(self,'Sum data','Enter scale for each pattern in summation','PWDR',TextList)
899	try:
900	if dlg.ShowModal() == wx.ID_OK:
901	lenX = 0
902	Xminmax = [0,0]
903	Xsum = []
904	Ysum = []
905	Vsum = []
906	result = dlg.GetData()
907	for i,item in enumerate(result[:-1]):
908	scale,name = item
909	data = DataList[i]
910	if scale:
911	Comments.append("%10.3f %s" % (scale,' * '+name))
912	x,y,w,yc,yb,yd = data #numpy arrays!
913	v = 1./w
914	if lenX:
915	if lenX != len(x):
916	self.ErrorDialog('Data length error','Data to be summed must have same number of points'+ \
917	'\nExpected:'+str(lenX)+ \
918	'\nFound: '+str(len(x))+'\nfor '+name)
919	return
920	else:
921	lenX = len(x)
922	if Xminmax[1]:
923	if Xminmax != [x[0],x[-1]]:
924	self.ErrorDialog('Data range error','Data to be summed must span same range'+ \
925	'\nExpected:'+str(Xminmax[0])+' '+str(Xminmax[1])+ \
926	'\nFound: '+str(x[0])+' '+str(x[-1])+'\nfor '+name)
927	return
928	else:
929	for j,yi in enumerate(y):
930	Ysum[j] += scale*yi
931	Vsum[j] += abs(scale)*v[j]
932	else:
933	Xminmax = [x[0],x[-1]]
934	YCsum = YBsum = YDsum = [0.0 for i in range(lenX)]
935	for j,yi in enumerate(y):
936	Xsum.append(x[j])
937	Ysum.append(scale*yi)
938	Vsum.append(abs(scale*v[j]))
939	Wsum = 1./np.array(Vsum)
940	outname = 'PWDR '+result[-1]
941	Id = 0
942	if outname in Names:
943	dlg2 = wx.MessageDialog(self,'Overwrite data?','Duplicate data name',wx.OK\|wx.CANCEL)
944	try:
945	if dlg2.ShowModal() == wx.ID_OK:
946	Id = G2gd.GetPatternTreeItemId(self,self.root,name)
947	self.PatternTree.Delete(Id)
948	finally:
949	dlg2.Destroy()
950	Id = self.PatternTree.AppendItem(parent=self.root,text=outname)
951	if Id:
952	Sample = G2pdG.SetDefaultSample()
953	self.PatternTree.SetItemPyData(Id,[[''],[np.array(Xsum),np.array(Ysum),np.array(Wsum),
954	np.array(YCsum),np.array(YBsum),np.array(YDsum)]])
955	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),Comments)
956	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
957	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
958	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
959	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Instrument Parameters'),Inst)
960	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
961	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Peak List'),[])
962	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Index Peak List'),[])
963	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
964	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
965	self.PatternTree.SelectItem(Id)
966	self.PatternTree.Expand(Id)
967
968	finally:
969	dlg.Destroy()
970
971	def OnImageSum(self,event):
972	TextList = []
973	DataList = []
974	SumList = []
975	Names = []
976	Inst = []
977	SumItemList = []
978	Comments = ['Sum equals: \n']
979	if self.PatternTree.GetCount():
980	item, cookie = self.PatternTree.GetFirstChild(self.root)
981	while item:
982	name = self.PatternTree.GetItemText(item)
983	Names.append(name)
984	if 'IMG' in name:
985	TextList.append([0.0,name])
986	DataList.append(self.PatternTree.GetItemPyData(item)) #Size,Image
987	Data = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,item,'Image Controls'))
988	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
989	if len(TextList) < 2:
990	self.ErrorDialog('Not enough data to sum','There must be more than one "IMG" pattern')
991	return
992	TextList.append('default_sum_name')
993	dlg = self.SumDialog(self,'Sum data','Enter scale for each image in summation','IMG',TextList)
994	try:
995	if dlg.ShowModal() == wx.ID_OK:
996	imSize = 0
997	result = dlg.GetData()
998	First = True
999	Found = False
1000	for i,item in enumerate(result[:-1]):
1001	scale,name = item
1002	data = DataList[i]
1003	if scale:
1004	Found = True
1005	Comments.append("%10.3f %s" % (scale,' * '+name))
1006	Npix,imagefile = data
1007	image = G2IO.GetImageData(self,imagefile,imageOnly=True)
1008	if First:
1009	newImage = np.zeros_like(image)
1010	First = False
1011	if imSize:
1012	if imSize != Npix:
1013	self.ErrorDialog('Image size error','Images to be summed must be same size'+ \
1014	'\nExpected:'+str(imSize)+ \
1015	'\nFound: '+str(Npix)+'\nfor '+name)
1016	return
1017	newImage = newImage+scale*image
1018	else:
1019	imSize = Npix
1020	newImage = newImage+scale*image
1021	del(image)
1022	if not Found:
1023	self.ErrorDialog('Image sum error','No nonzero image multipliers found')
1024	return
1025
1026	newImage = np.asfarray(newImage,dtype=np.float32)
1027	outname = 'IMG '+result[-1]
1028	Id = 0
1029	if outname in Names:
1030	dlg2 = wx.MessageDialog(self,'Overwrite data?','Duplicate data name',wx.OK\|wx.CANCEL)
1031	try:
1032	if dlg2.ShowModal() == wx.ID_OK:
1033	Id = G2gd.GetPatternTreeItemId(self,self.root,name)
1034	finally:
1035	dlg2.Destroy()
1036	else:
1037	Id = self.PatternTree.AppendItem(parent=self.root,text=outname)
1038	if Id:
1039	dlg = wx.FileDialog(self, 'Choose sum image filename', '.', '',
1040	'G2img files (.G2img)\|.G2img',
1041	wx.SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
1042	if dlg.ShowModal() == wx.ID_OK:
1043	newimagefile = dlg.GetPath()
1044	newimagefile = FileDlgFixExt(dlg,newimagefile)
1045	G2IO.PutG2Image(newimagefile,Comments,Data,Npix,newImage)
1046	Imax = np.amax(newImage)
1047	Imin = np.amin(newImage)
1048	newImage = []
1049	self.PatternTree.SetItemPyData(Id,[imSize,newimagefile])
1050	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),Comments)
1051	del(newImage)
1052	if self.imageDefault:
1053	Data = copy.copy(self.imageDefault)
1054	Data['showLines'] = True
1055	Data['ring'] = []
1056	Data['rings'] = []
1057	Data['cutoff'] = 10
1058	Data['pixLimit'] = 20
1059	Data['ellipses'] = []
1060	Data['calibrant'] = ''
1061	Data['range'] = [(Imin,Imax),[Imin,Imax]]
1062	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Image Controls'),Data)
1063	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Thresholds':[(Imin,Imax),[Imin,Imax]]}
1064	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Masks'),Masks)
1065	self.PatternTree.SelectItem(Id)
1066	self.PatternTree.Expand(Id)
1067	self.PickId = G2gd.GetPatternTreeItemId(self,self.root,outname)
1068	self.Image = self.PickId
1069	finally:
1070	dlg.Destroy()
1071
1072	def OnAddPhase(self,event):
1073	if not G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
1074	sub = self.PatternTree.AppendItem(parent=self.root,text='Phases')
1075	else:
1076	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
1077	PhaseName = ''
1078	dlg = wx.TextEntryDialog(None,'Enter a name for this phase','Phase Name Entry','New phase',
1079	style=wx.OK)
1080	if dlg.ShowModal() == wx.ID_OK:
1081	PhaseName = dlg.GetValue()
1082	dlg.Destroy()
1083	sub = self.PatternTree.AppendItem(parent=sub,text=PhaseName)
1084	E,SGData = G2spc.SpcGroup('P 1')
1085	self.PatternTree.SetItemPyData(sub, {
1086	'General':{
1087	'Name':PhaseName,
1088	'Type':'nuclear',
1089	'SGData':SGData,
1090	'Cell':[False,10.,10.,10.,90.,90.,90,1000.],
1091	'Pawley dmin':1.0,
1092	'Data plot type':'Mustrain',
1093	'SH Texture':{
1094	'Order':0,
1095	'Model':'cylindrical',
1096	'Sample omega':[False,0.0],
1097	'Sample chi':[False,0.0],
1098	'Sample phi':[False,0.0],
1099	'SH Coeff':[False,{}],
1100	'SHShow':False,
1101	'PFhkl':[0,0,1],
1102	'PFxyz':[0,0,1],
1103	'PlotType':'Pole figure'}},
1104	'Atoms':[],
1105	'Drawing':{},
1106	'Histograms':{},
1107	'Pawley ref':[],
1108	'Models':{},
1109	})
1110
1111	def OnDeletePhase(self,event):
1112	#Hmm, also need to delete this phase from Reflection Lists for each PWDR histogram
1113	if self.dataFrame:
1114	self.dataFrame.Clear()
1115	TextList = []
1116	DelList = []
1117	DelItemList = []
1118	if G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
1119	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
1120	else:
1121	return
1122	if sub:
1123	item, cookie = self.PatternTree.GetFirstChild(sub)
1124	while item:
1125	TextList.append(self.PatternTree.GetItemText(item))
1126	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
1127	dlg = wx.MultiChoiceDialog(self, 'Which phase to delete?', 'Delete phase', TextList, wx.CHOICEDLG_STYLE)
1128	try:
1129	if dlg.ShowModal() == wx.ID_OK:
1130	result = dlg.GetSelections()
1131	for i in result: DelList.append([i,TextList[i]])
1132	item, cookie = self.PatternTree.GetFirstChild(sub)
1133	i = 0
1134	while item:
1135	if [i,self.PatternTree.GetItemText(item)] in DelList: DelItemList.append(item)
1136	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
1137	i += 1
1138	for item in DelItemList:
1139	name = self.PatternTree.GetItemText(item)
1140	self.PatternTree.Delete(item)
1141	self.G2plotNB.Delete(name)
1142	item, cookie = self.PatternTree.GetFirstChild(self.root)
1143	while item:
1144	name = self.PatternTree.GetItemText(item)
1145	if 'PWDR' in name:
1146	Id = G2gd.GetPatternTreeItemId(self,item, 'Reflection Lists')
1147	refList = self.PatternTree.GetItemPyData(Id)
1148	for i,item in DelList:
1149	del(refList[item])
1150	self.PatternTree.SetItemPyData(Id,refList)
1151	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
1152	finally:
1153	dlg.Destroy()
1154
1155	def OnRenameData(self,event):
1156	name = self.PatternTree.GetItemText(self.PickId)
1157	if 'PWDR' in name or 'HKLF' in name or 'IMG' in name:
1158	dataType = name[:name.index(' ')+1] #includes the ' '
1159	dlg = wx.TextEntryDialog(self,'Data name: '+dataType,'Change data name',
1160	defaultValue=name[name.index(' ')+1:])
1161	try:
1162	if dlg.ShowModal() == wx.ID_OK:
1163	self.PatternTree.SetItemText(self.PickId,dataType+dlg.GetValue())
1164	finally:
1165	dlg.Destroy()
1166
1167	def GetFileList(self,fileType,skip=None): #potentially useful?
1168	fileList = []
1169	Source = ''
1170	id, cookie = self.PatternTree.GetFirstChild(self.root)
1171	while id:
1172	name = self.PatternTree.GetItemText(id)
1173	if fileType in name:
1174	if id == skip:
1175	Source = name
1176	else:
1177	fileList.append([False,name,id])
1178	id, cookie = self.PatternTree.GetNextChild(self.root, cookie)
1179	if skip:
1180	return fileList,Source
1181	else:
1182	return fileList
1183
1184	def OnDataDelete(self, event):
1185	TextList = ['All Data']
1186	DelList = []
1187	DelItemList = []
1188	ifPWDR = False
1189	ifIMG = False
1190	ifHKLF = False
1191	ifPDF = False
1192	if self.PatternTree.GetCount():
1193	item, cookie = self.PatternTree.GetFirstChild(self.root)
1194	while item:
1195	name = self.PatternTree.GetItemText(item)
1196	if name not in ['Notebook','Controls','Covariance','Constraints','Restraints','Phases']:
1197	if 'PWDR' in name: ifPWDR = True
1198	if 'IMG' in name: ifIMG = True
1199	if 'HKLF' in name: ifHKLF = True
1200	if 'PDF' in name: ifPDF = True
1201	TextList.append(name)
1202	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
1203	if ifPWDR: TextList.insert(1,'All PWDR')
1204	if ifIMG: TextList.insert(1,'All IMG')
1205	if ifHKLF: TextList.insert(1,'All HKLF')
1206	if ifPDF: TextList.insert(1,'All PDF')
1207	dlg = wx.MultiChoiceDialog(self, 'Which data to delete?', 'Delete data', TextList, wx.CHOICEDLG_STYLE)
1208	try:
1209	if dlg.ShowModal() == wx.ID_OK:
1210	result = dlg.GetSelections()
1211	for i in result: DelList.append(TextList[i])
1212	if 'All Data' in DelList:
1213	DelList = [item for item in TextList if item[:3] != 'All']
1214	elif 'All PWDR' in DelList:
1215	DelList = [item for item in TextList if item[:4] == 'PWDR']
1216	elif 'All IMG' in DelList:
1217	DelList = [item for item in TextList if item[:3] == 'IMG']
1218	elif 'All HKLF' in DelList:
1219	DelList = [item for item in TextList if item[:4] == 'HKLF']
1220	elif 'All PDF' in DelList:
1221	DelList = [item for item in TextList if item[:3] == 'PDF']
1222	item, cookie = self.PatternTree.GetFirstChild(self.root)
1223	while item:
1224	if self.PatternTree.GetItemText(item) in DelList: DelItemList.append(item)
1225	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
1226	for item in DelItemList:
1227	self.PatternTree.Delete(item)
1228	G2plt.PlotPatterns(self,True) #so plot gets updated
1229	finally:
1230	dlg.Destroy()
1231
1232	def OnFileOpen(self, event):
1233	result = ''
1234	Id = 0
1235	if self.PatternTree.GetChildrenCount(self.root,False):
1236	if self.dataFrame:
1237	self.dataFrame.Clear()
1238	dlg = wx.MessageDialog(self, 'Overwrite?','Project exists!', wx.OK \| wx.CANCEL)
1239	try:
1240	result = dlg.ShowModal()
1241	if result == wx.ID_OK:
1242	self.PatternTree.DeleteChildren(self.root)
1243	self.GSASprojectfile = ''
1244	# self.PatternTree.DeleteChildren(self.root)
1245	if self.HKL: self.HKL = []
1246	if self.G2plotNB.plotList:
1247	self.G2plotNB.clear()
1248	finally:
1249	dlg.Destroy()
1250	if result != wx.ID_CANCEL:
1251	if self.dataDisplay: self.dataDisplay.Destroy()
1252	dlg = wx.FileDialog(self, 'Choose GSAS-II project file', '.', '',
1253	'GSAS-II project file (.gpx)\|.gpx',wx.OPEN\|wx.CHANGE_DIR)
1254	try:
1255	if dlg.ShowModal() == wx.ID_OK:
1256	self.GSASprojectfile = dlg.GetPath()
1257	self.GSASprojectfile = FileDlgFixExt(dlg,self.GSASprojectfile)
1258	self.dirname = dlg.GetDirectory()
1259	G2IO.ProjFileOpen(self)
1260	self.PatternTree.SetItemText(self.root,'Loaded Data: '+self.GSASprojectfile)
1261	self.PatternTree.Expand(self.root)
1262	self.HKL = []
1263	item, cookie = self.PatternTree.GetFirstChild(self.root)
1264	while item and not Id:
1265	name = self.PatternTree.GetItemText(item)
1266	if name[:4] in ['PWDR','HKLF','IMG ','PDF ']:
1267	Id = item
1268	elif name == 'Controls':
1269	data = self.PatternTree.GetItemPyData(item)
1270	if data:
1271	self.Refine.Enable(True)
1272	self.SeqRefine.Enable(True)
1273	self.Solve.Enable(True) #not right but something needed here
1274	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
1275	if Id:
1276	self.PatternTree.SelectItem(Id)
1277	self.CheckNotebook()
1278	finally:
1279	dlg.Destroy()
1280
1281
1282	def OnFileClose(self, event):
1283	if self.dataFrame:
1284	self.dataFrame.Clear()
1285	self.dataFrame.SetLabel('GSAS-II data display')
1286	dlg = wx.MessageDialog(self, 'Save current project?', ' ', wx.YES \| wx.NO \| wx.CANCEL)
1287	try:
1288	result = dlg.ShowModal()
1289	if result == wx.ID_OK:
1290	self.OnFileSaveMenu(event)
1291	if result != wx.ID_CANCEL:
1292	self.GSASprojectfile = ''
1293	self.PatternTree.SetItemText(self.root,'Loaded Data: ')
1294	self.PatternTree.DeleteChildren(self.root)
1295	if self.HKL: self.HKL = []
1296	if self.G2plotNB.plotList:
1297	self.G2plotNB.clear()
1298	finally:
1299	dlg.Destroy()
1300
1301	def OnFileSave(self, event):
1302	if self.GSASprojectfile:
1303	self.PatternTree.SetItemText(self.root,'Loaded Data: '+self.GSASprojectfile)
1304	G2IO.ProjFileSave(self)
1305	else:
1306	self.OnFileSaveas(event)
1307
1308	def OnFileSaveas(self, event):
1309	dlg = wx.FileDialog(self, 'Choose GSAS-II project file name', '.', '',
1310	'GSAS-II project file (.gpx)\|.gpx',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
1311	try:
1312	if dlg.ShowModal() == wx.ID_OK:
1313	self.GSASprojectfile = dlg.GetPath()
1314	self.GSASprojectfile = FileDlgFixExt(dlg,self.GSASprojectfile)
1315	self.PatternTree.SetItemText(self.root,'Loaded Data: '+self.GSASprojectfile)
1316	G2IO.ProjFileSave(self)
1317	self.dirname = dlg.GetDirectory()
1318	finally:
1319	dlg.Destroy()
1320
1321	def ExitMain(self, event):
1322	if self.undofile:
1323	os.remove(self.undofile)
1324	sys.exit()
1325
1326	def OnFileExit(self, event):
1327	if self.dataFrame:
1328	self.dataFrame.Clear()
1329	self.dataFrame.Destroy()
1330	self.Close()
1331
1332	def OnImportPattern(self,event):
1333	dlg = wx.FileDialog(self, 'Choose nonGSAS powder file', '.', '',
1334	'(.)\|.',wx.OPEN\|wx.CHANGE_DIR)
1335	try:
1336	if dlg.ShowModal() == wx.ID_OK:
1337	self.powderfile = dlg.GetPath()
1338	finally:
1339	dlg.Destroy()
1340
1341	def OnImportHKL(self,event):
1342	dlg = wx.FileDialog(self, 'Choose structure factor file', '.', '',
1343	'(.)\|.',wx.OPEN\|wx.CHANGE_DIR)
1344	try:
1345	if dlg.ShowModal() == wx.ID_OK:
1346	self.HKLfile = dlg.GetPath()
1347	finally:
1348	dlg.Destroy()
1349
1350	''' replaced -- delete soon
1351	def OnImportPhase(self,event):
1352	dlg = wx.FileDialog(self, 'Choose GSAS EXP file', '.', '',
1353	'EXP file (.EXP)\|.EXP',wx.OPEN\|wx.CHANGE_DIR)
1354	try:
1355	Phase = {}
1356	if dlg.ShowModal() == wx.ID_OK:
1357	EXPfile = dlg.GetPath()
1358	Phase = G2IO.ReadEXPPhase(self,EXPfile)
1359	finally:
1360	dlg.Destroy()
1361	if Phase:
1362	PhaseName = Phase['General']['Name']
1363	if not G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
1364	sub = self.PatternTree.AppendItem(parent=self.root,text='Phases')
1365	else:
1366	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
1367	sub = self.PatternTree.AppendItem(parent=sub,text=PhaseName)
1368	self.PatternTree.SetItemPyData(sub,Phase)
1369
1370	def OnImportPDB(self,event):
1371	dlg = wx.FileDialog(self, 'Choose PDB file', '.', '',
1372	'PDB file (.pdb,.ent)\|.pdb;.ent\|All files (.)\|.',wx.OPEN\|wx.CHANGE_DIR)
1373	try:
1374	if dlg.ShowModal() == wx.ID_OK:
1375	PDBfile = dlg.GetPath()
1376	Phase = G2IO.ReadPDBPhase(PDBfile)
1377	finally:
1378	dlg.Destroy()
1379	if Phase:
1380	PhaseName = Phase['General']['Name']
1381	if not G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
1382	sub = self.PatternTree.AppendItem(parent=self.root,text='Phases')
1383	else:
1384	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
1385	sub = self.PatternTree.AppendItem(parent=sub,text=PhaseName)
1386	self.PatternTree.SetItemPyData(sub,Phase)
1387
1388	def OnImportCIF(self,event):
1389	def ReadCIFPhase(filename):
1390	import random as ran
1391	import GSASIIlattice as G2lat
1392	anisoNames = ['aniso_u_11','aniso_u_22','aniso_u_33','aniso_u_12','aniso_u_13','aniso_u_23']
1393	file = open(filename, 'Ur')
1394	Phase = {}
1395	Title = ospath.split(filename)[-1]
1396	print '\n Reading cif file: ',Title
1397	Compnd = ''
1398	Atoms = []
1399	A = np.zeros(shape=(3,3))
1400	S = file.readline()
1401	while S:
1402	if '_symmetry_space_group_name_H-M' in S:
1403	SpGrp = S.split("_symmetry_space_group_name_H-M")[1].strip().strip('"').strip("'")
1404	E,SGData = G2spc.SpcGroup(SpGrp)
1405	if E:
1406	print ' ERROR in space group symbol ',SpGrp,' in file ',filename
1407	print ' N.B.: make sure spaces separate axial fields in symbol'
1408	print G2spc.SGErrors(E)
1409	return None
1410	S = file.readline()
1411	elif '_cell' in S:
1412	if '_cell_length_a' in S:
1413	a = S.split('_cell_length_a')[1].strip().strip('"').strip("'").split('(')[0]
1414	elif '_cell_length_b' in S:
1415	b = S.split('_cell_length_b')[1].strip().strip('"').strip("'").split('(')[0]
1416	elif '_cell_length_c' in S:
1417	c = S.split('_cell_length_c')[1].strip().strip('"').strip("'").split('(')[0]
1418	elif '_cell_angle_alpha' in S:
1419	alp = S.split('_cell_angle_alpha')[1].strip().strip('"').strip("'").split('(')[0]
1420	elif '_cell_angle_beta' in S:
1421	bet = S.split('_cell_angle_beta')[1].strip().strip('"').strip("'").split('(')[0]
1422	elif '_cell_angle_gamma' in S:
1423	gam = S.split('_cell_angle_gamma')[1].strip().strip('"').strip("'").split('(')[0]
1424	S = file.readline()
1425	elif 'loop_' in S:
1426	labels = {}
1427	i = 0
1428	while S:
1429	S = file.readline()
1430	if '_atom_site' in S.strip()[:10]:
1431	labels[S.strip().split('_atom_site_')[1].lower()] = i
1432	i += 1
1433	else:
1434	break
1435	if labels:
1436	if 'aniso_label' not in labels:
1437	while S:
1438	atom = ['','','',0,0,0,1.0,'','','I',0.01,0,0,0,0,0,0]
1439	S.strip()
1440	if len(S.split()) != len(labels):
1441	if 'loop_' in S:
1442	break
1443	S += file.readline().strip()
1444	data = S.split()
1445	if len(data) != len(labels):
1446	break
1447	for key in labels:
1448	if key == 'type_symbol':
1449	atom[1] = data[labels[key]]
1450	elif key == 'label':
1451	atom[0] = data[labels[key]]
1452	elif key == 'fract_x':
1453	atom[3] = float(data[labels[key]].split('(')[0])
1454	elif key == 'fract_y':
1455	atom[4] = float(data[labels[key]].split('(')[0])
1456	elif key == 'fract_z':
1457	atom[5] = float(data[labels[key]].split('(')[0])
1458	elif key == 'occupancy':
1459	atom[6] = float(data[labels[key]].split('(')[0])
1460	elif key == 'thermal_displace_type':
1461	if data[labels[key]].lower() == 'uiso':
1462	atom[9] = 'I'
1463	atom[10] = float(data[labels['u_iso_or_equiv']].split('(')[0])
1464	else:
1465	atom[9] = 'A'
1466	atom[10] = 0.0
1467
1468	atom[7],atom[8] = G2spc.SytSym(atom[3:6],SGData)
1469	atom.append(ran.randint(0,sys.maxint))
1470	Atoms.append(atom)
1471	S = file.readline()
1472	else:
1473	while S:
1474	S.strip()
1475	data = S.split()
1476	if len(data) != len(labels):
1477	break
1478	name = data[labels['aniso_label']]
1479	for atom in Atoms:
1480	if name == atom[0]:
1481	for i,uname in enumerate(anisoNames):
1482	atom[i+11] = float(data[labels[uname]].split('(')[0])
1483	S = file.readline()
1484
1485	else:
1486	S = file.readline()
1487	file.close()
1488	if Title:
1489	PhaseName = Title
1490	else:
1491	PhaseName = 'None'
1492	SGlines = G2spc.SGPrint(SGData)
1493	for line in SGlines: print line
1494	cell = [float(a),float(b),float(c),float(alp),float(bet),float(gam)]
1495	Volume = G2lat.calc_V(G2lat.cell2A(cell))
1496	Phase['General'] = {'Name':PhaseName,'Type':'nuclear','SGData':SGData,
1497	'Cell':[False,]+cell+[Volume,]}
1498	Phase['Atoms'] = Atoms
1499	Phase['Drawing'] = {}
1500	Phase['Histograms'] = {}
1501
1502	return Phase
1503
1504	dlg = wx.FileDialog(self, 'Choose CIF file', '.', '',
1505	'CIF file (.cif)\|.cif',wx.OPEN\|wx.CHANGE_DIR)
1506	try:
1507	if dlg.ShowModal() == wx.ID_OK:
1508	CIFfile = dlg.GetPath()
1509	Phase = ReadCIFPhase(CIFfile)
1510	finally:
1511	dlg.Destroy()
1512	if Phase:
1513	PhaseName = Phase['General']['Name']
1514	if not G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
1515	sub = self.PatternTree.AppendItem(parent=self.root,text='Phases')
1516	else:
1517	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
1518	sub = self.PatternTree.AppendItem(parent=sub,text=PhaseName)
1519	self.PatternTree.SetItemPyData(sub,Phase)
1520	print Phase
1521	'''
1522
1523	def OnExportPatterns(self,event):
1524	names = ['All']
1525	exports = []
1526	item, cookie = self.PatternTree.GetFirstChild(self.root)
1527	while item:
1528	name = self.PatternTree.GetItemText(item)
1529	if 'PWDR' in name:
1530	names.append(name)
1531	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
1532	if names:
1533	dlg = wx.MultiChoiceDialog(self,'Select','Powder patterns to export',names)
1534	if dlg.ShowModal() == wx.ID_OK:
1535	sel = dlg.GetSelections()
1536	if sel[0] == 0:
1537	exports = names[1:]
1538	else:
1539	for x in sel:
1540	exports.append(names[x])
1541	dlg.Destroy()
1542	if exports:
1543	dlg = wx.FileDialog(self, 'Choose output powder file name', '.', '',
1544	'GSAS fxye file (.fxye)\|.fxye\|xye file (.xye)\|.xye',
1545	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
1546	try:
1547	if dlg.ShowModal() == wx.ID_OK:
1548	powderfile = dlg.GetPath()
1549	powderfile = FileDlgFixExt(dlg,powderfile)
1550	if 'fxye' in powderfile:
1551	G2IO.powderFxyeSave(self,exports,powderfile)
1552	else: #just xye
1553	G2IO.powderXyeSave(self,exports,powderfile)
1554	finally:
1555	dlg.Destroy()
1556
1557	def OnExportPeakList(self,event):
1558	dlg = wx.FileDialog(self, 'Choose output peak list file name', '.', '',
1559	'(.)\|.',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
1560	try:
1561	if dlg.ShowModal() == wx.ID_OK:
1562	self.peaklistfile = dlg.GetPath()
1563	self.peaklistfile = FileDlgFixExt(dlg,self.peaklistfile)
1564	file = open(self.peaklistfile,'w')
1565	item, cookie = self.PatternTree.GetFirstChild(self.root)
1566	while item:
1567	name = self.PatternTree.GetItemText(item)
1568	if 'PWDR' in name:
1569	item2, cookie2 = self.PatternTree.GetFirstChild(item)
1570	while item2:
1571	name2 = self.PatternTree.GetItemText(item2)
1572	if name2 == 'Peak List':
1573	peaks = self.PatternTree.GetItemPyData(item2)
1574	file.write("%s \n" % (name+' Peak List'))
1575	for peak in peaks:
1576	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1577	(peak[0],peak[2],peak[4],peak[6]))
1578	item2, cookie2 = self.PatternTree.GetNextChild(item, cookie2)
1579	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
1580	file.close()
1581	finally:
1582	dlg.Destroy()
1583
1584	def OnExportHKL(self,event):
1585	event.Skip()
1586
1587	def OnExportPDF(self,event):
1588	#need S(Q) and G(R) to be saved here - probably best from selection?
1589	names = ['All']
1590	exports = []
1591	item, cookie = self.PatternTree.GetFirstChild(self.root)
1592	while item:
1593	name = self.PatternTree.GetItemText(item)
1594	if 'PDF' in name:
1595	names.append(name)
1596	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
1597	if names:
1598	dlg = wx.MultiChoiceDialog(self,'Select','PDF patterns to export',names)
1599	if dlg.ShowModal() == wx.ID_OK:
1600	sel = dlg.GetSelections()
1601	if sel[0] == 0:
1602	exports = names[1:]
1603	else:
1604	for x in sel:
1605	exports.append(names[x])
1606	dlg.Destroy()
1607	if exports:
1608	G2IO.PDFSave(self,exports)
1609
1610	def OnExportPhase(self,event):
1611	event.Skip()
1612
1613	def OnExportCIF(self,event):
1614	event.Skip()
1615
1616	def OnMakePDFs(self,event):
1617	tth2q = lambda t,w:4.0math.pisind(t/2.0)/w
1618	TextList = ['All PWDR']
1619	PDFlist = []
1620	Names = []
1621	if self.PatternTree.GetCount():
1622	id, cookie = self.PatternTree.GetFirstChild(self.root)
1623	while id:
1624	name = self.PatternTree.GetItemText(id)
1625	Names.append(name)
1626	if 'PWDR' in name:
1627	TextList.append(name)
1628	id, cookie = self.PatternTree.GetNextChild(self.root, cookie)
1629	if len(TextList) == 1:
1630	self.ErrorDialog('Nothing to make PDFs for','There must be at least one "PWDR" pattern')
1631	return
1632	dlg = wx.MultiChoiceDialog(self,'Make PDF controls','Make PDF controls for:',TextList, wx.CHOICEDLG_STYLE)
1633	try:
1634	if dlg.ShowModal() == wx.ID_OK:
1635	result = dlg.GetSelections()
1636	for i in result: PDFlist.append(TextList[i])
1637	if 0 in result:
1638	PDFlist = [item for item in TextList if item[:4] == 'PWDR']
1639	for item in PDFlist:
1640	PWDRname = item[4:]
1641	Id = self.PatternTree.AppendItem(parent=self.root,text='PDF '+PWDRname)
1642	Data = {
1643	'Sample':{'Name':item,'Mult':1.0,'Add':0.0},
1644	'Sample Bkg.':{'Name':'','Mult':-1.0,'Add':0.0},
1645	'Container':{'Name':'','Mult':-1.0,'Add':0.0},
1646	'Container Bkg.':{'Name':'','Mult':-1.0,'Add':0.0},'ElList':{},
1647	'Geometry':'Cylinder','Diam':1.0,'Pack':0.50,'Form Vol':10.0,
1648	'DetType':'Image plate','ObliqCoeff':0.2,'Ruland':0.025,'QScaleLim':[0,100],
1649	'Lorch':True,}
1650	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='PDF Controls'),Data)
1651	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='I(Q)'+PWDRname),[])
1652	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='S(Q)'+PWDRname),[])
1653	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='F(Q)'+PWDRname),[])
1654	self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='G(R)'+PWDRname),[])
1655	self.ExportPDF.Enable(True)
1656	finally:
1657	dlg.Destroy()
1658
1659	def GetPWDRdatafromTree(self,PWDRname):
1660	''' Returns powder data from GSASII tree
1661	input:
1662	PWDRname = powder histogram name as obtained from GetHistogramNames
1663	return:
1664	PWDRdata = powder data dictionary with:
1665	Data - powder data arrays, Limits, Instrument Parameters, Sample Parameters
1666	'''
1667	PWDRdata = {}
1668	PWDRdata['Data'] = self.PatternTree.GetItemPyData(PWDRname)[1] #powder data arrays
1669	PWDRdata['Limits'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Limits'))
1670	PWDRdata['Background'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Background'))
1671	PWDRdata['Instrument Parameters'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Instrument Parameters'))
1672	PWDRdata['Sample Parameters'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Sample Parameters'))
1673	PWDRdata['Reflection Lists'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Reflection Lists'))
1674	return PWDRdata
1675
1676	def GetHKLFdatafromTree(self,HKLFname):
1677	''' Returns single crystal data from GSASII tree
1678	input:
1679	HKLFname = single crystal histogram name as obtained from GetHistogramNames
1680	return:
1681	HKLFdata = single crystal data list of reflections: for each reflection:
1682	HKLF = [np.array([h,k,l]),FoSq,sigFoSq,FcSq,Fcp,Fcpp,phase]
1683	'''
1684	HKLFdata = []
1685	while True:
1686	data = self.PatternTree.GetItemPyData(HKLFname)
1687	datum = data[0]
1688	if datum[0] == HKLFname:
1689	HKLFdata = datum[1:][0]
1690	return HKLFdata
1691
1692	def GetUsedHistogramsAndPhasesfromTree(self):
1693	''' Returns all histograms that are found in any phase
1694	and any phase that uses a histogram
1695	return:
1696	Histograms = dictionary of histograms as {name:data,...}
1697	Phases = dictionary of phases that use histograms
1698	'''
1699	phaseData = {}
1700	if G2gd.GetPatternTreeItemId(self,self.root,'Phases'):
1701	sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases')
1702	else:
1703	print 'no phases to be refined'
1704	return
1705	if sub:
1706	item, cookie = self.PatternTree.GetFirstChild(sub)
1707	while item:
1708	phaseData[self.PatternTree.GetItemText(item)] = self.PatternTree.GetItemPyData(item)
1709	item, cookie = self.PatternTree.GetNextChild(sub, cookie)
1710	Histograms = {}
1711	Phases = {}
1712	pId = 0
1713	hId = 0
1714	for phase in phaseData:
1715	Phase = phaseData[phase]
1716	if Phase['Histograms']:
1717	if phase not in Phases:
1718	Phase['pId'] = pId
1719	pId += 1
1720	Phases[phase] = Phase
1721	for hist in Phase['Histograms']:
1722	if hist not in Histograms:
1723	item = G2gd.GetPatternTreeItemId(self,self.root,hist)
1724	if 'PWDR' in hist[:4]:
1725	Histograms[hist] = self.GetPWDRdatafromTree(item)
1726	elif 'HKLF' in hist[:4]:
1727	Histograms[hist] = self.GetHKLFdatafromTree(item)
1728	#future restraint, etc. histograms here
1729	Histograms[hist]['hId'] = hId
1730	hId += 1
1731	return Histograms,Phases
1732
1733	class ViewParmDialog(wx.Dialog):
1734	def __init__(self,parent,title,parmDict):
1735	wx.Dialog.__init__(self,parent,-1,title,size=(260,430),
1736	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1737	panel = wx.Panel(self,size=(260,430))
1738	parmNames = parmDict.keys()
1739	parmNames.sort()
1740	parmText = ' p:h:Parameter refine? value\n'
1741	for name in parmNames:
1742	parmData = parmDict[name]
1743	try:
1744	parmText += ' %s \t%12.4g \n'%(name.ljust(19)+'\t'+parmData[1],parmData[0])
1745	except TypeError:
1746	pass
1747	parmTable = wx.TextCtrl(panel,-1,parmText,
1748	style=wx.TE_MULTILINE\|wx.TE_READONLY,size=(250,400))
1749	mainSizer = wx.BoxSizer(wx.VERTICAL)
1750	mainSizer.Add(parmTable)
1751	panel.SetSizer(mainSizer)
1752
1753	def OnViewLSParms(self,event):
1754	parmDict = {}
1755	Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree()
1756	Natoms,phaseVary,phaseDict,pawleyLookup,FFtable,BLtable = G2str.GetPhaseData(Phases,Print=False)
1757	hapVary,hapDict,controlDict = G2str.GetHistogramPhaseData(Phases,Histograms,Print=False)
1758	histVary,histDict,controlDict = G2str.GetHistogramData(Histograms,Print=False)
1759	varyList = phaseVary+hapVary+histVary
1760	parmDict.update(phaseDict)
1761	parmDict.update(hapDict)
1762	parmDict.update(histDict)
1763	for parm in parmDict:
1764	if parm.split(':')[-1] in ['Azimuth','Gonio. radius','Lam1','Lam2','Omega','Chi','Phi']:
1765	parmDict[parm] = [parmDict[parm],' ']
1766	elif parm.split(':')[-2] in ['Ax','Ay','Az','SHmodel','SHord']:
1767	parmDict[parm] = [parmDict[parm],' ']
1768	elif parm in varyList:
1769	parmDict[parm] = [parmDict[parm],'True']
1770	else:
1771	parmDict[parm] = [parmDict[parm],'False']
1772	dlg = self.ViewParmDialog(self,'Parameters for least squares',parmDict)
1773	try:
1774	if dlg.ShowModal() == wx.ID_OK:
1775	print 'do something with changes?? - No!'
1776	finally:
1777	dlg.Destroy()
1778
1779	def OnRefine(self,event):
1780	self.OnFileSave(event)
1781	#works - but it'd be better if it could restore plots
1782	dlg = wx.ProgressDialog('Residual','Powder profile Rwp =',101.0,
1783	style = wx.PD_ELAPSED_TIME\|wx.PD_AUTO_HIDE\|wx.PD_CAN_ABORT)
1784	screenSize = wx.ClientDisplayRect()
1785	Size = dlg.GetSize()
1786	Size = (int(Size[0]*1.2),Size[1]) # increase size a bit along x
1787	dlg.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5))
1788	dlg.SetSize(Size)
1789	Rwp = 100.00
1790	try:
1791	Rwp = G2str.Refine(self.GSASprojectfile,dlg)
1792	finally:
1793	dlg.Destroy()
1794	dlg = wx.MessageDialog(self,'Load new result?','Refinement results, Rwp =%.3f'%(Rwp),wx.OK\|wx.CANCEL)
1795	try:
1796	if dlg.ShowModal() == wx.ID_OK:
1797	Id = 0
1798	self.PatternTree.DeleteChildren(self.root)
1799	if self.HKL: self.HKL = []
1800	if self.G2plotNB.plotList:
1801	self.G2plotNB.clear()
1802	G2IO.ProjFileOpen(self)
1803	item, cookie = self.PatternTree.GetFirstChild(self.root)
1804	while item and not Id:
1805	name = self.PatternTree.GetItemText(item)
1806	if name[:4] in ['PWDR','HKLF']:
1807	Id = item
1808	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
1809	if Id:
1810	self.PatternTree.SelectItem(Id)
1811	finally:
1812	dlg.Destroy()
1813
1814	def OnSeqRefine(self,event):
1815	Id = G2gd.GetPatternTreeItemId(self,self.root,'Sequental results')
1816	if not Id:
1817	Id = self.PatternTree.AppendItem(self.root,text='Sequental results')
1818	self.PatternTree.SetItemPyData(Id,{})
1819	self.OnFileSave(event)
1820	dlg = wx.ProgressDialog('Residual for histogram 0','Powder profile Rwp =',101.0,
1821	style = wx.PD_ELAPSED_TIME\|wx.PD_AUTO_HIDE\|wx.PD_CAN_ABORT)
1822	screenSize = wx.ClientDisplayRect()
1823	Size = dlg.GetSize()
1824	Size = (int(Size[0]*1.2),Size[1]) # increase size a bit along x
1825	dlg.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5))
1826	dlg.SetSize(Size)
1827	try:
1828	G2str.SeqRefine(self.GSASprojectfile,dlg)
1829	finally:
1830	dlg.Destroy()
1831	dlg = wx.MessageDialog(self,'Load new result?','Refinement results',wx.OK\|wx.CANCEL)
1832	try:
1833	if dlg.ShowModal() == wx.ID_OK:
1834	Id = 0
1835	self.PatternTree.DeleteChildren(self.root)
1836	if self.HKL: self.HKL = []
1837	if self.G2plotNB.plotList:
1838	self.G2plotNB.clear()
1839	G2IO.ProjFileOpen(self)
1840	item, cookie = self.PatternTree.GetFirstChild(self.root)
1841	while item and not Id:
1842	name = self.PatternTree.GetItemText(item)
1843	if name[:4] in ['PWDR','HKLF']:
1844	Id = item
1845	item, cookie = self.PatternTree.GetNextChild(self.root, cookie)
1846	if Id:
1847	self.PatternTree.SelectItem(Id)
1848	finally:
1849	dlg.Destroy()
1850
1851	def OnSolve(self,event):
1852	#works - but it'd be better if it could restore plots
1853	G2sol.Solve(self.GSASprojectfile)
1854	dlg = wx.MessageDialog(self,'Load new result?','Structure solution results',wx.OK\|wx.CANCEL)
1855	try:
1856	if dlg.ShowModal() == wx.ID_OK:
1857	self.PatternTree.DeleteChildren(self.root)
1858	if self.HKL: self.HKL = []
1859	if self.G2plotNB.plotList:
1860	self.G2plotNB.clear()
1861	G2IO.ProjFileOpen(self)
1862	finally:
1863	dlg.Destroy()
1864
1865	def ErrorDialog(self,title,message):
1866	dlg = wx.MessageDialog(self, message, title, wx.OK)
1867	try:
1868	result = dlg.ShowModal()
1869	finally:
1870	dlg.Destroy()
1871
1872	class GSASIImain(wx.App):
1873	def OnInit(self):
1874	self.main = GSASII(None)
1875	self.main.Show()
1876	self.SetTopWindow(self.main)
1877	return True
1878
1879	def main():
1880	application = GSASIImain(0)
1881	if wxInspector: wxeye.InspectionTool().Show()
1882
1883	#application.main.OnRefine(None)
1884	application.MainLoop()
1885
1886	if __name__ == '__main__':
1887	main()

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