Changeset 3681

Timestamp:

Oct 17, 2018 1:37:42 PM (5 years ago)

Author:

vondreele

Message:

change Panalytical importer to read multi xrdMeasurement blocks - can each have multiple scans; all recorded as separate PWDR histograms.
Begin implementation of access to Bilbao SUBGROUPS routine
some work on incommensurate magnetic structure stuff
Add new option for PWDR contour plots to show temperature on y-axis

Location:

trunk

Files:

• GSASIIdataGUI.py (modified) (4 diffs)
• GSASIIphsGUI.py (modified) (1 diff)
• GSASIIplot.py (modified) (9 diffs)
• GSASIIpwdGUI.py (modified) (5 diffs)
• GSASIIspc.py (modified) (5 diffs)
• imports/G2pwd_Panalytical.py (modified) (2 diffs)

trunk/GSASIIdataGUI.py

@@ -2785 +2785 @@
         self.ErrorBars = False
         self.Contour = False
+        self.TforYaxis = False
         self.Legend = False
         self.SinglePlot = True
@@ -5123 +5124 @@
         # PDR / Unit Cells List
         G2G.Define_wxId('wxID_INDEXPEAKS', 'wxID_REFINECELL', 'wxID_COPYCELL', 'wxID_MAKENEWPHASE',
-            'wxID_EXPORTCELLS','wxID_LOADCELL','wxID_IMPORTCELL','wxID_TRANSFORMCELL','wxID_RUNSUBMAG')
+            'wxID_EXPORTCELLS','wxID_LOADCELL','wxID_IMPORTCELL','wxID_TRANSFORMCELL','wxID_RUNSUB','wxID_RUNSUBMAG')
         self.IndexMenu = wx.MenuBar()
         self.PrefillDataMenu(self.IndexMenu)
@@ -5130 +5131 @@
         self.IndexPeaks = self.IndexEdit.Append(G2G.wxID_INDEXPEAKS,'Index Cell',
             'Find cells that index fitted peaks')
+        self.RunSubGroups = self.IndexEdit.Append(G2G.wxID_RUNSUB,'Run SUBGROUPS',
+            'If disabled, do Load Cell first')
         self.RunSubGroupsMag = self.IndexEdit.Append(G2G.wxID_RUNSUBMAG,'Run k-SUBGROUPMAG',
             'If disabled, do Load Cell first')
@@ -5147 +5150 @@
         self.PostfillDataMenu()
         self.IndexPeaks.Enable(False)
+        self.RunSubGroups.Enable(False)
         self.RunSubGroupsMag.Enable(False)
         self.CopyCell.Enable(False)

trunk/GSASIIphsGUI.py

@@ -4974 +4974 @@
                             if waveTyp in ['ZigZag','Block','SawTooth','Crenel']:
                                 nx = 1
-                            CSI = G2spc.GetSSfxuinel(waveTyp,Stype,1,xyz,SGData,SSGData)
+                            CSI = G2spc.GetSSfxuinel(waveTyp,Stype,1,xyz,SGData,SSGData,debug=True)[0]
                         else:
                             CSI = G2spc.GetSSfxuinel('Fourier',Stype,iwave+1-nx,xyz,SGData,SSGData)

trunk/GSASIIplot.py

@@ -1620 +1620 @@
     global DifLine # BHT: probably does not need to be global
     global Ymax
-    global Pattern,mcolors,Plot,Page
+    global Pattern,mcolors,Plot,Page,imgAx,Temps
     plottype = plotType
     
@@ -1766 +1766 @@
                 Page.plotStyle['sqPlot'] = not Page.plotStyle['sqPlot']
         elif event.key == 't' and 'PWDR' in plottype:
-            Page.plotStyle['dPlot'] = not Page.plotStyle['dPlot']
-            if Page.plotStyle['dPlot']:
-                G2frame.Contour = False                
-                G2frame.Weight = False
-            Page.plotStyle['qPlot'] = False
-            newPlot = True      
+            if G2frame.Contour:
+                G2frame.TforYaxis = not G2frame.TforYaxis
+            else:
+                Page.plotStyle['dPlot'] = not Page.plotStyle['dPlot']
+                if Page.plotStyle['dPlot']:
+                    G2frame.Contour = False                
+                    G2frame.Weight = False
+                Page.plotStyle['qPlot'] = False
+                newPlot = True      
         elif event.key == 'm':
             Page.plotStyle['sqrtPlot'] = False
@@ -1817 +1820 @@
         
     def OnMotion(event):
+        if event.button and G2frame.Contour and G2frame.TforYaxis:
+            ytics = imgAx.get_yticks()
+            ytics = np.where(ytics<len(Temps),ytics,-1)
+            ylabs = [np.where(0<=i ,Temps[int(i)],' ') for i in ytics]
+            imgAx.set_yticklabels(ylabs)            
         xpos = event.xdata
         if xpos is None: return  #avoid out of frame mouse position
@@ -2386 +2394 @@
     if G2frame.Contour:
         Page.Choice = (' key press','d: lower contour max','u: raise contour max','o: reset contour max',
-            'i: interpolation method','s: color scheme','c: contour off')
+            'i: interpolation method','s: color scheme','c: contour off','t: temperature for y-axis')
     else:
         if Page.plotStyle['logPlot']:
@@ -2469 +2477 @@
         ParmList = []
         SampleList = []
+        Temps = []
         if G2frame.selections is None:
             choices = G2gd.GetGPXtreeDataNames(G2frame,plotType)
@@ -2491 +2500 @@
             SampleList.append(G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,
                 id, 'Sample Parameters')))
+            Temps.append('%.1fK'%SampleList[-1]['Temperature'])
         if not G2frame.Contour:
             PlotList.reverse()
@@ -2497 +2507 @@
     lenX = 0
     Ymax = None
-    for Pattern in PlotList:
+    for ip,Pattern in enumerate(PlotList):
         xye = Pattern[1]
         bxye = G2pdG.GetFileBackground(G2frame,xye,Pattern)
@@ -2682 +2692 @@
                     ContourX = range(lenX)
                 Nseq += 1
-                Plot.set_ylabel('Data sequence',fontsize=12)
+                if G2frame.TforYaxis:
+                    Plot.set_ylabel('Temperature',fontsize=14)
+                else:
+                    Plot.set_ylabel('Data sequence',fontsize=14)
         else:
             if G2frame.plusPlot:
@@ -2899 +2912 @@
         Img = Plot.imshow(ContourZ,cmap=acolor,vmin=0,vmax=Ymax*G2frame.Cmax,interpolation=G2frame.Interpolate, 
             extent=[ContourX[0],ContourX[-1],ContourY[0],ContourY[-1]],aspect='auto',origin='lower')
+        if G2frame.TforYaxis:
+            imgAx = Img.axes
+            ytics = imgAx.get_yticks()
+            ylabs = [Temps[int(i)] for i in ytics[:-1]]
+            imgAx.set_yticklabels(ylabs)
         Page.figure.colorbar(Img)
     else:

trunk/GSASIIpwdGUI.py

@@ -3117 +3117 @@
             ssopt['SGData'] = SGData
         data = [controls,bravais,cells,dminx,ssopt,magcells]
+        G2frame.dataWindow.RunSubGroups.Enable(True)
         G2frame.GPXtree.SetItemPyData(UnitCellsId,data)
         OnHklShow(None)
@@ -3162 +3163 @@
             if not ssopt.get('Use',False):
                 G2frame.dataWindow.RunSubGroupsMag.Enable(True)
+        G2frame.dataWindow.RunSubGroups.Enable(True)
         G2frame.GPXtree.SetItemPyData(UnitCellsId,data)
         G2frame.dataWindow.RefineCell.Enable(True)
@@ -3187 +3189 @@
         controls[13] = SGData['SpGrp']
 #        G2frame.GPXtree.SetItemPyData(UnitCellsId,[controls,bravais,cells,dmin,ssopt])
+        G2frame.dataWindow.RunSubGroups.Enable(True)
         G2frame.dataWindow.RefineCell.Enable(True)
         OnHklShow(None)
@@ -3627 +3630 @@
             phase['Keep'] = False
         return uAtms
+
+    def OnRunSubs(event):
+#        import SUBGROUPS as kSUB
+        G2frame.dataWindow.RunSubGroupsMag.Enable(False)
+        pUCid = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Unit Cells List')
+        controls,bravais,cells,dminx,ssopt,magcells = G2frame.GPXtree.GetItemPyData(pUCid)
+        E,SGData = G2spc.SpcGroup(controls[13])
+        kvec = ['0','0','0',' ',' ',' ',' ',' ',' ',' ']
+        Kx = [' ','0','1/2','-1/2','1/3','-1/3','2/3','1']
+        Ky = [' ','0','1/2','1/3','2/3','1']
+        Kz = [' ','0','1/2','3/2','1/3','2/3','1']
+        dlg = G2G.MultiDataDialog(G2frame,title='SUBGROUPS options',
+            prompts=[' kx1 as fr.',' ky1 as fr.',' kz1 as fr.',' kx2 as fr.',' ky2 as fr.',' kz2 as fr.', \
+                     ' kx3 as fr.',' ky3 as fr.',' kz3 as fr.', \
+                     ' Use whole star',' Filter by','preserve axes','max unique'],
+            values=kvec[:9]+[False,'',True,100],
+            limits=[Kx[1:],Ky[1:],Kz[1:],Kx,Ky,Kz,Kx,Ky,Kz,[True,False],['',' Landau transition',' Only maximal subgroups',],
+                [True,False],[1,100]],
+            formats=['choice','choice','choice','choice','choice','choice','choice','choice','choice','bool','choice',
+                    'bool','%d',])
+        if dlg.ShowModal() == wx.ID_OK:
+            subcells = []
+            newVals = dlg.GetValues()
+            kvec[:9] = newVals[:9]
+            nkvec = kvec.index(' ')
+            star = newVals[9]
+            filterby = newVals[10]
+            keepaxes = newVals[11]
+            maxequiv = newVals[12]
+            if 'maximal' in filterby:
+                maximal = True
+                Landau = False
+            elif 'Landau' in filterby:
+                maximal = False
+                Landau = True
+            else:
+                maximal = False
+                Landau = False            
+            if nkvec not in [0,3,6,9]:
+                wx.MessageBox('Error: check your propagation vector(s)',
+                    caption='Bilbao SUBGROUPS setup error',style=wx.ICON_EXCLAMATION)
+                return
+            if nkvec in [6,9] and Landau:
+                wx.MessageBox('Error, multi k-vectors & Landau not compatible',
+                    caption='Bilbao SUBGROUPS setup error',style=wx.ICON_EXCLAMATION)
+                return
+        print('run Bilbao SUBGROUPS - TBD')
         
     def OnRunSubsMag(event):
         import kSUBGROUPSMAG as kMAG
+        G2frame.dataWindow.RunSubGroups.Enable(False)
         pUCid = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Unit Cells List')
         controls,bravais,cells,dminx,ssopt,magcells = G2frame.GPXtree.GetItemPyData(pUCid)
@@ -3731 +3782 @@
     G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.IndexMenu)
     G2frame.Bind(wx.EVT_MENU, OnIndexPeaks, id=G2G.wxID_INDEXPEAKS)
+    G2frame.Bind(wx.EVT_MENU, OnRunSubs, id=G2G.wxID_RUNSUB)
     G2frame.Bind(wx.EVT_MENU, OnRunSubsMag, id=G2G.wxID_RUNSUBMAG)
     G2frame.Bind(wx.EVT_MENU, CopyUnitCell, id=G2G.wxID_COPYCELL)

trunk/GSASIIspc.py

@@ -2830 +2830 @@
     
     def DoMag():
+        dM = []
+        dMTP = []
         CSI = [[1,0,0],[2,0,0],[3,0,0], [4,0,0],[5,0,0],[6,0,0]],6*[[1.,0.,0.],]
         if siteSym == '1':
@@ -2836 +2838 @@
             CSI = 3*[[0,0,0],]+[[1,0,0],[2,0,0],[3,0,0]],3*[[0.,0.,0.],]+3*[[1.,0.,0.],]
         else:
+            tau = np.linspace(0,1,49,True)
             delt6 = np.eye(6)*0.001
             dM = posFourier(tau,nH,delt6[:3],delt6[3:]) #+np.array(Mxyz)[:,nxs,nxs]
@@ -2906 +2909 @@
                     CSI[1][i][0] = 1.0
 
-        return CSI,None,None
+        return list(CSI),dM,dMTP
         
     if debug: print ('super space group: '+SSGData['SSpGrp'])
@@ -2948 +2951 @@
     elif Stype == 'Smag':
         CSI,dF,dFTP = DoMag()
-        
+
     if debug:
         return CSI,dF,dFTP
@@ -3481 +3484 @@
         NA += len(SGOps)
     M,T = SGOps[nA]
-    if SGData['SGGray']:        #no nonzero moments for gray groups!
+    if SGData['SGGray']:
         newMom = -np.inner(Mom,M).T*nl.det(M)*SGData['SpnFlp'][NA+nC]
     else:

trunk/imports/G2pwd_Panalytical.py

@@ -62 +62 @@
         sample = self.root.find(tag+'sample')
         self.idstring = ospath.basename(filename) + ' Scan '+str(blockNum)
-        data = self.root.find(tag+'xrdMeasurement')
+        blks = self.root.findall(tag+'xrdMeasurement')
+        scans = []
+        for data in blks:
+            scans += data.findall(tag+'scan')
+        data = self.root.find(tag+'xrdMeasurement')        
         wave = data.find(tag+'usedWavelength')
         incident = data.find(tag+'incidentBeamPath')
         radius = float(incident.find(tag+'radius').text)
         tube = incident.find(tag+'xRayTube')
-        scans = data.findall(tag+'scan')
         if len(scans) > 1:
             self.repeat = True
@@ -108 +111 @@
             ]
         conditions = scan.find(tag+'nonAmbientPoints')
-        if conditions:
+        if conditions is not None:
             kind = conditions.attrib['type']
             if kind == 'Temperature':