| 95 | | # PATCH: for Mavericks (OS X 10.9.x), wx produces an annoying warning about LucidaGrandeUI. |
| 96 | | # In case stderr has been suppressed there, redirect python error output to stdout. Nobody |
| 97 | | # else should care much about this. |
| 98 | | sys.stderr = sys.stdout |
| 99 | | |
| 100 | | def create(parent): |
| 101 | | return GSASII(parent) |
| 102 | | |
| 103 | | def SetDefaultDData(dType,histoName,NShkl=0,NDij=0): |
| 104 | | if dType in ['SXC','SNC']: |
| 105 | | return {'Histogram':histoName,'Show':False,'Scale':[1.0,True], |
| 106 | | 'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}, |
| 107 | | 'Extinction':['Lorentzian','None', {'Tbar':0.1,'Cos2TM':0.955, |
| 108 | | 'Eg':[1.e-10,False],'Es':[1.e-10,False],'Ep':[1.e-10,False]}], |
| 109 | | 'Flack':[0.0,False]} |
| 110 | | elif dType == 'SNT': |
| 111 | | return {'Histogram':histoName,'Show':False,'Scale':[1.0,True], |
| 112 | | 'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}, |
| 113 | | 'Extinction':['Lorentzian','None', { |
| 114 | | 'Eg':[1.e-10,False],'Es':[1.e-10,False],'Ep':[1.e-10,False]}]} |
| 115 | | elif 'P' in dType: |
| 116 | | return {'Histogram':histoName,'Show':False,'Scale':[1.0,False], |
| 117 | | 'Pref.Ori.':['MD',1.0,False,[0,0,1],0,{},[],0.1], |
| 118 | | 'Size':['isotropic',[1.,1.,1.],[False,False,False],[0,0,1], |
| 119 | | [1.,1.,1.,0.,0.,0.],6*[False,]], |
| 120 | | 'Mustrain':['isotropic',[1000.0,1000.0,1.0],[False,False,False],[0,0,1], |
| 121 | | NShkl*[0.01,],NShkl*[False,]], |
| 122 | | 'HStrain':[NDij*[0.0,],NDij*[False,]], |
| 123 | | 'Extinction':[0.0,False],'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}} |
| 124 | | |
| 125 | | class GSASII(wx.Frame): |
| 126 | | '''Define the main GSAS-II frame and its associated menu items |
| 127 | | ''' |
| 128 | | def MenuBinding(self,event): |
| 129 | | '''Called when a menu is clicked upon; looks up the binding in table |
| 130 | | ''' |
| 131 | | log.InvokeMenuCommand(event.GetId(),self,event) |
| 132 | | |
| 133 | | def Bind(self,eventtype,handler,*args,**kwargs): |
| 134 | | '''Override the Bind function so that we can wrap calls that will be logged. |
| 135 | | |
| 136 | | N.B. This is a bit kludgy. Menu bindings with an id are wrapped and |
| 137 | | menu bindings with an object and no id are not. |
| 138 | | ''' |
| 139 | | if eventtype == wx.EVT_MENU and 'id' in kwargs: |
| 140 | | menulabels = log.SaveMenuCommand(kwargs['id'],self,handler) |
| 141 | | if menulabels: |
| 142 | | wx.Frame.Bind(self,eventtype,self.MenuBinding,*args,**kwargs) |
| 143 | | return |
| 144 | | wx.Frame.Bind(self,eventtype,handler,*args,**kwargs) |
| 145 | | |
| 146 | | def _Add_FileMenuItems(self, parent): |
| 147 | | item = parent.Append( |
| 148 | | help='Open a GSAS-II project file (*.gpx)', id=wx.ID_ANY, |
| 149 | | kind=wx.ITEM_NORMAL,text='&Open project...') |
| 150 | | self.Bind(wx.EVT_MENU, self.OnFileOpen, id=item.GetId()) |
| 151 | | item = parent.Append( |
| 152 | | help='Save project under current name', id=wx.ID_ANY, |
| 153 | | kind=wx.ITEM_NORMAL,text='&Save project') |
| 154 | | self.Bind(wx.EVT_MENU, self.OnFileSave, id=item.GetId()) |
| 155 | | item = parent.Append( |
| 156 | | help='Save current project to new file', id=wx.ID_ANY, |
| 157 | | kind=wx.ITEM_NORMAL,text='Save project as...') |
| 158 | | self.Bind(wx.EVT_MENU, self.OnFileSaveas, id=item.GetId()) |
| 159 | | item = parent.Append( |
| 160 | | help='Create empty new project, saving current is optional', id=wx.ID_ANY, |
| 161 | | kind=wx.ITEM_NORMAL,text='&New project') |
| 162 | | self.Bind(wx.EVT_MENU, self.OnFileClose, id=item.GetId()) |
| 163 | | item = parent.Append(wx.ID_PREFERENCES, text = "&Preferences") |
| 164 | | self.Bind(wx.EVT_MENU, self.OnPreferences, item) |
| 165 | | if GSASIIpath.GetConfigValue('debug'): |
| 166 | | def OnIPython(event): |
| 167 | | GSASIIpath.IPyBreak() |
| 168 | | item = parent.Append(wx.ID_ANY, text = "IPython Console") |
| 169 | | self.Bind(wx.EVT_MENU, OnIPython, item) |
| 170 | | item = parent.Append( |
| 171 | | help='Exit from GSAS-II', id=wx.ID_ANY, |
| 172 | | kind=wx.ITEM_NORMAL,text='&Exit') |
| 173 | | self.Bind(wx.EVT_MENU, self.OnFileExit, id=item.GetId()) |
| 174 | | |
| 175 | | def _Add_DataMenuItems(self,parent): |
| 176 | | item = parent.Append( |
| 177 | | help='',id=wx.ID_ANY, |
| 178 | | kind=wx.ITEM_NORMAL, |
| 179 | | text='Read image data...') |
| 180 | | self.Bind(wx.EVT_MENU, self.OnImageRead, id=item.GetId()) |
| 181 | | item = parent.Append( |
| 182 | | help='',id=wx.ID_ANY, |
| 183 | | kind=wx.ITEM_NORMAL, |
| 184 | | text='Read Powder Pattern Peaks...') |
| 185 | | self.Bind(wx.EVT_MENU, self.OnReadPowderPeaks, id=item.GetId()) |
| 186 | | item = parent.Append( |
| 187 | | help='',id=wx.ID_ANY, |
| 188 | | kind=wx.ITEM_NORMAL, |
| 189 | | text='Sum powder data') |
| 190 | | self.Bind(wx.EVT_MENU, self.OnPwdrSum, id=item.GetId()) |
| 191 | | item = parent.Append( |
| 192 | | help='',id=wx.ID_ANY, |
| 193 | | kind=wx.ITEM_NORMAL, |
| 194 | | text='Sum image data') |
| 195 | | self.Bind(wx.EVT_MENU, self.OnImageSum, id=item.GetId()) |
| 196 | | item = parent.Append( |
| 197 | | help='',id=wx.ID_ANY, |
| 198 | | kind=wx.ITEM_NORMAL, |
| 199 | | text='Add new phase') |
| 200 | | self.Bind(wx.EVT_MENU, self.OnAddPhase, id=item.GetId()) |
| 201 | | item = parent.Append( |
| 202 | | help='',id=wx.ID_ANY, |
| 203 | | kind=wx.ITEM_NORMAL, |
| 204 | | text='Delete phase') |
| 205 | | self.Bind(wx.EVT_MENU, self.OnDeletePhase, id=item.GetId()) |
| 206 | | item = parent.Append( |
| 207 | | help='Rename the selected data tree item (PWDR, HKLF or IMG)',id=wx.ID_ANY, |
| 208 | | kind=wx.ITEM_NORMAL, |
| 209 | | text='Rename tree item') |
| 210 | | self.Bind(wx.EVT_MENU, self.OnRenameData, id=item.GetId()) |
| 211 | | item = parent.Append( |
| 212 | | help='Delete selected data items from data tree',id=wx.ID_ANY, |
| 213 | | kind=wx.ITEM_NORMAL, |
| 214 | | text='Delete tree items') |
| 215 | | self.Bind(wx.EVT_MENU, self.OnDataDelete, id=item.GetId()) |
| 216 | | expandmenu = wx.Menu() |
| 217 | | item = parent.AppendMenu( |
| 218 | | wx.ID_ANY, 'Expand tree items', expandmenu, |
| 219 | | help='Expand items of type in GSAS-II data tree') |
| 220 | | for s in 'all','IMG','PWDR','PDF','HKLF','SASD','REFD': |
| 221 | | if s == 'all': |
| 222 | | help = 'Expand all items in GSAS-II data tree' |
| 223 | | else: |
| 224 | | help = 'Expand '+s+' type items in GSAS-II data tree' |
| 225 | | item = expandmenu.Append(wx.ID_ANY,kind=wx.ITEM_NORMAL,text=s,help=help) |
| 226 | | self.Bind(wx.EVT_MENU,self.ExpandAll,id=item.GetId()) |
| 227 | | movemenu = wx.Menu() |
| 228 | | item = parent.AppendMenu( |
| 229 | | wx.ID_ANY, 'Move tree items', movemenu, |
| 230 | | help='Move items of type items to end of GSAS-II data tree') |
| 231 | | for s in 'IMG','PWDR','PDF','HKLF','SASD','REFD','Phase': |
| 232 | | help = 'Move '+s+' type items to end of GSAS-II data tree' |
| 233 | | item = movemenu.Append(wx.ID_ANY,kind=wx.ITEM_NORMAL,text=s,help=help) |
| 234 | | self.Bind(wx.EVT_MENU,self.MoveTreeItems,id=item.GetId()) |
| 235 | | |
| 236 | | def _Add_CalculateMenuItems(self,parent): |
| 237 | | item = parent.Append(help='Create PDF tree entries for selected powder patterns', |
| 238 | | id=wx.ID_ANY, kind=wx.ITEM_NORMAL,text='Setup PDFs') |
| 239 | | self.MakePDF.append(item) |
| 240 | | self.Bind(wx.EVT_MENU, self.OnMakePDFs, id=item.GetId()) |
| 241 | | |
| 242 | | item = parent.Append(help='View least squares parameters', |
| 243 | | id=wx.ID_ANY, kind=wx.ITEM_NORMAL,text='&View LS parms') |
| 244 | | self.Bind(wx.EVT_MENU, self.OnShowLSParms, id=item.GetId()) |
| 245 | | |
| 246 | | item = parent.Append(help='', id=wx.ID_ANY, kind=wx.ITEM_NORMAL, |
| 247 | | text='&Refine') |
| 248 | | if len(self.Refine): # extend state for new menus to match main (on mac) |
| 249 | | state = self.Refine[0].IsEnabled() |
| 250 | | else: |
| 251 | | state = False |
| 252 | | item.Enable(state) |
| 253 | | self.Refine.append(item) |
| 254 | | self.Bind(wx.EVT_MENU, self.OnRefine, id=item.GetId()) |
| 255 | | |
| 256 | | item = parent.Append(help='', id=wx.ID_ANY, kind=wx.ITEM_NORMAL, |
| 257 | | text='Sequential refine') |
| 258 | | self.Bind(wx.EVT_MENU, self.OnSeqRefine, id=item.GetId()) |
| 259 | | if len(self.SeqRefine): # extend state for new menus to match main (on mac) |
| 260 | | state = self.SeqRefine[0].IsEnabled() |
| 261 | | else: |
| 262 | | state = False |
| 263 | | item.Enable(state) |
| 264 | | self.SeqRefine.append(item) # save menu obj for use in self.EnableSeqRefineMenu |
| 265 | | # if GSASIIpath.GetConfigValue('debug'): # allow exceptions for debugging |
| 266 | | # item = parent.Append(help='', id=wx.ID_ANY, kind=wx.ITEM_NORMAL, |
| 267 | | # text='tree test') |
| 268 | | # self.Bind(wx.EVT_MENU, self.TreeTest, id=item.GetId()) |
| 269 | | |
| 270 | | def _init_Imports(self): |
| 271 | | '''import all the G2phase*.py & G2sfact*.py & G2pwd*.py files that |
| 272 | | are found in the path |
| 273 | | ''' |
| 274 | | |
| 275 | | self.ImportPhaseReaderlist = [] |
| 276 | | self._init_Import_routines('phase',self.ImportPhaseReaderlist,'Phase') |
| 277 | | self.ImportSfactReaderlist = [] |
| 278 | | self._init_Import_routines('sfact',self.ImportSfactReaderlist,'Struct_Factor') |
| 279 | | self.ImportPowderReaderlist = [] |
| 280 | | self._init_Import_routines('pwd',self.ImportPowderReaderlist,'Powder_Data') |
| 281 | | self.ImportSmallAngleReaderlist = [] |
| 282 | | self._init_Import_routines('sad',self.ImportSmallAngleReaderlist,'SmallAngle_Data') |
| 283 | | self.ImportReflectometryReaderlist = [] |
| 284 | | self._init_Import_routines('rfd',self.ImportReflectometryReaderlist,'Reflectometry_Data') |
| 285 | | self.ImportPDFReaderlist = [] |
| 286 | | self._init_Import_routines('pdf',self.ImportPDFReaderlist,'PDF_Data') |
| 287 | | self.ImportImageReaderlist = [] |
| 288 | | self._init_Import_routines('img',self.ImportImageReaderlist,'Images') |
| 289 | | self.ImportMenuId = {} |
| 290 | | |
| 291 | | def _init_Import_routines(self,prefix,readerlist,errprefix): |
| 292 | | '''import all the import readers matching the prefix |
| 293 | | ''' |
| 294 | | #path2GSAS2 = os.path.dirname(os.path.realpath(__file__)) # location of this file |
| 295 | | #pathlist = sys.path[:] |
| 296 | | #if path2GSAS2 not in pathlist: pathlist.append(path2GSAS2) |
| 297 | | #path2GSAS2 = os.path.join( |
| 298 | | # os.path.dirname(os.path.realpath(__file__)), # location of this file |
| 299 | | # 'imports') |
| 300 | | pathlist = sys.path[:] |
| 301 | | #if path2GSAS2 not in pathlist: pathlist.append(path2GSAS2) |
| 302 | | if '.' not in pathlist: pathlist.append('.') # insert the directory where G2 is started |
| 303 | | |
| 304 | | filelist = [] |
| 305 | | for path in pathlist: |
| 306 | | for filename in glob.iglob(os.path.join( |
| 307 | | path, |
| 308 | | "G2"+prefix+"*.py")): |
| 309 | | filelist.append(filename) |
| 310 | | #print 'debug: found',filename |
| 311 | | filelist = sorted(list(set(filelist))) # remove duplicates |
| 312 | | for filename in filelist: |
| 313 | | path,rootname = os.path.split(filename) |
| 314 | | pkg = os.path.splitext(rootname)[0] |
| 315 | | try: |
| 316 | | fp = None |
| 317 | | fp, fppath,desc = imp.find_module(pkg,[path,]) |
| 318 | | pkg = imp.load_module(pkg,fp,fppath,desc) |
| 319 | | for clss in inspect.getmembers(pkg): # find classes defined in package |
| 320 | | if clss[0].startswith('_'): continue |
| 321 | | if inspect.isclass(clss[1]): |
| 322 | | # check if we have the required methods |
| 323 | | for m in 'Reader','ExtensionValidator','ContentsValidator': |
| 324 | | if not hasattr(clss[1],m): break |
| 325 | | if not callable(getattr(clss[1],m)): break |
| 326 | | else: |
| 327 | | reader = clss[1]() # create an import instance |
| 328 | | if reader.UseReader: |
| 329 | | readerlist.append(reader) |
| 330 | | except AttributeError: |
| 331 | | print 'Import_'+errprefix+': Attribute Error '+ filename |
| 332 | | #except ImportError: |
| 333 | | # print 'Import_'+errprefix+': Error importing file '+ filename |
| 334 | | except Exception,errmsg: |
| 335 | | print('\nImport_'+errprefix+': Error importing file '+ filename) |
| 336 | | print(u'Error message: {}\n'.format(errmsg)) |
| 337 | | if fp: fp.close() |
| 338 | | |
| 339 | | def EnableSeqRefineMenu(self): |
| 340 | | '''Enable or disable the sequential refinement menu items based on the |
| 341 | | contents of the Controls 'Seq Data' item (if present) |
| 342 | | ''' |
| 343 | | controls = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.root, 'Controls')) |
| 344 | | if controls.get('Seq Data'): |
| 345 | | for i in self.SeqRefine: i.Enable(True) |
| 346 | | else: |
| 347 | | for i in self.SeqRefine: i.Enable(False) |
| 348 | | |
| 349 | | def PreviewFile(self,filename,fp): |
| 350 | | 'confirm we have the right file' |
| 351 | | rdmsg = 'File '+ filename +' begins:\n\n' |
| 352 | | try: |
| 353 | | rdmsg += fp.read(80) |
| 354 | | rdmsg += '\n\nDo you want to read this file?' |
| 355 | | except UnicodeDecodeError: |
| 356 | | rdmsg = None |
| 357 | | if rdmsg is None or not all([ord(c) < 128 and ord(c) != 0 for c in rdmsg]): # show only if ASCII |
| 358 | | rdmsg = 'File '+ filename +' is a binary file. Do you want to read this file?' |
| 359 | | # it would be better to use something that |
| 360 | | # would resize better, but this will do for now |
| 361 | | dlg = wx.MessageDialog( |
| 362 | | self, rdmsg, |
| 363 | | 'Is this the file you want?', |
| 364 | | wx.YES_NO | wx.ICON_QUESTION, |
| 365 | | ) |
| 366 | | dlg.SetSize((700,300)) # does not resize on Mac |
| 367 | | result = wx.ID_NO |
| 368 | | try: |
| 369 | | result = dlg.ShowModal() |
| 370 | | finally: |
| 371 | | dlg.Destroy() |
| 372 | | if result == wx.ID_NO: return True |
| 373 | | return False |
| 374 | | |
| 375 | | def OnImportGeneric(self,reader,readerlist,label,multiple=False, |
| 376 | | usedRanIdList=[],Preview=True,load2Tree=False): |
| 377 | | '''Used for all imports, including Phases, datasets, images... |
| 378 | | |
| 379 | | Called from :meth:`GSASII.OnImportPhase`, :meth:`GSASII.OnImportImage`, |
| 380 | | :meth:`GSASII.OnImportSfact`, :meth:`GSASII.OnImportPowder`, |
| 381 | | :meth:`GSASII.OnImportSmallAngle` and :meth:'GSASII.OnImportReflectometry` |
| 382 | | |
| 383 | | Uses reader_objects subclassed from :class:`GSASIIobj.ImportPhase`, |
| 384 | | :class:`GSASIIobj.ImportStructFactor`, |
| 385 | | :class:`GSASIIobj.ImportPowderData`, |
| 386 | | :class:`GSASIIobj.ImportSmallAngleData` |
| 387 | | :class:`GSASIIobj.ImportReflectometryData` or |
| 388 | | :class:`GSASIIobj.ImportImage`. |
| 389 | | If a specific reader is specified, only that method will be called, |
| 390 | | but if no reader is specified, every one that is potentially |
| 391 | | compatible (by file extension) will be tried on the file(s) |
| 392 | | selected in the Open File dialog. |
| 393 | | |
| 394 | | :param reader_object reader: This will be a reference to |
| 395 | | a particular object to be used to read a file or None, |
| 396 | | if every appropriate reader should be used. |
| 397 | | |
| 398 | | :param list readerlist: a list of reader objects appropriate for |
| 399 | | the current read attempt. At present, this will be either |
| 400 | | self.ImportPhaseReaderlist, self.ImportSfactReaderlist |
| 401 | | self.ImportPowderReaderlist or self.ImportImageReaderlist |
| 402 | | (defined in _init_Imports from the files found in the path), |
| 403 | | but in theory this list could be tailored. |
| 404 | | Used only when reader is None. |
| 405 | | |
| 406 | | :param str label: string to place on the open file dialog: |
| 407 | | Open `label` input file |
| 408 | | |
| 409 | | :param bool multiple: True if multiple files can be selected |
| 410 | | in the file dialog. False is default. At present True is used |
| 411 | | only for reading of powder data. |
| 412 | | |
| 413 | | :param list usedRanIdList: an optional list of random Ids that |
| 414 | | have been used and should not be reused |
| 415 | | |
| 416 | | :param bool Preview: indicates if a preview of the file should |
| 417 | | be shown. Default is True, but set to False for image files |
| 418 | | which are all binary. |
| 419 | | |
| 420 | | :param bool load2Tree: indicates if the file should be loaded |
| 421 | | into the data tree immediately (used for images only). True |
| 422 | | only when called from :meth:`OnImportImage`; causes return |
| 423 | | value to change to a list of True values rather than |
| 424 | | reader objects. |
| 425 | | |
| 426 | | :returns: a list of reader objects (rd_list) that were able |
| 427 | | to read the specified file(s). This list may be empty. |
| 428 | | ''' |
| 429 | | self.lastimport = '' |
| 430 | | self.zipfile = None |
| 431 | | singlereader = True |
| 432 | | if reader is None: |
| 433 | | singlereader = False |
| 434 | | multiple = False |
| 435 | | #print "use all formats" |
| 436 | | choices = "any file (*.*)|*.*" |
| 437 | | choices += "|zip archive (.zip)|*.zip" |
| 438 | | extdict = {} |
| 439 | | # compile a list of allowed extensions |
| 440 | | for rd in readerlist: |
| 441 | | fmt = rd.formatName |
| 442 | | for extn in rd.extensionlist: |
| 443 | | if not extdict.get(extn): extdict[extn] = [] |
| 444 | | extdict[extn] += [fmt,] |
| 445 | | for extn in sorted(extdict.keys(),cmp=lambda x,y: cmp(x.lower(), y.lower())): |
| 446 | | fmt = '' |
| 447 | | for f in extdict[extn]: |
| 448 | | if fmt != "": fmt += ', ' |
| 449 | | fmt += f |
| 450 | | choices += "|" + fmt + " file (*" + extn + ")|*" + extn |
| 451 | | else: |
| 452 | | readerlist = [reader,] |
| 453 | | # compile a list of allowed extensions |
| 454 | | choices = reader.formatName + " file (" |
| 455 | | w = "" |
| 456 | | for extn in reader.extensionlist: |
| 457 | | if w != "": w += ";" |
| 458 | | w += "*" + extn |
| 459 | | choices += w + ")|" + w |
| 460 | | choices += "|zip archive (.zip)|*.zip" |
| 461 | | if not reader.strictExtension: |
| 462 | | choices += "|any file (*.*)|*.*" |
| 463 | | # get the file(s) |
| 464 | | if multiple: |
| 465 | | mode = wx.OPEN|wx.MULTIPLE |
| 466 | | else: |
| 467 | | mode = wx.OPEN |
| 468 | | filelist = G2G.GetImportFile(self,message="Choose "+label+" input file", |
| 469 | | defaultFile="",wildcard=choices,style=mode) |
| 470 | | rd_list = [] |
| 471 | | filelist1 = [] |
| 472 | | for filename in filelist: |
| 473 | | # is this a zip file? |
| 474 | | if os.path.splitext(filename)[1].lower() == '.zip': |
| 475 | | extractedfiles = G2IO.ExtractFileFromZip( |
| 476 | | filename,parent=self, |
| 477 | | multipleselect=True) |
| 478 | | if extractedfiles is None: continue # error or Cancel |
| 479 | | if extractedfiles != filename: |
| 480 | | self.zipfile = filename # save zip name |
| 481 | | filelist1 += extractedfiles |
| 482 | | continue |
| 483 | | filelist1.append(filename) |
| 484 | | filelist = filelist1 |
| 485 | | Start = True #1st time read - clear selections below |
| 486 | | for filename in filelist: |
| 487 | | # is this a zip file? |
| 488 | | if os.path.splitext(filename)[1].lower() == '.zip': |
| 489 | | extractedfile = G2IO.ExtractFileFromZip(filename,parent=self) |
| 490 | | if extractedfile is None: continue # error or Cancel |
| 491 | | if extractedfile != filename: |
| 492 | | filename,self.zipfile = extractedfile,filename # now use the file that was created |
| 493 | | # determine which formats are compatible with this file |
| 494 | | primaryReaders = [] |
| 495 | | secondaryReaders = [] |
| 496 | | for rd in readerlist: |
| 497 | | flag = rd.ExtensionValidator(filename) |
| 498 | | if flag is None: |
| 499 | | secondaryReaders.append(rd) |
| 500 | | elif flag: |
| 501 | | primaryReaders.append(rd) |
| 502 | | if len(secondaryReaders) + len(primaryReaders) == 0 and reader: |
| 503 | | self.ErrorDialog('Not supported','The selected reader cannot read file '+filename) |
| 504 | | return [] |
| 505 | | elif len(secondaryReaders) + len(primaryReaders) == 0: |
| 506 | | self.ErrorDialog('No Format','No matching format for file '+filename) |
| 507 | | return [] |
| 508 | | |
| 509 | | fp = None |
| 510 | | msg = '' |
| 511 | | fp = open(filename,'Ur') |
| 512 | | if len(filelist) == 1 and Preview: |
| 513 | | if self.PreviewFile(filename,fp): return [] |
| 514 | | self.lastimport = filename # this is probably not what I want to do -- it saves only the |
| 515 | | # last name in a series. See rd.readfilename for a better name. |
| 516 | | |
| 517 | | # try the file first with Readers that specify the |
| 518 | | # file's extension and later with ones that merely allow it |
| 519 | | errorReport = '' |
| 520 | | for rd in primaryReaders+secondaryReaders: |
| 521 | | if Start: #clear old bank selections to allow new ones to be selected by user |
| 522 | | rd.selections = [] |
| 523 | | rd.dnames = [] |
| 524 | | rd.ReInitialize() # purge anything from a previous read |
| 525 | | fp.seek(0) # rewind |
| 526 | | rd.errors = "" # clear out any old errors |
| 527 | | if not rd.ContentsValidator(fp): # rejected on cursory check |
| 528 | | errorReport += "\n "+rd.formatName + ' validator error' |
| 529 | | if rd.errors: |
| 530 | | errorReport += ': '+rd.errors |
| 531 | | continue |
| 532 | | if len(rd.selections)>1 and Start: |
| 533 | | dlg = G2G.G2MultiChoiceDialog(self,'Dataset Selector','Select data to read from the list below',rd.dnames) |
| 534 | | if dlg.ShowModal() == wx.ID_OK: |
| 535 | | rd.selections = dlg.GetSelections() |
| 536 | | Start = False |
| 537 | | dlg.Destroy() |
| 538 | | repeat = True |
| 539 | | rdbuffer = {} # create temporary storage for file reader |
| 540 | | block = 0 |
| 541 | | fp.seek(0) # rewind |
| 542 | | while repeat: # loop if the reader asks for another pass on the file |
| 543 | | block += 1 |
| 544 | | repeat = False |
| 545 | | rd.objname = os.path.basename(filename) |
| 546 | | flag = False |
| 547 | | if GSASIIpath.GetConfigValue('debug'): # allow exceptions for debugging |
| 548 | | flag = rd.Reader(filename,fp,self,buffer=rdbuffer,blocknum=block, |
| 549 | | usedRanIdList=usedRanIdList,) |
| 550 | | else: |
| 551 | | try: |
| 552 | | flag = rd.Reader(filename,fp,self,buffer=rdbuffer, |
| 553 | | blocknum=block,usedRanIdList=usedRanIdList,) |
| 554 | | except rd.ImportException as detail: |
| 555 | | rd.errors += "\n Read exception: "+str(detail) |
| 556 | | except Exception as detail: |
| 557 | | import traceback |
| 558 | | rd.errors += "\n Unhandled read exception: "+str(detail) |
| 559 | | rd.errors += "\n Traceback info:\n"+str(traceback.format_exc()) |
| 560 | | if flag: # this read succeeded |
| 561 | | if rd.SciPy: #was default read by scipy; needs 1 time fixes |
| 562 | | G2IO.EditImageParms(self,rd.Data,rd.Comments,rd.Image,filename) |
| 563 | | rd.SciPy = False |
| 564 | | rd.readfilename = filename |
| 565 | | if load2Tree: #images only |
| 566 | | if rd.repeatcount == 1 and not rd.repeat: # skip image number if only one in set |
| 567 | | rd.Data['ImageTag'] = None |
| 568 | | else: |
| 569 | | rd.Data['ImageTag'] = rd.repeatcount |
| 570 | | rd.Data['formatName'] = rd.formatName |
| 571 | | if rd.sumfile: |
| 572 | | rd.readfilename = rd.sumfile |
| 573 | | G2IO.LoadImage2Tree(rd.readfilename,self,rd.Comments,rd.Data,rd.Npix,rd.Image) |
| 574 | | rd_list.append(True) # save a stub the result before it is written over |
| 575 | | del rd.Image |
| 576 | | else: |
| 577 | | rd_list.append(copy.deepcopy(rd)) # save the result before it is written over |
| 578 | | if rd.repeat: |
| 579 | | repeat = True |
| 580 | | continue |
| 581 | | errorReport += '\n'+rd.formatName + ' read error' |
| 582 | | if rd.errors: |
| 583 | | errorReport += ': '+rd.errors |
| 584 | | if rd_list: # read succeeded, was there a warning or any errors? |
| 585 | | if rd.warnings: |
| 586 | | self.ErrorDialog('Read Warning','The '+ rd.formatName+ |
| 587 | | ' reader reported a warning message:\n\n'+rd.warnings) |
| 588 | | break # success in reading, try no further |
| 589 | | else: |
| 590 | | if singlereader: |
| 591 | | print('The '+ rd.formatName+' reader was not able to read file '+filename+msg) |
| 592 | | try: |
| 593 | | print('\n\nError message(s):\n\t'+errorReport) |
| 594 | | except: |
| 595 | | pass |
| 596 | | self.ErrorDialog('Read Error','The '+ rd.formatName+ |
| 597 | | ' reader was not able to read file '+filename+msg) |
| 598 | | else: |
| 599 | | print('No reader was able to read file '+filename+msg) |
| 600 | | try: |
| 601 | | print('\n\nError message(s):\n\t'+errorReport) |
| 602 | | except: |
| 603 | | pass |
| 604 | | self.ErrorDialog('Read Error','No reader was able to read file '+filename+msg) |
| 605 | | if fp: fp.close() |
| 606 | | return rd_list |
| 607 | | |
| 608 | | def _Add_ImportMenu_Phase(self,parent): |
| 609 | | '''configure the Import Phase menus accord to the readers found in _init_Imports |
| 610 | | ''' |
| 611 | | submenu = wx.Menu() |
| 612 | | item = parent.AppendMenu(wx.ID_ANY, 'Phase', |
| 613 | | submenu, help='Import phase data') |
| 614 | | for reader in self.ImportPhaseReaderlist: |
| 615 | | item = submenu.Append(wx.ID_ANY,help=reader.longFormatName, |
| 616 | | kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file') |
| 617 | | self.ImportMenuId[item.GetId()] = reader |
| 618 | | self.Bind(wx.EVT_MENU, self.OnImportPhase, id=item.GetId()) |
| 619 | | item = submenu.Append(wx.ID_ANY,help='Import phase data, use file to try to determine format', |
| 620 | | kind=wx.ITEM_NORMAL,text='guess format from file') |
| 621 | | self.Bind(wx.EVT_MENU, self.OnImportPhase, id=item.GetId()) |
| 622 | | |
| 623 | | def OnImportPhase(self,event): |
| 624 | | '''Called in response to an Import/Phase/... menu item |
| 625 | | to read phase information. |
| 626 | | dict self.ImportMenuId is used to look up the specific |
| 627 | | reader item associated with the menu item, which will be |
| 628 | | None for the last menu item, which is the "guess" option |
| 629 | | where all appropriate formats will be tried. |
| 630 | | ''' |
| 631 | | # look up which format was requested |
| 632 | | reqrdr = self.ImportMenuId.get(event.GetId()) |
| 633 | | |
| 634 | | # make a list of phase names, ranId's and the histograms used in those phases |
| 635 | | phaseRIdList,usedHistograms = self.GetPhaseInfofromTree() |
| 636 | | phaseNameList = usedHistograms.keys() # phase names in use |
| 637 | | usedHKLFhists = [] # used single-crystal histograms |
| 638 | | for p in usedHistograms: |
| 639 | | for h in usedHistograms[p]: |
| 640 | | if h.startswith('HKLF ') and h not in usedHKLFhists: |
| 641 | | usedHKLFhists.append(h) |
| 642 | | |
| 643 | | |
| 644 | | rdlist = self.OnImportGeneric(reqrdr,self.ImportPhaseReaderlist, |
| 645 | | 'phase',usedRanIdList=phaseRIdList) |
| 646 | | if len(rdlist) == 0: return |
| 647 | | # for now rdlist is only expected to have one element |
| 648 | | # but below will allow multiple phases to be imported |
| 649 | | # if ever the import routines ever implement multiple phase reads. |
| 650 | | self.CheckNotebook() |
| 651 | | newPhaseList = [] |
| 652 | | for rd in rdlist: |
| 653 | | PhaseName = '' |
| 654 | | dlg = wx.TextEntryDialog(self, 'Enter the name for the new phase', |
| 655 | | 'Edit phase name', rd.Phase['General']['Name'],style=wx.OK) |
| 656 | | while PhaseName == '': |
| 657 | | dlg.CenterOnParent() |
| 658 | | if dlg.ShowModal() == wx.ID_OK: |
| 659 | | PhaseName = dlg.GetValue().strip() |
| 660 | | else: |
| 661 | | dlg.Destroy() |
| 662 | | return |
| 663 | | dlg.Destroy() |
| 664 | | # make new phase names unique |
| 665 | | rd.Phase['General']['Name'] = G2obj.MakeUniqueLabel(PhaseName,phaseNameList) |
| 666 | | PhaseName = rd.Phase['General']['Name'][:] |
| 667 | | newPhaseList.append(PhaseName) |
| 668 | | print(u'Read phase {} from file {}'.format(PhaseName,self.lastimport)) |
| 669 | | if not G2gd.GetPatternTreeItemId(self,self.root,'Phases'): |
| 670 | | sub = self.PatternTree.AppendItem(parent=self.root,text='Phases') |
| 671 | | else: |
| 672 | | sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases') |
| 673 | | psub = self.PatternTree.AppendItem(parent=sub,text=PhaseName) |
| 674 | | self.PatternTree.SetItemPyData(psub,rd.Phase) |
| 675 | | self.PatternTree.Expand(self.root) # make sure phases are seen |
| 676 | | self.PatternTree.Expand(sub) |
| 677 | | self.PatternTree.Expand(psub) |
| 678 | | wx.CallAfter(G2gd.SelectDataTreeItem,self,psub) #bring up new phase General tab |
| 679 | | |
| 680 | | if rd.Constraints: |
| 681 | | sub = G2gd.GetPatternTreeItemId(self,self.root,'Constraints') # was created in CheckNotebook if needed |
| 682 | | Constraints = self.PatternTree.GetItemPyData(sub) |
| 683 | | # TODO: make sure that NEWVAR names are unique here? |
| 684 | | for i in rd.Constraints: |
| 685 | | if type(i) is dict: |
| 686 | | #for j in i: print j,' --> ',i[j] |
| 687 | | if '_Explain' not in Constraints: Constraints['_Explain'] = {} |
| 688 | | Constraints['_Explain'].update(i) |
| 689 | | continue |
| 690 | | Constraints['Phase'].append(i) |
| 691 | | if not newPhaseList: return # somehow, no new phases |
| 692 | | # get a list of existing histograms |
| 693 | | PWDRlist = [] |
| 694 | | HKLFlist = [] |
| 695 | | if self.PatternTree.GetCount(): |
| 696 | | item, cookie = self.PatternTree.GetFirstChild(self.root) |
| 697 | | while item: |
| 698 | | name = self.PatternTree.GetItemText(item) |
| 699 | | if name.startswith('PWDR ') and name not in PWDRlist: |
| 700 | | PWDRlist.append(name) |
| 701 | | if name.startswith('HKLF ') and name not in HKLFlist: |
| 702 | | HKLFlist.append(name) |
| 703 | | item, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 704 | | TextList = PWDRlist + HKLFlist |
| 705 | | if not TextList: |
| 706 | | return #no histograms |
| 707 | | header = 'Select histogram(s) to add to new phase(s):' |
| 708 | | for phaseName in newPhaseList: |
| 709 | | header += '\n '+phaseName |
| 710 | | |
| 711 | | notOK = True |
| 712 | | while notOK: |
| 713 | | result = G2G.ItemSelector(TextList,self,header,header='Add histogram(s)',multiple=True) |
| 714 | | if not result: return |
| 715 | | # check that selected single crystal histograms are not already in use! |
| 716 | | used = [TextList[i] for i in result if TextList[i] in usedHKLFhists] |
| 717 | | #for i in result: |
| 718 | | # if TextList[i] in usedHKLFhists: used.append(TextList[i]) |
| 719 | | if used: |
| 720 | | msg = 'The following single crystal histogram(s) are already in use' |
| 721 | | for i in used: |
| 722 | | msg += '\n '+str(i) |
| 723 | | msg += '\nAre you sure you want to add them to this phase? ' |
| 724 | | msg += 'Associating a single crystal dataset to >1 histogram is usually an error, ' |
| 725 | | msg += 'so No is suggested here.' |
| 726 | | if self.ErrorDialog('Likely error',msg,self,wtype=wx.YES_NO) == wx.ID_YES: notOK = False |
| 727 | | else: |
| 728 | | notOK = False |
| 729 | | # connect new phases to histograms |
| 730 | | sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases') |
| 731 | | if not sub: |
| 732 | | raise Exception('ERROR -- why are there no phases here?') |
| 733 | | wx.BeginBusyCursor() |
| 734 | | item, cookie = self.PatternTree.GetFirstChild(sub) |
| 735 | | while item: # loop over (new) phases |
| 736 | | phaseName = self.PatternTree.GetItemText(item) |
| 737 | | data = self.PatternTree.GetItemPyData(item) |
| 738 | | item, cookie = self.PatternTree.GetNextChild(sub, cookie) |
| 739 | | if phaseName not in newPhaseList: continue |
| 740 | | generalData = data['General'] |
| 741 | | SGData = generalData['SGData'] |
| 742 | | Super = generalData.get('Super',0) |
| 743 | | SuperVec = [] |
| 744 | | if Super: |
| 745 | | SuperVec = np.array(generalData['SuperVec'][0]) |
| 746 | | UseList = data['Histograms'] |
| 747 | | NShkl = len(G2spc.MustrainNames(SGData)) |
| 748 | | NDij = len(G2spc.HStrainNames(SGData)) |
| 749 | | for i in result: |
| 750 | | histoName = TextList[i] |
| 751 | | if histoName in HKLFlist: |
| 752 | | #redo UpdateHKLFdata(histoName) here: |
| 753 | | Id = G2gd.GetPatternTreeItemId(self,self.root,histoName) |
| 754 | | refDict,reflData = self.PatternTree.GetItemPyData(Id) |
| 755 | | G,g = G2lat.cell2Gmat(generalData['Cell'][1:7]) |
| 756 | | Super = reflData.get('Super',0) |
| 757 | | for iref,ref in enumerate(reflData['RefList']): |
| 758 | | hkl = ref[:3] |
| 759 | | if Super: |
| 760 | | H = list(hkl+SuperVec*ref[3]) |
| 761 | | else: |
| 762 | | H = hkl |
| 763 | | ref[4+Super] = np.sqrt(1./G2lat.calc_rDsq2(H,G)) |
| 764 | | iabsnt = G2spc.GenHKLf(H,SGData)[0] |
| 765 | | if iabsnt: #flag space gp. absences |
| 766 | | if Super: |
| 767 | | if not ref[2+Super]: |
| 768 | | ref[3+Super] = 0 |
| 769 | | else: |
| 770 | | ref[3+Super] = 1 #twin id |
| 771 | | else: |
| 772 | | ref[3] = 0 |
| 773 | | UseList[histoName] = SetDefaultDData(reflData['Type'],histoName) |
| 774 | | elif histoName in PWDRlist: |
| 775 | | Id = G2gd.GetPatternTreeItemId(self,self.root,histoName) |
| 776 | | refList = self.PatternTree.GetItemPyData( |
| 777 | | G2gd.GetPatternTreeItemId(self,Id,'Reflection Lists')) |
| 778 | | refList[generalData['Name']] = {} |
| 779 | | UseList[histoName] = SetDefaultDData('PWDR',histoName,NShkl=NShkl,NDij=NDij) |
| 780 | | else: |
| 781 | | raise Exception('Unexpected histogram '+histoName) |
| 782 | | wx.EndBusyCursor() |
| 783 | | self.EnableRefineCommand() |
| 784 | | |
| 785 | | return # success |
| 786 | | |
| 787 | | def _Add_ImportMenu_Image(self,parent): |
| 788 | | '''configure the Import Image menus accord to the readers found in _init_Imports |
| 789 | | ''' |
| 790 | | submenu = wx.Menu() |
| 791 | | item = parent.AppendMenu(wx.ID_ANY, 'Image', |
| 792 | | submenu, help='Import image file') |
| 793 | | for reader in self.ImportImageReaderlist: |
| 794 | | item = submenu.Append(wx.ID_ANY,help=reader.longFormatName, |
| 795 | | kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file') |
| 796 | | self.ImportMenuId[item.GetId()] = reader |
| 797 | | self.Bind(wx.EVT_MENU, self.OnImportImage, id=item.GetId()) |
| 798 | | item = submenu.Append(wx.ID_ANY,help='Import image data, use file to try to determine format', |
| 799 | | kind=wx.ITEM_NORMAL,text='guess format from file') |
| 800 | | self.Bind(wx.EVT_MENU, self.OnImportImage, id=item.GetId()) |
| 801 | | |
| 802 | | def OnImportImage(self,event): |
| 803 | | '''Called in response to an Import/Image/... menu item |
| 804 | | to read an image from a file. Like all the other imports, |
| 805 | | dict self.ImportMenuId is used to look up the specific |
| 806 | | reader item associated with the menu item, which will be |
| 807 | | None for the last menu item, which is the "guess" option |
| 808 | | where all appropriate formats will be tried. |
| 809 | | |
| 810 | | A reader object is filled each time an image is read. |
| 811 | | ''' |
| 812 | | self.CheckNotebook() |
| 813 | | # look up which format was requested |
| 814 | | reqrdr = self.ImportMenuId.get(event.GetId()) |
| 815 | | rdlist = self.OnImportGeneric(reqrdr,self.ImportImageReaderlist, |
| 816 | | 'image',multiple=True,Preview=False,load2Tree=True) |
| 817 | | if rdlist: |
| 818 | | self.PatternTree.SelectItem(G2gd.GetPatternTreeItemId(self,self.Image,'Image Controls')) #show last image to have beeen read |
| 819 | | |
| 820 | | def _Add_ImportMenu_Sfact(self,parent): |
| 821 | | '''configure the Import Structure Factor menus accord to the readers found in _init_Imports |
| 822 | | ''' |
| 823 | | submenu = wx.Menu() |
| 824 | | item = parent.AppendMenu(wx.ID_ANY, 'Structure Factor', |
| 825 | | submenu, help='Import Structure Factor data') |
| 826 | | for reader in self.ImportSfactReaderlist: |
| 827 | | item = submenu.Append(wx.ID_ANY,help=reader.longFormatName, |
| 828 | | kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file') |
| 829 | | self.ImportMenuId[item.GetId()] = reader |
| 830 | | self.Bind(wx.EVT_MENU, self.OnImportSfact, id=item.GetId()) |
| 831 | | item = submenu.Append(wx.ID_ANY, |
| 832 | | help='Import Structure Factor, use file to try to determine format', |
| 833 | | kind=wx.ITEM_NORMAL, |
| 834 | | text='guess format from file') |
| 835 | | self.Bind(wx.EVT_MENU, self.OnImportSfact, id=item.GetId()) |
| 836 | | |
| 837 | | def OnImportSfact(self,event): |
| 838 | | '''Called in response to an Import/Structure Factor/... menu item |
| 839 | | to read single crystal datasets. |
| 840 | | dict self.ImportMenuId is used to look up the specific |
| 841 | | reader item associated with the menu item, which will be |
| 842 | | None for the last menu item, which is the "guess" option |
| 843 | | where all appropriate formats will be tried. |
| 844 | | ''' |
| 845 | | # get a list of existing histograms |
| 846 | | HKLFlist = [] |
| 847 | | if self.PatternTree.GetCount(): |
| 848 | | item, cookie = self.PatternTree.GetFirstChild(self.root) |
| 849 | | while item: |
| 850 | | name = self.PatternTree.GetItemText(item) |
| 851 | | if name.startswith('HKLF ') and name not in HKLFlist: |
| 852 | | HKLFlist.append(name) |
| 853 | | item, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 854 | | # look up which format was requested |
| 855 | | reqrdr = self.ImportMenuId.get(event.GetId()) |
| 856 | | rdlist = self.OnImportGeneric(reqrdr,self.ImportSfactReaderlist, |
| 857 | | 'Structure Factor',multiple=True) |
| 858 | | if len(rdlist) == 0: return |
| 859 | | self.CheckNotebook() |
| 860 | | newHistList = [] |
| 861 | | for rd in rdlist: |
| 862 | | HistName = rd.objname |
| 863 | | if len(rdlist) <= 2: |
| 864 | | dlg = wx.TextEntryDialog( # allow editing of Structure Factor name |
| 865 | | self, 'Enter the name for the new Structure Factor', |
| 866 | | 'Edit Structure Factor name', HistName, |
| 867 | | style=wx.OK) |
| 868 | | dlg.CenterOnParent() |
| 869 | | if dlg.ShowModal() == wx.ID_OK: |
| 870 | | HistName = dlg.GetValue() |
| 871 | | dlg.Destroy() |
| 872 | | HistName = 'HKLF '+G2obj.StripUnicode(HistName,'_') |
| 873 | | # make new histogram names unique |
| 874 | | if len(rd.Banks): |
| 875 | | for Bank in rd.Banks: |
| 876 | | valuesdict = {'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxint),} |
| 877 | | HistName = G2obj.MakeUniqueLabel(HistName,HKLFlist) |
| 878 | | print 'Read structure factor table '+HistName+' from file '+self.lastimport |
| 879 | | Id = self.PatternTree.AppendItem(parent=self.root,text=HistName) |
| 880 | | if not Bank['RefDict'].get('FF'): |
| 881 | | Bank['RefDict']['FF'] = {} |
| 882 | | self.PatternTree.SetItemPyData(Id,[valuesdict,Bank['RefDict']]) |
| 883 | | Sub = self.PatternTree.AppendItem(Id,text='Instrument Parameters') |
| 884 | | self.PatternTree.SetItemPyData(Sub,copy.copy(rd.Parameters)) |
| 885 | | self.PatternTree.SetItemPyData( |
| 886 | | self.PatternTree.AppendItem(Id,text='Reflection List'),{}) #dummy entry for GUI use |
| 887 | | newHistList.append(HistName) |
| 888 | | else: |
| 889 | | valuesdict = {'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxint),} |
| 890 | | HistName = G2obj.MakeUniqueLabel(HistName,HKLFlist) |
| 891 | | print 'Read structure factor table '+HistName+' from file '+self.lastimport |
| 892 | | if not rd.RefDict.get('FF'): |
| 893 | | rd.RefDict['FF'] = {} |
| 894 | | Id = self.PatternTree.AppendItem(parent=self.root,text=HistName) |
| 895 | | self.PatternTree.SetItemPyData(Id,[valuesdict,rd.RefDict]) |
| 896 | | Sub = self.PatternTree.AppendItem(Id,text='Instrument Parameters') |
| 897 | | self.PatternTree.SetItemPyData(Sub,rd.Parameters) |
| 898 | | self.PatternTree.SetItemPyData( |
| 899 | | self.PatternTree.AppendItem(Id,text='Reflection List'),{}) #dummy entry for GUI use |
| 900 | | newHistList.append(HistName) |
| 901 | | |
| 902 | | self.PatternTree.SelectItem(Id) |
| 903 | | self.PatternTree.Expand(Id) |
| 904 | | self.Sngl = True |
| 905 | | |
| 906 | | if not newHistList: return # somehow, no new histograms |
| 907 | | # make a list of phase names |
| 908 | | phaseRIdList,usedHistograms = self.GetPhaseInfofromTree() |
| 909 | | phaseNameList = usedHistograms.keys() # phase names in use |
| 910 | | if not phaseNameList: return # no phases yet, nothing to do |
| 911 | | header = 'Select phase(s) to add the new\nsingle crystal dataset(s) to:' |
| 912 | | for Name in newHistList: |
| 913 | | header += '\n '+str(Name) |
| 914 | | result = G2G.ItemSelector(phaseNameList,self,header,header='Add to phase(s)',multiple=True) |
| 915 | | if not result: return |
| 916 | | # connect new phases to histograms |
| 917 | | sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases') |
| 918 | | if not sub: |
| 919 | | raise Exception('ERROR -- why are there no phases here?') |
| 920 | | wx.BeginBusyCursor() |
| 921 | | item, cookie = self.PatternTree.GetFirstChild(sub) |
| 922 | | iph = -1 |
| 923 | | while item: # loop over (new) phases |
| 924 | | iph += 1 |
| 925 | | data = self.PatternTree.GetItemPyData(item) |
| 926 | | item, cookie = self.PatternTree.GetNextChild(sub, cookie) |
| 927 | | if iph not in result: continue |
| 928 | | generalData = data['General'] |
| 929 | | SGData = generalData['SGData'] |
| 930 | | Super = generalData.get('Super',0) |
| 931 | | SuperVec = [] |
| 932 | | if Super: |
| 933 | | SuperVec = np.array(generalData['SuperVec'][0]) |
| 934 | | UseList = data['Histograms'] |
| 935 | | for histoName in newHistList: |
| 936 | | #redo UpdateHKLFdata(histoName) here: |
| 937 | | Id = G2gd.GetPatternTreeItemId(self,self.root,histoName) |
| 938 | | refDict,reflData = self.PatternTree.GetItemPyData(Id) |
| 939 | | UseList[histoName] = SetDefaultDData(reflData['Type'],histoName) |
| 940 | | G,g = G2lat.cell2Gmat(generalData['Cell'][1:7]) |
| 941 | | if 'TwMax' in reflData: #nonmerohedral twins present |
| 942 | | UseList[histoName]['Twins'] = [] |
| 943 | | for iT in range(reflData['TwMax'][0]+1): |
| 944 | | if iT in reflData['TwMax'][1]: |
| 945 | | UseList[histoName]['Twins'].append([False,0.0]) |
| 946 | | else: |
| 947 | | UseList[histoName]['Twins'].append([np.array([[1,0,0],[0,1,0],[0,0,1]]),[1.0,False,reflData['TwMax'][0]]]) |
| 948 | | else: #no nonmerohedral twins |
| 949 | | UseList[histoName]['Twins'] = [[np.array([[1,0,0],[0,1,0],[0,0,1]]),[1.0,False,0]],] |
| 950 | | for iref,ref in enumerate(reflData['RefList']): |
| 951 | | hkl = ref[:3] |
| 952 | | if Super: |
| 953 | | H = list(hkl+SuperVec*ref[3]) |
| 954 | | else: |
| 955 | | H = hkl |
| 956 | | ref[4+Super] = np.sqrt(1./G2lat.calc_rDsq2(H,G)) |
| 957 | | iabsnt,mul,Uniq,phi = G2spc.GenHKLf(H,SGData) |
| 958 | | if iabsnt: #flag space gp. absences |
| 959 | | if Super: |
| 960 | | if not ref[2+Super]: |
| 961 | | ref[3+Super] = 0 |
| 962 | | else: |
| 963 | | ref[3+Super] = 1 #twin id? |
| 964 | | else: |
| 965 | | ref[3] = 0 |
| 966 | | wx.EndBusyCursor() |
| 967 | | self.EnableRefineCommand() |
| 968 | | return # success |
| 969 | | |
| 970 | | def _Add_ImportMenu_powder(self,parent): |
| 971 | | '''configure the Powder Data menus accord to the readers found in _init_Imports |
| 972 | | ''' |
| 973 | | submenu = wx.Menu() |
| 974 | | item = parent.AppendMenu(wx.ID_ANY, 'Powder Data', |
| 975 | | submenu, help='Import Powder data') |
| 976 | | for reader in self.ImportPowderReaderlist: |
| 977 | | item = submenu.Append(wx.ID_ANY,help=reader.longFormatName, |
| 978 | | kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file') |
| 979 | | self.ImportMenuId[item.GetId()] = reader |
| 980 | | self.Bind(wx.EVT_MENU, self.OnImportPowder, id=item.GetId()) |
| 981 | | item = submenu.Append(wx.ID_ANY, |
| 982 | | help='Import powder data, use file to try to determine format', |
| 983 | | kind=wx.ITEM_NORMAL,text='guess format from file') |
| 984 | | self.Bind(wx.EVT_MENU, self.OnImportPowder, id=item.GetId()) |
| 985 | | submenu.AppendSeparator() |
| 986 | | item = submenu.Append(wx.ID_ANY, |
| 987 | | help='Create a powder data set entry that will be simulated', |
| 988 | | kind=wx.ITEM_NORMAL,text='Simulate a dataset') |
| 989 | | self.Bind(wx.EVT_MENU, self.OnDummyPowder, id=item.GetId()) |
| 990 | | |
| 991 | | def OpenPowderInstprm(self,instfile): |
| 992 | | '''Read a GSAS-II (new) instrument parameter file |
| 993 | | |
| 994 | | :param str instfile: name of instrument parameter file |
| 995 | | |
| 996 | | ''' |
| 997 | | File = open(instfile,'r') |
| 998 | | lines = File.readlines() |
| 999 | | File.close() |
| 1000 | | return lines |
| 1001 | | |
| 1002 | | def ReadPowderInstprm(self,instLines,bank,databanks,rd): |
| 1003 | | '''Read lines from a GSAS-II (new) instrument parameter file |
| 1004 | | similar to G2pwdGUI.OnLoad |
| 1005 | | If instprm file has multiple banks each with header #Bank n: ..., this |
| 1006 | | finds matching bank no. to load - problem with nonmatches? |
| 1007 | | |
| 1008 | | :param list instLines: strings from GSAS-II parameter file; can be concatenated with ';' |
| 1009 | | :param int bank: bank number to check when instprm file has '#BANK n:...' strings |
| 1010 | | when bank = n then use parameters; otherwise skip that set. Ignored if BANK n: |
| 1011 | | not present. NB: this kind of instprm file made by a Save all profile command in Instrument Parameters |
| 1012 | | :return dict: Inst instrument parameter dict if OK, or |
| 1013 | | str: Error message if failed |
| 1014 | | ''' |
| 1015 | | if 'GSAS-II' not in instLines[0]: # not a valid file |
| 1016 | | return 'Not a valid GSAS-II instprm file' |
| 1017 | | newItems = [] |
| 1018 | | newVals = [] |
| 1019 | | Found = False |
| 1020 | | il = 0 |
| 1021 | | if bank is None: # no bank was specified in the input file, is more than one present in file? |
| 1022 | | banklist = set([]) |
| 1023 | | for S in instLines: |
| 1024 | | if S[0] == '#' and 'Bank' in S: |
| 1025 | | banklist.add(int(S.split(':')[0].split()[1])) |
| 1026 | | if len(banklist) > 1: # yes, the user must make a selection |
| 1027 | | choices = [str(i) for i in banklist] |
| 1028 | | bank = int(G2G.ItemSelector(choices,self.G2frame,multiple=False)) |
| 1029 | | else: |
| 1030 | | bank = 1 |
| 1031 | | rd.powderentry[2] = bank |
| 1032 | | while il < len(instLines): |
| 1033 | | S = instLines[il] |
| 1034 | | if S[0] == '#': |
| 1035 | | if Found: |
| 1036 | | break |
| 1037 | | if 'Bank' in S: |
| 1038 | | if bank == int(S.split(':')[0].split()[1]): |
| 1039 | | il += 1 |
| 1040 | | S = instLines[il] |
| 1041 | | else: |
| 1042 | | il += 1 |
| 1043 | | S = instLines[il] |
| 1044 | | while il < len(instLines) and '#Bank' not in S: |
| 1045 | | il += 1 |
| 1046 | | if il == len(instLines): |
| 1047 | | return 'Bank %d not found in instprm file'%(bank) |
| 1048 | | S = instLines[il] |
| 1049 | | continue |
| 1050 | | else: #a non #Bank file |
| 1051 | | il += 1 |
| 1052 | | S = instLines[il] |
| 1053 | | Found = True |
| 1054 | | if '"""' in S: |
| 1055 | | delim = '"""' |
| 1056 | | elif "'''" in S: |
| 1057 | | delim = "'''" |
| 1058 | | else: |
| 1059 | | S = S.replace(' ','') |
| 1060 | | SS = S.strip().split(';') |
| 1061 | | for s in SS: |
| 1062 | | [item,val] = s.split(':',1) |
| 1063 | | newItems.append(item) |
| 1064 | | try: |
| 1065 | | newVals.append(float(val)) |
| 1066 | | except ValueError: |
| 1067 | | newVals.append(val) |
| 1068 | | il += 1 |
| 1069 | | continue |
| 1070 | | # read multiline values, delimited by ''' or """ |
| 1071 | | item,val = S.strip().split(':',1) |
| 1072 | | val = val.replace(delim,'').rstrip() |
| 1073 | | val += '\n' |
| 1074 | | while True: |
| 1075 | | il += 1 |
| 1076 | | if il >= len(instLines): break |
| 1077 | | S = instLines[il] |
| 1078 | | if delim in S: |
| 1079 | | val += S.replace(delim,'').rstrip() |
| 1080 | | val += '\n' |
| 1081 | | break |
| 1082 | | else: |
| 1083 | | val += S.rstrip() |
| 1084 | | val += '\n' |
| 1085 | | newItems.append(item) |
| 1086 | | newVals.append(val) |
| 1087 | | il += 1 |
| 1088 | | return [G2IO.makeInstDict(newItems,newVals,len(newVals)*[False,]),{}] |
| 1089 | | |
| 1090 | | def ReadPowderIparm(self,instfile,bank,databanks,rd): |
| 1091 | | '''Read a GSAS (old) instrument parameter file |
| 1092 | | |
| 1093 | | :param str instfile: name of instrument parameter file |
| 1094 | | :param int bank: the bank number read in the raw data file |
| 1095 | | :param int databanks: the number of banks in the raw data file. |
| 1096 | | If the number of banks in the data and instrument parameter files |
| 1097 | | agree, then the sets of banks are assumed to match up and bank |
| 1098 | | is used to select the instrument parameter file. If not and not TOF, |
| 1099 | | the user is asked to make a selection. |
| 1100 | | :param obj rd: the raw data (histogram) data object. This |
| 1101 | | sets rd.instbank. |
| 1102 | | |
| 1103 | | ''' |
| 1104 | | if not os.path.exists(instfile): # no such file |
| 1105 | | return {} |
| 1106 | | fp = 0 |
| 1107 | | try: |
| 1108 | | fp = open(instfile,'Ur') |
| 1109 | | Iparm = {} |
| 1110 | | for S in fp: |
| 1111 | | if '#' in S[0]: |
| 1112 | | continue |
| 1113 | | Iparm[S[:12]] = S[12:-1] |
| 1114 | | except IOError: |
| 1115 | | print(u'Error reading file: {}'.format(instfile)) |
| 1116 | | if fp: |
| 1117 | | fp.close() |
| 1118 | | |
| 1119 | | ibanks = int(Iparm.get('INS BANK ','1').strip()) |
| 1120 | | if ibanks == 1: # there is only one bank here, return it |
| 1121 | | rd.instbank = 1 |
| 1122 | | rd.powderentry[2] = 1 |
| 1123 | | return Iparm |
| 1124 | | if 'PNT' in Iparm['INS HTYPE ']: #allow mismatch between banks in data iparm file for TOF |
| 1125 | | rd.instbank = bank |
| 1126 | | elif ibanks != databanks or bank is None: |
| 1127 | | choices = [] |
| 1128 | | for i in range(1,1+ibanks): |
| 1129 | | choices.append('Bank '+str(i)) |
| 1130 | | bank = 1 + G2IO.BlockSelector( |
| 1131 | | choices, self, |
| 1132 | | title='Select an instrument parameter bank for '+ |
| 1133 | | os.path.split(rd.powderentry[0])[1]+' BANK '+str(bank)+ |
| 1134 | | '\nOr use Cancel to select from the default parameter sets', |
| 1135 | | header='Block Selector') |
| 1136 | | if bank is None: return {} |
| 1137 | | # pull out requested bank # bank from the data, and change the bank to 1 |
| 1138 | | IparmS = {} |
| 1139 | | for key in Iparm: |
| 1140 | | if 'INS' in key[:3]: #skip around rubbish lines in some old iparm files |
| 1141 | | if key[4:6] == " ": |
| 1142 | | IparmS[key] = Iparm[key] |
| 1143 | | elif int(key[4:6].strip()) == bank: |
| 1144 | | IparmS[key[:4]+' 1'+key[6:]] = Iparm[key] |
| 1145 | | rd.instbank = bank |
| 1146 | | return IparmS |
| 1147 | | |
| 1148 | | def GetPowderIparm(self,rd, prevIparm, lastIparmfile, lastdatafile): |
| 1149 | | '''Open and read an instrument parameter file for a data file |
| 1150 | | Returns the list of parameters used in the data tree |
| 1151 | | |
| 1152 | | :param obj rd: the raw data (histogram) data object. |
| 1153 | | |
| 1154 | | :param str prevIparm: not used |
| 1155 | | |
| 1156 | | :param str lastIparmfile: Name of last instrument parameter |
| 1157 | | file that was read, or a empty string. |
| 1158 | | |
| 1159 | | :param str lastdatafile: Name of last data file that was read. |
| 1160 | | |
| 1161 | | :returns: a list of two dicts, the first containing instrument parameters |
| 1162 | | and the second used for TOF lookup tables for profile coeff. |
| 1163 | | |
| 1164 | | ''' |
| 1165 | | def SetPowderInstParms(Iparm, rd): |
| 1166 | | '''extracts values from instrument parameters in rd.instdict |
| 1167 | | or in array Iparm. |
| 1168 | | Create and return the contents of the instrument parameter tree entry. |
| 1169 | | ''' |
| 1170 | | Irads = {0:' ',1:'CrKa',2:'FeKa',3:'CuKa',4:'MoKa',5:'AgKa',6:'TiKa',7:'CoKa'} |
| 1171 | | DataType = Iparm['INS HTYPE '].strip()[:3] # take 1st 3 chars |
| 1172 | | # override inst values with values read from data file |
| 1173 | | Bank = rd.powderentry[2] #should be used in multibank iparm files |
| 1174 | | if rd.instdict.get('type'): |
| 1175 | | DataType = rd.instdict.get('type') |
| 1176 | | data = [DataType,] |
| 1177 | | instname = Iparm.get('INS 1INAME ') |
| 1178 | | irad = int(Iparm.get('INS 1 IRAD ','0')) |
| 1179 | | if instname: |
| 1180 | | rd.Sample['InstrName'] = instname.strip() |
| 1181 | | if 'C' in DataType: |
| 1182 | | wave1 = None |
| 1183 | | wave2 = 0.0 |
| 1184 | | if rd.instdict.get('wave'): |
| 1185 | | wl = rd.instdict.get('wave') |
| 1186 | | wave1 = wl[0] |
| 1187 | | if len(wl) > 1: wave2 = wl[1] |
| 1188 | | s = Iparm['INS 1 ICONS'] |
| 1189 | | if not wave1: |
| 1190 | | wave1 = G2IO.sfloat(s[:10]) |
| 1191 | | wave2 = G2IO.sfloat(s[10:20]) |
| 1192 | | v = (wave1,wave2, |
| 1193 | | G2IO.sfloat(s[20:30])/100.,G2IO.sfloat(s[55:65]),G2IO.sfloat(s[40:50])) #get lam1, lam2, zero, pola & ratio |
| 1194 | | if not v[1]: |
| 1195 | | names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth'] |
| 1196 | | v = (v[0],v[2],v[4]) |
| 1197 | | codes = [0,0,0,0] |
| 1198 | | rd.Sample.update({'Type':'Debye-Scherrer','Absorption':[0.,False],'DisplaceX':[0.,False],'DisplaceY':[0.,False]}) |
| 1199 | | else: |
| 1200 | | names = ['Type','Lam1','Lam2','Zero','I(L2)/I(L1)','Polariz.','U','V','W','X','Y','SH/L','Azimuth'] |
| 1201 | | codes = [0,0,0,0,0,0] |
| 1202 | | rd.Sample.update({'Type':'Bragg-Brentano','Shift':[0.,False],'Transparency':[0.,False], |
| 1203 | | 'SurfRoughA':[0.,False],'SurfRoughB':[0.,False]}) |
| 1204 | | data.extend(v) |
| 1205 | | if 'INS 1PRCF ' in Iparm: |
| 1206 | | v1 = Iparm['INS 1PRCF '].split() |
| 1207 | | v = Iparm['INS 1PRCF 1'].split() |
| 1208 | | data.extend([float(v[0]),float(v[1]),float(v[2])]) #get GU, GV & GW - always here |
| 1209 | | azm = float(Iparm.get('INS 1DETAZM','0.0')) |
| 1210 | | v = Iparm['INS 1PRCF 2'].split() |
| 1211 | | if v1[0] == 3: |
| 1212 | | data.extend([float(v[0]),float(v[1]),float(v[2])+float(v[3],azm)]) #get LX, LY, S+H/L & azimuth |
| 1213 | | else: |
| 1214 | | data.extend([0.0,0.0,0.002,azm]) #OK defaults if fxn #3 not 1st in iprm file |
| 1215 | | else: |
| 1216 | | v1 = Iparm['INS 1PRCF1 '].split() |
| 1217 | | v = Iparm['INS 1PRCF11'].split() |
| 1218 | | data.extend([float(v[0]),float(v[1]),float(v[2])]) #get GU, GV & GW - always here |
| 1219 | | azm = float(Iparm.get('INS 1DETAZM','0.0')) |
| 1220 | | v = Iparm['INS 1PRCF12'].split() |
| 1221 | | if v1[0] == 3: |
| 1222 | | data.extend([float(v[0]),float(v[1]),float(v[2])+float(v[3],azm)]) #get LX, LY, S+H/L & azimuth |
| 1223 | | else: |
| 1224 | | data.extend([0.0,0.0,0.002,azm]) #OK defaults if fxn #3 not 1st in iprm file |
| 1225 | | codes.extend([0,0,0,0,0,0,0]) |
| 1226 | | Iparm1 = G2IO.makeInstDict(names,data,codes) |
| 1227 | | Iparm1['Source'] = [Irads[irad],Irads[irad]] |
| 1228 | | Iparm1['Bank'] = [Bank,Bank,0] |
| 1229 | | return [Iparm1,{}] |
| 1230 | | elif 'T' in DataType: |
| 1231 | | names = ['Type','fltPath','2-theta','difC','difA', 'difB','Zero','alpha','beta-0','beta-1', |
| 1232 | | 'beta-q','sig-0','sig-1','sig-2','sig-q', 'X','Y','Azimuth',] |
| 1233 | | codes = [0,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0, 0,0,0,] |
| 1234 | | azm = 0. |
| 1235 | | if 'INS 1DETAZM' in Iparm: |
| 1236 | | azm = float(Iparm['INS 1DETAZM']) |
| 1237 | | rd.Sample['Azimuth'] = azm |
| 1238 | | fltPath0 = 20. #arbitrary |
| 1239 | | if 'INS FPATH1' in Iparm: |
| 1240 | | s = Iparm['INS FPATH1'].split() |
| 1241 | | fltPath0 = G2IO.sfloat(s[0]) |
| 1242 | | if 'INS 1BNKPAR' not in Iparm: #bank missing from Iparm file |
| 1243 | | return [] |
| 1244 | | s = Iparm['INS 1BNKPAR'].split() |
| 1245 | | fltPath1 = G2IO.sfloat(s[0]) |
| 1246 | | data.extend([fltPath0+fltPath1,]) #Flight path source-sample-detector |
| 1247 | | data.extend([G2IO.sfloat(s[1]),]) #2-theta for bank |
| 1248 | | s = Iparm['INS 1 ICONS'].split() |
| 1249 | | data.extend([G2IO.sfloat(s[0]),G2IO.sfloat(s[1]),0.0,G2IO.sfloat(s[2])]) #difC,difA,difB,Zero |
| 1250 | | if 'INS 1PRCF ' in Iparm: |
| 1251 | | s = Iparm['INS 1PRCF '].split() |
| 1252 | | pfType = int(s[0]) |
| 1253 | | s = Iparm['INS 1PRCF 1'].split() |
| 1254 | | if abs(pfType) == 1: |
| 1255 | | data.extend([G2IO.sfloat(s[1]),G2IO.sfloat(s[2]),G2IO.sfloat(s[3])]) #alpha, beta-0, beta-1 |
| 1256 | | s = Iparm['INS 1PRCF 2'].split() |
| 1257 | | data.extend([0.0,0.0,G2IO.sfloat(s[1]),G2IO.sfloat(s[2]),0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y |
| 1258 | | elif abs(pfType) in [3,4,5]: |
| 1259 | | data.extend([G2IO.sfloat(s[0]),G2IO.sfloat(s[1]),G2IO.sfloat(s[2])]) #alpha, beta-0, beta-1 |
| 1260 | | if abs(pfType) == 4: |
| 1261 | | data.extend([0.0,0.0,G2IO.sfloat(s[3]),0.0,0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y |
| 1262 | | else: |
| 1263 | | s = Iparm['INS 1PRCF 2'].split() |
| 1264 | | data.extend([0.0,0.0,G2IO.sfloat(s[0]),G2IO.sfloat(s[1]),0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y |
| 1265 | | elif abs(pfType) == 2: |
| 1266 | | data.extend([G2IO.sfloat(s[1]),0.0,1./G2IO.sfloat(s[3])]) #alpha, beta-0, beta-1 |
| 1267 | | data.extend([0.0,0.0,G2IO.sfloat(s[1]),0.0,0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y |
| 1268 | | else: |
| 1269 | | s = Iparm['INS 1PRCF1 '].split() |
| 1270 | | pfType = int(s[0]) |
| 1271 | | s = Iparm['INS 1PRCF11'].split() |
| 1272 | | if abs(pfType) == 1: |
| 1273 | | data.extend([G2IO.sfloat(s[1]),G2IO.sfloat(s[2]),G2IO.sfloat(s[3])]) #alpha, beta-0, beta-1 |
| 1274 | | s = Iparm['INS 1PRCF12'].split() |
| 1275 | | data.extend([0.0,0.0,G2IO.sfloat(s[1]),G2IO.sfloat(s[2]),0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y |
| 1276 | | elif abs(pfType) in [3,4,5]: |
| 1277 | | data.extend([G2IO.sfloat(s[0]),G2IO.sfloat(s[1]),G2IO.sfloat(s[2])]) #alpha, beta-0, beta-1 |
| 1278 | | if abs(pfType) == 4: |
| 1279 | | data.extend([0.0,0.0,G2IO.sfloat(s[3]),0.0,0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y |
| 1280 | | else: |
| 1281 | | s = Iparm['INS 1PRCF12'].split() |
| 1282 | | data.extend([0.0,0.0,G2IO.sfloat(s[0]),G2IO.sfloat(s[1]),0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y |
| 1283 | | Inst1 = G2IO.makeInstDict(names,data,codes) |
| 1284 | | Inst1['Bank'] = [Bank,Bank,0] |
| 1285 | | Inst2 = {} |
| 1286 | | if pfType < 0: |
| 1287 | | Ipab = 'INS 1PAB'+str(-pfType) |
| 1288 | | Npab = int(Iparm[Ipab+' '].strip()) |
| 1289 | | Inst2['Pdabc'] = [] |
| 1290 | | for i in range(Npab): |
| 1291 | | k = Ipab+str(i+1).rjust(2) |
| 1292 | | s = Iparm[k].split() |
| 1293 | | Inst2['Pdabc'].append([float(t) for t in s]) |
| 1294 | | Inst2['Pdabc'] = np.array(Inst2['Pdabc']) |
| 1295 | | Inst2['Pdabc'].T[3] += Inst2['Pdabc'].T[0]*Inst1['difC'][0] #turn 3rd col into TOF |
| 1296 | | if 'INS 1I ITYP' in Iparm: |
| 1297 | | s = Iparm['INS 1I ITYP'].split() |
| 1298 | | Ityp = int(s[0]) |
| 1299 | | Tminmax = [float(s[1])*1000.,float(s[2])*1000.] |
| 1300 | | Itypes = ['Exponential','Maxwell/Exponential','','Maxwell/Chebyschev',''] |
| 1301 | | if Ityp in [1,2,4]: |
| 1302 | | Inst2['Itype'] = Itypes[Ityp-1] |
| 1303 | | Inst2['Tminmax'] = Tminmax |
| 1304 | | Icoeff = [] |
| 1305 | | Iesd = [] |
| 1306 | | Icovar = [] |
| 1307 | | for i in range(3): |
| 1308 | | s = Iparm['INS 1ICOFF'+str(i+1)].split() |
| 1309 | | Icoeff += [float(S) for S in s] |
| 1310 | | s = Iparm['INS 1IECOF'+str(i+1)].split() |
| 1311 | | Iesd += [float(S) for S in s] |
| 1312 | | NT = 10 |
| 1313 | | for i in range(8): |
| 1314 | | s = Iparm['INS 1IECOR'+str(i+1)] |
| 1315 | | if i == 7: |
| 1316 | | NT = 8 |
| 1317 | | Icovar += [float(s[6*j:6*j+6]) for j in range(NT)] |
| 1318 | | Inst2['Icoeff'] = Icoeff |
| 1319 | | Inst2['Iesd'] = Iesd |
| 1320 | | Inst2['Icovar'] = Icovar |
| 1321 | | return [Inst1,Inst2] |
| 1322 | | |
| 1323 | | def GetDefaultParms(self,rd): |
| 1324 | | '''Solicits from user a default set of parameters & returns Inst parm dict |
| 1325 | | param: self: refers to the GSASII main class |
| 1326 | | param: rd: importer data structure |
| 1327 | | returns: dict: Instrument parameter dictionary |
| 1328 | | ''' |
| 1329 | | sind = lambda x: math.sin(x*math.pi/180.) |
| 1330 | | tand = lambda x: math.tan(x*math.pi/180.) |
| 1331 | | import defaultIparms as dI |
| 1332 | | while True: # loop until we get a choice |
| 1333 | | choices = [] |
| 1334 | | head = 'Select from default instrument parameters for '+rd.idstring |
| 1335 | | |
| 1336 | | for l in dI.defaultIparm_lbl: |
| 1337 | | choices.append('Defaults for '+l) |
| 1338 | | res = G2IO.BlockSelector(choices,ParentFrame=self,title=head, |
| 1339 | | header='Select default inst parms',useCancel=True) |
| 1340 | | if res is None: return None |
| 1341 | | rd.instfile = '' |
| 1342 | | if 'lab data' in choices[res]: |
| 1343 | | rd.Sample.update({'Type':'Bragg-Brentano','Shift':[0.,False],'Transparency':[0.,False], |
| 1344 | | 'SurfRoughA':[0.,False],'SurfRoughB':[0.,False]}) |
| 1345 | | else: |
| 1346 | | rd.Sample.update({'Type':'Debye-Scherrer','Absorption':[0.,False],'DisplaceX':[0.,False], |
| 1347 | | 'DisplaceY':[0.,False]}) |
| 1348 | | if 'Generic' in choices[res]: |
| 1349 | | dlg = G2G.MultiFloatDialog(self,title='Generic TOF detector bank', |
| 1350 | | prompts=['Total FP','2-theta',],values=[25.0,150.,], |
| 1351 | | limits=[[6.,200.],[5.,175.],],formats=['%6.2f','%6.1f',]) |
| 1352 | | if dlg.ShowModal() == wx.ID_OK: #strictly empirical approx. |
| 1353 | | FP,tth = dlg.GetValues() |
| 1354 | | difC = 505.632*FP*sind(tth/2.) |
| 1355 | | sig1 = 50.+2.5e-6*(difC/tand(tth/2.))**2 |
| 1356 | | bet1 = .00226+7.76e+11/difC**4 |
| 1357 | | rd.instmsg = 'default: '+dI.defaultIparm_lbl[res] |
| 1358 | | Inst = self.ReadPowderInstprm(dI.defaultIparms[res],bank,numbanks,rd) |
| 1359 | | Inst[0]['difC'] = [difC,difC,0] |
| 1360 | | Inst[0]['sig-1'] = [sig1,sig1,0] |
| 1361 | | Inst[0]['beta-1'] = [bet1,bet1,0] |
| 1362 | | return Inst #this is [Inst1,Inst2] a pair of dicts |
| 1363 | | dlg.Destroy() |
| 1364 | | else: |
| 1365 | | rd.instmsg = 'default: '+dI.defaultIparm_lbl[res] |
| 1366 | | return self.ReadPowderInstprm(dI.defaultIparms[res],bank,numbanks,rd) #this is [Inst1,Inst2] a pair of dicts |
| 1367 | | |
| 1368 | | # stuff we might need from the reader |
| 1369 | | filename = rd.powderentry[0] |
| 1370 | | bank = rd.powderentry[2] |
| 1371 | | numbanks = rd.numbanks |
| 1372 | | #1st priority: is there an instrument parameter file matching the current file |
| 1373 | | # with extension .instprm, .prm, .inst, or .ins? If so read it |
| 1374 | | basename = os.path.splitext(filename)[0] |
| 1375 | | for ext in '.prm','.inst','.ins','.instprm': |
| 1376 | | if self.zipfile: |
| 1377 | | instfile = G2IO.ExtractFileFromZip(self.zipfile, |
| 1378 | | selection=os.path.split(basename + ext)[1],parent=self) |
| 1379 | | if instfile == None: |
| 1380 | | continue |
| 1381 | | else: |
| 1382 | | instfile = basename + ext |
| 1383 | | if not os.path.exists(instfile): |
| 1384 | | continue |
| 1385 | | if 'instprm' in instfile: |
| 1386 | | Lines = self.OpenPowderInstprm(instfile) |
| 1387 | | instParmList = self.ReadPowderInstprm(Lines,bank,numbanks,rd) #this is [Inst1,Inst2] a pair of dicts |
| 1388 | | if 'list' in str(type(instParmList)): |
| 1389 | | rd.instfile = instfile |
| 1390 | | rd.instmsg = 'GSAS-II file '+instfile |
| 1391 | | return instParmList |
| 1392 | | else: |
| 1393 | | #print 'debug: open/read failed',instfile |
| 1394 | | pass # fail silently |
| 1395 | | else: |
| 1396 | | Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd) |
| 1397 | | if Iparm: |
| 1398 | | #print 'debug: success' |
| 1399 | | rd.instfile = instfile |
| 1400 | | rd.instmsg = instfile + ' bank ' + str(rd.instbank) |
| 1401 | | return SetPowderInstParms(Iparm,rd) |
| 1402 | | else: |
| 1403 | | #print 'debug: open/read failed',instfile |
| 1404 | | pass # fail silently |
| 1405 | | |
| 1406 | | #2nd priority: is there an instrument parameter file defined for the current data set? |
| 1407 | | # or if this is a read on a set of set of files, use the last one again |
| 1408 | | #if rd.instparm as found in data file header or (lastdatafile == filename and lastIparmfile): |
| 1409 | | if rd.instparm or lastIparmfile: |
| 1410 | | if rd.instparm: |
| 1411 | | instfile = os.path.join(os.path.split(filename)[0],rd.instparm) |
| 1412 | | else: |
| 1413 | | # for multiple reads of one data file, reuse the inst parm file |
| 1414 | | instfile = lastIparmfile |
| 1415 | | # if self.zipfile: |
| 1416 | | # instfile = G2IO.ExtractFileFromZip(self.zipfile, |
| 1417 | | # selection=os.path.split(instfile)[1],parent=self) |
| 1418 | | if instfile != None and os.path.exists(instfile): |
| 1419 | | #print 'debug: try read',instfile |
| 1420 | | if 'instprm' in instfile: #GSAS-II file must have .instprm as extension |
| 1421 | | Lines = self.OpenPowderInstprm(instfile) |
| 1422 | | if Lines is not None: |
| 1423 | | instParmList = self.ReadPowderInstprm(Lines,bank,numbanks,rd) #this is [Inst1,Inst2] a pair of dicts |
| 1424 | | else: #old GSAS style iparm file - could be named anything! |
| 1425 | | Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd) |
| 1426 | | if Iparm: |
| 1427 | | #print 'debug: success' |
| 1428 | | rd.instfile = instfile |
| 1429 | | rd.instmsg = instfile + ' bank ' + str(rd.instbank) |
| 1430 | | instParmList = SetPowderInstParms(Iparm,rd) #this is [Inst1,Inst2] a pair of dicts |
| 1431 | | if 'list' in str(type(instParmList)): #record stuff & return stuff |
| 1432 | | rd.instfile = instfile |
| 1433 | | rd.instmsg = 'GSAS-II file '+instfile |
| 1434 | | return instParmList |
| 1435 | | else: #bad iparms - try default |
| 1436 | | rd.instmsg = instParmList #an error message |
| 1437 | | return GetDefaultParms(self,rd) |
| 1438 | | else: |
| 1439 | | self.ErrorDialog('Open Error',u'Error opening instrument parameter file ' \ |
| 1440 | | +'{} requested by file '.format(instfile,filename)) |
| 1441 | | #Finally - ask user for Instrument parametrs file - seems it can't be in a zip file |
| 1442 | | while True: # loop until we get a file that works or we get a cancel |
| 1443 | | instfile = '' |
| 1444 | | pth = G2G.GetImportPath(self) |
| 1445 | | if not pth: pth = '.' |
| 1446 | | dlg = wx.FileDialog(self, |
| 1447 | | 'Choose inst. param file for "'+rd.idstring+'" (or Cancel for default)', |
| 1448 | | pth, '', |
| 1449 | | 'GSAS iparm file (*.prm,*.inst,*.ins)|*.prm;*.inst;*.ins|' |
| 1450 | | 'GSAS-II iparm file (*.instprm)|*.instprm|' |
| 1451 | | 'All files (*.*)|*.*', wx.OPEN) |
| 1452 | | if os.path.exists(lastIparmfile): |
| 1453 | | dlg.SetFilename(lastIparmfile) |
| 1454 | | if dlg.ShowModal() == wx.ID_OK: |
| 1455 | | instfile = dlg.GetPath() |
| 1456 | | dlg.Destroy() |
| 1457 | | if not instfile: |
| 1458 | | return GetDefaultParms(self,rd) #on Cancel/break |
| 1459 | | if 'instprm' in instfile: |
| 1460 | | Lines = self.OpenPowderInstprm(instfile) |
| 1461 | | if Lines is not None: |
| 1462 | | instParmList = self.ReadPowderInstprm(Lines,bank,numbanks,rd) #this is [Inst1,Inst2] a pair of dicts |
| 1463 | | if 'list' in str(type(instParmList)): |
| 1464 | | rd.instfile = instfile |
| 1465 | | rd.instmsg = 'GSAS-II file '+instfile |
| 1466 | | return instParmList |
| 1467 | | else: |
| 1468 | | rd.instmsg = instParmList #an error message |
| 1469 | | return GetDefaultParms(self,rd) |
| 1470 | | else: |
| 1471 | | Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd) |
| 1472 | | if Iparm: |
| 1473 | | #print 'debug: success with',instfile |
| 1474 | | rd.instfile = instfile |
| 1475 | | rd.instmsg = instfile + ' bank ' + str(rd.instbank) |
| 1476 | | return SetPowderInstParms(Iparm,rd) |
| 1477 | | else: |
| 1478 | | self.ErrorDialog('Read Error', |
| 1479 | | u'Error opening/reading file {}'.format(instfile)) |
| 1480 | | def EnableRefineCommand(self): |
| 1481 | | haveData = False |
| 1482 | | # check for phases connected to histograms |
| 1483 | | sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases') |
| 1484 | | if not sub: return |
| 1485 | | item, cookie = self.PatternTree.GetFirstChild(sub) |
| 1486 | | while item: # loop over phases |
| 1487 | | data = self.PatternTree.GetItemPyData(item) |
| 1488 | | item, cookie = self.PatternTree.GetNextChild(sub, cookie) |
| 1489 | | UseList = data['Histograms'] |
| 1490 | | if UseList: haveData = True |
| 1491 | | if haveData: |
| 1492 | | self.dataFrame.DataMenu.Enable(G2gd.wxID_DATADELETE,True) |
| 1493 | | for item in self.Refine: item.Enable(True) |
| 1494 | | else: |
| 1495 | | self.dataFrame.DataMenu.Enable(G2gd.wxID_DATADELETE,False) |
| 1496 | | for item in self.Refine: item.Enable(False) |
| 1497 | | |
| 1498 | | |
| 1499 | | def OnImportPowder(self,event): |
| 1500 | | '''Called in response to an Import/Powder Data/... menu item |
| 1501 | | to read a powder diffraction data set. |
| 1502 | | dict self.ImportMenuId is used to look up the specific |
| 1503 | | reader item associated with the menu item, which will be |
| 1504 | | None for the last menu item, which is the "guess" option |
| 1505 | | where all appropriate formats will be tried. |
| 1506 | | |
| 1507 | | Also reads an instrument parameter file for each dataset. |
| 1508 | | ''' |
| 1509 | | # get a list of existing histograms |
| 1510 | | PWDRlist = [] |
| 1511 | | if self.PatternTree.GetCount(): |
| 1512 | | item, cookie = self.PatternTree.GetFirstChild(self.root) |
| 1513 | | while item: |
| 1514 | | name = self.PatternTree.GetItemText(item) |
| 1515 | | if name.startswith('PWDR ') and name not in PWDRlist: |
| 1516 | | PWDRlist.append(name) |
| 1517 | | item, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 1518 | | # look up which format was requested |
| 1519 | | reqrdr = self.ImportMenuId.get(event.GetId()) |
| 1520 | | rdlist = self.OnImportGeneric( |
| 1521 | | reqrdr,self.ImportPowderReaderlist,'Powder Data',multiple=True) |
| 1522 | | if len(rdlist) == 0: return |
| 1523 | | self.CheckNotebook() |
| 1524 | | Iparm = None |
| 1525 | | lastIparmfile = '' |
| 1526 | | lastdatafile = '' |
| 1527 | | newHistList = [] |
| 1528 | | # lastVals = [] |
| 1529 | | self.EnablePlot = False |
| 1530 | | for rd in rdlist: |
| 1531 | | if 'Instrument Parameters' in rd.pwdparms: |
| 1532 | | Iparm1,Iparm2 = rd.pwdparms['Instrument Parameters'] |
| 1533 | | else: |
| 1534 | | # get instrument parameters for each dataset, unless already set |
| 1535 | | # if lastIparmfile: # is this histogram like previous? |
| 1536 | | # if lastVals != (rd.powderdata[0].min(),rd.powderdata[0].max(),len(rd.powderdata[0])): |
| 1537 | | # lastIparmfile = '' |
| 1538 | | Iparms = self.GetPowderIparm(rd, Iparm, lastIparmfile, lastdatafile) |
| 1539 | | if not Iparms: #may have bailed out |
| 1540 | | Id = 0 |
| 1541 | | continue |
| 1542 | | Iparm1,Iparm2 = Iparms |
| 1543 | | if rd.repeat_instparm: |
| 1544 | | lastIparmfile = rd.instfile |
| 1545 | | # lastVals = (rd.powderdata[0].min(),rd.powderdata[0].max(),len(rd.powderdata[0])) |
| 1546 | | # override any keys in read instrument parameters with ones set in import |
| 1547 | | for key in Iparm1: |
| 1548 | | if key in rd.instdict: |
| 1549 | | Iparm1[key] = rd.instdict[key] |
| 1550 | | lastdatafile = rd.powderentry[0] |
| 1551 | | HistName = 'PWDR '+G2obj.StripUnicode(rd.idstring,'_') |
| 1552 | | # make new histogram names unique |
| 1553 | | if HistName in PWDRlist: |
| 1554 | | dlg = wx.MessageDialog(self,'Skip %s?'%(HistName),'Duplicate data name',wx.YES_NO) |
| 1555 | | try: |
| 1556 | | if dlg.ShowModal() == wx.ID_YES: |
| 1557 | | Id = 0 |
| 1558 | | continue |
| 1559 | | finally: |
| 1560 | | dlg.Destroy() |
| 1561 | | HistName = G2obj.MakeUniqueLabel(HistName,PWDRlist) |
| 1562 | | print('Read powder data '+HistName+ |
| 1563 | | ' from file '+rd.readfilename + |
| 1564 | | ' (format: '+ rd.formatName + |
| 1565 | | '). Inst parameters from '+rd.instmsg) |
| 1566 | | # data are read, now store them in the tree |
| 1567 | | Id = self.PatternTree.AppendItem(parent=self.root,text=HistName) |
| 1568 | | if 'T' in Iparm1['Type'][0]: |
| 1569 | | if not rd.clockWd and rd.GSAS: |
| 1570 | | rd.powderdata[0] *= 100. #put back the CW centideg correction |
| 1571 | | cw = np.diff(rd.powderdata[0]) |
| 1572 | | rd.powderdata[0] = rd.powderdata[0][:-1]+cw/2. |
| 1573 | | if rd.GSAS: #NB: old GSAS wanted intensities*CW even if normalized! |
| 1574 | | npts = min(len(rd.powderdata[0]),len(rd.powderdata[1]),len(cw)) |
| 1575 | | rd.powderdata[1] = rd.powderdata[1][:npts]/cw[:npts] |
| 1576 | | rd.powderdata[2] = rd.powderdata[2][:npts]*cw[:npts]**2 #1/var=w at this point |
| 1577 | | else: #NB: from topas/fullprof type files |
| 1578 | | rd.powderdata[1] = rd.powderdata[1][:-1] |
| 1579 | | rd.powderdata[2] = rd.powderdata[2][:-1] |
| 1580 | | if 'Itype' in Iparm2: |
| 1581 | | Ibeg = np.searchsorted(rd.powderdata[0],Iparm2['Tminmax'][0]) |
| 1582 | | Ifin = np.searchsorted(rd.powderdata[0],Iparm2['Tminmax'][1]) |
| 1583 | | rd.powderdata[0] = rd.powderdata[0][Ibeg:Ifin] |
| 1584 | | YI,WYI = G2pwd.calcIncident(Iparm2,rd.powderdata[0]) |
| 1585 | | rd.powderdata[1] = rd.powderdata[1][Ibeg:Ifin]/YI |
| 1586 | | var = 1./rd.powderdata[2][Ibeg:Ifin] |
| 1587 | | var += WYI*rd.powderdata[1]**2 |
| 1588 | | var /= YI**2 |
| 1589 | | rd.powderdata[2] = 1./var |
| 1590 | | rd.powderdata[3] = np.zeros_like(rd.powderdata[0]) |
| 1591 | | rd.powderdata[4] = np.zeros_like(rd.powderdata[0]) |
| 1592 | | rd.powderdata[5] = np.zeros_like(rd.powderdata[0]) |
| 1593 | | Ymin = np.min(rd.powderdata[1]) |
| 1594 | | Ymax = np.max(rd.powderdata[1]) |
| 1595 | | valuesdict = { |
| 1596 | | 'wtFactor':1.0, |
| 1597 | | 'Dummy':False, |
| 1598 | | 'ranId':ran.randint(0,sys.maxint), |
| 1599 | | 'Offset':[0.0,0.0],'delOffset':0.02*Ymax,'refOffset':-.1*Ymax,'refDelt':0.1*Ymax, |
| 1600 | | 'qPlot':False,'dPlot':False,'sqrtPlot':False,'Yminmax':[Ymin,Ymax] |
| 1601 | | } |
| 1602 | | # apply user-supplied corrections to powder data |
| 1603 | | if 'CorrectionCode' in Iparm1: |
| 1604 | | print('Applying corrections from instprm file') |
| 1605 | | corr = Iparm1['CorrectionCode'][0] |
| 1606 | | try: |
| 1607 | | exec(corr) |
| 1608 | | print('done') |
| 1609 | | except Exception as err: |
| 1610 | | print(u'error: {}'.format(err)) |
| 1611 | | print('with commands -------------------') |
| 1612 | | print(corr) |
| 1613 | | print('---------------------------------') |
| 1614 | | finally: |
| 1615 | | del Iparm1['CorrectionCode'] |
| 1616 | | rd.Sample['ranId'] = valuesdict['ranId'] # this should be removed someday |
| 1617 | | self.PatternTree.SetItemPyData(Id,[valuesdict,rd.powderdata]) |
| 1618 | | self.PatternTree.SetItemPyData( |
| 1619 | | self.PatternTree.AppendItem(Id,text='Comments'), |
| 1620 | | rd.comments) |
| 1621 | | Tmin = min(rd.powderdata[0]) |
| 1622 | | Tmax = max(rd.powderdata[0]) |
| 1623 | | Tmin1 = Tmin |
| 1624 | | if 'NT' in Iparm1['Type'][0] and G2lat.Pos2dsp(Iparm1,Tmin) < 0.4: |
| 1625 | | Tmin1 = G2lat.Dsp2pos(Iparm1,0.4) |
| 1626 | | self.PatternTree.SetItemPyData( |
| 1627 | | self.PatternTree.AppendItem(Id,text='Limits'), |
| 1628 | | rd.pwdparms.get('Limits',[(Tmin,Tmax),[Tmin1,Tmax]]) |
| 1629 | | ) |
| 1630 | | self.PatternId = G2gd.GetPatternTreeItemId(self,Id,'Limits') |
| 1631 | | self.PatternTree.SetItemPyData( |
| 1632 | | self.PatternTree.AppendItem(Id,text='Background'), |
| 1633 | | rd.pwdparms.get('Background', |
| 1634 | | [['chebyschev',True,3,1.0,0.0,0.0],{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}]) |
| 1635 | | ) |
| 1636 | | self.PatternTree.SetItemPyData( |
| 1637 | | self.PatternTree.AppendItem(Id,text='Instrument Parameters'), |
| 1638 | | [Iparm1,Iparm2]) |
| 1639 | | self.PatternTree.SetItemPyData( |
| 1640 | | self.PatternTree.AppendItem(Id,text='Sample Parameters'), |
| 1641 | | rd.Sample) |
| 1642 | | self.PatternTree.SetItemPyData( |
| 1643 | | self.PatternTree.AppendItem(Id,text='Peak List') |
| 1644 | | ,{'peaks':[],'sigDict':{}}) |
| 1645 | | self.PatternTree.SetItemPyData( |
| 1646 | | self.PatternTree.AppendItem(Id,text='Index Peak List'), |
| 1647 | | [[],[]]) |
| 1648 | | self.PatternTree.SetItemPyData( |
| 1649 | | self.PatternTree.AppendItem(Id,text='Unit Cells List'), |
| 1650 | | []) |
| 1651 | | self.PatternTree.SetItemPyData( |
| 1652 | | self.PatternTree.AppendItem(Id,text='Reflection Lists'), |
| 1653 | | {}) |
| 1654 | | # if any Control values have been set, move them into tree |
| 1655 | | Controls = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.root, 'Controls')) |
| 1656 | | Controls.update(rd.Controls) |
| 1657 | | newHistList.append(HistName) |
| 1658 | | rd.repeat_instparm = False #clear the iparm reuse flag |
| 1659 | | else: |
| 1660 | | self.EnablePlot = True |
| 1661 | | if Id: |
| 1662 | | self.PatternTree.Expand(Id) |
| 1663 | | self.PatternTree.SelectItem(Id) |
| 1664 | | |
| 1665 | | if not newHistList: return # somehow, no new histograms |
| 1666 | | # make a list of phase names |
| 1667 | | phaseRIdList,usedHistograms = self.GetPhaseInfofromTree() |
| 1668 | | phaseNameList = usedHistograms.keys() # phase names in use |
| 1669 | | if not phaseNameList: return # no phases yet, nothing to do |
| 1670 | | header = 'Select phase(s) to link\nto the newly-read data:' |
| 1671 | | for Name in newHistList: |
| 1672 | | header += '\n '+str(Name) |
| 1673 | | |
| 1674 | | result = G2G.ItemSelector(phaseNameList,self,header,header='Add to phase(s)',multiple=True) |
| 1675 | | if not result: return |
| 1676 | | # connect new phases to histograms |
| 1677 | | sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases') |
| 1678 | | if not sub: |
| 1679 | | raise Exception('ERROR -- why are there no phases here?') |
| 1680 | | item, cookie = self.PatternTree.GetFirstChild(sub) |
| 1681 | | iph = -1 |
| 1682 | | while item: # loop over (new) phases |
| 1683 | | iph += 1 |
| 1684 | | data = self.PatternTree.GetItemPyData(item) |
| 1685 | | item, cookie = self.PatternTree.GetNextChild(sub, cookie) |
| 1686 | | if iph not in result: continue |
| 1687 | | generalData = data['General'] |
| 1688 | | SGData = generalData['SGData'] |
| 1689 | | UseList = data['Histograms'] |
| 1690 | | NShkl = len(G2spc.MustrainNames(SGData)) |
| 1691 | | NDij = len(G2spc.HStrainNames(SGData)) |
| 1692 | | for histoName in newHistList: |
| 1693 | | UseList[histoName] = SetDefaultDData('PWDR',histoName,NShkl=NShkl,NDij=NDij) |
| 1694 | | Id = G2gd.GetPatternTreeItemId(self,self.root,histoName) |
| 1695 | | refList = self.PatternTree.GetItemPyData( |
| 1696 | | G2gd.GetPatternTreeItemId(self,Id,'Reflection Lists')) |
| 1697 | | refList[generalData['Name']] = [] |
| 1698 | | self.EnableRefineCommand() |
| 1699 | | return # success |
| 1700 | | |
| 1701 | | def OnDummyPowder(self,event): |
| 1702 | | '''Called in response to Import/Powder Data/Simulate menu item |
| 1703 | | to create a Dummy powder diffraction data set. |
| 1704 | | |
| 1705 | | Reads an instrument parameter file and then gets input from the user |
| 1706 | | ''' |
| 1707 | | # get a list of existing histograms |
| 1708 | | PWDRlist = [] |
| 1709 | | if self.PatternTree.GetCount(): |
| 1710 | | item, cookie = self.PatternTree.GetFirstChild(self.root) |
| 1711 | | while item: |
| 1712 | | name = self.PatternTree.GetItemText(item) |
| 1713 | | if name.startswith('PWDR ') and name not in PWDRlist: |
| 1714 | | PWDRlist.append(name) |
| 1715 | | item, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 1716 | | # Initialize a base class reader |
| 1717 | | rd = G2obj.ImportPowderData( |
| 1718 | | extensionlist=tuple(), |
| 1719 | | strictExtension=False, |
| 1720 | | formatName = 'Simulate dataset', |
| 1721 | | longFormatName = 'Compute a simulated pattern') |
| 1722 | | rd.powderentry[0] = '' # no filename |
| 1723 | | # #self.powderentry[1] = pos # bank offset (N/A here) |
| 1724 | | rd.powderentry[2] = 1 # only one bank |
| 1725 | | rd.comments.append('This is a dummy dataset for powder pattern simulation') |
| 1726 | | self.CheckNotebook() |
| 1727 | | Iparm = None |
| 1728 | | lastdatafile = '' |
| 1729 | | self.zipfile = None |
| 1730 | | # get instrument parameters for it |
| 1731 | | Iparm1,Iparm2 = self.GetPowderIparm(rd, Iparm, '', lastdatafile) |
| 1732 | | if 'T' in Iparm1['Type'][0]: |
| 1733 | | print('TOF simulation not supported yet') |
| 1734 | | return False |
| 1735 | | else: |
| 1736 | | # need to get name, 2theta start, end, step |
| 1737 | | rd.idstring = ' CW' |
| 1738 | | if 'X' in Iparm1['Type'][0]: |
| 1739 | | rd.idstring = 'CW x-ray simulation' |
| 1740 | | else: |
| 1741 | | rd.idstring = 'CW neutron simulation' |
| 1742 | | # base initial range on wavelength |
| 1743 | | wave = Iparm1.get('Lam') |
| 1744 | | if wave: |
| 1745 | | wave = wave[0] |
| 1746 | | else: |
| 1747 | | wave = Iparm1.get('Lam1') |
| 1748 | | if wave: |
| 1749 | | wave = wave[0] |
| 1750 | | N = 0 |
| 1751 | | while (N < 3): # insist on a dataset with a few points |
| 1752 | | names = ('dataset name', 'start angle', 'end angle', 'step size') |
| 1753 | | if not wave or wave < 1.0: |
| 1754 | | inp = [rd.idstring, 10.,40.,0.005] # see names for what's what |
| 1755 | | else: |
| 1756 | | inp = [rd.idstring, 10.,80.,0.01] # see names for what's what |
| 1757 | | dlg = G2G.ScrolledMultiEditor( |
| 1758 | | self,[inp] * len(inp),range(len(inp)),names, |
| 1759 | | header='Enter simulation name and range', |
| 1760 | | minvals=(None,0.001,0.001,0.0001), |
| 1761 | | maxvals=(None,180.,180.,.1), |
| 1762 | | sizevals=((225,-1),) |
| 1763 | | ) |
| 1764 | | dlg.CenterOnParent() |
| 1765 | | if dlg.ShowModal() == wx.ID_OK: |
| 1766 | | if inp[1] > inp[2]: |
| 1767 | | end,start,step = inp[1:] |
| 1768 | | else: |
| 1769 | | start,end,step = inp[1:] |
| 1770 | | step = abs(step) |
| 1771 | | else: |
| 1772 | | return False |
| 1773 | | N = int((end-start)/step)+1 |
| 1774 | | x = np.linspace(start,end,N,True) |
| 1775 | | N = len(x) |
| 1776 | | rd.powderdata = [ |
| 1777 | | np.array(x), # x-axis values |
| 1778 | | np.zeros_like(x), # powder pattern intensities |
| 1779 | | np.ones_like(x), # 1/sig(intensity)^2 values (weights) |
| 1780 | | np.zeros_like(x), # calc. intensities (zero) |
| 1781 | | np.zeros_like(x), # calc. background (zero) |
| 1782 | | np.zeros_like(x), # obs-calc profiles |
| 1783 | | ] |
| 1784 | | Tmin = rd.powderdata[0][0] |
| 1785 | | Tmax = rd.powderdata[0][-1] |
| 1786 | | # data are read, now store them in the tree |
| 1787 | | HistName = inp[0] |
| 1788 | | HistName = 'PWDR '+HistName |
| 1789 | | HistName = G2obj.MakeUniqueLabel(HistName,PWDRlist) # make new histogram names unique |
| 1790 | | Id = self.PatternTree.AppendItem(parent=self.root,text=HistName) |
| 1791 | | Ymin = np.min(rd.powderdata[1]) |
| 1792 | | Ymax = np.max(rd.powderdata[1]) |
| 1793 | | valuesdict = { |
| 1794 | | 'wtFactor':1.0, |
| 1795 | | 'Dummy':True, |
| 1796 | | 'ranId':ran.randint(0,sys.maxint), |
| 1797 | | 'Offset':[0.0,0.0],'delOffset':0.02*Ymax,'refOffset':-.1*Ymax,'refDelt':0.1*Ymax, |
| 1798 | | 'qPlot':False,'dPlot':False,'sqrtPlot':False,'Yminmax':[Ymin,Ymax] |
| 1799 | | } |
| 1800 | | self.PatternTree.SetItemPyData(Id,[valuesdict,rd.powderdata]) |
| 1801 | | self.PatternTree.SetItemPyData( |
| 1802 | | self.PatternTree.AppendItem(Id,text='Comments'), |
| 1803 | | rd.comments) |
| 1804 | | self.PatternTree.SetItemPyData( |
| 1805 | | self.PatternTree.AppendItem(Id,text='Limits'), |
| 1806 | | [(Tmin,Tmax),[Tmin,Tmax]]) |
| 1807 | | self.PatternId = G2gd.GetPatternTreeItemId(self,Id,'Limits') |
| 1808 | | self.PatternTree.SetItemPyData( |
| 1809 | | self.PatternTree.AppendItem(Id,text='Background'), |
| 1810 | | [['chebyschev',True,3,1.0,0.0,0.0], |
| 1811 | | {'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}]) |
| 1812 | | self.PatternTree.SetItemPyData( |
| 1813 | | self.PatternTree.AppendItem(Id,text='Instrument Parameters'), |
| 1814 | | [Iparm1,Iparm2]) |
| 1815 | | self.PatternTree.SetItemPyData( |
| 1816 | | self.PatternTree.AppendItem(Id,text='Sample Parameters'), |
| 1817 | | rd.Sample) |
| 1818 | | self.PatternTree.SetItemPyData( |
| 1819 | | self.PatternTree.AppendItem(Id,text='Peak List') |
| 1820 | | ,{'peaks':[],'sigDict':{}}) |
| 1821 | | self.PatternTree.SetItemPyData( |
| 1822 | | self.PatternTree.AppendItem(Id,text='Index Peak List'), |
| 1823 | | [[],[]]) |
| 1824 | | self.PatternTree.SetItemPyData( |
| 1825 | | self.PatternTree.AppendItem(Id,text='Unit Cells List'), |
| 1826 | | []) |
| 1827 | | self.PatternTree.SetItemPyData( |
| 1828 | | self.PatternTree.AppendItem(Id,text='Reflection Lists'), |
| 1829 | | {}) |
| 1830 | | self.PatternTree.Expand(Id) |
| 1831 | | self.PatternTree.SelectItem(Id) |
| 1832 | | print(u'Added simulation powder data {}'.format(HistName)+ |
| 1833 | | ' with parameters from {}'.format(rd.instmsg)) |
| 1834 | | |
| 1835 | | # make a list of phase names |
| 1836 | | phaseRIdList,usedHistograms = self.GetPhaseInfofromTree() |
| 1837 | | phaseNameList = usedHistograms.keys() # phase names in use |
| 1838 | | if not phaseNameList: return # no phases yet, nothing to do |
| 1839 | | header = 'Select phase(s) to add the new\npowder simulation (dummy) dataset to:' |
| 1840 | | result = G2G.ItemSelector(phaseNameList,self,header,header='Add to phase(s)',multiple=True) |
| 1841 | | if not result: return |
| 1842 | | # connect new phases to histograms |
| 1843 | | sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases') |
| 1844 | | if not sub: |
| 1845 | | raise Exception('ERROR -- why are there no phases here?') |
| 1846 | | item, cookie = self.PatternTree.GetFirstChild(sub) |
| 1847 | | iph = -1 |
| 1848 | | while item: # loop over (new) phases |
| 1849 | | iph += 1 |
| 1850 | | data = self.PatternTree.GetItemPyData(item) |
| 1851 | | item, cookie = self.PatternTree.GetNextChild(sub, cookie) |
| 1852 | | if iph not in result: continue |
| 1853 | | generalData = data['General'] |
| 1854 | | SGData = generalData['SGData'] |
| 1855 | | UseList = data['Histograms'] |
| 1856 | | NShkl = len(G2spc.MustrainNames(SGData)) |
| 1857 | | NDij = len(G2spc.HStrainNames(SGData)) |
| 1858 | | UseList[HistName] = SetDefaultDData('PWDR',HistName,NShkl=NShkl,NDij=NDij) |
| 1859 | | Id = G2gd.GetPatternTreeItemId(self,self.root,HistName) |
| 1860 | | refList = self.PatternTree.GetItemPyData( |
| 1861 | | G2gd.GetPatternTreeItemId(self,Id,'Reflection Lists')) |
| 1862 | | refList[generalData['Name']] = [] |
| 1863 | | self.EnableRefineCommand() |
| 1864 | | return # success |
| 1865 | | |
| 1866 | | def OnPreferences(self,event): |
| 1867 | | 'Edit the GSAS-II configuration variables' |
| 1868 | | dlg = G2G.SelectConfigSetting(self) |
| 1869 | | dlg.ShowModal() == wx.ID_OK |
| 1870 | | dlg.Destroy() |
| 1871 | | |
| 1872 | | def _Add_ImportMenu_smallangle(self,parent): |
| 1873 | | '''configure the Small Angle Data menus accord to the readers found in _init_Imports |
| 1874 | | ''' |
| 1875 | | submenu = wx.Menu() |
| 1876 | | item = parent.AppendMenu(wx.ID_ANY, 'Small Angle Data', |
| 1877 | | submenu, help='Import small angle data') |
| 1878 | | for reader in self.ImportSmallAngleReaderlist: |
| 1879 | | item = submenu.Append(wx.ID_ANY,help=reader.longFormatName, |
| 1880 | | kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file') |
| 1881 | | self.ImportMenuId[item.GetId()] = reader |
| 1882 | | self.Bind(wx.EVT_MENU, self.OnImportSmallAngle, id=item.GetId()) |
| 1883 | | # item = submenu.Append(wx.ID_ANY, |
| 1884 | | # help='Import small angle data, use file to try to determine format', |
| 1885 | | # kind=wx.ITEM_NORMAL,text='guess format from file') |
| 1886 | | # self.Bind(wx.EVT_MENU, self.OnImportSmallAngle, id=item.GetId()) |
| 1887 | | |
| 1888 | | def OnImportSmallAngle(self,event): |
| 1889 | | '''Called in response to an Import/Small Angle Data/... menu item |
| 1890 | | to read a small angle diffraction data set. |
| 1891 | | dict self.ImportMenuId is used to look up the specific |
| 1892 | | reader item associated with the menu item, which will be |
| 1893 | | None for the last menu item, which is the "guess" option |
| 1894 | | where all appropriate formats will be tried. |
| 1895 | | |
| 1896 | | ''' |
| 1897 | | |
| 1898 | | def GetSASDIparm(reader): |
| 1899 | | parm = reader.instdict |
| 1900 | | Iparm = {'Type':[parm['type'],parm['type'],0],'Lam':[parm['wave'], |
| 1901 | | parm['wave'],0],'Azimuth':[0.,0.,0]} |
| 1902 | | return Iparm,{} |
| 1903 | | |
| 1904 | | # get a list of existing histograms |
| 1905 | | SASDlist = [] |
| 1906 | | if self.PatternTree.GetCount(): |
| 1907 | | item, cookie = self.PatternTree.GetFirstChild(self.root) |
| 1908 | | while item: |
| 1909 | | name = self.PatternTree.GetItemText(item) |
| 1910 | | if name.startswith('SASD ') and name not in SASDlist: |
| 1911 | | SASDlist.append(name) |
| 1912 | | item, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 1913 | | # look up which format was requested |
| 1914 | | reqrdr = self.ImportMenuId.get(event.GetId()) |
| 1915 | | rdlist = self.OnImportGeneric( |
| 1916 | | reqrdr,self.ImportSmallAngleReaderlist,'Small Angle Data',multiple=True) |
| 1917 | | if len(rdlist) == 0: return |
| 1918 | | self.CheckNotebook() |
| 1919 | | newHistList = [] |
| 1920 | | self.EnablePlot = False |
| 1921 | | for rd in rdlist: |
| 1922 | | HistName = rd.idstring |
| 1923 | | HistName = 'SASD '+HistName |
| 1924 | | # make new histogram names unique |
| 1925 | | HistName = G2obj.MakeUniqueLabel(HistName,SASDlist) |
| 1926 | | print 'Read small angle data '+HistName+ \ |
| 1927 | | ' from file '+self.lastimport |
| 1928 | | # data are read, now store them in the tree |
| 1929 | | Id = self.PatternTree.AppendItem(parent=self.root,text=HistName) |
| 1930 | | Iparm1,Iparm2 = GetSASDIparm(rd) |
| 1931 | | # if 'T' in Iparm1['Type'][0]: |
| 1932 | | # if not rd.clockWd and rd.GSAS: |
| 1933 | | # rd.powderdata[0] *= 100. #put back the CW centideg correction |
| 1934 | | # cw = np.diff(rd.powderdata[0]) |
| 1935 | | # rd.powderdata[0] = rd.powderdata[0][:-1]+cw/2. |
| 1936 | | # rd.powderdata[1] = rd.powderdata[1][:-1]/cw |
| 1937 | | # rd.powderdata[2] = rd.powderdata[2][:-1]*cw**2 #1/var=w at this point |
| 1938 | | # if 'Itype' in Iparm2: |
| 1939 | | # Ibeg = np.searchsorted(rd.powderdata[0],Iparm2['Tminmax'][0]) |
| 1940 | | # Ifin = np.searchsorted(rd.powderdata[0],Iparm2['Tminmax'][1]) |
| 1941 | | # rd.powderdata[0] = rd.powderdata[0][Ibeg:Ifin] |
| 1942 | | # YI,WYI = G2pwd.calcIncident(Iparm2,rd.powderdata[0]) |
| 1943 | | # rd.powderdata[1] = rd.powderdata[1][Ibeg:Ifin]/YI |
| 1944 | | # var = 1./rd.powderdata[2][Ibeg:Ifin] |
| 1945 | | # var += WYI*rd.powderdata[1]**2 |
| 1946 | | # var /= YI**2 |
| 1947 | | # rd.powderdata[2] = 1./var |
| 1948 | | # rd.powderdata[3] = np.zeros_like(rd.powderdata[0]) |
| 1949 | | # rd.powderdata[4] = np.zeros_like(rd.powderdata[0]) |
| 1950 | | # rd.powderdata[5] = np.zeros_like(rd.powderdata[0]) |
| 1951 | | Tmin = min(rd.smallangledata[0]) |
| 1952 | | Tmax = max(rd.smallangledata[0]) |
| 1953 | | valuesdict = { |
| 1954 | | 'wtFactor':1.0, |
| 1955 | | 'Dummy':False, |
| 1956 | | 'ranId':ran.randint(0,sys.maxint), |
| 1957 | | 'Offset':[0.0,0.0], |
| 1958 | | } |
| 1959 | | rd.Sample['ranId'] = valuesdict['ranId'] # this should be removed someday |
| 1960 | | self.PatternTree.SetItemPyData(Id,[valuesdict,rd.smallangledata]) |
| 1961 | | self.PatternTree.SetItemPyData( |
| 1962 | | self.PatternTree.AppendItem(Id,text='Comments'), |
| 1963 | | rd.comments) |
| 1964 | | self.PatternTree.SetItemPyData( |
| 1965 | | self.PatternTree.AppendItem(Id,text='Limits'), |
| 1966 | | [(Tmin,Tmax),[Tmin,Tmax]]) |
| 1967 | | self.PatternId = G2gd.GetPatternTreeItemId(self,Id,'Limits') |
| 1968 | | self.PatternTree.SetItemPyData( |
| 1969 | | self.PatternTree.AppendItem(Id,text='Instrument Parameters'), |
| 1970 | | [Iparm1,Iparm2]) |
| 1971 | | self.PatternTree.SetItemPyData( |
| 1972 | | self.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances()) |
| 1973 | | self.PatternTree.SetItemPyData( |
| 1974 | | self.PatternTree.AppendItem(Id,text='Sample Parameters'), |
| 1975 | | rd.Sample) |
| 1976 | | self.PatternTree.SetItemPyData( |
| 1977 | | self.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel()) |
| 1978 | | newHistList.append(HistName) |
| 1979 | | else: |
| 1980 | | self.EnablePlot = True |
| 1981 | | self.PatternTree.Expand(Id) |
| 1982 | | self.PatternTree.SelectItem(Id) |
| 1983 | | |
| 1984 | | if not newHistList: return # somehow, no new histograms |
| 1985 | | return # success |
| 1986 | | |
| 1987 | | def _Add_ImportMenu_reflectometry(self,parent): |
| 1988 | | '''configure the reflectometry Data menus accord to the readers found in _init_Imports |
| 1989 | | ''' |
| 1990 | | submenu = wx.Menu() |
| 1991 | | item = parent.AppendMenu(wx.ID_ANY, 'Reflectometry Data', |
| 1992 | | submenu, help='Import reflectometry data') |
| 1993 | | for reader in self.ImportReflectometryReaderlist: |
| 1994 | | item = submenu.Append(wx.ID_ANY,help=reader.longFormatName, |
| 1995 | | kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file') |
| 1996 | | self.ImportMenuId[item.GetId()] = reader |
| 1997 | | self.Bind(wx.EVT_MENU, self.OnImportReflectometry, id=item.GetId()) |
| 1998 | | # item = submenu.Append(wx.ID_ANY, |
| 1999 | | # help='Import reflectometry data, use file to try to determine format', |
| 2000 | | # kind=wx.ITEM_NORMAL,text='guess format from file') |
| 2001 | | # self.Bind(wx.EVT_MENU, self.OnImportReflectometry, id=item.GetId()) |
| 2002 | | |
| 2003 | | def OnImportReflectometry(self,event): |
| 2004 | | '''Called in response to an Import/Reflectometry Data/... menu item |
| 2005 | | to read a reflectometry data set. |
| 2006 | | dict self.ImportMenuId is used to look up the specific |
| 2007 | | reader item associated with the menu item, which will be |
| 2008 | | None for the last menu item, which is the "guess" option |
| 2009 | | where all appropriate formats will be tried. |
| 2010 | | |
| 2011 | | ''' |
| 2012 | | |
| 2013 | | def GetREFDIparm(reader): |
| 2014 | | parm = reader.instdict |
| 2015 | | Iparm = {'Type':[parm['type'],parm['type'],0],'Lam':[parm['wave'], |
| 2016 | | parm['wave'],0],'Azimuth':[0.,0.,0]} |
| 2017 | | return Iparm,{} |
| 2018 | | |
| 2019 | | # get a list of existing histograms |
| 2020 | | REFDlist = [] |
| 2021 | | if self.PatternTree.GetCount(): |
| 2022 | | item, cookie = self.PatternTree.GetFirstChild(self.root) |
| 2023 | | while item: |
| 2024 | | name = self.PatternTree.GetItemText(item) |
| 2025 | | if name.startswith('REFD ') and name not in REFDlist: |
| 2026 | | REFDlist.append(name) |
| 2027 | | item, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 2028 | | # look up which format was requested |
| 2029 | | reqrdr = self.ImportMenuId.get(event.GetId()) |
| 2030 | | rdlist = self.OnImportGeneric( |
| 2031 | | reqrdr,self.ImportReflectometryReaderlist,'Reflectometry Data',multiple=True) |
| 2032 | | if len(rdlist) == 0: return |
| 2033 | | self.CheckNotebook() |
| 2034 | | newHistList = [] |
| 2035 | | self.EnablePlot = False |
| 2036 | | for rd in rdlist: |
| 2037 | | HistName = rd.idstring |
| 2038 | | HistName = 'REFD '+HistName |
| 2039 | | # make new histogram names unique |
| 2040 | | HistName = G2obj.MakeUniqueLabel(HistName,REFDlist) |
| 2041 | | print 'Read reflectometry data '+HistName+ \ |
| 2042 | | ' from file '+self.lastimport |
| 2043 | | # data are read, now store them in the tree |
| 2044 | | Id = self.PatternTree.AppendItem(parent=self.root,text=HistName) |
| 2045 | | Iparm1,Iparm2 = GetREFDIparm(rd) |
| 2046 | | # if 'T' in Iparm1['Type'][0]: |
| 2047 | | # if not rd.clockWd and rd.GSAS: |
| 2048 | | # rd.powderdata[0] *= 100. #put back the CW centideg correction |
| 2049 | | # cw = np.diff(rd.powderdata[0]) |
| 2050 | | # rd.powderdata[0] = rd.powderdata[0][:-1]+cw/2. |
| 2051 | | # rd.powderdata[1] = rd.powderdata[1][:-1]/cw |
| 2052 | | # rd.powderdata[2] = rd.powderdata[2][:-1]*cw**2 #1/var=w at this point |
| 2053 | | # if 'Itype' in Iparm2: |
| 2054 | | # Ibeg = np.searchsorted(rd.powderdata[0],Iparm2['Tminmax'][0]) |
| 2055 | | # Ifin = np.searchsorted(rd.powderdata[0],Iparm2['Tminmax'][1]) |
| 2056 | | # rd.powderdata[0] = rd.powderdata[0][Ibeg:Ifin] |
| 2057 | | # YI,WYI = G2pwd.calcIncident(Iparm2,rd.powderdata[0]) |
| 2058 | | # rd.powderdata[1] = rd.powderdata[1][Ibeg:Ifin]/YI |
| 2059 | | # var = 1./rd.powderdata[2][Ibeg:Ifin] |
| 2060 | | # var += WYI*rd.powderdata[1]**2 |
| 2061 | | # var /= YI**2 |
| 2062 | | # rd.powderdata[2] = 1./var |
| 2063 | | # rd.powderdata[3] = np.zeros_like(rd.powderdata[0]) |
| 2064 | | # rd.powderdata[4] = np.zeros_like(rd.powderdata[0]) |
| 2065 | | # rd.powderdata[5] = np.zeros_like(rd.powderdata[0]) |
| 2066 | | Tmin = min(rd.reflectometrydata[0]) |
| 2067 | | Tmax = max(rd.reflectometrydata[0]) |
| 2068 | | ifDQ = np.any(rd.reflectometrydata[5]) |
| 2069 | | valuesdict = { |
| 2070 | | 'wtFactor':1.0, |
| 2071 | | 'Dummy':False, |
| 2072 | | 'ranId':ran.randint(0,sys.maxint), |
| 2073 | | 'Offset':[0.0,0.0], |
| 2074 | | 'ifDQ':ifDQ |
| 2075 | | } |
| 2076 | | rd.Sample['ranId'] = valuesdict['ranId'] # this should be removed someday |
| 2077 | | self.PatternTree.SetItemPyData(Id,[valuesdict,rd.reflectometrydata]) |
| 2078 | | self.PatternTree.SetItemPyData( |
| 2079 | | self.PatternTree.AppendItem(Id,text='Comments'), |
| 2080 | | rd.comments) |
| 2081 | | self.PatternTree.SetItemPyData( |
| 2082 | | self.PatternTree.AppendItem(Id,text='Limits'), |
| 2083 | | [(Tmin,Tmax),[Tmin,Tmax]]) |
| 2084 | | self.PatternId = G2gd.GetPatternTreeItemId(self,Id,'Limits') |
| 2085 | | self.PatternTree.SetItemPyData( |
| 2086 | | self.PatternTree.AppendItem(Id,text='Instrument Parameters'), |
| 2087 | | [Iparm1,Iparm2]) |
| 2088 | | self.PatternTree.SetItemPyData( |
| 2089 | | self.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances()) |
| 2090 | | self.PatternTree.SetItemPyData( |
| 2091 | | self.PatternTree.AppendItem(Id,text='Sample Parameters'), |
| 2092 | | rd.Sample) |
| 2093 | | self.PatternTree.SetItemPyData( |
| 2094 | | self.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultREFDModel()) |
| 2095 | | newHistList.append(HistName) |
| 2096 | | else: |
| 2097 | | self.EnablePlot = True |
| 2098 | | self.PatternTree.Expand(Id) |
| 2099 | | self.PatternTree.SelectItem(Id) |
| 2100 | | |
| 2101 | | if not newHistList: return # somehow, no new histograms |
| 2102 | | return # success |
| 2103 | | |
| 2104 | | def _Add_ImportMenu_PDF(self,parent): |
| 2105 | | '''configure the PDF Data menus accord to the readers found in _init_Imports |
| 2106 | | ''' |
| 2107 | | submenu = wx.Menu() |
| 2108 | | item = parent.AppendMenu(wx.ID_ANY, 'PDF G(R) Data', |
| 2109 | | submenu, help='Import PDF G(R) data') |
| 2110 | | for reader in self.ImportPDFReaderlist: |
| 2111 | | item = submenu.Append(wx.ID_ANY,help=reader.longFormatName, |
| 2112 | | kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file') |
| 2113 | | self.ImportMenuId[item.GetId()] = reader |
| 2114 | | self.Bind(wx.EVT_MENU, self.OnImportPDF, id=item.GetId()) |
| 2115 | | # item = submenu.Append(wx.ID_ANY, |
| 2116 | | # help='Import reflectometry data, use file to try to determine format', |
| 2117 | | # kind=wx.ITEM_NORMAL,text='guess format from file') |
| 2118 | | # self.Bind(wx.EVT_MENU, self.OnImportReflectometry, id=item.GetId()) |
| 2119 | | |
| 2120 | | def OnImportPDF(self,event): |
| 2121 | | '''Called in response to an Import/PDF G(R) Data/... menu item |
| 2122 | | to read a PDF G(R) data set. |
| 2123 | | dict self.ImportMenuId is used to look up the specific |
| 2124 | | reader item associated with the menu item, which will be |
| 2125 | | None for the last menu item, which is the "guess" option |
| 2126 | | where all appropriate formats will be tried. |
| 2127 | | |
| 2128 | | ''' |
| 2129 | | |
| 2130 | | # get a list of existing histograms |
| 2131 | | PDFlist = [] |
| 2132 | | if self.PatternTree.GetCount(): |
| 2133 | | item, cookie = self.PatternTree.GetFirstChild(self.root) |
| 2134 | | while item: |
| 2135 | | name = self.PatternTree.GetItemText(item) |
| 2136 | | if name.startswith('PDF ') and name not in PDFlist: |
| 2137 | | PDFlist.append(name) |
| 2138 | | item, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 2139 | | # look up which format was requested |
| 2140 | | reqrdr = self.ImportMenuId.get(event.GetId()) |
| 2141 | | rdlist = self.OnImportGeneric( |
| 2142 | | reqrdr,self.ImportPDFReaderlist,'PDF G(R) Data',multiple=True) |
| 2143 | | if len(rdlist) == 0: return |
| 2144 | | self.CheckNotebook() |
| 2145 | | newHistList = [] |
| 2146 | | self.EnablePlot = False |
| 2147 | | for rd in rdlist: |
| 2148 | | HistName = rd.idstring |
| 2149 | | HistName = 'PDF '+HistName |
| 2150 | | # make new histogram names unique |
| 2151 | | HistName = G2obj.MakeUniqueLabel(HistName,PDFlist) |
| 2152 | | print 'Read PDF G(R) data '+HistName+ \ |
| 2153 | | ' from file '+self.lastimport |
| 2154 | | # data are read, now store them in the tree |
| 2155 | | Id = self.PatternTree.AppendItem(self.root,text=HistName) |
| 2156 | | Ymin = np.min(rd.pdfdata[1]) |
| 2157 | | Ymax = np.max(rd.pdfdata[1]) |
| 2158 | | valuesdict = { |
| 2159 | | 'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxint), |
| 2160 | | 'Offset':[0.0,0.0],'delOffset':0.02*Ymax, |
| 2161 | | 'qPlot':False,'dPlot':False,'sqrtPlot':False,'Yminmax':[Ymin,Ymax] |
| 2162 | | } |
| 2163 | | self.PatternTree.SetItemPyData( |
| 2164 | | self.PatternTree.AppendItem(Id,text='PDF Controls'), |
| 2165 | | {'G(R)':[valuesdict,rd.pdfdata,HistName],'diffGRname':'','diffMult':1.0}) |
| 2166 | | self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='PDF Peaks'), |
| 2167 | | {'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]}) |
| 2168 | | else: |
| 2169 | | self.EnablePlot = True |
| 2170 | | self.PatternTree.Expand(Id) |
| 2171 | | self.PatternTree.SelectItem(Id) |
| 2172 | | |
| 2173 | | if not newHistList: return # somehow, no new histograms |
| 2174 | | return # success |
| 2175 | | |
| 2176 | | ############################################################################### |
| 2177 | | #Command logging |
| 2178 | | ############################################################################### |
| 2179 | | |
| 2180 | | def OnMacroRecordStatus(self,event,setvalue=None): |
| 2181 | | '''Called when the record macro menu item is used which toggles the |
| 2182 | | value. Alternately a value to be set can be provided. Note that this |
| 2183 | | routine is made more complex because on the Mac there are lots of menu |
| 2184 | | items (listed in self.MacroStatusList) and this loops over all of them. |
| 2185 | | ''' |
| 2186 | | nextvalue = log.ShowLogStatus() != True |
| 2187 | | if setvalue is not None: |
| 2188 | | nextvalue = setvalue |
| 2189 | | if nextvalue: |
| 2190 | | log.LogOn() |
| 2191 | | set2 = True |
| 2192 | | else: |
| 2193 | | log.LogOff() |
| 2194 | | set2 = False |
| 2195 | | for menuitem in self.MacroStatusList: |
| 2196 | | menuitem.Check(set2) |
| 2197 | | |
| 2198 | | def _init_Macro(self): |
| 2199 | | '''Define the items in the macro menu. |
| 2200 | | ''' |
| 2201 | | menu = self.MacroMenu |
| 2202 | | item = menu.Append( |
| 2203 | | help='Start or stop recording of menu actions, etc.', id=wx.ID_ANY, |
| 2204 | | kind=wx.ITEM_CHECK,text='Record actions') |
| 2205 | | self.MacroStatusList.append(item) |
| 2206 | | item.Check(log.ShowLogStatus()) |
| 2207 | | self.Bind(wx.EVT_MENU, self.OnMacroRecordStatus, item) |
| 2208 | | |
| 2209 | | # this may only be of value for development work |
| 2210 | | item = menu.Append( |
| 2211 | | help='Show logged commands', id=wx.ID_ANY, |
| 2212 | | kind=wx.ITEM_NORMAL,text='Show log') |
| 2213 | | def OnShowLog(event): |
| 2214 | | print 70*'=' |
| 2215 | | print 'List of logged actions' |
| 2216 | | for i,line in enumerate(log.G2logList): |
| 2217 | | if line: print i,line |
| 2218 | | print 70*'=' |
| 2219 | | self.Bind(wx.EVT_MENU, OnShowLog, item) |
| 2220 | | |
| 2221 | | item = menu.Append( |
| 2222 | | help='Clear logged commands', id=wx.ID_ANY, |
| 2223 | | kind=wx.ITEM_NORMAL,text='Clear log') |
| 2224 | | def OnClearLog(event): log.G2logList=[None] |
| 2225 | | self.Bind(wx.EVT_MENU, OnClearLog, item) |
| 2226 | | |
| 2227 | | item = menu.Append( |
| 2228 | | help='Save logged commands to file', id=wx.ID_ANY, |
| 2229 | | kind=wx.ITEM_NORMAL,text='Save log') |
| 2230 | | def OnSaveLog(event): |
| 2231 | | import cPickle |
| 2232 | | defnam = os.path.splitext( |
| 2233 | | os.path.split(self.GSASprojectfile)[1] |
| 2234 | | )[0]+'.gcmd' |
| 2235 | | dlg = wx.FileDialog(self, |
| 2236 | | 'Choose an file to save past actions', '.', defnam, |
| 2237 | | 'GSAS-II cmd output (*.gcmd)|*.gcmd', |
| 2238 | | wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) |
| 2239 | | dlg.CenterOnParent() |
| 2240 | | try: |
| 2241 | | if dlg.ShowModal() == wx.ID_OK: |
| 2242 | | filename = dlg.GetPath() |
| 2243 | | # make sure extension is correct |
| 2244 | | filename = os.path.splitext(filename)[0]+'.gcmd' |
| 2245 | | else: |
| 2246 | | filename = None |
| 2247 | | finally: |
| 2248 | | dlg.Destroy() |
| 2249 | | if filename: |
| 2250 | | fp = open(filename,'wb') |
| 2251 | | fp.write(str(len(log.G2logList)-1)+'\n') |
| 2252 | | for item in log.G2logList: |
| 2253 | | if item: cPickle.dump(item,fp) |
| 2254 | | fp.close() |
| 2255 | | self.Bind(wx.EVT_MENU, OnSaveLog, item) |
| 2256 | | |
| 2257 | | item = menu.Append( |
| 2258 | | help='Load logged commands from file', id=wx.ID_ANY, |
| 2259 | | kind=wx.ITEM_NORMAL,text='Load log') |
| 2260 | | def OnLoadLog(event): |
| 2261 | | # this appends. Perhaps we should ask to clear? |
| 2262 | | import cPickle |
| 2263 | | defnam = os.path.splitext( |
| 2264 | | os.path.split(self.GSASprojectfile)[1] |
| 2265 | | )[0]+'.gcmd' |
| 2266 | | dlg = wx.FileDialog(self, |
| 2267 | | 'Choose an file to read saved actions', '.', defnam, |
| 2268 | | 'GSAS-II cmd output (*.gcmd)|*.gcmd', |
| 2269 | | wx.OPEN) |
| 2270 | | dlg.CenterOnParent() |
| 2271 | | try: |
| 2272 | | if dlg.ShowModal() == wx.ID_OK: |
| 2273 | | filename = dlg.GetPath() |
| 2274 | | # make sure extension is correct |
| 2275 | | filename = os.path.splitext(filename)[0]+'.gcmd' |
| 2276 | | else: |
| 2277 | | filename = None |
| 2278 | | finally: |
| 2279 | | dlg.Destroy() |
| 2280 | | if filename and os.path.exists(filename): |
| 2281 | | fp = open(filename,'rb') |
| 2282 | | lines = fp.readline() |
| 2283 | | for i in range(int(lines)): |
| 2284 | | log.G2logList.append(cPickle.load(fp)) |
| 2285 | | fp.close() |
| 2286 | | self.Bind(wx.EVT_MENU, OnLoadLog, item) |
| 2287 | | |
| 2288 | | item = menu.Append( |
| 2289 | | help='Replay saved commands', id=wx.ID_ANY, |
| 2290 | | kind=wx.ITEM_NORMAL,text='Replay log') |
| 2291 | | self.Bind(wx.EVT_MENU, log.ReplayLog, item) |
| 2292 | | |
| 2293 | | def _init_Exports(self,menu): |
| 2294 | | '''Find exporter routines and add them into menus |
| 2295 | | ''' |
| 2296 | | # set up the top-level menus |
| 2297 | | projectmenu = wx.Menu() |
| 2298 | | item = menu.AppendMenu( |
| 2299 | | wx.ID_ANY, 'Entire project as', |
| 2300 | | projectmenu, help='Export entire project') |
| 2301 | | |
| 2302 | | phasemenu = wx.Menu() |
| 2303 | | item = menu.AppendMenu( |
| 2304 | | wx.ID_ANY, 'Phase as', |
| 2305 | | phasemenu, help='Export phase or sometimes phases') |
| 2306 | | |
| 2307 | | powdermenu = wx.Menu() |
| 2308 | | item = menu.AppendMenu( |
| 2309 | | wx.ID_ANY, 'Powder data as', |
| 2310 | | powdermenu, help='Export powder diffraction histogram(s)') |
| 2311 | | |
| 2312 | | singlemenu = wx.Menu() |
| 2313 | | item = menu.AppendMenu( |
| 2314 | | wx.ID_ANY, 'Single crystal data as', |
| 2315 | | singlemenu, help='Export single crystal histogram(s)') |
| 2316 | | |
| 2317 | | imagemenu = wx.Menu() |
| 2318 | | item = menu.AppendMenu( |
| 2319 | | wx.ID_ANY, 'Image data as', |
| 2320 | | imagemenu, help='Export powder image(s) data') |
| 2321 | | |
| 2322 | | mapmenu = wx.Menu() |
| 2323 | | item = menu.AppendMenu( |
| 2324 | | wx.ID_ANY, 'Maps as', |
| 2325 | | mapmenu, help='Export density map(s)') |
| 2326 | | |
| 2327 | | # pdfmenu = wx.Menu() |
| 2328 | | # item = menu.AppendMenu( |
| 2329 | | # wx.ID_ANY, 'PDFs as', |
| 2330 | | # pdfmenu, help='Export pair distribution function(s)') |
| 2331 | | |
| 2332 | | # find all the exporter files |
| 2333 | | if not self.exporterlist: # this only needs to be done once |
| 2334 | | pathlist = sys.path |
| 2335 | | filelist = [] |
| 2336 | | for path in pathlist: |
| 2337 | | for filename in glob.iglob(os.path.join(path,"G2export*.py")): |
| 2338 | | filelist.append(filename) |
| 2339 | | filelist = sorted(list(set(filelist))) # remove duplicates |
| 2340 | | # go through the routines and import them, saving objects that |
| 2341 | | # have export routines (method Exporter) |
| 2342 | | for filename in filelist: |
| 2343 | | path,rootname = os.path.split(filename) |
| 2344 | | pkg = os.path.splitext(rootname)[0] |
| 2345 | | # try: |
| 2346 | | fp = None |
| 2347 | | fp, fppath,desc = imp.find_module(pkg,[path,]) |
| 2348 | | pkg = imp.load_module(pkg,fp,fppath,desc) |
| 2349 | | for clss in inspect.getmembers(pkg): # find classes defined in package |
| 2350 | | if clss[0].startswith('_'): continue |
| 2351 | | if inspect.isclass(clss[1]): |
| 2352 | | # check if we have the required methods |
| 2353 | | for m in 'Exporter','loadParmDict': |
| 2354 | | if not hasattr(clss[1],m): break |
| 2355 | | if not callable(getattr(clss[1],m)): break |
| 2356 | | else: |
| 2357 | | exporter = clss[1](self) # create an export instance |
| 2358 | | self.exporterlist.append(exporter) |
| 2359 | | # except AttributeError: |
| 2360 | | # print 'Import_'+errprefix+': Attribute Error'+str(filename) |
| 2361 | | # pass |
| 2362 | | # except ImportError: |
| 2363 | | # print 'Import_'+errprefix+': Error importing file'+str(filename) |
| 2364 | | # pass |
| 2365 | | if fp: fp.close() |
| 2366 | | # Add submenu item(s) for each Exporter by its self-declared type (can be more than one) |
| 2367 | | for obj in self.exporterlist: |
| 2368 | | #print 'exporter',obj |
| 2369 | | for typ in obj.exporttype: |
| 2370 | | if typ == "project": |
| 2371 | | submenu = projectmenu |
| 2372 | | elif typ == "phase": |
| 2373 | | submenu = phasemenu |
| 2374 | | elif typ == "powder": |
| 2375 | | submenu = powdermenu |
| 2376 | | elif typ == "single": |
| 2377 | | submenu = singlemenu |
| 2378 | | elif typ == "image": |
| 2379 | | submenu = imagemenu |
| 2380 | | elif typ == "map": |
| 2381 | | submenu = mapmenu |
| 2382 | | # elif typ == "pdf": |
| 2383 | | # submenu = pdfmenu |
| 2384 | | else: |
| 2385 | | print("Error, unknown type in "+str(obj)) |
| 2386 | | break |
| 2387 | | item = submenu.Append( |
| 2388 | | wx.ID_ANY, |
| 2389 | | help=obj.longFormatName, |
| 2390 | | kind=wx.ITEM_NORMAL, |
| 2391 | | text=obj.formatName) |
| 2392 | | self.Bind(wx.EVT_MENU, obj.Exporter, id=item.GetId()) |
| 2393 | | self.ExportLookup[item.GetId()] = typ # lookup table for submenu item |
| 2394 | | item = imagemenu.Append(wx.ID_ANY, |
| 2395 | | help='Export image controls and masks for multiple images', |
| 2396 | | kind=wx.ITEM_NORMAL, |
| 2397 | | text='Multiple image controls and masks') |
| 2398 | | self.Bind(wx.EVT_MENU, self.OnSaveMultipleImg, id=item.GetId()) |
| 2399 | | #code to debug an Exporter. hard-code the routine below, to allow a reload before use |
| 2400 | | # def DebugExport(event): |
| 2401 | | # print 'start reload' |
| 2402 | | # reload(G2IO) |
| 2403 | | # import G2export_pwdr as dev |
| 2404 | | # reload(dev) |
| 2405 | | # dev.ExportPowderFXYE(self).Exporter(event) |
| 2406 | | # item = menu.Append( |
| 2407 | | # wx.ID_ANY,kind=wx.ITEM_NORMAL, |
| 2408 | | # help="debug exporter",text="test Export FXYE") |
| 2409 | | # self.Bind(wx.EVT_MENU, DebugExport, id=item.GetId()) |
| 2410 | | # # #self.ExportLookup[item.GetId()] = 'image' |
| 2411 | | # self.ExportLookup[item.GetId()] = 'powder' |
| 2412 | | |
| 2413 | | ############################################################################### |
| 2414 | | # Exporters |
| 2415 | | ############################################################################### |
| 2416 | | |
| 2417 | | def _Add_ExportMenuItems(self,parent): |
| 2418 | | # item = parent.Append( |
| 2419 | | # help='Select PWDR item to enable',id=wx.ID_ANY, |
| 2420 | | # kind=wx.ITEM_NORMAL, |
| 2421 | | # text='Export Powder Patterns...') |
| 2422 | | # self.ExportPattern.append(item) |
| 2423 | | # item.Enable(False) |
| 2424 | | # self.Bind(wx.EVT_MENU, self.OnExportPatterns, id=item.GetId()) |
| 2425 | | |
| 2426 | | item = parent.Append( |
| 2427 | | help='',id=wx.ID_ANY, |
| 2428 | | kind=wx.ITEM_NORMAL, |
| 2429 | | text='Export All Peak Lists...') |
| 2430 | | self.ExportPeakList.append(item) |
| 2431 | | item.Enable(True) |
| 2432 | | self.Bind(wx.EVT_MENU, self.OnExportPeakList, id=item.GetId()) |
| 2433 | | |
| 2434 | | item = parent.Append( |
| 2435 | | help='',id=wx.ID_ANY, |
| 2436 | | kind=wx.ITEM_NORMAL, |
| 2437 | | text='Export HKLs...') |
| 2438 | | self.ExportHKL.append(item) |
| 2439 | | self.Bind(wx.EVT_MENU, self.OnExportHKL, id=item.GetId()) |
| 2440 | | |
| 2441 | | item = parent.Append( |
| 2442 | | help='Select PDF item to enable', |
| 2443 | | id=wx.ID_ANY, |
| 2444 | | kind=wx.ITEM_NORMAL, |
| 2445 | | text='Export PDF...') |
| 2446 | | self.ExportPDF.append(item) |
| 2447 | | item.Enable(False) |
| 2448 | | self.Bind(wx.EVT_MENU, self.OnExportPDF, id=item.GetId()) |
| 2449 | | |
| 2450 | | def FillMainMenu(self,menubar,addhelp=True): |
| 2451 | | '''Define contents of the main GSAS-II menu for the (main) data tree window. |
| 2452 | | For the mac, this is also called for the data item windows as well so that |
| 2453 | | the main menu items are data menu as well. |
| 2454 | | ''' |
| 2455 | | File = wx.Menu(title='') |
| 2456 | | menubar.Append(menu=File, title='&File') |
| 2457 | | self._Add_FileMenuItems(File) |
| 2458 | | Data = wx.Menu(title='') |
| 2459 | | menubar.Append(menu=Data, title='Data') |
| 2460 | | self._Add_DataMenuItems(Data) |
| 2461 | | Calculate = wx.Menu(title='') |
| 2462 | | menubar.Append(menu=Calculate, title='&Calculate') |
| 2463 | | self._Add_CalculateMenuItems(Calculate) |
| 2464 | | Import = wx.Menu(title='') |
| 2465 | | menubar.Append(menu=Import, title='Import') |
| 2466 | | self._Add_ImportMenu_Image(Import) |
| 2467 | | self._Add_ImportMenu_Phase(Import) |
| 2468 | | self._Add_ImportMenu_powder(Import) |
| 2469 | | self._Add_ImportMenu_Sfact(Import) |
| 2470 | | self._Add_ImportMenu_smallangle(Import) |
| 2471 | | self._Add_ImportMenu_reflectometry(Import) |
| 2472 | | self._Add_ImportMenu_PDF(Import) |
| 2473 | | |
| 2474 | | #====================================================================== |
| 2475 | | # Code to help develop/debug an importer, much is hard-coded below |
| 2476 | | # but module is reloaded before each use, allowing faster testing |
| 2477 | | # def DebugImport(event): |
| 2478 | | # print 'start reload' |
| 2479 | | # import G2phase_ISO as dev |
| 2480 | | # reload(dev) |
| 2481 | | # rd = dev.ISODISTORTPhaseReader() |
| 2482 | | # self.ImportMenuId[event.GetId()] = rd |
| 2483 | | # self.OnImportPhase(event) |
| 2484 | | # or ---------------------------------------------------------------------- |
| 2485 | | #self.OnImportGeneric(rd,[],'test of ISODISTORTPhaseReader') |
| 2486 | | # special debug code |
| 2487 | | # or ---------------------------------------------------------------------- |
| 2488 | | # filename = '/Users/toby/projects/branton/subgroup_cif.txt' |
| 2489 | | # fp = open(filename,'Ur') |
| 2490 | | # if not rd.ContentsValidator(fp): |
| 2491 | | # print 'not validated' |
| 2492 | | # # make a list of used phase ranId's |
| 2493 | | # phaseRIdList = [] |
| 2494 | | # sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases') |
| 2495 | | # if sub: |
| 2496 | | # item, cookie = self.PatternTree.GetFirstChild(sub) |
| 2497 | | # while item: |
| 2498 | | # phaseName = self.PatternTree.GetItemText(item) |
| 2499 | | # ranId = self.PatternTree.GetItemPyData(item).get('ranId') |
| 2500 | | # if ranId: phaseRIdList.append(ranId) |
| 2501 | | # item, cookie = self.PatternTree.GetNextChild(sub, cookie) |
| 2502 | | # if rd.Reader(filename,fp,usedRanIdList=phaseRIdList): |
| 2503 | | # print 'read OK' |
| 2504 | | # item = Import.Append( |
| 2505 | | # wx.ID_ANY,kind=wx.ITEM_NORMAL, |
| 2506 | | # help="debug importer",text="test importer") |
| 2507 | | # self.Bind(wx.EVT_MENU, DebugImport, id=item.GetId()) |
| 2508 | | #====================================================================== |
| 2509 | | self.ExportMenu = wx.Menu(title='') |
| 2510 | | menubar.Append(menu=self.ExportMenu, title='Export') |
| 2511 | | self._init_Exports(self.ExportMenu) |
| 2512 | | self._Add_ExportMenuItems(self.ExportMenu) |
| 2513 | | if GSASIIpath.GetConfigValue('Enable_logging'): |
| 2514 | | self.MacroMenu = wx.Menu(title='') |
| 2515 | | menubar.Append(menu=self.MacroMenu, title='Macro') |
| 2516 | | self._init_Macro() |
| 2517 | | if addhelp: |
| 2518 | | HelpMenu=G2G.MyHelp(self,includeTree=True, |
| 2519 | | morehelpitems=[('&Tutorials','Tutorials'),]) |
| 2520 | | menubar.Append(menu=HelpMenu,title='&Help') |
| 2521 | | |
| 2522 | | def _init_ctrls(self, parent): |
| 2523 | | wx.Frame.__init__(self, name='GSASII', parent=parent, |
| 2524 | | size=wx.Size(400, 250),style=wx.DEFAULT_FRAME_STYLE, title='GSAS-II data tree') |
| 2525 | | clientSize = wx.ClientDisplayRect() |
| 2526 | | Size = self.GetSize() |
| 2527 | | xPos = clientSize[2]-Size[0] |
| 2528 | | self.SetPosition(wx.Point(xPos,clientSize[1])) |
| 2529 | | self._init_Imports() |
| 2530 | | #initialize Menu item objects (these contain lists of menu items that are enabled or disabled) |
| 2531 | | self.MakePDF = [] |
| 2532 | | self.Refine = [] |
| 2533 | | self.SeqRefine = [] # pointer(s) to Sequential Refinement menu objects |
| 2534 | | #self.ExportPattern = [] |
| 2535 | | self.ExportPeakList = [] |
| 2536 | | self.ExportHKL = [] |
| 2537 | | self.ExportPDF = [] |
| 2538 | | self.ExportPhase = [] |
| 2539 | | self.ExportCIF = [] |
| 2540 | | # |
| 2541 | | self.GSASIIMenu = wx.MenuBar() |
| 2542 | | # create a list of all dataframe menus (appended in PrefillDataMenu) |
| 2543 | | self.dataMenuBars = [self.GSASIIMenu] |
| 2544 | | self.MacroStatusList = [] |
| 2545 | | self.FillMainMenu(self.GSASIIMenu) |
| 2546 | | self.SetMenuBar(self.GSASIIMenu) |
| 2547 | | self.Bind(wx.EVT_SIZE, self.OnSize) |
| 2548 | | self.Status = self.CreateStatusBar() |
| 2549 | | self.mainPanel = wx.Panel(self,-1) |
| 2550 | | |
| 2551 | | wxID_PATTERNTREE = wx.NewId() |
| 2552 | | #self.PatternTree = wx.TreeCtrl(id=wxID_PATTERNTREE, # replaced for logging |
| 2553 | | self.PatternTree = G2G.G2TreeCtrl(id=wxID_PATTERNTREE, |
| 2554 | | parent=self.mainPanel, pos=wx.Point(0, 0),style=wx.TR_DEFAULT_STYLE ) |
| 2555 | | self.PatternTree.Bind(wx.EVT_TREE_SEL_CHANGED,self.OnDataTreeSelChanged) |
| 2556 | | self.PatternTree.Bind(wx.EVT_TREE_ITEM_RIGHT_CLICK,self.OnDataTreeSelChanged) |
| 2557 | | self.PatternTree.Bind(wx.EVT_TREE_ITEM_COLLAPSED, |
| 2558 | | self.OnPatternTreeItemCollapsed, id=wxID_PATTERNTREE) |
| 2559 | | self.PatternTree.Bind(wx.EVT_TREE_ITEM_EXPANDED, |
| 2560 | | self.OnPatternTreeItemExpanded, id=wxID_PATTERNTREE) |
| 2561 | | self.PatternTree.Bind(wx.EVT_TREE_DELETE_ITEM, |
| 2562 | | self.OnPatternTreeItemDelete, id=wxID_PATTERNTREE) |
| 2563 | | self.PatternTree.Bind(wx.EVT_TREE_KEY_DOWN, |
| 2564 | | self.OnPatternTreeKeyDown, id=wxID_PATTERNTREE) |
| 2565 | | self.PatternTree.Bind(wx.EVT_TREE_BEGIN_RDRAG, |
| 2566 | | self.OnPatternTreeBeginRDrag, id=wxID_PATTERNTREE) |
| 2567 | | self.PatternTree.Bind(wx.EVT_TREE_END_DRAG, |
| 2568 | | self.OnPatternTreeEndDrag, id=wxID_PATTERNTREE) |
| 2569 | | #self.root = self.PatternTree.AddRoot('Loaded Data: ') |
| 2570 | | self.root = self.PatternTree.root |
| 2571 | | plotFrame = wx.Frame(None,-1,'GSASII Plots',size=wx.Size(700,600), \ |
| 2572 | | style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX) |
| 2573 | | self.G2plotNB = G2plt.G2PlotNoteBook(plotFrame,G2frame=self) |
| 2574 | | plotFrame.Show() |
| 2575 | | |
| 2576 | | self.dataDisplay = None |
| 2577 | | |
| 2578 | | def __init__(self, parent): |
| 2579 | | self.ExportLookup = {} |
| 2580 | | self.exporterlist = [] |
| 2581 | | self._init_ctrls(parent) |
| 2582 | | self.Image = wx.Image( |
| 2583 | | os.path.join(GSASIIpath.path2GSAS2,'gsas2.ico'), |
| 2584 | | wx.BITMAP_TYPE_ICO) |
| 2585 | | if "wxMSW" in wx.PlatformInfo: |
| 2586 | | img = self.Image.Scale(16, 16).ConvertToBitmap() |
| 2587 | | elif "wxGTK" in wx.PlatformInfo: |
| 2588 | | img = self.Image.Scale(22, 22).ConvertToBitmap() |
| 2589 | | else: |
| 2590 | | img = self.Image.ConvertToBitmap() |
| 2591 | | self.SetIcon(wx.IconFromBitmap(img)) |
| 2592 | | self.Bind(wx.EVT_CLOSE, self.ExitMain) |
| 2593 | | # various defaults |
| 2594 | | self.oldFocus = None |
| 2595 | | self.GSASprojectfile = '' |
| 2596 | | self.undofile = '' |
| 2597 | | self.TreeItemDelete = False |
| 2598 | | self.plotStyle = {'qPlot':False,'dPlot':False,'sqrtPlot':False,'sqPlot':False} |
| 2599 | | self.Weight = False |
| 2600 | | self.IfPlot = False |
| 2601 | | self.DDShowAll = False |
| 2602 | | self.atmSel = '' |
| 2603 | | self.PatternId = 0 |
| 2604 | | self.PickId = 0 |
| 2605 | | self.PickIdText = None |
| 2606 | | self.PeakTable = [] |
| 2607 | | self.LimitsTable = [] |
| 2608 | | self.ifX20 = True #use M20 /= (1+X20) in powder indexing, etc. |
| 2609 | | self.HKL = [] |
| 2610 | | self.Lines = [] |
| 2611 | | self.itemPicked = None |
| 2612 | | self.dataFrame = None |
| 2613 | | self.Interpolate = 'nearest' |
| 2614 | | self.ContourColor = GSASIIpath.GetConfigValue('Contour_color','Paired') |
| 2615 | | self.VcovColor = 'RdYlGn' |
| 2616 | | self.RamaColor = 'Blues' |
| 2617 | | self.Projection = 'equal area' |
| 2618 | | self.logPlot = False |
| 2619 | | self.plusPlot = True |
| 2620 | | self.ErrorBars = False |
| 2621 | | self.Contour = False |
| 2622 | | self.Legend = False |
| 2623 | | self.SinglePlot = True |
| 2624 | | self.Waterfall = False |
| 2625 | | self.selections= None |
| 2626 | | self.PDFselections = None |
| 2627 | | self.SubBack = False |
| 2628 | | self.seqReverse = False |
| 2629 | | self.seqLines = True #draw lines between points |
| 2630 | | self.plotView = 0 |
| 2631 | | self.Image = 0 |
| 2632 | | self.oldImagefile = '' # the name of the last image file read |
| 2633 | | self.oldImageTag = None # the name of the tag for multi-image files |
| 2634 | | self.PauseIntegration = False |
| 2635 | | self.ImageZ = [] |
| 2636 | | self.Integrate = 0 |
| 2637 | | self.imageDefault = {} |
| 2638 | | self.IntgOutList = [] # list of integration tree item Ids created in G2IO.SaveIntegration |
| 2639 | | self.AutointPWDRnames = [] # list of autoint created PWDR tree item names (to be deleted on a reset) |
| 2640 | | self.autoIntFrame = None |
| 2641 | | self.IntegratedList = [] # list of already integrated IMG tree items |
| 2642 | | self.Sngl = False |
| 2643 | | self.ifGetRing = False |
| 2644 | | self.MaskKey = '' #trigger for making image masks |
| 2645 | | self.MskDelete = False #trigger for mask delete |
| 2646 | | self.StrainKey = '' #ditto for new strain d-zeros |
| 2647 | | self.EnablePlot = True |
| 2648 | | self.hist = '' # selected histogram in Phase/Data tab |
| 2649 | | self.dirname = os.path.abspath(os.path.expanduser('~')) #start in the users home directory by default; may be meaningless |
| 2650 | | self.TutorialImportDir = None # location to read tutorial files, set when a tutorial is viewed |
| 2651 | | self.LastImportDir = None # last-used directory where an import was done |
| 2652 | | self.LastGPXdir = None # directory where a GPX file was last read |
| 2653 | | self.LastExportDir = None # the last directory used for exports, if any. |
| 2654 | | self.dataDisplayPhaseText = '' |
| 2655 | | self.lastTreeSetting = [] |
| 2656 | | self.ExpandingAll = False |
| 2657 | | self.SeqTblHideList = [] |
| 2658 | | |
| 2659 | | arg = sys.argv |
| 2660 | | if len(arg) > 1 and arg[1]: |
| 2661 | | self.GSASprojectfile = os.path.splitext(arg[1])[0]+'.gpx' |
| 2662 | | self.dirname = os.path.abspath(os.path.dirname(arg[1])) |
| 2663 | | if self.dirname: os.chdir(self.dirname) |
| 2664 | | try: |
| 2665 | | self.StartProject() #open the file if possible |
| 2666 | | return |
| 2667 | | except Exception: |
| 2668 | | print 'Error opening or reading file',arg[1] |
| 2669 | | import traceback |
| 2670 | | print traceback.format_exc() |
| 2671 | | |
| 2672 | | if GSASIIpath.GetConfigValue('Starting_directory'): |
| 2673 | | try: |
| 2674 | | pth = GSASIIpath.GetConfigValue('Starting_directory') |
| 2675 | | pth = os.path.expanduser(pth) |
| 2676 | | os.chdir(pth) |
| 2677 | | self.LastGPXdir = pth |
| 2678 | | except: |
| 2679 | | print('Ignoring Config Starting_directory value: '+ |
| 2680 | | GSASIIpath.GetConfigValue('Starting_directory')) |
| 2681 | | |
| 2682 | | def GetTreeItemsList(self,item): |
| 2683 | | return self.PatternTree._getTreeItemsList(item) |
| 2684 | | |
| 2685 | | def OnSize(self,event): |
| 2686 | | 'Called to make PatternTree fill mainPanel' |
| 2687 | | w,h = self.GetClientSizeTuple() |
| 2688 | | self.mainPanel.SetSize(wx.Size(w,h)) |
| 2689 | | self.PatternTree.SetSize(wx.Size(w,h)) |
| 2690 | | |
| 2691 | | def OnDataTreeSelChanged(self, event): |
| 2692 | | '''Called when a data tree item is selected''' |
| 2693 | | if self.TreeItemDelete: |
| 2694 | | self.TreeItemDelete = False |
| 2695 | | else: |
| 2696 | | if self.ExpandingAll: |
| 2697 | | if GSASIIpath.GetConfigValue('debug'): print('Skipping Tree selection due to ExpandAll') |
| 2698 | | return |
| 2699 | | pltNum = self.G2plotNB.nb.GetSelection() |
| 2700 | | if pltNum >= 0: #to avoid the startup with no plot! |
| 2701 | | self.G2plotNB.nb.GetPage(pltNum) |
| 2702 | | item = event.GetItem() |
| 2703 | | wx.CallAfter(G2gd.SelectDataTreeItem,self,item,self.oldFocus) |
| 2704 | | #if self.oldFocus: # now done via last parameter on SelectDataTreeItem |
| 2705 | | # wx.CallAfter(self.oldFocus.SetFocus) |
| 2706 | | |
| 2707 | | def OnPatternTreeItemCollapsed(self, event): |
| 2708 | | 'Called when a tree item is collapsed - all children will be collapsed' |
| 2709 | | self.PatternTree.CollapseAllChildren(event.GetItem()) |
| 2710 | | |
| 2711 | | def OnPatternTreeItemExpanded(self, event): |
| 2712 | | 'Called when a tree item is expanded' |
| 2713 | | self.OnDataTreeSelChanged(event) |
| 2714 | | event.Skip() |
| 2715 | | |
| 2716 | | def OnPatternTreeItemDelete(self, event): |
| 2717 | | 'Called when a tree item is deleted -- not sure what this does' |
| 2718 | | self.TreeItemDelete = True |
| 2719 | | |
| 2720 | | def OnPatternTreeItemActivated(self, event): |
| 2721 | | 'Called when a tree item is activated' |
| 2722 | | event.Skip() |
| 2723 | | |
| 2724 | | def OnPatternTreeBeginRDrag(self,event): |
| 2725 | | event.Allow() |
| 2726 | | self.BeginDragId = event.GetItem() |
| 2727 | | self.ParentId = self.PatternTree.GetItemParent(self.BeginDragId) |
| 2728 | | DragText = self.PatternTree.GetItemText(self.BeginDragId) |
| 2729 | | self.DragData = [[DragText,self.PatternTree.GetItemPyData(self.BeginDragId)],] |
| 2730 | | item, cookie = self.PatternTree.GetFirstChild(self.BeginDragId) |
| 2731 | | while item: #G2 data tree has no sub children under a child of a tree item |
| 2732 | | name = self.PatternTree.GetItemText(item) |
| 2733 | | self.DragData.append([name,self.PatternTree.GetItemPyData(item)]) |
| 2734 | | item, cookie = self.PatternTree.GetNextChild(self.BeginDragId, cookie) |
| 2735 | | |
| 2736 | | def OnPatternTreeEndDrag(self,event): |
| 2737 | | event.Allow() |
| 2738 | | self.EndDragId = event.GetItem() |
| 2739 | | try: |
| 2740 | | NewParent = self.PatternTree.GetItemParent(self.EndDragId) |
| 2741 | | except: |
| 2742 | | self.EndDragId = self.PatternTree.GetLastChild(self.root) |
| 2743 | | NewParent = self.root |
| 2744 | | if self.ParentId != NewParent: |
| 2745 | | self.ErrorDialog('Drag not allowed','Wrong parent for item dragged') |
| 2746 | | else: |
| 2747 | | Name,Item = self.DragData[0] |
| 2748 | | NewId = self.PatternTree.InsertItem(self.ParentId,self.EndDragId,Name,data=None) |
| 2749 | | self.PatternTree.SetItemPyData(NewId,Item) |
| 2750 | | for name,item in self.DragData[1:]: #loop over children |
| 2751 | | Id = self.PatternTree.AppendItem(parent=NewId,text=name) |
| 2752 | | self.PatternTree.SetItemPyData(Id,item) |
| 2753 | | self.PatternTree.Delete(self.BeginDragId) |
| 2754 | | G2gd.SelectDataTreeItem(self,NewId) |
| 2755 | | |
| 2756 | | def OnPatternTreeKeyDown(self,event): #doesn't exactly work right with Shift key down |
| 2757 | | 'Allows stepping through the tree with the up/down arrow keys' |
| 2758 | | self.oldFocus = wx.Window.FindFocus() |
| 2759 | | keyevt = event.GetKeyEvent() |
| 2760 | | key = event.GetKeyCode() |
| 2761 | | item = self.PatternTree.GetSelection() |
| 2762 | | if type(item) is int: return # is this the toplevel in tree? |
| 2763 | | name = self.PatternTree.GetItemText(item) |
| 2764 | | parent = self.PatternTree.GetItemParent(item) |
| 2765 | | if key == wx.WXK_UP: |
| 2766 | | if keyevt.GetModifiers() == wx.MOD_SHIFT and parent != self.root: |
| 2767 | | if type(parent) is int: return # is this the toplevel in tree? |
| 2768 | | prev = self.PatternTree.GetPrevSibling(parent) |
| 2769 | | NewId = G2gd.GetPatternTreeItemId(self,prev,name) |
| 2770 | | if NewId: |
| 2771 | | self.PatternTree.Collapse(parent) |
| 2772 | | self.PatternTree.Expand(prev) |
| 2773 | | self.oldFocus = wx.Window.FindFocus() |
| 2774 | | wx.CallAfter(self.PatternTree.SelectItem,NewId) |
| 2775 | | else: |
| 2776 | | wx.CallAfter(self.PatternTree.SelectItem,item) |
| 2777 | | elif sys.platform == "win32": |
| 2778 | | self.PatternTree.GetPrevSibling(item) |
| 2779 | | self.PatternTree.SelectItem(item) |
| 2780 | | else: |
| 2781 | | item = self.PatternTree.GetPrevSibling(item) |
| 2782 | | if item.IsOk(): self.PatternTree.SelectItem(item) |
| 2783 | | elif key == wx.WXK_DOWN: |
| 2784 | | if keyevt.GetModifiers() == wx.MOD_SHIFT and parent != self.root: |
| 2785 | | next = self.PatternTree.GetNextSibling(parent) |
| 2786 | | NewId = G2gd.GetPatternTreeItemId(self,next,name) |
| 2787 | | if NewId: |
| 2788 | | self.PatternTree.Collapse(parent) |
| 2789 | | self.PatternTree.Expand(next) |
| 2790 | | self.oldFocus = wx.Window.FindFocus() |
| 2791 | | wx.CallAfter(self.PatternTree.SelectItem,NewId) |
| 2792 | | else: |
| 2793 | | wx.CallAfter(self.PatternTree.SelectItem,item) |
| 2794 | | elif sys.platform == "win32": |
| 2795 | | self.PatternTree.GetNextSibling(item) |
| 2796 | | self.PatternTree.SelectItem(item) |
| 2797 | | else: |
| 2798 | | item = self.PatternTree.GetNextSibling(item) |
| 2799 | | if item.IsOk(): self.PatternTree.SelectItem(item) |
| 2800 | | |
| 2801 | | def OnReadPowderPeaks(self,event): |
| 2802 | | 'Bound to menu Data/Read Powder Peaks' |
| 2803 | | self.CheckNotebook() |
| 2804 | | pth = G2G.GetImportPath(self) |
| 2805 | | if not pth: pth = '.' |
| 2806 | | dlg = wx.FileDialog(self, 'Choose file with peak list', pth, '', |
| 2807 | | 'peak files (*.txt)|*.txt|All files (*.*)|*.*',wx.OPEN) |
| 2808 | | try: |
| 2809 | | if dlg.ShowModal() == wx.ID_OK: |
| 2810 | | self.HKL = [] |
| 2811 | | self.powderfile = dlg.GetPath() |
| 2812 | | comments,peaks,limits,wave = G2IO.GetPowderPeaks(self.powderfile) |
| 2813 | | Id = self.PatternTree.AppendItem(parent=self.root,text='PKS '+os.path.basename(self.powderfile)) |
| 2814 | | data = ['PKS',wave,0.0] |
| 2815 | | names = ['Type','Lam','Zero'] |
| 2816 | | codes = [0,0,0] |
| 2817 | | inst = [G2IO.makeInstDict(names,data,codes),{}] |
| 2818 | | self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst) |
| 2819 | | self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),comments) |
| 2820 | | self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Limits'),[tuple(limits),limits]) |
| 2821 | | self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Index Peak List'),[peaks,[]]) |
| 2822 | | self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Unit Cells List'),[]) |
| 2823 | | self.PatternTree.Expand(Id) |
| 2824 | | self.PatternTree.SelectItem(Id) |
| 2825 | | os.chdir(dlg.GetDirectory()) # to get Mac/Linux to change directory! |
| 2826 | | finally: |
| 2827 | | dlg.Destroy() |
| 2828 | | |
| 2829 | | def OnImageRead(self,event): |
| 2830 | | '''Called to read in an image in any known format. *** Depreciated. *** |
| 2831 | | ''' |
| 2832 | | G2G.G2MessageBox(self,'Please use the Import/Image/... menu item rather than this','depreciating menu item') |
| 2833 | | |
| 2834 | | def CheckNotebook(self): |
| 2835 | | '''Make sure the data tree has the minimally expected controls. |
| 2836 | | ''' |
| 2837 | | if not G2gd.GetPatternTreeItemId(self,self.root,'Notebook'): |
| 2838 | | sub = self.PatternTree.AppendItem(parent=self.root,text='Notebook') |
| 2839 | | self.PatternTree.SetItemPyData(sub,['']) |
| 2840 | | if not G2gd.GetPatternTreeItemId(self,self.root,'Controls'): |
| 2841 | | sub = self.PatternTree.AppendItem(parent=self.root,text='Controls') |
| 2842 | | self.PatternTree.SetItemPyData(sub,copy.copy(G2obj.DefaultControls)) |
| 2843 | | if not G2gd.GetPatternTreeItemId(self,self.root,'Covariance'): |
| 2844 | | sub = self.PatternTree.AppendItem(parent=self.root,text='Covariance') |
| 2845 | | self.PatternTree.SetItemPyData(sub,{}) |
| 2846 | | if not G2gd.GetPatternTreeItemId(self,self.root,'Constraints'): |
| 2847 | | sub = self.PatternTree.AppendItem(parent=self.root,text='Constraints') |
| 2848 | | self.PatternTree.SetItemPyData(sub,{'Hist':[],'HAP':[],'Phase':[]}) |
| 2849 | | if not G2gd.GetPatternTreeItemId(self,self.root,'Restraints'): |
| 2850 | | sub = self.PatternTree.AppendItem(parent=self.root,text='Restraints') |
| 2851 | | self.PatternTree.SetItemPyData(sub,{}) |
| 2852 | | if not G2gd.GetPatternTreeItemId(self,self.root,'Rigid bodies'): |
| 2853 | | sub = self.PatternTree.AppendItem(parent=self.root,text='Rigid bodies') |
| 2854 | | self.PatternTree.SetItemPyData(sub,{'Vector':{'AtInfo':{}}, |
| 2855 | | 'Residue':{'AtInfo':{}},'RBIds':{'Vector':[],'Residue':[]}}) |
| 2856 | | |
| 2857 | | class CopyDialog(wx.Dialog): |
| 2858 | | '''Creates a dialog for copying control settings between |
| 2859 | | data tree items''' |
| 2860 | | def __init__(self,parent,title,text,data): |
| 2861 | | wx.Dialog.__init__(self,parent,-1,title, |
| 2862 | | pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE) |
| 2863 | | self.data = data |
| 2864 | | panel = wx.Panel(self) |
| 2865 | | mainSizer = wx.BoxSizer(wx.VERTICAL) |
| 2866 | | topLabl = wx.StaticText(panel,-1,text) |
| 2867 | | mainSizer.Add((10,10),1) |
| 2868 | | mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL|wx.LEFT,10) |
| 2869 | | mainSizer.Add((10,10),1) |
| 2870 | | ncols = len(data)/40+1 |
| 2871 | | dataGridSizer = wx.FlexGridSizer(cols=ncols,hgap=2,vgap=2) |
| 2872 | | for id,item in enumerate(self.data): |
| 2873 | | ckbox = wx.CheckBox(panel,id,item[1]) |
| 2874 | | ckbox.Bind(wx.EVT_CHECKBOX,self.OnCopyChange) |
| 2875 | | dataGridSizer.Add(ckbox,0,wx.LEFT,10) |
| 2876 | | mainSizer.Add(dataGridSizer,0,wx.EXPAND) |
| 2877 | | OkBtn = wx.Button(panel,-1,"Ok") |
| 2878 | | OkBtn.Bind(wx.EVT_BUTTON, self.OnOk) |
| 2879 | | cancelBtn = wx.Button(panel,-1,"Cancel") |
| 2880 | | cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel) |
| 2881 | | btnSizer = wx.BoxSizer(wx.HORIZONTAL) |
| 2882 | | btnSizer.Add((20,20),1) |
| 2883 | | btnSizer.Add(OkBtn) |
| 2884 | | btnSizer.Add((20,20),1) |
| 2885 | | btnSizer.Add(cancelBtn) |
| 2886 | | btnSizer.Add((20,20),1) |
| 2887 | | |
| 2888 | | mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10) |
| 2889 | | panel.SetSizer(mainSizer) |
| 2890 | | panel.Fit() |
| 2891 | | self.Fit() |
| 2892 | | |
| 2893 | | def OnCopyChange(self,event): |
| 2894 | | id = event.GetId() |
| 2895 | | self.data[id][0] = self.FindWindowById(id).GetValue() |
| 2896 | | |
| 2897 | | def OnOk(self,event): |
| 2898 | | parent = self.GetParent() |
| 2899 | | parent.Raise() |
| 2900 | | self.EndModal(wx.ID_OK) |
| 2901 | | |
| 2902 | | def OnCancel(self,event): |
| 2903 | | parent = self.GetParent() |
| 2904 | | parent.Raise() |
| 2905 | | self.EndModal(wx.ID_CANCEL) |
| 2906 | | |
| 2907 | | def GetData(self): |
| 2908 | | return self.data |
| 2909 | | |
| 2910 | | class SumDialog(wx.Dialog): |
| 2911 | | '''Allows user to supply scale factor(s) when summing data - |
| 2912 | | TODO: CAN WE PREVIEW RESULT HERE?''' |
| 2913 | | def __init__(self,parent,title,text,dataType,data,dataList): |
| 2914 | | wx.Dialog.__init__(self,parent,-1,title,size=(400,250), |
| 2915 | | pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER) |
| 2916 | | self.plotFrame = wx.Frame(self,-1,'Sum Plots',size=wx.Size(700,600), \ |
| 2917 | | style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX) |
| 2918 | | self.G2plotNB = G2plt.G2PlotNoteBook(self.plotFrame,G2frame=self) |
| 2919 | | self.data = data |
| 2920 | | self.dataList = dataList |
| 2921 | | self.dataType = dataType |
| 2922 | | size = (450,350) |
| 2923 | | panel = wxscroll.ScrolledPanel(self, wx.ID_ANY,size=size, |
| 2924 | | style = wx.TAB_TRAVERSAL|wx.SUNKEN_BORDER) |
| 2925 | | mainSizer = wx.BoxSizer(wx.VERTICAL) |
| 2926 | | topLabl = wx.StaticText(panel,-1,text) |
| 2927 | | mainSizer.Add((10,10),1) |
| 2928 | | mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL|wx.LEFT,10) |
| 2929 | | mainSizer.Add((10,10),1) |
| 2930 | | self.dataGridSizer = wx.FlexGridSizer(cols=2,hgap=2,vgap=2) |
| 2931 | | for id,item in enumerate(self.data[:-1]): |
| 2932 | | name = wx.TextCtrl(panel,-1,item[1],size=wx.Size(300,20)) |
| 2933 | | name.SetEditable(False) |
| 2934 | | # azmthOff = G2G.ValidatedTxtCtrl(G2frame.dataDisplay,data,'azmthOff',nDig=(10,2),typeHint=float,OnLeave=OnAzmthOff) |
| 2935 | | scale = wx.TextCtrl(panel,id,'%.3f'%(item[0]),style=wx.TE_PROCESS_ENTER) |
| 2936 | | scale.Bind(wx.EVT_TEXT_ENTER,self.OnScaleChange) |
| 2937 | | scale.Bind(wx.EVT_KILL_FOCUS,self.OnScaleChange) |
| 2938 | | self.dataGridSizer.Add(scale,0,wx.LEFT,10) |
| 2939 | | self.dataGridSizer.Add(name,0,wx.RIGHT,10) |
| 2940 | | if self.dataType: |
| 2941 | | self.dataGridSizer.Add(wx.StaticText(panel,-1,'Sum result name: '+self.dataType),0, \ |
| 2942 | | wx.LEFT|wx.TOP|wx.ALIGN_CENTER_VERTICAL,10) |
| 2943 | | self.name = wx.TextCtrl(panel,-1,self.data[-1],size=wx.Size(300,20),style=wx.TE_PROCESS_ENTER) |
| 2944 | | self.name.Bind(wx.EVT_TEXT_ENTER,self.OnNameChange) |
| 2945 | | self.name.Bind(wx.EVT_KILL_FOCUS,self.OnNameChange) |
| 2946 | | self.dataGridSizer.Add(self.name,0,wx.RIGHT|wx.TOP,10) |
| 2947 | | self.dataGridSizer.Add(wx.StaticText(panel,label='All scales value: '),0, \ |
| 2948 | | wx.LEFT|wx.TOP|wx.ALIGN_CENTER_VERTICAL,10) |
| 2949 | | # azmthOff = G2G.ValidatedTxtCtrl(G2frame.dataDisplay,data,'azmthOff',nDig=(10,2),typeHint=float,OnLeave=OnAzmthOff) |
| 2950 | | allScale = wx.TextCtrl(panel,value='',style=wx.TE_PROCESS_ENTER) |
| 2951 | | allScale.Bind(wx.EVT_TEXT_ENTER,self.OnAllScale) |
| 2952 | | allScale.Bind(wx.EVT_KILL_FOCUS,self.OnAllScale) |
| 2953 | | self.dataGridSizer.Add(allScale,0,WACV) |
| 2954 | | mainSizer.Add(self.dataGridSizer,0,wx.EXPAND) |
| 2955 | | OkBtn = wx.Button(panel,-1,"Ok") |
| 2956 | | OkBtn.Bind(wx.EVT_BUTTON, self.OnOk) |
| 2957 | | cancelBtn = wx.Button(panel,-1,"Cancel") |
| 2958 | | cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel) |
| 2959 | | btnSizer = wx.FlexGridSizer(0,3,10,20) |
| 2960 | | if self.dataType =='PWDR': |
| 2961 | | TestBtn = wx.Button(panel,-1,"Test") |
| 2962 | | TestBtn.Bind(wx.EVT_BUTTON, self.OnTest) |
| 2963 | | btnSizer.Add(TestBtn) |
| 2964 | | btnSizer.Add(OkBtn) |
| 2965 | | btnSizer.Add(cancelBtn) |
| 2966 | | |
| 2967 | | panel.SetSizer(mainSizer) |
| 2968 | | panel.SetAutoLayout(1) |
| 2969 | | panel.SetupScrolling() |
| 2970 | | mainSizer.Add((10,10),1) |
| 2971 | | mainSizer.Add(btnSizer,0,wx.CENTER) |
| 2972 | | panel.SetSizer(mainSizer) |
| 2973 | | panel.Fit() |
| 2974 | | self.Fit() |
| 2975 | | |
| 2976 | | def OnScaleChange(self,event): |
| 2977 | | event.Skip() |
| 2978 | | id = event.GetId() |
| 2979 | | value = self.FindWindowById(id).GetValue() |
| 2980 | | try: |
| 2981 | | self.data[id][0] = float(value) |
| 2982 | | self.FindWindowById(id).SetValue('%.3f'%(self.data[id][0])) |
| 2983 | | except ValueError: |
| 2984 | | if value and '-' not in value[0]: |
| 2985 | | print 'bad input - numbers only' |
| 2986 | | self.FindWindowById(id).SetValue('0.000') |
| 2987 | | |
| 2988 | | def OnAllScale(self,event): |
| 2989 | | event.Skip() |
| 2990 | | id = event.GetId() |
| 2991 | | try: |
| 2992 | | scale = float(self.FindWindowById(id).GetValue()) |
| 2993 | | self.FindWindowById(id).SetValue('%.3f'%(scale)) |
| 2994 | | entries = self.dataGridSizer.GetChildren() |
| 2995 | | for i,item in enumerate(self.data[:-1]): |
| 2996 | | item[0] = scale |
| 2997 | | entries[2*i].GetWindow().SetValue('%.3f'%(scale)) |
| 2998 | | |
| 2999 | | except ValueError: |
| 3000 | | print 'bad input - numbers only' |
| 3001 | | self.FindWindowById(id).SetValue('') |
| 3002 | | |
| 3003 | | |
| 3004 | | def OnNameChange(self,event): |
| 3005 | | event.Skip() |
| 3006 | | self.data[-1] = self.name.GetValue() |
| 3007 | | |
| 3008 | | def OnTest(self,event): |
| 3009 | | lenX = 0 |
| 3010 | | Xminmax = [0,0] |
| 3011 | | XY = [] |
| 3012 | | Xsum = [] |
| 3013 | | Ysum = [] |
| 3014 | | Vsum = [] |
| 3015 | | result = self.data |
| 3016 | | for i,item in enumerate(result[:-1]): |
| 3017 | | scale,name = item |
| 3018 | | data = self.dataList[i] |
| 3019 | | if scale: |
| 3020 | | x,y,w,yc,yb,yd = data #numpy arrays! |
| 3021 | | XY.append([x,scale*y]) |
| 3022 | | v = 1./w |
| 3023 | | if lenX: |
| 3024 | | if lenX != len(x): |
| 3025 | | self.ErrorDialog('Data length error','Data to be summed must have same number of points'+ \ |
| 3026 | | '\nExpected:'+str(lenX)+ \ |
| 3027 | | '\nFound: '+str(len(x))+'\nfor '+name) |
| 3028 | | self.OnCancel(event) |
| 3029 | | else: |
| 3030 | | lenX = len(x) |
| 3031 | | if Xminmax[1]: |
| 3032 | | if Xminmax != [x[0],x[-1]]: |
| 3033 | | self.ErrorDialog('Data range error','Data to be summed must span same range'+ \ |
| 3034 | | '\nExpected:'+str(Xminmax[0])+' '+str(Xminmax[1])+ \ |
| 3035 | | '\nFound: '+str(x[0])+' '+str(x[-1])+'\nfor '+name) |
| 3036 | | self.OnCancel(event) |
| 3037 | | else: |
| 3038 | | for j,yi in enumerate(y): |
| 3039 | | Ysum[j] += scale*yi |
| 3040 | | Vsum[j] += abs(scale)*v[j] |
| 3041 | | else: |
| 3042 | | Xminmax = [x[0],x[-1]] |
| 3043 | | Xsum = x |
| 3044 | | Ysum = scale*y |
| 3045 | | Vsum = abs(scale*v) |
| 3046 | | Wsum = 1./np.array(Vsum) |
| 3047 | | YCsum = np.zeros(lenX) |
| 3048 | | YBsum = np.zeros(lenX) |
| 3049 | | YDsum = np.zeros(lenX) |
| 3050 | | XY.append([Xsum,Ysum]) |
| 3051 | | self.result = [Xsum,Ysum,Wsum,YCsum,YBsum,YDsum] |
| 3052 | | # N.B. PlotXY expects the first arg to point to G2frame. In this case, we |
| 3053 | | # create a duplicate (temporary) Plot notebook window that is a child of the |
| 3054 | | # modal SumDialog dialog (self). This nicely gets deleted when the dialog is destroyed, |
| 3055 | | # but the plot window is not fully functional, at least on the Mac. |
| 3056 | | G2plt.PlotXY(self,XY,lines=True,Title='Sum:'+self.data[-1],labelY='Intensity',) |
| 3057 | | self.plotFrame.Show() |
| 3058 | | |
| 3059 | | def OnOk(self,event): |
| 3060 | | if self.dataType == 'PWDR': self.OnTest(event) |
| 3061 | | parent = self.GetParent() |
| 3062 | | parent.Raise() |
| 3063 | | self.EndModal(wx.ID_OK) |
| 3064 | | |
| 3065 | | def OnCancel(self,event): |
| 3066 | | parent = self.GetParent() |
| 3067 | | parent.Raise() |
| 3068 | | self.EndModal(wx.ID_CANCEL) |
| 3069 | | |
| 3070 | | def GetData(self): |
| 3071 | | if self.dataType == 'PWDR': |
| 3072 | | return self.data,self.result |
| 3073 | | else: |
| 3074 | | return self.data |
| 3075 | | |
| 3076 | | def OnPwdrSum(self,event): |
| 3077 | | 'Sum together powder data(?)' |
| 3078 | | TextList = [] |
| 3079 | | DataList = [] |
| 3080 | | Names = [] |
| 3081 | | Inst = None |
| 3082 | | Comments = ['Sum equals: \n'] |
| 3083 | | if self.PatternTree.GetCount(): |
| 3084 | | item, cookie = self.PatternTree.GetFirstChild(self.root) |
| 3085 | | while item: |
| 3086 | | name = self.PatternTree.GetItemText(item) |
| 3087 | | Names.append(name) |
| 3088 | | if 'PWDR' in name: |
| 3089 | | TextList.append([0.0,name]) |
| 3090 | | DataList.append(self.PatternTree.GetItemPyData(item)[1]) # (x,y,w,yc,yb,yd) |
| 3091 | | if not Inst: |
| 3092 | | Inst = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,item, 'Instrument Parameters')) |
| 3093 | | item, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 3094 | | if len(TextList) < 2: |
| 3095 | | self.ErrorDialog('Not enough data to sum','There must be more than one "PWDR" pattern') |
| 3096 | | return |
| 3097 | | TextList.append('default_sum_name') |
| 3098 | | dlg = self.SumDialog(self,'Sum data','Enter scale for each pattern in summation','PWDR',TextList,DataList) |
| 3099 | | try: |
| 3100 | | if dlg.ShowModal() == wx.ID_OK: |
| 3101 | | result,sumData = dlg.GetData() |
| 3102 | | Xsum,Ysum,Wsum,YCsum,YBsum,YDsum = sumData |
| 3103 | | Xminmax = [Xsum[0],Xsum[-1]] |
| 3104 | | outname = 'PWDR '+result[-1] |
| 3105 | | Id = 0 |
| 3106 | | if outname in Names: |
| 3107 | | dlg2 = wx.MessageDialog(self,'Overwrite data?','Duplicate data name',wx.OK|wx.CANCEL) |
| 3108 | | try: |
| 3109 | | if dlg2.ShowModal() == wx.ID_OK: |
| 3110 | | Id = G2gd.GetPatternTreeItemId(self,self.root,name) |
| 3111 | | self.PatternTree.Delete(Id) |
| 3112 | | finally: |
| 3113 | | dlg2.Destroy() |
| 3114 | | Id = self.PatternTree.AppendItem(parent=self.root,text=outname) |
| 3115 | | if Id: |
| 3116 | | Sample = G2obj.SetDefaultSample() |
| 3117 | | Ymin = np.min(Ysum) |
| 3118 | | Ymax = np.max(Ysum) |
| 3119 | | valuesdict = { |
| 3120 | | 'wtFactor':1.0, |
| 3121 | | 'Dummy':False, |
| 3122 | | 'ranId':ran.randint(0,sys.maxint), |
| 3123 | | 'Offset':[0.0,0.0],'delOffset':0.02*Ymax,'refOffset':-.1*Ymax,'refDelt':0.1*Ymax, |
| 3124 | | 'qPlot':False,'dPlot':False,'sqrtPlot':False,'Yminmax':[Ymin,Ymax] |
| 3125 | | } |
| 3126 | | self.PatternTree.SetItemPyData(Id,[valuesdict,[np.array(Xsum),np.array(Ysum),np.array(Wsum), |
| 3127 | | np.array(YCsum),np.array(YBsum),np.array(YDsum)]]) |
| 3128 | | self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),Comments) |
| 3129 | | self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax]) |
| 3130 | | self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',True,3,1.0,0.0,0.0], |
| 3131 | | {'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}]) |
| 3132 | | self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Instrument Parameters'),Inst) |
| 3133 | | self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample) |
| 3134 | | self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Peak List'),{'peaks':[],'sigDict':{}}) |
| 3135 | | self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Index Peak List'),[[],[]]) |
| 3136 | | self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Unit Cells List'),[]) |
| 3137 | | self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Reflection Lists'),{}) |
| 3138 | | self.PatternTree.SelectItem(Id) |
| 3139 | | self.PatternTree.Expand(Id) |
| 3140 | | finally: |
| 3141 | | dlg.Destroy() |
| 3142 | | |
| 3143 | | def OnImageSum(self,event): |
| 3144 | | 'Sum together image data' |
| 3145 | | TextList = [] |
| 3146 | | DataList = [] |
| 3147 | | IdList = [] |
| 3148 | | Names = [] |
| 3149 | | Comments = ['Sum equals: \n'] |
| 3150 | | if self.PatternTree.GetCount(): |
| 3151 | | item, cookie = self.PatternTree.GetFirstChild(self.root) |
| 3152 | | while item: |
| 3153 | | name = self.PatternTree.GetItemText(item) |
| 3154 | | Names.append(name) |
| 3155 | | if 'IMG' in name: |
| 3156 | | TextList.append([0.0,name]) |
| 3157 | | DataList.append(self.PatternTree.GetImageLoc(item)) #Size,Image,Tag |
| 3158 | | IdList.append(item) |
| 3159 | | Data = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,item,'Image Controls')) |
| 3160 | | item, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 3161 | | if len(TextList) < 2: |
| 3162 | | self.ErrorDialog('Not enough data to sum','There must be more than one "IMG" pattern') |
| 3163 | | return |
| 3164 | | TextList.append('default_sum_name') |
| 3165 | | dlg = self.SumDialog(self,'Sum data','Enter scale for each image in summation','IMG',TextList,DataList) |
| 3166 | | try: |
| 3167 | | if dlg.ShowModal() == wx.ID_OK: |
| 3168 | | imSize = 0 |
| 3169 | | result = dlg.GetData() |
| 3170 | | First = True |
| 3171 | | Found = False |
| 3172 | | for i,item in enumerate(result[:-1]): |
| 3173 | | scale,name = item |
| 3174 | | if scale: |
| 3175 | | Found = True |
| 3176 | | Comments.append("%10.3f %s" % (scale,' * '+name)) |
| 3177 | | Npix,imagefile,imagetag = DataList[i] |
| 3178 | | imagefile = G2IO.GetCheckImageFile(self,IdList[i])[1] |
| 3179 | | image = G2IO.GetImageData(self,imagefile,imageOnly=True,ImageTag=imagetag) |
| 3180 | | if First: |
| 3181 | | newImage = np.zeros_like(image) |
| 3182 | | First = False |
| 3183 | | if imSize: |
| 3184 | | if imSize != Npix: |
| 3185 | | self.ErrorDialog('Image size error','Images to be summed must be same size'+ \ |
| 3186 | | '\nExpected:'+str(imSize)+ \ |
| 3187 | | '\nFound: '+str(Npix)+'\nfor '+name) |
| 3188 | | return |
| 3189 | | newImage = newImage+scale*image |
| 3190 | | else: |
| 3191 | | imSize = Npix |
| 3192 | | newImage = newImage+scale*image |
| 3193 | | del(image) |
| 3194 | | if not Found: |
| 3195 | | self.ErrorDialog('Image sum error','No nonzero image multipliers found') |
| 3196 | | return |
| 3197 | | |
| 3198 | | |
| 3199 | | newImage = np.array(newImage,dtype=np.int32) |
| 3200 | | outname = 'IMG '+result[-1] |
| 3201 | | Id = 0 |
| 3202 | | if outname in Names: |
| 3203 | | dlg2 = wx.MessageDialog(self,'Overwrite data?','Duplicate data name',wx.OK|wx.CANCEL) |
| 3204 | | try: |
| 3205 | | if dlg2.ShowModal() == wx.ID_OK: |
| 3206 | | Id = G2gd.GetPatternTreeItemId(self,self.root,name) |
| 3207 | | finally: |
| 3208 | | dlg2.Destroy() |
| 3209 | | else: |
| 3210 | | Id = self.PatternTree.AppendItem(parent=self.root,text=outname) |
| 3211 | | if Id: |
| 3212 | | pth = G2G.GetExportPath(self) |
| 3213 | | dlg = wx.FileDialog(self, 'Choose sum image filename', pth,outname.split('IMG ')[1], |
| 3214 | | 'G2img files (*.G2img)|*.G2img', |
| 3215 | | wx.SAVE|wx.FD_OVERWRITE_PROMPT) |
| 3216 | | if dlg.ShowModal() == wx.ID_OK: |
| 3217 | | newimagefile = dlg.GetPath() |
| 3218 | | newimagefile = G2IO.FileDlgFixExt(dlg,newimagefile) |
| 3219 | | G2IO.PutG2Image(newimagefile,Comments,Data,Npix,newImage) |
| 3220 | | Imax = np.amax(newImage) |
| 3221 | | Imin = np.amin(newImage) |
| 3222 | | newImage = [] |
| 3223 | | self.PatternTree.SetItemPyData(Id,[imSize,newimagefile]) |
| 3224 | | self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),Comments) |
| 3225 | | del(newImage) |
| 3226 | | if self.imageDefault: |
| 3227 | | Data = copy.copy(self.imageDefault) |
| 3228 | | Data['formatName'] = 'GSAS-II image' |
| 3229 | | Data['showLines'] = True |
| 3230 | | Data['ring'] = [] |
| 3231 | | Data['rings'] = [] |
| 3232 | | Data['cutoff'] = 10 |
| 3233 | | Data['pixLimit'] = 20 |
| 3234 | | Data['ellipses'] = [] |
| 3235 | | Data['calibrant'] = '' |
| 3236 | | Data['range'] = [(Imin,Imax),[Imin,Imax]] |
| 3237 | | self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Image Controls'),Data) |
| 3238 | | Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(Imin,Imax),[Imin,Imax]]} |
| 3239 | | self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Masks'),Masks) |
| 3240 | | self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Stress/Strain'), |
| 3241 | | {'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0}) |
| 3242 | | self.PatternTree.SelectItem(Id) |
| 3243 | | self.PatternTree.Expand(Id) |
| 3244 | | self.PickId = G2gd.GetPatternTreeItemId(self,self.root,outname) |
| 3245 | | self.Image = self.PickId |
| 3246 | | finally: |
| 3247 | | dlg.Destroy() |
| 3248 | | |
| 3249 | | def OnAddPhase(self,event): |
| 3250 | | 'Add a new, empty phase to the tree. Called by Data/Add Phase menu' |
| 3251 | | if not G2gd.GetPatternTreeItemId(self,self.root,'Phases'): |
| 3252 | | sub = self.PatternTree.AppendItem(parent=self.root,text='Phases') |
| 3253 | | else: |
| 3254 | | sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases') |
| 3255 | | PhaseName = '' |
| 3256 | | dlg = wx.TextEntryDialog(None,'Enter a name for this phase','Phase Name Entry','New phase', |
| 3257 | | style=wx.OK) |
| 3258 | | if dlg.ShowModal() == wx.ID_OK: |
| 3259 | | PhaseName = dlg.GetValue() |
| 3260 | | dlg.Destroy() |
| 3261 | | sub = self.PatternTree.AppendItem(parent=sub,text=PhaseName) |
| 3262 | | E,SGData = G2spc.SpcGroup('P 1') |
| 3263 | | self.PatternTree.SetItemPyData(sub,G2obj.SetNewPhase(Name=PhaseName,SGData=SGData)) |
| 3264 | | G2gd.SelectDataTreeItem(self,sub) #bring up new phase General tab |
| 3265 | | |
| 3266 | | def OnDeletePhase(self,event): |
| 3267 | | 'Delete a phase from the tree. Called by Data/Delete Phase menu' |
| 3268 | | #Hmm, also need to delete this phase from Reflection Lists for each PWDR histogram |
| 3269 | | if self.dataFrame: |
| 3270 | | self.dataFrame.Clear() |
| 3271 | | TextList = [] |
| 3272 | | DelList = [] |
| 3273 | | DelItemList = [] |
| 3274 | | if G2gd.GetPatternTreeItemId(self,self.root,'Phases'): |
| 3275 | | sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases') |
| 3276 | | else: |
| 3277 | | return |
| 3278 | | if sub: |
| 3279 | | item, cookie = self.PatternTree.GetFirstChild(sub) |
| 3280 | | while item: |
| 3281 | | TextList.append(self.PatternTree.GetItemText(item)) |
| 3282 | | item, cookie = self.PatternTree.GetNextChild(sub, cookie) |
| 3283 | | dlg = wx.MultiChoiceDialog(self, 'Which phase to delete?', 'Delete phase', TextList, wx.CHOICEDLG_STYLE) |
| 3284 | | try: |
| 3285 | | if dlg.ShowModal() == wx.ID_OK: |
| 3286 | | result = dlg.GetSelections() |
| 3287 | | for i in result: DelList.append([i,TextList[i]]) |
| 3288 | | item, cookie = self.PatternTree.GetFirstChild(sub) |
| 3289 | | i = 0 |
| 3290 | | while item: |
| 3291 | | if [i,self.PatternTree.GetItemText(item)] in DelList: DelItemList.append(item) |
| 3292 | | item, cookie = self.PatternTree.GetNextChild(sub, cookie) |
| 3293 | | i += 1 |
| 3294 | | for item in DelItemList: |
| 3295 | | name = self.PatternTree.GetItemText(item) |
| 3296 | | self.PatternTree.Delete(item) |
| 3297 | | self.G2plotNB.Delete(name) |
| 3298 | | item, cookie = self.PatternTree.GetFirstChild(self.root) |
| 3299 | | while item: |
| 3300 | | name = self.PatternTree.GetItemText(item) |
| 3301 | | if 'PWDR' in name: |
| 3302 | | Id = G2gd.GetPatternTreeItemId(self,item, 'Reflection Lists') |
| 3303 | | refList = self.PatternTree.GetItemPyData(Id) |
| 3304 | | if len(refList): |
| 3305 | | for i,item in DelList: |
| 3306 | | if item in refList: |
| 3307 | | del(refList[item]) |
| 3308 | | # self.PatternTree.SetItemPyData(Id,refList) |
| 3309 | | elif 'HKLF' in name: |
| 3310 | | data = self.PatternTree.GetItemPyData(item) |
| 3311 | | data[0] = {} |
| 3312 | | # self.PatternTree.SetItemPyData(item,data) |
| 3313 | | |
| 3314 | | item, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 3315 | | finally: |
| 3316 | | dlg.Destroy() |
| 3317 | | |
| 3318 | | def OnRenameData(self,event): |
| 3319 | | 'Renames an existing phase. Called by Data/Rename Phase menu' |
| 3320 | | name = self.PatternTree.GetItemText(self.PickId) |
| 3321 | | if 'PWDR' in name or 'HKLF' in name or 'IMG' in name: |
| 3322 | | if 'Bank' in name: |
| 3323 | | names = name.split('Bank') |
| 3324 | | names[1] = ' Bank'+names[1] |
| 3325 | | elif 'Azm' in name: |
| 3326 | | names = name.split('Azm') |
| 3327 | | names[1] = ' Azm'+names[1] |
| 3328 | | else: |
| 3329 | | names = [name,''] |
| 3330 | | dataType = names[0][:names[0].index(' ')+1] #includes the ' ' |
| 3331 | | dlg = wx.TextEntryDialog(self,'Data name: '+name,'Change data name', |
| 3332 | | defaultValue=names[0][names[0].index(' ')+1:]) |
| 3333 | | try: |
| 3334 | | if dlg.ShowModal() == wx.ID_OK: |
| 3335 | | name = dataType+dlg.GetValue()+names[1] |
| 3336 | | self.PatternTree.SetItemText(self.PickId,name) |
| 3337 | | finally: |
| 3338 | | dlg.Destroy() |
| 3339 | | |
| 3340 | | def GetFileList(self,fileType,skip=None): #potentially useful? |
| 3341 | | 'Appears unused. Note routine of same name in GSASIIpwdGUI' |
| 3342 | | fileList = [] |
| 3343 | | Source = '' |
| 3344 | | id, cookie = self.PatternTree.GetFirstChild(self.root) |
| 3345 | | while id: |
| 3346 | | name = self.PatternTree.GetItemText(id) |
| 3347 | | if fileType in name: |
| 3348 | | if id == skip: |
| 3349 | | Source = name |
| 3350 | | else: |
| 3351 | | fileList.append([False,name,id]) |
| 3352 | | id, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 3353 | | if skip: |
| 3354 | | return fileList,Source |
| 3355 | | else: |
| 3356 | | return fileList |
| 3357 | | |
| 3358 | | def OnDataDelete(self, event): |
| 3359 | | '''Delete one or more histograms from data tree. Called by the |
| 3360 | | Data/DeleteData menu |
| 3361 | | ''' |
| 3362 | | TextList = [] |
| 3363 | | DelList = [] |
| 3364 | | DelItemList = [] |
| 3365 | | nItems = {'PWDR':0,'SASD':0,'REFD':0,'IMG':0,'HKLF':0,'PDF':0} |
| 3366 | | PDFnames = [] |
| 3367 | | if self.PatternTree.GetCount(): |
| 3368 | | item, cookie = self.PatternTree.GetFirstChild(self.root) |
| 3369 | | while item: |
| 3370 | | name = self.PatternTree.GetItemText(item) |
| 3371 | | if name not in ['Notebook','Controls','Covariance','Constraints', |
| 3372 | | 'Restraints','Phases','Rigid bodies'] and 'Sequential' not in name: |
| 3373 | | if 'PWDR' in name[:4]: nItems['PWDR'] += 1 |
| 3374 | | if 'SASD' in name[:4]: nItems['SASD'] += 1 |
| 3375 | | if 'REFD' in name[:4]: nItems['REFD'] += 1 |
| 3376 | | if 'IMG' in name[:3]: nItems['IMG'] += 1 |
| 3377 | | if 'HKLF' in name[:4]: nItems['HKLF'] += 1 |
| 3378 | | if 'PDF' in name[:3]: |
| 3379 | | PDFnames.append(name) |
| 3380 | | nItems['PDF'] += 1 |
| 3381 | | TextList.append(name) |
| 3382 | | item, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 3383 | | for pdfName in PDFnames: |
| 3384 | | try: |
| 3385 | | TextList.remove('PWDR'+pdfName[4:]) |
| 3386 | | except ValueError: |
| 3387 | | print 'PWDR'+pdfName[4:]+' for '+pdfName+' not found' |
| 3388 | | dlg = G2G.G2MultiChoiceDialog(self, 'Which data to delete?', 'Delete data', TextList, wx.CHOICEDLG_STYLE) |
| 3389 | | try: |
| 3390 | | if dlg.ShowModal() == wx.ID_OK: |
| 3391 | | result = dlg.GetSelections() |
| 3392 | | for i in result: DelList.append(TextList[i]) |
| 3393 | | item, cookie = self.PatternTree.GetFirstChild(self.root) |
| 3394 | | while item: |
| 3395 | | itemName = self.PatternTree.GetItemText(item) |
| 3396 | | if itemName in DelList: |
| 3397 | | if 'PWDR' in itemName[:4]: nItems['PWDR'] -= 1 |
| 3398 | | elif 'SASD' in itemName[:4]: nItems['SASD'] -= 1 |
| 3399 | | elif 'REFD' in itemName[:4]: nItems['REFD'] -= 1 |
| 3400 | | elif 'IMG' in itemName[:3]: nItems['IMG'] -= 1 |
| 3401 | | elif 'HKLF' in itemName[:4]: nItems['HKLF'] -= 1 |
| 3402 | | elif 'PDF' in itemName[:3]: nItems['PDF'] -= 1 |
| 3403 | | DelItemList.append(item) |
| 3404 | | item, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 3405 | | for item in DelItemList: |
| 3406 | | self.PatternTree.Delete(item) |
| 3407 | | self.PickId = 0 |
| 3408 | | self.PickIdText = None |
| 3409 | | self.PatternId = 0 |
| 3410 | | if nItems['PWDR']: |
| 3411 | | wx.CallAfter(G2plt.PlotPatterns,self,True) |
| 3412 | | else: |
| 3413 | | self.G2plotNB.Delete('Powder Patterns') |
| 3414 | | if not nItems['IMG']: |
| 3415 | | self.G2plotNB.Delete('2D Powder Image') |
| 3416 | | if not nItems['HKLF']: |
| 3417 | | self.G2plotNB.Delete('Structure Factors') |
| 3418 | | if '3D Structure Factors' in self.G2plotNB.plotList: |
| 3419 | | self.G2plotNB.Delete('3D Structure Factors') |
| 3420 | | finally: |
| 3421 | | dlg.Destroy() |
| 3422 | | |
| 3423 | | def OnFileOpen(self, event, filename=None): |
| 3424 | | '''Gets a GSAS-II .gpx project file in response to the |
| 3425 | | File/Open Project menu button |
| 3426 | | ''' |
| 3427 | | result = wx.ID_OK |
| 3428 | | self.EnablePlot = False |
| 3429 | | if self.PatternTree.GetChildrenCount(self.root,False): |
| 3430 | | if self.dataFrame: |
| 3431 | | self.dataFrame.Clear() |
| 3432 | | dlg = wx.MessageDialog( |
| 3433 | | self, |
| 3434 | | 'Do you want to overwrite the current project? '+ |
| 3435 | | 'Any unsaved changes in current project will be lost. Press OK to continue.', |
| 3436 | | 'Overwrite?', wx.OK | wx.CANCEL) |
| 3437 | | try: |
| 3438 | | result = dlg.ShowModal() |
| 3439 | | if result == wx.ID_OK: |
| 3440 | | self.PatternTree.DeleteChildren(self.root) |
| 3441 | | self.GSASprojectfile = '' |
| 3442 | | self.HKL = [] |
| 3443 | | if self.G2plotNB.plotList: |
| 3444 | | self.G2plotNB.clear() |
| 3445 | | finally: |
| 3446 | | dlg.Destroy() |
| 3447 | | if result != wx.ID_OK: return |
| 3448 | | |
| 3449 | | if not filename: |
| 3450 | | if self.dataDisplay: self.dataDisplay.Destroy() |
| 3451 | | if self.LastGPXdir: |
| 3452 | | pth = self.LastGPXdir |
| 3453 | | else: |
| 3454 | | pth = '.' |
| 3455 | | dlg = wx.FileDialog(self, 'Choose GSAS-II project file', pth, |
| 3456 | | wildcard='GSAS-II project file (*.gpx)|*.gpx',style=wx.OPEN) |
| 3457 | | try: |
| 3458 | | if dlg.ShowModal() != wx.ID_OK: return |
| 3459 | | self.GSASprojectfile = dlg.GetPath() |
| 3460 | | self.GSASprojectfile = G2IO.FileDlgFixExt(dlg,self.GSASprojectfile) |
| 3461 | | self.dirname = dlg.GetDirectory() |
| 3462 | | finally: |
| 3463 | | dlg.Destroy() |
| 3464 | | else: |
| 3465 | | self.GSASprojectfile = os.path.splitext(filename)[0]+'.gpx' |
| 3466 | | self.dirname = os.path.split(filename)[0] |
| 3467 | | |
| 3468 | | try: |
| 3469 | | self.StartProject() #open the file if possible |
| 3470 | | except: |
| 3471 | | print '\nError opening file ',filename |
| 3472 | | import traceback |
| 3473 | | print traceback.format_exc() |
| 3474 | | |
| 3475 | | def StartProject(self): |
| 3476 | | '''Opens a GSAS-II project file & selects the 1st available data set to |
| 3477 | | display (PWDR, HKLF, REFD or SASD) |
| 3478 | | ''' |
| 3479 | | |
| 3480 | | Id = 0 |
| 3481 | | phaseId = None |
| 3482 | | G2IO.ProjFileOpen(self) |
| 3483 | | self.PatternTree.SetItemText(self.root,'Loaded Data: '+self.GSASprojectfile) |
| 3484 | | self.PatternTree.Expand(self.root) |
| 3485 | | self.HKL = [] |
| 3486 | | item, cookie = self.PatternTree.GetFirstChild(self.root) |
| 3487 | | while item and not Id: |
| 3488 | | name = self.PatternTree.GetItemText(item) |
| 3489 | | if name[:4] in ['PWDR','HKLF','IMG ','PDF ','SASD','REFD']: |
| 3490 | | Id = item |
| 3491 | | elif name == "Phases": |
| 3492 | | phaseId = item |
| 3493 | | elif name == 'Controls': |
| 3494 | | data = self.PatternTree.GetItemPyData(item) |
| 3495 | | if data: |
| 3496 | | for item in self.Refine: item.Enable(True) |
| 3497 | | self.EnableSeqRefineMenu() |
| 3498 | | item, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 3499 | | if phaseId: # show all phases |
| 3500 | | self.PatternTree.Expand(phaseId) |
| 3501 | | if Id: |
| 3502 | | self.EnablePlot = True |
| 3503 | | self.PatternTree.SelectItem(Id) |
| 3504 | | self.PatternTree.Expand(Id) |
| 3505 | | elif phaseId: |
| 3506 | | self.PatternTree.SelectItem(phaseId) |
| 3507 | | self.CheckNotebook() |
| 3508 | | if self.dirname: os.chdir(self.dirname) # to get Mac/Linux to change directory! |
| 3509 | | pth = os.path.split(os.path.abspath(self.GSASprojectfile))[0] |
| 3510 | | if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth) |
| 3511 | | self.LastGPXdir = pth |
| 3512 | | |
| 3513 | | def OnFileClose(self, event): |
| 3514 | | '''Clears the data tree in response to the |
| 3515 | | File/New Project menu button. User is given option to save |
| 3516 | | the project. |
| 3517 | | ''' |
| 3518 | | if self.dataFrame: |
| 3519 | | self.dataFrame.Clear() |
| 3520 | | self.dataFrame.SetLabel('GSAS-II data display') |
| 3521 | | dlg = wx.MessageDialog(self, 'Save current project?', ' ', wx.YES | wx.NO | wx.CANCEL) |
| 3522 | | try: |
| 3523 | | result = dlg.ShowModal() |
| 3524 | | if result == wx.ID_OK: |
| 3525 | | self.OnFileSaveMenu(event) |
| 3526 | | if result != wx.ID_CANCEL: |
| 3527 | | self.GSASprojectfile = '' |
| 3528 | | self.PatternTree.SetItemText(self.root,'Loaded Data: ') |
| 3529 | | self.PatternTree.DeleteChildren(self.root) |
| 3530 | | if self.HKL: self.HKL = [] |
| 3531 | | if self.G2plotNB.plotList: |
| 3532 | | self.G2plotNB.clear() |
| 3533 | | finally: |
| 3534 | | dlg.Destroy() |
| 3535 | | |
| 3536 | | def OnFileSave(self, event): |
| 3537 | | '''Save the current project in response to the |
| 3538 | | File/Save Project menu button |
| 3539 | | ''' |
| 3540 | | |
| 3541 | | if self.GSASprojectfile: |
| 3542 | | self.PatternTree.SetItemText(self.root,'Loaded Data: '+self.GSASprojectfile) |
| 3543 | | self.CheckNotebook() |
| 3544 | | G2IO.ProjFileSave(self) |
| 3545 | | else: |
| 3546 | | self.OnFileSaveas(event) |
| 3547 | | |
| 3548 | | def OnFileSaveas(self, event): |
| 3549 | | '''Save the current project in response to the |
| 3550 | | File/Save as menu button |
| 3551 | | ''' |
| 3552 | | if GSASIIpath.GetConfigValue('Starting_directory'): |
| 3553 | | pth = GSASIIpath.GetConfigValue('Starting_directory') |
| 3554 | | pth = os.path.expanduser(pth) |
| 3555 | | elif self.LastGPXdir: |
| 3556 | | pth = self.LastGPXdir |
| 3557 | | else: |
| 3558 | | pth = '.' |
| 3559 | | dlg = wx.FileDialog(self, 'Choose GSAS-II project file name', pth, '', |
| 3560 | | 'GSAS-II project file (*.gpx)|*.gpx',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) |
| 3561 | | try: |
| 3562 | | if dlg.ShowModal() == wx.ID_OK: |
| 3563 | | self.GSASprojectfile = dlg.GetPath() |
| 3564 | | self.GSASprojectfile = G2IO.FileDlgFixExt(dlg,self.GSASprojectfile) |
| 3565 | | self.PatternTree.SetItemText(self.root,'Saving project as'+self.GSASprojectfile) |
| 3566 | | self.SetTitle("GSAS-II data tree: "+os.path.split(self.GSASprojectfile)[1]) |
| 3567 | | self.CheckNotebook() |
| 3568 | | G2IO.ProjFileSave(self) |
| 3569 | | os.chdir(dlg.GetDirectory()) # to get Mac/Linux to change directory! |
| 3570 | | finally: |
| 3571 | | dlg.Destroy() |
| 3572 | | |
| 3573 | | def ExpandAll(self,event): |
| 3574 | | '''Expand all tree items or those of a single type |
| 3575 | | ''' |
| 3576 | | txt = self.GetMenuBar().GetLabel(event.Id) |
| 3577 | | if txt == 'all': |
| 3578 | | self.ExpandingAll = True |
| 3579 | | try: |
| 3580 | | self.PatternTree.ExpandAll() |
| 3581 | | finally: |
| 3582 | | self.ExpandingAll = False |
| 3583 | | else: |
| 3584 | | self.ExpandingAll = True |
| 3585 | | try: |
| 3586 | | item, cookie = self.PatternTree.GetFirstChild(self.root) |
| 3587 | | while item: |
| 3588 | | name = self.PatternTree.GetItemText(item) |
| 3589 | | if name.startswith(txt+' '): self.PatternTree.Expand(item) |
| 3590 | | item, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 3591 | | finally: |
| 3592 | | self.ExpandingAll = False |
| 3593 | | |
| 3594 | | def MoveTreeItems(self,event): |
| 3595 | | '''Move tree items of a single type to the end of the tree |
| 3596 | | ''' |
| 3597 | | txt = self.GetMenuBar().GetLabel(event.Id) |
| 3598 | | # make a list of items to copy |
| 3599 | | copyList = [] |
| 3600 | | item, cookie = self.PatternTree.GetFirstChild(self.root) |
| 3601 | | while item: |
| 3602 | | if self.PatternTree.GetItemText(item).startswith(txt+' '): |
| 3603 | | copyList.append(item) |
| 3604 | | item, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 3605 | | |
| 3606 | | self.ExpandingAll = True |
| 3607 | | try: |
| 3608 | | for item in copyList: |
| 3609 | | name = self.PatternTree.GetItemText(item) |
| 3610 | | newId = self.PatternTree.AppendItem(self.root,name) |
| 3611 | | self.PatternTree.SetItemPyData(newId,self.PatternTree.GetItemPyData(item)) |
| 3612 | | chld, chldcookie = self.PatternTree.GetFirstChild(item) |
| 3613 | | while chld: |
| 3614 | | chname = self.PatternTree.GetItemText(chld) |
| 3615 | | newCh = self.PatternTree.AppendItem(newId,chname) |
| 3616 | | self.PatternTree.SetItemPyData(newCh,self.PatternTree.GetItemPyData(chld)) |
| 3617 | | chld, chldcookie = self.PatternTree.GetNextChild(item, chldcookie) |
| 3618 | | self.PatternTree.Delete(item) |
| 3619 | | finally: |
| 3620 | | self.ExpandingAll = False |
| 3621 | | G2gd.SelectDataTreeItem(self,self.root) |
| 3622 | | |
| 3623 | | def ExitMain(self, event): |
| 3624 | | '''Called if the main window is closed''' |
| 3625 | | if self.G2plotNB: |
| 3626 | | self.G2plotNB.Destroy() |
| 3627 | | if self.dataFrame: |
| 3628 | | self.dataFrame.Clear() |
| 3629 | | self.dataFrame.Destroy() |
| 3630 | | if self.undofile: |
| 3631 | | os.remove(self.undofile) |
| 3632 | | sys.exit() |
| 3633 | | |
| 3634 | | def OnFileExit(self, event): |
| 3635 | | '''Called in response to the File/Quit menu button''' |
| 3636 | | if self.G2plotNB: |
| 3637 | | self.G2plotNB.Destroy() |
| 3638 | | if self.dataFrame: |
| 3639 | | self.dataFrame.Clear() |
| 3640 | | self.dataFrame.Destroy() |
| 3641 | | self.Close() |
| 3642 | | |
| 3643 | | def OnExportPeakList(self,event): |
| 3644 | | nptand = lambda x: np.tan(x*math.pi/180.) |
| 3645 | | pth = G2G.GetExportPath(self) |
| 3646 | | dlg = wx.FileDialog(self, 'Choose output peak list file name', pth, '', |
| 3647 | | '(*.*)|*.*',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) |
| 3648 | | try: |
| 3649 | | if dlg.ShowModal() == wx.ID_OK: |
| 3650 | | self.peaklistfile = dlg.GetPath() |
| 3651 | | self.peaklistfile = G2IO.FileDlgFixExt(dlg,self.peaklistfile) |
| 3652 | | file = open(self.peaklistfile,'w') |
| 3653 | | item, cookie = self.PatternTree.GetFirstChild(self.root) |
| 3654 | | while item: |
| 3655 | | name = self.PatternTree.GetItemText(item) |
| 3656 | | if 'PWDR' in name: |
| 3657 | | item2, cookie2 = self.PatternTree.GetFirstChild(item) |
| 3658 | | wave = 0.0 |
| 3659 | | while item2: |
| 3660 | | name2 = self.PatternTree.GetItemText(item2) |
| 3661 | | if name2 == 'Instrument Parameters': |
| 3662 | | Inst = self.PatternTree.GetItemPyData(item2)[0] |
| 3663 | | Type = Inst['Type'][0] |
| 3664 | | if 'T' not in Type: |
| 3665 | | wave = G2mth.getWave(Inst) |
| 3666 | | elif name2 == 'Peak List': |
| 3667 | | pkdata = self.PatternTree.GetItemPyData(item2) |
| 3668 | | peaks = pkdata['peaks'] |
| 3669 | | sigDict = pkdata['sigDict'] |
| 3670 | | item2, cookie2 = self.PatternTree.GetNextChild(item, cookie2) |
| 3671 | | file.write("#%s \n" % (name+' Peak List')) |
| 3672 | | if wave: |
| 3673 | | file.write('#wavelength = %10.6f\n'%(wave)) |
| 3674 | | if 'T' in Type: |
| 3675 | | file.write('#%9s %10s %10s %12s %10s %10s %10s %10s %10s\n'%('pos','dsp','esd','int','alp','bet','sig','gam','FWHM')) |
| 3676 | | else: |
| 3677 | | file.write('#%9s %10s %10s %12s %10s %10s %10s\n'%('pos','dsp','esd','int','sig','gam','FWHM')) |
| 3678 | | for ip,peak in enumerate(peaks): |
| 3679 | | dsp = G2lat.Pos2dsp(Inst,peak[0]) |
| 3680 | | if 'T' in Type: #TOF - more cols |
| 3681 | | esds = {'pos':0.,'int':0.,'alp':0.,'bet':0.,'sig':0.,'gam':0.} |
| 3682 | | for name in esds.keys(): |
| 3683 | | esds[name] = sigDict.get('%s%d'%(name,ip),0.) |
| 3684 | | sig = np.sqrt(peak[8]) |
| 3685 | | gam = peak[10] |
| 3686 | | esddsp = G2lat.Pos2dsp(Inst,esds['pos']) |
| 3687 | | FWHM = G2pwd.getgamFW(gam,sig) #to get delta-TOF from Gam(peak) |
| 3688 | | file.write("%10.2f %10.5f %10.5f %12.2f %10.3f %10.3f %10.3f %10.3f %10.3f\n" % \ |
| 3689 | | (peak[0],dsp,esddsp,peak[2],np.sqrt(max(0.0001,peak[4])),peak[6],peak[8],peak[10],FWHM)) |
| 3690 | | else: #CW |
| 3691 | | #get esds from sigDict for each peak & put in output - esds for sig & gam from UVWXY? |
| 3692 | | esds = {'pos':0.,'int':0.,'sig':0.,'gam':0.} |
| 3693 | | for name in esds.keys(): |
| 3694 | | esds[name] = sigDict.get('%s%d'%(name,ip),0.) |
| 3695 | | sig = np.sqrt(peak[4]) #var -> sig |
| 3696 | | gam = peak[6] |
| 3697 | | esddsp = 0.5*esds['pos']*dsp/nptand(peak[0]/2.) |
| 3698 | | FWHM = G2pwd.getgamFW(gam,sig) #to get delta-2-theta in deg. from Gam(peak) |
| 3699 | | file.write("%10.4f %10.5f %10.5f %12.2f %10.5f %10.5f %10.5f \n" % \ |
| 3700 | | (peak[0],dsp,esddsp,peak[2],np.sqrt(max(0.0001,peak[4]))/100.,peak[6]/100.,FWHM/100.)) #convert to deg |
| 3701 | | item, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 3702 | | file.close() |
| 3703 | | finally: |
| 3704 | | dlg.Destroy() |
| 3705 | | |
| 3706 | | def OnExportHKL(self,event): |
| 3707 | | pth = G2G.GetExportPath(self) |
| 3708 | | dlg = wx.FileDialog(self, 'Choose output reflection list file name', pth, '', |
| 3709 | | '(*.*)|*.*',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) |
| 3710 | | try: |
| 3711 | | if dlg.ShowModal() == wx.ID_OK: |
| 3712 | | self.peaklistfile = dlg.GetPath() |
| 3713 | | self.peaklistfile = G2IO.FileDlgFixExt(dlg,self.peaklistfile) |
| 3714 | | file = open(self.peaklistfile,'w') |
| 3715 | | item, cookie = self.PatternTree.GetFirstChild(self.root) |
| 3716 | | while item: |
| 3717 | | name = self.PatternTree.GetItemText(item) |
| 3718 | | if 'PWDR' in name: |
| 3719 | | item2, cookie2 = self.PatternTree.GetFirstChild(item) |
| 3720 | | while item2: |
| 3721 | | name2 = self.PatternTree.GetItemText(item2) |
| 3722 | | if name2 == 'Reflection Lists': |
| 3723 | | data = self.PatternTree.GetItemPyData(item2) |
| 3724 | | phases = data.keys() |
| 3725 | | for phase in phases: |
| 3726 | | peaks = data[phase] |
| 3727 | | I100 = peaks['RefList'].T[8]*np.array([refl[11] for refl in peaks['RefList']]) |
| 3728 | | Imax = np.max(I100) |
| 3729 | | if Imax: |
| 3730 | | I100 *= 100.0/Imax |
| 3731 | | file.write("%s %s %s \n" % (name,phase,' Reflection List')) |
| 3732 | | if 'T' in peaks.get('Type','PXC'): |
| 3733 | | file.write('%s \n'%(' h k l m d-space TOF wid Fo**2 Fc**2 Icorr Prfo Trans ExtP I100')) |
| 3734 | | else: |
| 3735 | | file.write('%s \n'%(' h k l m d-space 2-theta wid Fo**2 Fc**2 Icorr Prfo Trans ExtP I100')) |
| 3736 | | for ipk,peak in enumerate(peaks['RefList']): |
| 3737 | | if 'T' in peaks.get('Type','PXC'): |
| 3738 | | sig = np.sqrt(peak[6]) |
| 3739 | | gam = peak[7] |
| 3740 | | FWHM = G2pwd.getgamFW(gam,sig) |
| 3741 | | file.write(" %3d %3d %3d %3d%10.5f%10.2f%10.5f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" % \ |
| 3742 | | (int(peak[0]),int(peak[1]),int(peak[2]),int(peak[3]),peak[4],peak[5],FWHM,peak[8], |
| 3743 | | peak[9],peak[11],peak[12],peak[13],peak[14],I100[ipk])) |
| 3744 | | else: |
| 3745 | | sig = np.sqrt(peak[6]) |
| 3746 | | gam = peak[7] |
| 3747 | | FWHM = G2pwd.getgamFW(gam,sig) |
| 3748 | | file.write(" %3d %3d %3d %3d%10.5f%10.5f%10.5f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" % \ |
| 3749 | | (int(peak[0]),int(peak[1]),int(peak[2]),int(peak[3]),peak[4],peak[5],FWHM/100., |
| 3750 | | peak[8],peak[9],peak[11],peak[12],peak[13],peak[14],I100[ipk])) |
| 3751 | | item2, cookie2 = self.PatternTree.GetNextChild(item, cookie2) |
| 3752 | | item, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 3753 | | file.close() |
| 3754 | | finally: |
| 3755 | | dlg.Destroy() |
| 3756 | | |
| 3757 | | def OnExportPDF(self,event): |
| 3758 | | #need S(Q) and G(R) to be saved here - probably best from selection? |
| 3759 | | names = G2pdG.GetFileList(self,'PDF') |
| 3760 | | exports = [] |
| 3761 | | if names: |
| 3762 | | od = {'label_1':'Export I(Q)','value_1':False,'label_2':'Export S(Q)','value_2':False, |
| 3763 | | 'label_3':'Export F(Q)','value_3':False,'label_4':'Export G(R)','value_4':True, |
| 3764 | | 'label_5':'Make G(R) for pdfGUI','value_5':False} |
| 3765 | | dlg = G2G.G2MultiChoiceDialog(self,'Select','PDF patterns to export',names,extraOpts=od) |
| 3766 | | if dlg.ShowModal() == wx.ID_OK: |
| 3767 | | sel = dlg.GetSelections() |
| 3768 | | for x in sel: |
| 3769 | | exports.append(names[x]) |
| 3770 | | dlg.Destroy() |
| 3771 | | if exports: |
| 3772 | | PDFsaves = [od['value_1'],od['value_2'],od['value_3'],od['value_4'],od['value_5']] |
| 3773 | | G2IO.PDFSave(self,exports,PDFsaves) |
| 3774 | | |
| 3775 | | def OnMakePDFs(self,event): |
| 3776 | | '''Sets up PDF data structure filled with defaults; if found chemical formula is inserted |
| 3777 | | so a default PDF can be made. |
| 3778 | | ''' |
| 3779 | | sind = lambda x: math.sin(x*math.pi/180.) |
| 3780 | | tth2q = lambda t,w:4.0*math.pi*sind(t/2.0)/w |
| 3781 | | tof2q = lambda t,C:2.0*math.pi*C/t |
| 3782 | | TextList = [] |
| 3783 | | ElLists = [] |
| 3784 | | Qlimits = [] |
| 3785 | | Names = [] |
| 3786 | | if self.PatternTree.GetCount(): |
| 3787 | | id, cookie = self.PatternTree.GetFirstChild(self.root) |
| 3788 | | while id: |
| 3789 | | name = self.PatternTree.GetItemText(id) |
| 3790 | | Names.append(name) |
| 3791 | | if 'PWDR' in name: |
| 3792 | | TextList.append(name) |
| 3793 | | Data = self.PatternTree.GetItemPyData(id)[1] |
| 3794 | | pwdrMin = np.min(Data[1]) |
| 3795 | | Comments = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,id,'Comments')) |
| 3796 | | Parms = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,id,'Instrument Parameters'))[0] |
| 3797 | | fullLimits = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,id,'Limits'))[0] |
| 3798 | | if 'C' in Parms['Type'][0]: |
| 3799 | | wave = G2mth.getWave(Parms) |
| 3800 | | qMax = tth2q(fullLimits[1],wave) |
| 3801 | | else: #'T'of |
| 3802 | | qMax = tof2q(fullLimits[0],Parms['difC'][1]) |
| 3803 | | Qlimits.append([0.9*qMax,qMax]) |
| 3804 | | ElList = {} |
| 3805 | | sumnum = 1. |
| 3806 | | for item in Comments: #grab chemical formula from Comments |
| 3807 | | if 'formula' in item[:15].lower(): |
| 3808 | | formula = item.split('=')[1].split() |
| 3809 | | try: |
| 3810 | | elems = formula[::2] |
| 3811 | | nums = formula[1::2] |
| 3812 | | Formula = zip(elems,nums) |
| 3813 | | sumnum = 0. |
| 3814 | | for [elem,num] in Formula: |
| 3815 | | ElData = G2elem.GetElInfo(elem,Parms) |
| 3816 | | ElData['FormulaNo'] = float(num) |
| 3817 | | sumnum += float(num) |
| 3818 | | ElList[elem] = ElData |
| 3819 | | |
| 3820 | | except ValueError: |
| 3821 | | ElData = G2elem.GetElInfo(formula[0],Parms) |
| 3822 | | ElData['FormulaNo'] = 1.0 |
| 3823 | | ElList[elem] = ElData |
| 3824 | | ElLists.append(ElList) |
| 3825 | | id, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 3826 | | if len(TextList) < 1: |
| 3827 | | self.ErrorDialog('Nothing to make PDFs for','There must be at least one "PWDR" pattern') |
| 3828 | | return |
| 3829 | | dlg = G2G.G2MultiChoiceDialog(self,'Make PDF controls','Make PDF controls for:',TextList, wx.CHOICEDLG_STYLE) |
| 3830 | | try: |
| 3831 | | if dlg.ShowModal() == wx.ID_OK: |
| 3832 | | for i in dlg.GetSelections(): |
| 3833 | | PDFnames = G2gd.GetPatternTreeDataNames(self,['PDF ',]) |
| 3834 | | G2obj.CreatePDFitems(self,TextList[i],ElLists[i],Qlimits[i],sumnum,pwdrMin,PDFnames) |
| 3835 | | for item in self.ExportPDF: item.Enable(True) |
| 3836 | | finally: |
| 3837 | | dlg.Destroy() |
| 3838 | | |
| 3839 | | def GetPWDRdatafromTree(self,PWDRname): |
| 3840 | | ''' Returns powder data from GSASII tree |
| 3841 | | |
| 3842 | | :param str PWDRname: a powder histogram name as obtained from |
| 3843 | | :meth:`GSASIIstruct.GetHistogramNames` |
| 3844 | | |
| 3845 | | :returns: PWDRdata = powder data dictionary with |
| 3846 | | Powder data arrays, Limits, Instrument Parameters, |
| 3847 | | Sample Parameters |
| 3848 | | ''' |
| 3849 | | PWDRdata = {} |
| 3850 | | try: |
| 3851 | | PWDRdata.update(self.PatternTree.GetItemPyData(PWDRname)[0]) #wtFactor + ? |
| 3852 | | except ValueError: |
| 3853 | | PWDRdata['wtFactor'] = 1.0 |
| 3854 | | PWDRdata['Data'] = self.PatternTree.GetItemPyData(PWDRname)[1] #powder data arrays |
| 3855 | | PWDRdata['Limits'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Limits')) |
| 3856 | | PWDRdata['Background'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Background')) |
| 3857 | | PWDRdata['Instrument Parameters'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Instrument Parameters')) |
| 3858 | | PWDRdata['Sample Parameters'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Sample Parameters')) |
| 3859 | | PWDRdata['Reflection Lists'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Reflection Lists')) |
| 3860 | | if 'ranId' not in PWDRdata: # patch, add a random Id |
| 3861 | | PWDRdata['ranId'] = ran.randint(0,sys.maxint) |
| 3862 | | if 'ranId' not in PWDRdata['Sample Parameters']: # I hope this becomes obsolete at some point |
| 3863 | | PWDRdata['Sample Parameters']['ranId'] = PWDRdata['ranId'] |
| 3864 | | return PWDRdata |
| 3865 | | |
| 3866 | | def GetHKLFdatafromTree(self,HKLFname): |
| 3867 | | ''' Returns single crystal data from GSASII tree |
| 3868 | | |
| 3869 | | :param str HKLFname: a single crystal histogram name as obtained |
| 3870 | | from |
| 3871 | | :meth:`GSASIIstruct.GetHistogramNames` |
| 3872 | | |
| 3873 | | :returns: HKLFdata = single crystal data list of reflections |
| 3874 | | |
| 3875 | | ''' |
| 3876 | | HKLFdata = {} |
| 3877 | | HKLFdata.update(self.PatternTree.GetItemPyData(HKLFname)[0]) #wtFactor + ? |
| 3878 | | # try: |
| 3879 | | # HKLFdata.update(self.PatternTree.GetItemPyData(HKLFname)[0]) #wtFactor + ? |
| 3880 | | # except ValueError: |
| 3881 | | # HKLFdata['wtFactor'] = 1.0 |
| 3882 | | HKLFdata['Data'] = self.PatternTree.GetItemPyData(HKLFname)[1] |
| 3883 | | HKLFdata['Instrument Parameters'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,HKLFname,'Instrument Parameters')) |
| 3884 | | return HKLFdata |
| 3885 | | |
| 3886 | | def GetPhaseData(self): |
| 3887 | | '''Returns a dict with defined phases. |
| 3888 | | Note routine :func:`GSASIIstrIO.GetPhaseData` also exists to |
| 3889 | | get same info from GPX file. |
| 3890 | | ''' |
| 3891 | | phaseData = {} |
| 3892 | | if G2gd.GetPatternTreeItemId(self,self.root,'Phases'): |
| 3893 | | sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases') |
| 3894 | | else: |
| 3895 | | print 'no phases found in GetPhaseData' |
| 3896 | | sub = None |
| 3897 | | if sub: |
| 3898 | | item, cookie = self.PatternTree.GetFirstChild(sub) |
| 3899 | | while item: |
| 3900 | | phaseName = self.PatternTree.GetItemText(item) |
| 3901 | | phaseData[phaseName] = self.PatternTree.GetItemPyData(item) |
| 3902 | | if 'ranId' not in phaseData[phaseName]: |
| 3903 | | phaseData[phaseName]['ranId'] = ran.randint(0,sys.maxint) |
| 3904 | | item, cookie = self.PatternTree.GetNextChild(sub, cookie) |
| 3905 | | return phaseData |
| 3906 | | |
| 3907 | | def GetPhaseInfofromTree(self): |
| 3908 | | '''Get the phase names and their rId values, |
| 3909 | | also the histograms used in each phase. |
| 3910 | | |
| 3911 | | :returns: (phaseRIdList, usedHistograms) where |
| 3912 | | |
| 3913 | | * phaseRIdList is a list of random Id values for each phase |
| 3914 | | * usedHistograms is a dict where the keys are the phase names |
| 3915 | | and the values for each key are a list of the histogram names |
| 3916 | | used in each phase. |
| 3917 | | ''' |
| 3918 | | phaseRIdList = [] |
| 3919 | | usedHistograms = {} |
| 3920 | | sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases') |
| 3921 | | if sub: |
| 3922 | | item, cookie = self.PatternTree.GetFirstChild(sub) |
| 3923 | | while item: |
| 3924 | | phaseName = self.PatternTree.GetItemText(item) |
| 3925 | | ranId = self.PatternTree.GetItemPyData(item).get('ranId') |
| 3926 | | if ranId: phaseRIdList.append(ranId) |
| 3927 | | data = self.PatternTree.GetItemPyData(item) |
| 3928 | | UseList = data['Histograms'] |
| 3929 | | usedHistograms[phaseName] = UseList.keys() |
| 3930 | | item, cookie = self.PatternTree.GetNextChild(sub, cookie) |
| 3931 | | return phaseRIdList,usedHistograms |
| 3932 | | |
| 3933 | | def GetPhaseNames(self): |
| 3934 | | '''Returns a list of defined phases. |
| 3935 | | Note routine :func:`GSASIIstrIO.GetPhaseNames` also exists to |
| 3936 | | get same info from GPX file. |
| 3937 | | ''' |
| 3938 | | phaseNames = [] |
| 3939 | | if G2gd.GetPatternTreeItemId(self,self.root,'Phases'): |
| 3940 | | sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases') |
| 3941 | | else: |
| 3942 | | print 'no phases found in GetPhaseNames' |
| 3943 | | sub = None |
| 3944 | | if sub: |
| 3945 | | item, cookie = self.PatternTree.GetFirstChild(sub) |
| 3946 | | while item: |
| 3947 | | phase = self.PatternTree.GetItemText(item) |
| 3948 | | phaseNames.append(phase) |
| 3949 | | item, cookie = self.PatternTree.GetNextChild(sub, cookie) |
| 3950 | | return phaseNames |
| 3951 | | |
| 3952 | | def GetHistogramNames(self,hType): |
| 3953 | | """ Returns a list of histogram names found in the GSASII data tree |
| 3954 | | Note routine :func:`GSASIIstrIO.GetHistogramNames` also exists to |
| 3955 | | get same info from GPX file. |
| 3956 | | |
| 3957 | | :param str hType: list of histogram types |
| 3958 | | :return: list of histogram names |
| 3959 | | |
| 3960 | | """ |
| 3961 | | HistogramNames = [] |
| 3962 | | if self.PatternTree.GetCount(): |
| 3963 | | item, cookie = self.PatternTree.GetFirstChild(self.root) |
| 3964 | | while item: |
| 3965 | | name = self.PatternTree.GetItemText(item) |
| 3966 | | if name[:4] in hType: |
| 3967 | | HistogramNames.append(name) |
| 3968 | | item, cookie = self.PatternTree.GetNextChild(self.root, cookie) |
| 3969 | | |
| 3970 | | return HistogramNames |
| 3971 | | |
| 3972 | | def GetUsedHistogramsAndPhasesfromTree(self): |
| 3973 | | ''' Returns all histograms that are found in any phase |
| 3974 | | and any phase that uses a histogram. |
| 3975 | | This also assigns numbers to used phases and histograms by the |
| 3976 | | order they appear in the file. |
| 3977 | | Note routine :func:`GSASIIstrIO.GetUsedHistogramsAndPhasesfromTree` also exists to |
| 3978 | | get same info from GPX file. |
| 3979 | | |
| 3980 | | :returns: (Histograms,Phases) |
| 3981 | | |
| 3982 | | * Histograms = dictionary of histograms as {name:data,...} |
| 3983 | | * Phases = dictionary of phases that use histograms |
| 3984 | | ''' |
| 3985 | | Histograms = {} |
| 3986 | | Phases = {} |
| 3987 | | phaseNames = self.GetPhaseNames() |
| 3988 | | phaseData = self.GetPhaseData() |
| 3989 | | histoList = self.GetHistogramNames(['PWDR','HKLF']) |
| 3990 | | |
| 3991 | | for phase in phaseData: |
| 3992 | | Phase = phaseData[phase] |
| 3993 | | pId = phaseNames.index(phase) |
| 3994 | | Phase['pId'] = pId |
| 3995 | | if Phase['Histograms']: |
| 3996 | | if phase not in Phases: |
| 3997 | | Phases[phase] = Phase |
| 3998 | | for hist in Phase['Histograms']: |
| 3999 | | if 'Use' not in Phase['Histograms'][hist]: #patch: add Use flag as True |
| 4000 | | Phase['Histograms'][hist]['Use'] = True |
| 4001 | | if hist not in Histograms and Phase['Histograms'][hist]['Use']: |
| 4002 | | item = G2gd.GetPatternTreeItemId(self,self.root,hist) |
| 4003 | | if item: |
| 4004 | | if 'PWDR' in hist[:4]: |
| 4005 | | Histograms[hist] = self.GetPWDRdatafromTree(item) |
| 4006 | | elif 'HKLF' in hist[:4]: |
| 4007 | | Histograms[hist] = self.GetHKLFdatafromTree(item) |
| 4008 | | hId = histoList.index(hist) |
| 4009 | | Histograms[hist]['hId'] = hId |
| 4010 | | else: # would happen if a referenced histogram were renamed or deleted |
| 4011 | | print('For phase "'+phase+ |
| 4012 | | '" unresolved reference to histogram "'+hist+'"') |
| 4013 | | #G2obj.IndexAllIds(Histograms=Histograms,Phases=Phases) |
| 4014 | | G2obj.IndexAllIds(Histograms=Histograms,Phases=phaseData) |
| 4015 | | return Histograms,Phases |
| 4016 | | |
| 4017 | | def MakeLSParmDict(self): |
| 4018 | | '''Load all parameters used for computation from the tree into a |
| 4019 | | dict of paired values [value, refine flag]. Note that this is |
| 4020 | | different than the parmDict used in the refinement, which only has |
| 4021 | | values. |
| 4022 | | |
| 4023 | | Note that similar things are done in |
| 4024 | | :meth:`GSASIIIO.ExportBaseclass.loadParmDict` (from the tree) and |
| 4025 | | :func:`GSASIIstrMain.Refine` and :func:`GSASIIstrMain.SeqRefine` (from |
| 4026 | | a GPX file). |
| 4027 | | |
| 4028 | | :returns: (parmDict,varyList) where: |
| 4029 | | |
| 4030 | | * parmDict is a dict with values and refinement flags |
| 4031 | | for each parameter and |
| 4032 | | * varyList is a list of variables (refined parameters). |
| 4033 | | ''' |
| 4034 | | parmDict = {} |
| 4035 | | Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree() |
| 4036 | | for phase in Phases: |
| 4037 | | if 'pId' not in Phases[phase]: |
| 4038 | | self.ErrorDialog('View parameter error','You must run least squares at least once') |
| 4039 | | raise Exception,'No pId for phase '+phase |
| 4040 | | rigidbodyDict = self.PatternTree.GetItemPyData( |
| 4041 | | G2gd.GetPatternTreeItemId(self,self.root,'Rigid bodies')) |
| 4042 | | rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False) |
| 4043 | | rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) |
| 4044 | | Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtable,BLtable,MFtable,maxSSwave = G2stIO.GetPhaseData(Phases,RestraintDict=None,rbIds=rbIds,Print=False) |
| 4045 | | hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(Phases,Histograms,Print=False) |
| 4046 | | histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False) |
| 4047 | | varyList = rbVary+phaseVary+hapVary+histVary |
| 4048 | | parmDict.update(rbDict) |
| 4049 | | parmDict.update(phaseDict) |
| 4050 | | parmDict.update(hapDict) |
| 4051 | | parmDict.update(histDict) |
| 4052 | | for parm in parmDict: |
| 4053 | | if parm.split(':')[-1] in ['Azimuth','Gonio. radius','Lam1','Lam2', |
| 4054 | | 'Omega','Chi','Phi','nDebye','nPeaks']: |
| 4055 | | parmDict[parm] = [parmDict[parm],'-'] |
| 4056 | | elif parm.split(':')[-2] in ['Ax','Ay','Az','SHmodel','SHord']: |
| 4057 | | parmDict[parm] = [parmDict[parm],'-'] |
| 4058 | | elif parm in varyList: |
| 4059 | | parmDict[parm] = [parmDict[parm],'T'] |
| 4060 | | else: |
| 4061 | | parmDict[parm] = [parmDict[parm],'F'] |
| 4062 | | # for i in parmDict: print i,'\t',parmDict[i] |
| 4063 | | # fl = open('parmDict.dat','wb') |
| 4064 | | # import cPickle |
| 4065 | | # cPickle.dump(parmDict,fl,1) |
| 4066 | | # fl.close() |
| 4067 | | return parmDict,varyList |
| 4068 | | |
| 4069 | | def OnShowLSParms(self,event): |
| 4070 | | '''Displays a window showing all parameters in the refinement. |
| 4071 | | Called from the Calculate/View LS Parms menu. |
| 4072 | | ''' |
| 4073 | | try: |
| 4074 | | parmDict,varyList = self.MakeLSParmDict() |
| 4075 | | except: |
| 4076 | | print('Error retrieving parameters') |
| 4077 | | return |
| 4078 | | parmValDict = {} |
| 4079 | | for i in parmDict: |
| 4080 | | parmValDict[i] = parmDict[i][0] |
| 4081 | | |
| 4082 | | reqVaryList = tuple(varyList) # save requested variables |
| 4083 | | try: |
| 4084 | | # process constraints |
| 4085 | | sub = G2gd.GetPatternTreeItemId(self,self.root,'Constraints') |
| 4086 | | Constraints = self.PatternTree.GetItemPyData(sub) |
| 4087 | | constList = [] |
| 4088 | | for item in Constraints: |
| 4089 | | if item.startswith('_'): continue |
| 4090 | | constList += Constraints[item] |
| 4091 | | G2mv.InitVars() |
| 4092 | | constrDict,fixedList,ignored = G2stIO.ProcessConstraints(constList) |
| 4093 | | groups,parmlist = G2mv.GroupConstraints(constrDict) |
| 4094 | | G2mv.GenerateConstraints(groups,parmlist,varyList,constrDict,fixedList,parmValDict) |
| 4095 | | G2mv.Map2Dict(parmValDict,varyList) |
| 4096 | | except: |
| 4097 | | pass |
| 4098 | | dlg = G2gd.ShowLSParms(self,'Least Squares Parameters',parmValDict,varyList,reqVaryList) |
| 4099 | | dlg.ShowModal() |
| 4100 | | dlg.Destroy() |
| 4101 | | |
| 4102 | | def OnRefine(self,event): |
| 4103 | | '''Perform a refinement. |
| 4104 | | Called from the Calculate/Refine menu. |
| 4105 | | ''' |
| 4106 | | Id = G2gd.GetPatternTreeItemId(self,self.root,'Sequential results') |
| 4107 | | if Id: |
| 4108 | | dlg = wx.MessageDialog( |
| 4109 | | self, |
| 4110 | | 'Your last refinement was sequential. Continue with "Refine", removing previous sequential results?', |
| 4111 | | 'Remove sequential results?',wx.OK|wx.CANCEL) |
| 4112 | | if dlg.ShowModal() == wx.ID_OK: |
| 4113 | | self.PatternTree.Delete(Id) |
| 4114 | | dlg.Destroy() |
| 4115 | | else: |
| 4116 | | dlg.Destroy() |
| 4117 | | return |
| 4118 | | self.OnFileSave(event) |
| 4119 | | # check that constraints are OK here |
| 4120 | | errmsg, warnmsg = G2stIO.ReadCheckConstraints(self.GSASprojectfile) |
| 4121 | | if errmsg: |
| 4122 | | self.ErrorDialog('Refinement error',errmsg) |
| 4123 | | return |
| 4124 | | if warnmsg: |
| 4125 | | print('Conflict between refinment flag settings and constraints:\n'+ |
| 4126 | | warnmsg+'\nRefinement not possible') |
| 4127 | | self.ErrorDialog('Refinement Flag Error', |
| 4128 | | 'Conflict between refinement flag settings and constraints:\n'+ |
| 4129 | | warnmsg+'\nRefinement not possible') |
| 4130 | | return |
| 4131 | | dlg = wx.ProgressDialog('Residual','All data Rw =',101.0, |
| 4132 | | style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT, |
| 4133 | | parent=self) |
| 4134 | | Size = dlg.GetSize() |
| 4135 | | if 50 < Size[0] < 500: # sanity check on size, since this fails w/Win & wx3.0 |
| 4136 | | dlg.SetSize((int(Size[0]*1.2),Size[1])) # increase size a bit along x |
| 4137 | | dlg.CenterOnParent() |
| 4138 | | Rw = 100.00 |
| 4139 | | self.SaveTreeSetting() |
| 4140 | | self.PatternTree.SaveExposedItems() |
| 4141 | | try: |
| 4142 | | OK,Msg = G2stMn.Refine(self.GSASprojectfile,dlg) #Msg is Rvals dict if Ok=True |
| 4143 | | finally: |
| 4144 | | dlg.Update(101.) # forces the Auto_Hide; needed after move w/Win & wx3.0 |
| 4145 | | dlg.Destroy() |
| 4146 | | wx.Yield() |
| 4147 | | if OK: |
| 4148 | | Rw = Msg['Rwp'] |
| 4149 | | lamMax = Msg.get('lamMax',0.001) |
| 4150 | | lst = os.path.splitext(os.path.abspath(self.GSASprojectfile))[0] |
| 4151 | | text = u'Detailed results are in '+lst+'.lst\n\nLoad new result?' |
| 4152 | | if lamMax >= 10.: |
| 4153 | | text += '\nWARNING: Steepest descents dominates;'+ \ |
| 4154 | | ' minimum may not have been reached\nor result may be false minimum.'+ \ |
| 4155 | | ' You should reconsider your parameter suite' |
| 4156 | | dlg2 = wx.MessageDialog(self,text,'Refinement results, Rw =%.3f'%(Rw),wx.OK|wx.CANCEL) |
| 4157 | | try: |
| 4158 | | if dlg2.ShowModal() == wx.ID_OK: |
| 4159 | | self.PatternTree.DeleteChildren(self.root) |
| 4160 | | self.HKL = [] |
| 4161 | | G2IO.ProjFileOpen(self,False) |
| 4162 | | self.PatternTree.RestoreExposedItems() |
| 4163 | | self.ResetPlots() |
| 4164 | | finally: |
| 4165 | | dlg2.Destroy() |
| 4166 | | else: |
| 4167 | | self.ErrorDialog('Refinement error',Msg) |
| 4168 | | |
| 4169 | | def SaveTreeSetting(self): |
| 4170 | | 'Save the last tree setting' |
| 4171 | | oldId = self.PatternTree.GetSelection() #retain current selection |
| 4172 | | oldPath = self.GetTreeItemsList(oldId) |
| 4173 | | self.lastTreeSetting = oldPath |
| 4174 | | # note that for reasons unclear, it does not seem necessary to reload the Atoms tab |
| 4175 | | #parentName = '' |
| 4176 | | #tabId = None |
| 4177 | | # parentId = self.PatternTree.GetItemParent(oldId) |
| 4178 | | # if parentId: |
| 4179 | | # parentName = self.PatternTree.GetItemText(parentId) #find the current data tree name |
| 4180 | | # if 'Phases' in parentName: |
| 4181 | | # tabId = self.dataDisplay.GetSelection() |
| 4182 | | #self.lastTreeSetting = oldPath,tabId |
| 4183 | | #GSASIIpath.IPyBreak() |
| 4184 | | |
| 4185 | | def TestResetPlot(self,event): |
| 4186 | | '''Debug code to test cleaning up plots after a refinement''' |
| 4187 | | #for i in range(self.G2plotNB.nb.GetPageCount()): |
| 4188 | | # [self.G2plotNB.nb.GetPageText(i) |
| 4189 | | # save current tree item and (if needed) atoms tab |
| 4190 | | self.SaveTreeSetting() |
| 4191 | | self.ResetPlots() |
| 4192 | | |
| 4193 | | def ResetPlots(self): |
| 4194 | | '''This reloads the current tree item, often drawing a plot. It refreshes any plots |
| 4195 | | that have registered a refresh routine (see G2plotNB.RegisterRedrawRoutine) |
| 4196 | | and deletes all plots that have not been refreshed and |
| 4197 | | require one (see G2plotNB.SetNoDelete). |
| 4198 | | ''' |
| 4199 | | lastRaisedPlotTab = self.G2plotNB.lastRaisedPlotTab # save the last page saved |
| 4200 | | #print 'lastRaisedPlotTab=',lastRaisedPlotTab |
| 4201 | | self.G2plotNB.lastRaisedPlotTab = None |
| 4202 | | # mark displayed plots as invalid |
| 4203 | | for lbl,frame in zip(self.G2plotNB.plotList,self.G2plotNB.panelList): |
| 4204 | | frame.plotInvalid = True |
| 4205 | | # reload current tree item, triggering the routine to redraw the data window and possibly a plot |
| 4206 | | #oldPath,tabId = self.lastTreeSetting |
| 4207 | | oldPath = self.lastTreeSetting |
| 4208 | | Id = self.root |
| 4209 | | for txt in oldPath: |
| 4210 | | Id = G2gd.GetPatternTreeItemId(self, Id, txt) |
| 4211 | | self.PickIdText = None #force reload of page |
| 4212 | | if Id: |
| 4213 | | self.PickId = Id |
| 4214 | | self.PatternTree.SelectItem(Id) |
| 4215 | | # update other self-updating plots |
| 4216 | | # for lbl,frame in zip(self.G2plotNB.plotList,self.G2plotNB.panelList): |
| 4217 | | # if frame.plotInvalid and frame.replotFunction: |
| 4218 | | # frame.replotFunction(*frame.replotArgs,**frame.replotKWargs) |
| 4219 | | # delete any remaining plots that are still invalid and need a refresh |
| 4220 | | for lbl,frame in zip(self.G2plotNB.plotList,self.G2plotNB.panelList): |
| 4221 | | if frame.plotInvalid and frame.plotRequiresRedraw: |
| 4222 | | self.G2plotNB.Delete(lbl) |
| 4223 | | # put the previously last-raised tab on top, if present. If not, use the one corresponding to |
| 4224 | | # the last tree item to be selected |
| 4225 | | wx.CallAfter(self.G2plotNB.RaiseLastPage,lastRaisedPlotTab,self.G2plotNB.lastRaisedPlotTab) |
| 4226 | | |
| 4227 | | def OnSeqRefine(self,event): |
| 4228 | | '''Perform a sequential refinement. |
| 4229 | | Called from the Calculate/Sequential refine menu. |
| 4230 | | ''' |
| 4231 | | Id = G2gd.GetPatternTreeItemId(self,self.root,'Sequential results') |
| 4232 | | if not Id: |
| 4233 | | Id = self.PatternTree.AppendItem(self.root,text='Sequential results') |
| 4234 | | self.PatternTree.SetItemPyData(Id,{}) |
| 4235 | | self.G2plotNB.Delete('Sequential refinement') #clear away probably invalid plot |
| 4236 | | Controls = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.root, 'Controls')) |
| 4237 | | if not Controls.get('Seq Data'): |
| 4238 | | print('Error: a sequential refinement has not been set up') |
| 4239 | | return |
| 4240 | | Controls['ShowCell'] = True |
| 4241 | | self.OnFileSave(event) |
| 4242 | | # check that constraints are OK here |
| 4243 | | errmsg, warnmsg = G2stIO.ReadCheckConstraints(self.GSASprojectfile) |
| 4244 | | if errmsg: |
| 4245 | | self.ErrorDialog('Refinement error',errmsg) |
| 4246 | | return |
| 4247 | | if warnmsg: |
| 4248 | | print('Conflict between refinment flag settings and constraints:\n'+ |
| 4249 | | warnmsg+'\nRefinement not possible') |
| 4250 | | self.ErrorDialog('Refinement Flag Error', |
| 4251 | | 'Conflict between refinment flag settings and constraints:\n'+ |
| 4252 | | warnmsg+'\nRefinement not possible') |
| 4253 | | return |
| 4254 | | self.PatternTree.SaveExposedItems() |
| 4255 | | dlg = wx.ProgressDialog('Residual for histogram 0','Powder profile Rwp =',101.0, |
| 4256 | | style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT, |
| 4257 | | parent=self) |
| 4258 | | Size = dlg.GetSize() |
| 4259 | | if 50 < Size[0] < 500: # sanity check on size, since this fails w/Win & wx3.0 |
| 4260 | | dlg.SetSize((int(Size[0]*1.2),Size[1])) # increase size a bit along x |
| 4261 | | dlg.CenterOnParent() |
| 4262 | | try: |
| 4263 | | OK,Msg = G2stMn.SeqRefine(self.GSASprojectfile,dlg,G2plt.SequentialPlotPattern,self) #Msg is Rvals dict if Ok=True |
| 4264 | | finally: |
| 4265 | | dlg.Update(101.) # forces the Auto_Hide; needed after move w/Win & wx3.0 |
| 4266 | | dlg.Destroy() |
| 4267 | | wx.Yield() |
| 4268 | | if OK: |
| 4269 | | dlg = wx.MessageDialog(self,'Load new result?','Refinement results',wx.OK|wx.CANCEL) |
| 4270 | | try: |
| 4271 | | if dlg.ShowModal() == wx.ID_OK: |
| 4272 | | self.PickIdText = None #force reload of PickId contents |
| 4273 | | self.PatternTree.DeleteChildren(self.root) |
| 4274 | | if len(self.HKL): self.HKL = [] |
| 4275 | | if self.G2plotNB.plotList: |
| 4276 | | self.G2plotNB.clear() |
| 4277 | | G2IO.ProjFileOpen(self,False) |
| 4278 | | self.PatternTree.RestoreExposedItems() |
| 4279 | | self.ResetPlots() |
| 4280 | | Id = G2gd.GetPatternTreeItemId(self,self.root,'Sequential results') |
| 4281 | | self.PatternTree.SelectItem(Id) |
| 4282 | | finally: |
| 4283 | | dlg.Destroy() |
| 4284 | | self.SeqTblHideList = [] |
| 4285 | | else: |
| 4286 | | self.ErrorDialog('Sequential refinement error',Msg) |
| 4287 | | |
| 4288 | | def ErrorDialog(self,title,message,parent=None, wtype=wx.OK): |
| 4289 | | 'Display an error message' |
| 4290 | | result = None |
| 4291 | | if parent is None: |
| 4292 | | dlg = wx.MessageDialog(self, message, title, wtype) |
| 4293 | | else: |
| 4294 | | dlg = wx.MessageDialog(parent, message, title, wtype) |
| 4295 | | dlg.CenterOnParent() # not working on Mac |
| 4296 | | try: |
| 4297 | | result = dlg.ShowModal() |
| 4298 | | finally: |
| 4299 | | dlg.Destroy() |
| 4300 | | return result |
| 4301 | | |
| 4302 | | def OnSaveMultipleImg(self,event): |
| 4303 | | '''Select and save multiple image parameter and mask files |
| 4304 | | ''' |
| 4305 | | G2IO.SaveMultipleImg(self) |
| 4306 | | |
| 4307 | | class GSASIImain(wx.App): |
| 4308 | | '''Defines a wxApp for GSAS-II |
| 4309 | | |
| 4310 | | Creates a wx frame (self.main) which contains the display of the |
| 4311 | | data tree. |
| 4312 | | ''' |
| 4313 | | def OnInit(self): |
| 4314 | | '''Called automatically when the app is created.''' |
| 4315 | | import platform |
| 4316 | | if '2.7' not in sys.version[:5]: |
| 4317 | | dlg = wx.MessageDialog(None, |
| 4318 | | 'GSAS-II requires Python 2.7.x\n Yours is '+sys.version.split()[0], |
| 4319 | | 'Python version error', wx.OK) |
| 4320 | | try: |
| 4321 | | dlg.ShowModal() |
| 4322 | | finally: |
| 4323 | | dlg.Destroy() |
| 4324 | | sys.exit() |
| 4325 | | self.main = GSASII(None) |
| 4326 | | self.main.Show() |
| 4327 | | self.SetTopWindow(self.main) |
| 4328 | | # save the current package versions |
| 4329 | | self.main.PackageVersions = [] |
| 4330 | | self.main.PackageVersions.append(['Python',sys.version.split()[0]]) |
| 4331 | | for p in (wx,mpl,np,sp,ogl): |
| 4332 | | self.main.PackageVersions.append([p.__name__,p.__version__]) |
| 4333 | | try: |
| 4334 | | self.main.PackageVersions.append([Image.__name__,Image.VERSION]) |
| 4335 | | except: |
| 4336 | | try: |
| 4337 | | from PIL import PILLOW_VERSION |
| 4338 | | self.main.PackageVersions.append([Image.__name__,PILLOW_VERSION]) |
| 4339 | | except: |
| 4340 | | pass |
| 4341 | | self.main.PackageVersions.append(['Platform',sys.platform+' '+platform.architecture()[0]+' '+platform.machine()]) |
| 4342 | | |
| 4343 | | return True |
| 4344 | | # def MacOpenFile(self, filename): |
| 4345 | | # '''Called on Mac every time a file is dropped on the app when it is running, |
| 4346 | | # treat this like a File/Open project menu action. |
| 4347 | | # Should be ignored on other platforms |
| 4348 | | # ''' |
| 4349 | | # # PATCH: Canopy 1.4 script main seems dropped on app; ignore .py files |
| 4350 | | # print 'MacOpen',filename |
| 4351 | | # if os.path.splitext(filename)[1] == '.py': return |
| 4352 | | # # end PATCH |
| 4353 | | # self.main.OnFileOpen(None,filename) |
| 4354 | | # removed because this gets triggered when a file is on the command line in canopy 1.4 -- not likely used anyway |
| 4355 | | |
| 4356 | | def main(): |
| 4357 | | '''Start up the GSAS-II application''' |
| 4358 | | #application = GSASIImain() # don't redirect output, someday we |
| 4359 | | # may want to do this if we can |
| 4360 | | application = GSASIImain(0) |
| 4361 | | if GSASIIpath.GetConfigValue('wxInspector'): |
| 4362 | | import wx.lib.inspection as wxeye |
| 4363 | | wxeye.InspectionTool().Show() |
| 4364 | | |
| 4365 | | #application.main.OnRefine(None) |
| 4366 | | application.MainLoop() |
| 4367 | | |
