Changeset 146
 Timestamp:
 Aug 5, 2010 2:41:33 PM (13 years ago)
 File:

 1 edited
Legend:
 Unmodified
 Added
 Removed

trunk/GSASIIphsGUI.py
r142 r146 4 4 import matplotlib as mpl 5 5 import math 6 import copy 6 7 import time 7 8 import cPickle … … 23 24 cosd = lambda x: math.cos(x*math.pi/180.) 24 25 asind = lambda x: 180.*math.asin(x)/math.pi 25 26 26 27 def UpdatePhaseData(self,item,data,oldPage): 28 29 class SymOpDialog(wx.Dialog): 30 def __init__(self,parent,SGData): 31 wx.Dialog.__init__(self,parent,1,'Select symmetry operator', 32 pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE) 33 panel = wx.Panel(self) 34 self.SGData = SGData 35 self.OpSelected = [0,0,0,0,0,0] 36 mainSizer = wx.BoxSizer(wx.VERTICAL) 37 mainSizer.Add((5,5),0) 38 if SGData['SGInv']: 39 choice = ['No','Yes'] 40 self.inv = wx.RadioBox(panel,1,'Choose inversion?',choices=choice) 41 self.inv.Bind(wx.EVT_RADIOBOX, self.OnOpSelect) 42 mainSizer.Add(self.inv,0,wx.ALIGN_CENTER_VERTICAL) 43 mainSizer.Add((5,5),0) 44 if SGData['SGLatt'] != 'P': 45 LattOp = G2spc.Latt2text(SGData['SGLatt']).split(';') 46 self.latt = wx.RadioBox(panel,1,'Choose cell centering?',choices=LattOp) 47 self.latt.Bind(wx.EVT_RADIOBOX, self.OnOpSelect) 48 mainSizer.Add(self.latt,0,wx.ALIGN_CENTER_VERTICAL) 49 mainSizer.Add((5,5),0) 50 if SGData['SGLaue'] in ['1','2/m','mmm','4/m','4/mmm']: 51 Ncol = 2 52 else: 53 Ncol = 3 54 OpList = [] 55 for M,T in SGData['SGOps']: 56 OpList.append(G2spc.MT2text(M,T)) 57 self.oprs = wx.RadioBox(panel,1,'Choose space group operator?',choices=OpList, 58 majorDimension=Ncol) 59 self.oprs.Bind(wx.EVT_RADIOBOX, self.OnOpSelect) 60 mainSizer.Add(self.oprs,0,wx.ALIGN_CENTER_VERTICAL) 61 mainSizer.Add((5,5),0) 62 mainSizer.Add(wx.StaticText(panel,1," Choose unit cell?"),0,wx.ALIGN_CENTER_VERTICAL) 63 mainSizer.Add((5,5),0) 64 cellSizer = wx.BoxSizer(wx.HORIZONTAL) 65 cellSizer.Add((5,0),0) 66 cellName = ['X','Y','Z'] 67 self.cell = [] 68 for i in range(3): 69 self.cell.append(wx.SpinCtrl(panel,1,cellName[i],size=wx.Size(50,20))) 70 self.cell[1].SetRange(3,3) 71 self.cell[1].SetValue(0) 72 self.cell[1].Bind(wx.EVT_SPINCTRL, self.OnOpSelect) 73 cellSizer.Add(self.cell[1],0,wx.ALIGN_CENTER_VERTICAL) 74 mainSizer.Add(cellSizer,0,) 75 choice = ['No','Yes'] 76 self.new = wx.RadioBox(panel,1,'Generate new positions?',choices=choice) 77 self.new.Bind(wx.EVT_RADIOBOX, self.OnOpSelect) 78 mainSizer.Add(self.new,0,wx.ALIGN_CENTER_VERTICAL) 79 mainSizer.Add((5,5),0) 80 81 OkBtn = wx.Button(panel,1,"Ok") 82 OkBtn.Bind(wx.EVT_BUTTON, self.OnOk) 83 cancelBtn = wx.Button(panel,1,"Cancel") 84 cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel) 85 btnSizer = wx.BoxSizer(wx.HORIZONTAL) 86 btnSizer.Add((20,20),1) 87 btnSizer.Add(OkBtn) 88 btnSizer.Add((20,20),1) 89 btnSizer.Add(cancelBtn) 90 btnSizer.Add((20,20),1) 91 92 mainSizer.Add(btnSizer,0,wx.EXPANDwx.BOTTOMwx.TOP, 10) 93 panel.SetSizer(mainSizer) 94 panel.Fit() 95 self.Fit() 96 97 def OnOpSelect(self,event): 98 self.OpSelected = [0,0,0,[],0] 99 if self.SGData['SGInv']: 100 self.OpSelected[0] = self.inv.GetSelection() 101 if self.SGData['SGLatt'] != 'P': 102 self.OpSelected[1] = self.latt.GetSelection() 103 self.OpSelected[2] = self.oprs.GetSelection() 104 for i in range(3): 105 self.OpSelected[3].append(float(self.cell[i].GetValue())) 106 self.OpSelected[4] = self.new.GetSelection() 107 108 def GetSelection(self): 109 return self.OpSelected 110 111 def OnOk(self,event): 112 parent = self.GetParent() 113 parent.Raise() 114 self.SetReturnCode(wx.ID_OK) 115 self.MakeModal(False) 116 self.Destroy() 117 118 def OnCancel(self,event): 119 parent = self.GetParent() 120 parent.Raise() 121 self.SetReturnCode(wx.ID_CANCEL) 122 self.MakeModal(False) 123 self.Destroy() 124 27 125 Atoms = [] 28 126 self.SelectedRow = 0 … … 84 182 else: 85 183 text = G2spc.SGPrint(SGData) 86 generalData[ SGData] = SGData184 generalData['SGData'] = SGData 87 185 msg = 'Space Group Information' 88 186 Style = wx.ICON_INFORMATION … … 200 298 201 299 r,c = event.GetRow(),event.GetCol() 202 if r < 0: #on col label! 300 if r < 0 and c < 0: 301 Atoms.ClearSelection() 302 if r < 0: #double click on col label! Change all atoms! 203 303 sel = 1 304 noSkip = True 204 305 if Atoms.GetColLabelValue(c) == 'refine': 205 choice = ['F  site fraction','X  coordinates','U  thermal parameters'] 306 Type = generalData['Type'] 307 if Type in ['nuclear','macromolecular']: 308 choice = ['F  site fraction','X  coordinates','U  thermal parameters'] 309 elif Type in ['magnetic',]: 310 choice = ['F  site fraction','X  coordinates','U  thermal parameters','M  magnetic moment'] 206 311 dlg = wx.MultiChoiceDialog(self,'Select','Refinement controls',choice) 207 312 if dlg.ShowModal() == wx.ID_OK: … … 209 314 parms = '' 210 315 for x in sel: 211 parms += choice[x][0] 316 parms += choice[x][0] 317 dlg.Destroy() 212 318 elif Atoms.GetColLabelValue(c) == 'I/A': 213 319 choice = ['Isotropic','Anisotropic'] … … 216 322 sel = dlg.GetSelection() 217 323 parms = choice[sel][0] 218 if sel >= 0: 324 dlg.Destroy() 325 elif Atoms.GetColLabelValue(c) == 'Type': 326 choice = generalData['AtomTypes'] 327 dlg = wx.SingleChoiceDialog(self,'Select','Atom types',choice) 328 if dlg.ShowModal() == wx.ID_OK: 329 sel = dlg.GetSelection() 330 parms = choice[sel] 331 noSkip = False 332 Atoms.ClearSelection() 333 for row in range(Atoms.GetNumberRows()): 334 if parms == atomData[row][c]: 335 Atoms.SelectRow(row,True) 336 elif Atoms.GetColLabelValue(c) == 'residue': 337 choice = [] 219 338 for r in range(Atoms.GetNumberRows()): 339 if str(atomData[r][c]) not in choice: 340 choice.append(str(atomData[r][c])) 341 choice.sort() 342 dlg = wx.SingleChoiceDialog(self,'Select','Residue',choice) 343 if dlg.ShowModal() == wx.ID_OK: 344 sel = dlg.GetSelection() 345 parms = choice[sel] 346 noSkip = False 347 Atoms.ClearSelection() 348 for row in range(Atoms.GetNumberRows()): 349 if parms == atomData[row][c]: 350 Atoms.SelectRow(row,True) 351 elif Atoms.GetColLabelValue(c) == 'res no': 352 choice = [] 353 for r in range(Atoms.GetNumberRows()): 354 if str(atomData[r][c]) not in choice: 355 choice.append(str(atomData[r][c])) 356 dlg = wx.SingleChoiceDialog(self,'Select','Residue no.',choice) 357 if dlg.ShowModal() == wx.ID_OK: 358 sel = dlg.GetSelection() 359 parms = choice[sel] 360 noSkip = False 361 Atoms.ClearSelection() 362 for row in range(Atoms.GetNumberRows()): 363 if int(parms) == atomData[row][c]: 364 Atoms.SelectRow(row,True) 365 elif Atoms.GetColLabelValue(c) == 'chain': 366 choice = [] 367 for r in range(Atoms.GetNumberRows()): 368 if atomData[r][c] not in choice: 369 choice.append(atomData[r][c]) 370 dlg = wx.SingleChoiceDialog(self,'Select','Chain',choice) 371 if dlg.ShowModal() == wx.ID_OK: 372 sel = dlg.GetSelection() 373 parms = choice[sel] 374 noSkip = False 375 Atoms.ClearSelection() 376 for row in range(Atoms.GetNumberRows()): 377 if parms == atomData[row][c]: 378 Atoms.SelectRow(row,True) 379 dlg.Destroy() 380 if sel >= 0 and noSkip: 381 ui = colLabels.index('U11') 382 us = colLabels.index('Uiso') 383 ss = colLabels.index('site sym') 384 for r in range(Atoms.GetNumberRows()): 385 if parms != atomData[r][c] and Atoms.GetColLabelValue(c) == 'I/A': 386 if parms == 'A': #'I' > 'A' 387 Uiso = atomData[r][us] 388 sytsym = atomData[r][ss] 389 CSI = G2spc.GetCSuinel(sytsym) 390 atomData[r][ui:ui+6] = Uiso*np.array(CSI[3]) 391 atomData[r][us] = '' 392 Atoms.SetCellRenderer(r,us,wg.GridCellStringRenderer()) 393 Atoms.SetCellStyle(r,us,VERY_LIGHT_GREY,True) 394 for i in range(6): 395 ci = ui+i 396 Atoms.SetCellRenderer(r,ci,wg.GridCellFloatRenderer(10,4)) 397 Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True) 398 if CSI[2][i]: 399 Atoms.SetCellStyle(r,ci,WHITE,False) 400 else: #'A' > 'I' 401 Uij = atomData[r][ui:ui+6] 402 atomData[r][us] = (Uij[0]+Uij[1]+Uij[2])/3.0 403 atomData[r][ui:ui+6] = [0,0,0,0,0,0] 404 Atoms.SetCellRenderer(r,us,wg.GridCellFloatRenderer(10,4)) 405 Atoms.SetCellStyle(r,us,WHITE,False) 406 for i in range(6): 407 ci = ui+i 408 Atoms.SetCellRenderer(r,ci,wg.GridCellStringRenderer()) 409 Atoms.SetCellValue(r,ci,'') 410 Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True) 220 411 Atoms.SetCellValue(r,c,parms) 221 412 elif c < 0: #picked atom row … … 273 464 if iUij == CSI[0][i]: 274 465 atomData[r][i+colLabels.index('U11')] = value*CSI[1][i] 466 Atoms.ForceRefresh() 467 468 def ChangeSelection(event): 469 r,c = event.GetRow(),event.GetCol() 470 if r < 0 and c < 0: 471 Atoms.ClearSelection() 472 if c < 0: 473 if r in Atoms.GetSelectedRows(): 474 Atoms.DeselectRow(r) 475 else: 476 Atoms.SelectRow(r,True) 477 if r < 0: 478 if c in Atoms.GetSelectedCols(): 479 Atoms.DeselectCol(c) 480 else: 481 Atoms.SelectCol(c,True) 275 482 276 483 def AtomTypeSelect(event): … … 291 498 wg.GRID_VALUE_STRING,wg.GRID_VALUE_NUMBER,wg.GRID_VALUE_CHOICE+":I,A", 292 499 wg.GRID_VALUE_FLOAT+':10,4', #Uiso 293 wg.GRID_VALUE_ FLOAT+':10,4',wg.GRID_VALUE_FLOAT+':10,4',wg.GRID_VALUE_FLOAT+':10,4', #Uij294 wg.GRID_VALUE_ FLOAT+':10,4',wg.GRID_VALUE_FLOAT+':10,4',wg.GRID_VALUE_FLOAT+':10,4']500 wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING, #Uij  placeholders 501 wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING] 295 502 colLabels = ['Name','Type','refine','x','y','z','frac','site sym','mult','I/A','Uiso','U11','U22','U33','U12','U13','U23'] 296 503 if generalData['Type'] == 'magnetic': … … 303 510 Types = [wg.GRID_VALUE_NUMBER, 304 511 wg.GRID_VALUE_CHOICE+": ,ALA,ARG,ASN,ASP,CYS,GLN,GLU,GLY,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER,THR,TRP,TYR,VAL,MSE,HOH,UNK", 305 wg.GRID_VALUE_STRING] + Types 512 wg.GRID_VALUE_STRING] + Types 513 elif generalData['Type'] == 'modulated': 514 Types += [] 515 colLabels += [] 306 516 table = [] 307 517 rowLabels = [] 308 518 for i,atom in enumerate(atomData): 309 table.append(atom) 519 if atom[colLabels.index('I/A')] == 'I': 520 table.append(atom[:colLabels.index('U11')]+['','','','','','']) 521 else: 522 table.append(atom) 310 523 rowLabels.append(str(i+1)) 311 524 atomTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types) … … 313 526 Atoms.Bind(wg.EVT_GRID_CELL_CHANGE, RefreshAtomGrid) 314 527 Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid) 528 Atoms.Bind(wg.EVT_GRID_LABEL_RIGHT_CLICK, ChangeSelection) 315 529 Atoms.Bind(wg.EVT_GRID_SELECT_CELL, AtomTypeSelect) 316 530 Atoms.SetMargins(0,0) … … 319 533 colSS = colLabels.index('site sym') 320 534 colIA = colLabels.index('I/A') 535 colU11 = colLabels.index('U11') 536 colUiso = colLabels.index('Uiso') 537 attr = wg.GridCellAttr() #to set Uij defaults 538 attr.SetBackgroundColour(VERY_LIGHT_GREY) 539 attr.SetReadOnly(True) 540 for i in range(colU11,colU11+6): 541 Atoms.SetColAttr(i,attr) 321 542 for row in range(Atoms.GetNumberRows()): 322 543 Atoms.SetReadOnly(row,colSS,True) #site sym 323 544 Atoms.SetReadOnly(row,colSS+1,True) #Mult 324 if Atoms.GetCellValue(row,colIA) == 'I': 325 for i in range(2,8): 326 Atoms.SetCellRenderer(row,colIA+i,wg.GridCellStringRenderer()) 327 Atoms.SetCellValue(row,colIA+i,'') 328 Atoms.SetCellStyle(row,colIA+i,VERY_LIGHT_GREY,True) 329 elif Atoms.GetCellValue(row,colIA) == 'A': 545 if Atoms.GetCellValue(row,colIA) == 'A': 330 546 CSI = G2spc.GetCSuinel(atomData[row][colLabels.index('site sym')]) 331 Atoms.SetCellRenderer(row,col IA+1,wg.GridCellStringRenderer())332 Atoms.SetCellStyle(row,col IA+1,VERY_LIGHT_GREY,True)333 Atoms.SetCellValue(row,col IA+1,'')547 Atoms.SetCellRenderer(row,colUiso,wg.GridCellStringRenderer()) 548 Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True) 549 Atoms.SetCellValue(row,colUiso,'') 334 550 for i in range(6): 335 ci = col IA+i+2336 Atoms.SetCell Style(row,ci,VERY_LIGHT_GREY,True)551 ci = colU11+i 552 Atoms.SetCellRenderer(row,ci,wg.GridCellFloatRenderer(10,4)) 337 553 if CSI[2][i]: 338 554 Atoms.SetCellStyle(row,ci,WHITE,False) … … 381 597 event.StopPropagation() 382 598 599 def AtomRefine(event): 600 indx = Atoms.GetSelectedRows() 601 if indx: 602 atomData = data['Atoms'] 603 generalData = data['General'] 604 Type = generalData['Type'] 605 if Type in ['nuclear','macromolecular']: 606 choice = ['F  site fraction','X  coordinates','U  thermal parameters'] 607 elif Type in ['magnetic',]: 608 choice = ['F  site fraction','X  coordinates','U  thermal parameters','M  magnetic moment'] 609 dlg = wx.MultiChoiceDialog(self,'Select','Refinement controls',choice) 610 if dlg.ShowModal() == wx.ID_OK: 611 sel = dlg.GetSelections() 612 parms = '' 613 for x in sel: 614 parms += choice[x][0] 615 dlg.Destroy() 616 colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())] 617 c = colLabels.index('refine') 618 for r in indx: 619 atomData[r][c] = parms 620 Atoms.ForceRefresh() 621 622 def AtomModify(event): 623 indx = Atoms.GetSelectedRows() 624 if indx: 625 atomData = data['Atoms'] 626 generalData = data['General'] 627 628 def AtomTransform(event): 629 indx = Atoms.GetSelectedRows() 630 if indx: 631 colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())] 632 cx = colLabels.index('x') 633 cuia = colLabels.index('I/A') 634 cuij = colLabels.index('U11') 635 css = colLabels.index('site sym') 636 atomData = data['Atoms'] 637 generalData = data['General'] 638 SGData = generalData['SGData'] 639 dlg = SymOpDialog(self,SGData) 640 try: 641 if dlg.ShowModal() == wx.ID_OK: 642 Inv,Cent,Opr,Cell,New = dlg.GetSelection() 643 Cell = np.array(Cell) 644 cent = SGData['SGCen'][Cent] 645 M,T = SGData['SGOps'][Opr] 646 for ind in indx: 647 XYZ = np.array(atomData[ind][cx:cx+3]) 648 XYZ = np.inner(M,XYZ)+T 649 if Inv: 650 XYZ = XYZ 651 XYZ = XYZ+cent+Cell 652 if New: 653 atom = copy.copy(atomData[ind]) 654 else: 655 atom = atomData[ind] 656 atom[cx:cx+3] = XYZ 657 atom[css:css+2] = G2spc.SytSym(XYZ,SGData) 658 if atom[cuia] == 'A': 659 Uij = atom[cuij:cuij+6] 660 U = G2spc.Uij2U(Uij) 661 U = np.inner(np.inner(M.T,U),M) 662 Uij = G2spc.U2Uij(U) 663 atom[cuij:cuij+6] = Uij 664 if New: 665 atomData.append(atom) 666 finally: 667 dlg.Destroy() 668 Atoms.ClearSelection() 669 if New: 670 FillAtomsGrid() 671 else: 672 Atoms.ForceRefresh() 673 383 674 def UpdateDrawing(): 384 675 print 'Drawing' … … 397 688 self.dataFrame.Bind(wx.EVT_MENU, AtomInsert, id=G2gd.wxID_ATOMSEDITINSERT) 398 689 self.dataFrame.Bind(wx.EVT_MENU, AtomDelete, id=G2gd.wxID_ATOMSEDITDELETE) 690 self.dataFrame.Bind(wx.EVT_MENU, AtomRefine, id=G2gd.wxID_ATOMSREFINE) 691 self.dataFrame.Bind(wx.EVT_MENU, AtomModify, id=G2gd.wxID_ATOMSMODIFY) 692 self.dataFrame.Bind(wx.EVT_MENU, AtomTransform, id=G2gd.wxID_ATOMSTRANSFORM) 399 693 FillAtomsGrid() 400 694 else: … … 407 701 self.dataFrame.SetMenuBar(self.dataFrame.BlankMenu) 408 702 self.dataFrame.SetLabel('Phase Data for '+PhaseName) 703 self.dataFrame.CreateStatusBar() 409 704 self.dataDisplay = G2gd.GSNoteBook(parent=self.dataFrame,size=self.dataFrame.GetClientSize()) 410 705 411 General = G2gd.GSGrid( parent=self.dataDisplay)706 General = G2gd.GSGrid(self.dataDisplay) 412 707 FillGeneralGrid() 413 708 self.dataDisplay.AddPage(General,'General') … … 415 710 GeneralData = data['General'] 416 711 if GeneralData['Type'] == 'Pawley': 417 PawleyRefl = G2gd.GSGrid( parent=self.dataDisplay)712 PawleyRefl = G2gd.GSGrid(self.dataDisplay) 418 713 self.dataDisplay.AddPage(PawleyRefl,'Pawley reflections') 419 714 else: 420 Atoms = G2gd.GSGrid( parent=self.dataDisplay)715 Atoms = G2gd.GSGrid(self.dataDisplay) 421 716 self.dataDisplay.AddPage(Atoms,'Atoms') 422 Drawing = wx.Window( parent=self.dataDisplay)717 Drawing = wx.Window(self.dataDisplay) 423 718 self.dataDisplay.AddPage(Drawing,'Drawing') 424 719
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