Changeset 4883 for trunk/exports/G2export_CIF.py
- Timestamp:
- Apr 13, 2021 1:15:13 PM (2 years ago)
- File:
-
- 1 edited
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trunk/exports/G2export_CIF.py (modified) (13 diffs)
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- Unmodified
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trunk/exports/G2export_CIF.py
r4879 r4883 582 582 G2mth.ValEsd(cellmass/Z,-0.09,True)) 583 583 584 585 584 class ExportCIF(G2IO.ExportBaseclass): 586 585 '''Base class for CIF exports … … 604 603 'Unicode not valid for CIF') 605 604 return True 605 606 def _CellSelectNeeded(self,phasenam): 607 '''Determines if selection is needed for a T value in a multiblock CIF 608 609 :returns: True if the choice of T is ambiguous and a human should 610 be asked. 611 ''' 612 phasedict = self.Phases[phasenam] # pointer to current phase info 613 Tlist = {} # histname & T values used for cell w/o Hstrain 614 DijTlist = {} # hId & T values used for cell w/Hstrain 615 # scan over histograms used in this phase to determine the best 616 # data collection T value 617 for h in phasedict['Histograms']: 618 if not phasedict['Histograms'][h]['Use']: continue 619 T = self.Histograms[h]['Sample Parameters']['Temperature'] 620 if np.any(abs(np.array(phasedict['Histograms'][h]['HStrain'][0])) > 1e-8): 621 DijTlist[h] = T 622 else: 623 Tlist[h] = T 624 if len(Tlist) > 0: 625 T = sum(Tlist.values())/len(Tlist) 626 if max(Tlist.values()) - T > 1: 627 return True # temperatures span more than 1 degree, user needs to pick one 628 return False 629 elif len(DijTlist) == 1: 630 return False 631 elif len(DijTlist) > 1: 632 # each histogram has different cell lengths, user needs to pick one 633 return True 634 635 def _CellSelectHist(self,phasenam): 636 '''Select T value for a phase in a multiblock CIF 637 638 :returns: T,h_ranId where T is a temperature (float) or '?' and 639 h_ranId is the random Id (ranId) for a histogram in the 640 current phase. This is stored in OverallParms['Controls']['CellHistSelection'] 641 ''' 642 phasedict = self.Phases[phasenam] # pointer to current phase info 643 Tlist = {} # histname & T values used for cell w/o Hstrain 644 DijTlist = {} # hId & T values used for cell w/Hstrain 645 # scan over histograms used in this phase to determine the best 646 # data collection T value 647 for h in phasedict['Histograms']: 648 if not phasedict['Histograms'][h]['Use']: continue 649 T = self.Histograms[h]['Sample Parameters']['Temperature'] 650 if np.any(abs(np.array(phasedict['Histograms'][h]['HStrain'][0])) > 1e-8): 651 DijTlist[h] = T 652 else: 653 Tlist[h] = T 654 if len(Tlist) > 0: 655 T = sum(Tlist.values())/len(Tlist) 656 if max(Tlist.values()) - T > 1: 657 # temperatures span more than 1 degree, user needs to pick one 658 choices = ["{} (unweighted average)".format(T)] 659 Ti = [T] 660 for h in Tlist: 661 choices += ["{} (hist {})".format(Tlist[h],h)] 662 Ti += [Tlist[h]] 663 msg = 'The cell parameters for phase {} are from\nhistograms with different temperatures.\n\nSelect a T value below'.format(phasenam) 664 dlg = wx.SingleChoiceDialog(self.G2frame,msg,'Select T',choices) 665 if dlg.ShowModal() == wx.ID_OK: 666 T = Ti[dlg.GetSelection()] 667 else: 668 T = '?' 669 dlg.Destroy() 670 return (T,None) 671 elif len(DijTlist) == 1: 672 h = list(DijTlist.keys())[0] 673 h_ranId = self.Histograms[h]['ranId'] 674 return (DijTlist[h],h_ranId) 675 elif len(DijTlist) > 1: 676 # each histogram has different cell lengths, user needs to pick one 677 choices = [] 678 hi = [] 679 for h in DijTlist: 680 choices += ["{} (hist {})".format(DijTlist[h],h)] 681 hi += [h] 682 msg = 'There are {} sets of cell parameters for phase {}\n due to refined Hstrain values.\n\nSelect the histogram to use with the phase form list below'.format(len(DijTlist),phasenam) 683 dlg = wx.SingleChoiceDialog(self.G2frame,msg,'Select cell',choices) 684 if dlg.ShowModal() == wx.ID_OK: 685 h = hi[dlg.GetSelection()] 686 h_ranId = self.Histograms[h]['ranId'] 687 T = DijTlist[h] 688 else: 689 T = '?' 690 h_ranId = None 691 dlg.Destroy() 692 return (T,h_ranId) 693 else: 694 print('Unexpected option in _CellSelectHist for',phasenam) 695 return ('?',None) 606 696 607 697 def _Exporter(self,event=None,phaseOnly=None,histOnly=None,IncludeOnlyHist=None): … … 1138 1228 WriteCIFitem(self.fp, line) 1139 1229 1140 def WritePhaseInfo(phasenam ):1230 def WritePhaseInfo(phasenam,quick=True,oneblock=True): 1141 1231 'Write out the phase information for the selected phase' 1142 1232 WriteCIFitem(self.fp, '\n# phase info for '+str(phasenam) + ' follows') … … 1144 1234 WriteCIFitem(self.fp, '_pd_phase_name', phasenam) 1145 1235 cellList,cellSig = self.GetCell(phasenam) 1236 if quick: # leave temperature as unknown 1237 WriteCIFitem(self.fp,"_cell_measurement_temperature","?") 1238 elif oneblock: 1239 pass # temperature should be written when the histogram saved later 1240 else: # get T set in _SelectPhaseT_CellSelectHist and possibly get new cell params 1241 T,hRanId = self.CellHistSelection.get(phasedict['ranId'], 1242 ('?',None)) 1243 try: 1244 T = G2mth.ValEsd(T,-1.0) 1245 except: 1246 pass 1247 WriteCIFitem(self.fp,"_cell_measurement_temperature",T) 1248 for h in phasedict['Histograms']: 1249 if self.Histograms[h]['ranId'] == hRanId: 1250 pId = phasedict['pId'] 1251 hId = self.Histograms[h]['hId'] 1252 cellList,cellSig = G2strIO.getCellSU(pId,hId, 1253 phasedict['General']['SGData'], 1254 self.parmDict, 1255 self.OverallParms['Covariance']) 1256 break 1257 else: 1258 T = '?' 1259 1146 1260 defsigL = 3*[-0.00001] + 3*[-0.001] + [-0.01] # significance to use when no sigma 1147 1261 names = ['length_a','length_b','length_c', … … 1717 1831 phasedict['General']['DisAglCtls'] = dlg.GetData() 1718 1832 dlg.Destroy() 1719 1833 1834 def SetCellT(event): 1835 '''Set the temperature value by selection of a histogram 1836 ''' 1837 but = event.GetEventObject() 1838 phasenam = but.phase 1839 rId = self.Phases[phasenam]['ranId'] 1840 self.CellHistSelection[rId] = self._CellSelectHist(phasenam) 1841 1720 1842 def EditCIFDefaults(): 1721 1843 '''Fills the CIF Defaults window with controls for editing various CIF export … … 1764 1886 but.Bind(wx.EVT_BUTTON,SelectDisAglFlags) # phase bond/angle ranges 1765 1887 cbox.Add(but,0,wx.ALIGN_LEFT,0) 1888 if self._CellSelectNeeded(phasenam): 1889 but = wx.Button(cpnl, wx.ID_ANY,'Select cell temperature') 1890 cbox.Add(but,0,wx.ALIGN_LEFT,0) 1891 cbox.Add((-1,2)) 1892 but.phase = phasenam # set a pointer to current phase info 1893 but.Bind(wx.EVT_BUTTON,SetCellT) 1766 1894 cbox.Add((-1,2)) 1767 1895 for i in sorted(self.powderDict.keys()): … … 1999 2127 s += '.' 2000 2128 self.CIFname = s 2129 2130 self.InitExport(event) 2131 # load all of the tree into a set of dicts 2132 self.loadTree() 2001 2133 # load saved CIF author name 2002 try: 2003 self.author = self.OverallParms['Controls'].get("Author",'?').strip() 2004 except KeyError: 2005 pass 2134 self.author = self.OverallParms['Controls'].get("Author",'?').strip() 2135 # initialize dict for Selection of Hist for unit cell reporting 2136 self.OverallParms['Controls']['CellHistSelection'] = self.OverallParms[ 2137 'Controls'].get('CellHistSelection',{}) 2138 self.CellHistSelection = self.OverallParms['Controls']['CellHistSelection'] 2006 2139 #================================================================= 2007 2140 # write quick CIFs … … 2033 2166 #phasenam = self.Phases.keys()[0] 2034 2167 WriteCIFitem(self.fp, 'data_'+self.CIFname) 2035 #print 'phasenam',phasenam2036 #phaseblk = self.Phases[phasenam] # pointer to current phase info2037 #instnam = instnam.replace(' ','')2038 #WriteCIFitem(self.fp, '_pd_block_id',2039 # str(self.CIFdate) + "|" + str(self.CIFname) + "|" +2040 # str(self.shortauthorname) + "|" + instnam + '|' + histname)2041 #WriteAudit()2042 #writeCIFtemplate(self.OverallParms['Controls'],'publ') # overall (publication) template2043 #WriteOverall()2044 #writeCIFtemplate(self.Phases[phasenam]['General'],'phase',phasenam) # write phase template2045 # report the phase info2046 #WritePhaseInfo(phasenam,hist)2047 # preferred orientation2048 #SH = FormatSH(phasenam)2049 #MD = FormatHAPpo(phasenam)2050 #if SH and MD:2051 # WriteCIFitem(self.fp, '_pd_proc_ls_pref_orient_corr', SH + '\n' + MD)2052 #elif SH or MD:2053 # WriteCIFitem(self.fp, '_pd_proc_ls_pref_orient_corr', SH + MD)2054 #else:2055 # WriteCIFitem(self.fp, '_pd_proc_ls_pref_orient_corr', 'none')2056 # report profile, since one-block: include both histogram and phase info2057 #WriteCIFitem(self.fp, '_pd_proc_ls_profile_function',2058 # FormatInstProfile(histblk["Instrument Parameters"],histblk['hId'])2059 # +'\n'+FormatPhaseProfile(phasenam))2060 2168 if hist.startswith("PWDR"): 2061 2169 WritePowderData(hist) 2062 2170 elif hist.startswith("HKLF"): 2063 2171 WriteSingleXtalData(hist) 2064 #writeCIFtemplate(histblk,'powder',histblk['InstrName']) # write powder template2065 #self.CloseFile()2066 2172 return 2067 #elif IncludeOnlyHist is not None: # truncate histogram list to only selected (for sequential export)2068 # self.Histograms = {IncludeOnlyHist:self.Histograms[IncludeOnlyHist]}2069 2070 2173 #=============================================================================== 2071 2174 # the export process for a full CIF starts here 2072 2175 #=============================================================================== 2073 self.InitExport(event)2074 # load all of the tree into a set of dicts2075 self.loadTree()2076 2176 # create a dict with refined values and their uncertainties 2077 2177 self.loadParmDict() … … 2149 2249 return 2150 2250 dlg.Destroy() 2151 # scan over histograms used in this phase for 2152 #pId = self.Phases[phasenam]['pId'] 2153 #for h in phasedict['Histograms']: 2154 # if not phasedict['Histograms'][h]['Use']: continue 2155 # hId = self.Histograms[h]['hId'] 2156 # T = self.Histograms[h]['Sample Parameters']['Temperature'] 2157 2251 2158 2252 # check if temperature values & pressure are defaulted 2159 2253 default = 0 … … 2195 2289 if not self.author: 2196 2290 self.author = self.OverallParms['Controls'].get("Author",'?').strip() 2197 self.shortauthorname = self.author.replace(',','').replace(' ','')[:20]2198 2291 if not self.author: 2199 2292 if not EditAuthor(): return 2200 2293 self.ValidateAscii([('Author name',self.author),]) # check for ASCII strings where needed, warn on problems 2294 self.shortauthorname = self.author.replace(',','').replace(' ','')[:20] 2201 2295 self.cifdefs = wx.Dialog( 2202 2296 self.G2frame, … … 2246 2340 writeCIFtemplate(self.Phases[phasenam]['General'],'phase',phasenam) # write phase template 2247 2341 # report the phase info 2248 WritePhaseInfo(phasenam )2342 WritePhaseInfo(phasenam,False) 2249 2343 if hist.startswith("PWDR"): # this is invoked for single-block CIFs 2250 2344 # preferred orientation … … 2271 2365 else: 2272 2366 #=== multiblock: multiple phases and/or histograms ==================== 2367 for phasenam in sorted(self.Phases.keys()): 2368 rId = phasedict['ranId'] 2369 if rId in self.CellHistSelection: continue 2370 self.CellHistSelection[rId] = self._CellSelectHist(phasenam) 2273 2371 nsteps = 1 + len(self.Phases) + len(self.powderDict) + len(self.xtalDict) 2274 2372 dlg = wx.ProgressDialog('CIF progress','starting',nsteps,parent=self.G2frame) 2275 # Size = dlg.GetSize()2276 # Size = (int(Size[0]*3),Size[1]) # increase size along x2277 # dlg.SetSize(Size)2278 2373 dlg.CenterOnParent() 2279 2374 … … 2344 2439 # report the phase 2345 2440 writeCIFtemplate(self.Phases[phasenam]['General'],'phase',phasenam) # write phase template 2346 WritePhaseInfo(phasenam )2441 WritePhaseInfo(phasenam,False,False) 2347 2442 # preferred orientation 2348 2443 if self.ifPWDR:
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