Changeset 757

Timestamp:

Sep 13, 2012 8:53:46 AM (11 years ago)

Author:

vondreele

Message:

remove inverse check from peak search - didn't work
implement Zshift in structure plot
fix (mostly) the view direction

Location:

trunk

Files:

• GSASIImath.py (modified) (1 diff)
• GSASIIphsGUI.py (modified) (9 diffs)
• GSASIIplot.py (modified) (2 diffs)

trunk/GSASIImath.py

@@ -934 +934 @@
         rho[rMM[0]:rMP[0],rMM[1]:rMP[1],rMM[2]:rMP[2]] = peakFunc(x1,rX,rY,rZ,rhoPeak,res,SGData['SGLaue'])
         rho = np.roll(np.roll(np.roll(rho,-rMI[2],axis=2),-rMI[1],axis=1),-rMI[0],axis=0)
-    if SGData['SGInv']:                 #check origin location & fix it if needed - centrosymmetric only
-        Ocheck = np.zeros_like(rho)
-        for ipeak in peaks:
-            for opeak in peaks:           
-                dx = ((opeak-ipeak)*incre)%incre
-                if np.any(dx):      #avoid self vector
-                    Ocheck[dx[0],dx[1],dx[2]] += 1
-        dxMax = np.unravel_index(np.argmax(Ocheck),rho.shape)
-        print ' Inversion at:',dxMax,' shift by ;',dxMax-mapHalf
-        rho = np.roll(np.roll(np.roll(rho,dxMax[2],axis=2),dxMax[1],axis=1),dxMax[0],axis=0)
-        for peak in peaks:
-            peak = (peak-(dxMax+mapHalf)/incre)%1.0
+#    if SGData['SGInv']:                 #check origin location & fix it if needed - centrosymmetric only
+#        Ocheck = np.zeros_like(rho)
+#        for ipeak in peaks:
+#            for opeak in peaks:           
+#                dx = ((opeak-ipeak)*incre)%incre
+#                if np.any(dx):      #avoid self vector
+#                    Ocheck[dx[0],dx[1],dx[2]] += 1
+#        dxMax = np.unravel_index(np.argmax(Ocheck),rho.shape)
+#        print ' Inversion at:',dxMax,' shift by ;',dxMax-mapHalf
+#        rho = np.roll(np.roll(np.roll(rho,dxMax[2],axis=2),dxMax[1],axis=1),dxMax[0],axis=0)
+#        for peak in peaks:
+#            peak = (peak-(dxMax+mapHalf)/incre)%1.0
         
     return np.array(peaks),np.array([mags,]).T,np.array([dzeros,]).T

trunk/GSASIIphsGUI.py

@@ -1555 +1555 @@
     def SetupDrawingData():
         generalData = data['General']
+        Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
         atomData = data['Atoms']
         AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
@@ -1561 +1562 @@
             'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' ']
         defaultDrawing = {'Atoms':[],'viewPoint':[[0.5,0.5,0.5],[]],'showHydrogen':True,
-            'backColor':[0,0,0],'depthFog':False,'Zclip':50.0,'cameraPos':50.,
+            'backColor':[0,0,0],'depthFog':False,'Zclip':50.0,'cameraPos':50.,'Zstep':0.5,
             'radiusFactor':0.85,'contourLevel':1.,'bondRadius':0.1,'ballScale':0.33,
             'vdwScale':0.67,'ellipseProb':50,'sizeH':0.50,'unitCellBox':False,
             'showABC':True,'selectedAtoms':[],'Atoms':[],'oldxy':[],
-            'Quaternion':[1.0,0.0,0.0,0.0],'bondList':{},'viewDir':[0,0,1]}
+            'bondList':{},'viewDir':[0,0,1]}
+        defaultDrawing['Quaternion'] = G2mth.AV2Q(2*np.pi,np.inner(Amat,[0,0,1]))
         try:
             drawingData = data['Drawing']
@@ -1573 +1575 @@
         if not drawingData:                 #fill with defaults if empty
             drawingData.update(defaultDrawing)
+        if 'Zstep' not in drawingData:
+            drawingData['Zstep'] = 0.5
         if 'contourLevel' not in drawingData:
             drawingData['contourLevel'] = 1.
@@ -1578 +1582 @@
             drawingData['viewDir'] = [0,0,1]
         if 'Quaternion' not in drawingData:
-            drawingData['Quaternion'] = [1.0,0.0,0.0,0.0]
+            drawingData['Quaternion'] = G2mth.AV2Q(2*np.pi,np.inner(Amat,[0,0,1]))
         cx,ct,cs,ci = [0,0,0,0]
         if generalData['Type'] == 'nuclear':
@@ -2436 +2440 @@
         import wx.lib.colourselect as wcs
         generalData = data['General']
+        Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
         SetupDrawingData()
         drawingData = data['Drawing']
@@ -2454 +2459 @@
                 drawingData['Zclip'] = Zclip.GetValue()
                 ZclipTxt.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
+                G2plt.PlotStructure(G2frame,data)
+                
+            def OnZstep(event):
+                try:
+                    step = float(Zstep.GetValue())
+                    if not (0.01 <= step <= 1.0):
+                        raise ValueError
+                except ValueError:
+                    step = drawingData['Zstep']
+                drawingData['Zstep'] = step
+                Zstep.SetValue('%.2fA'%(drawingData['Zstep']))
+                
+            def OnMoveZ(event):
+                move = MoveZ.GetValue()*drawingData['Zstep']
+                MoveZ.SetValue(0)
+                VP = np.inner(Amat,np.array(drawingData['viewPoint'][0]))
+                VD = np.inner(Amat,np.array(drawingData['viewDir']))
+                VD /= np.sqrt(np.sum(VD**2))
+                VP += move*VD
+                VP = np.inner(Bmat,VP)
+                drawingData['viewPoint'][0] = VP
+                panel = dataDisplay.GetChildren()
+                names = [child.GetName() for child in panel]
+                panel[names.index('viewPoint')].SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))                
                 G2plt.PlotStructure(G2frame,data)
                 
@@ -2505 +2534 @@
             Zclip.Bind(wx.EVT_SLIDER, OnZclip)
             slideSizer.Add(Zclip,1,wx.EXPAND|wx.RIGHT)
+            
+            ZstepSizer = wx.BoxSizer(wx.HORIZONTAL)
+            ZstepSizer.Add(wx.StaticText(dataDisplay,-1,' Z step:'),0,wx.ALIGN_CENTER_VERTICAL)
+            Zstep = wx.TextCtrl(dataDisplay,value='%.2f'%(drawingData['Zstep']),
+                style=wx.TE_PROCESS_ENTER)
+            Zstep.Bind(wx.EVT_TEXT_ENTER,OnZstep)
+            Zstep.Bind(wx.EVT_KILL_FOCUS,OnZstep)
+            ZstepSizer.Add(Zstep,0,wx.ALIGN_CENTER_VERTICAL)
+            slideSizer.Add(ZstepSizer)
+            MoveSizer = wx.BoxSizer(wx.HORIZONTAL)
+            MoveSizer.Add(wx.StaticText(dataDisplay,-1,'   Press to step:'),0,wx.ALIGN_CENTER_VERTICAL)
+            MoveZ = wx.SpinButton(dataDisplay,style=wx.SP_HORIZONTAL,size=wx.Size(100,20))
+            MoveZ.SetValue(0)
+            MoveZ.SetRange(-1,1)
+            MoveZ.Bind(wx.EVT_SPIN, OnMoveZ)
+            MoveSizer.Add(MoveZ)
+            slideSizer.Add(MoveSizer,1,wx.EXPAND|wx.RIGHT)
             
             vdwScaleTxt = wx.StaticText(dataDisplay,-1,' van der Waals scale: '+'%.2f'%(drawingData['vdwScale']))
@@ -2582 +2628 @@
                 
             def OnViewDir(event):
-                event.Skip()
                 Obj = event.GetEventObject()
                 viewDir = Obj.GetValue().split()
@@ -2588 +2633 @@
                     Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
                     VD = np.array([float(viewDir[i]) for i in range(3)])
-#                    VD = np.inner(Amat,VD)
-                    VD /= np.sqrt(np.sum(VD**2))
+                    VC = np.inner(Amat,VD)
+                    VC /= np.sqrt(np.sum(VC**2))
                     V = np.array(drawingData['viewDir'])
-#                    V = np.inner(Amat,V)
-                    V /= np.sqrt(np.sum(V**2))
-                    A = acosd(np.sum(V*VD))
-                    VX = np.cross(V,VD)
+                    VB = np.inner(Amat,V)
+                    VB /= np.sqrt(np.sum(VB**2))
+                    VX = np.cross(VC,VB)
+                    A = acosd(max((2.-np.sum((VB-VC)**2))/2.,-1.))
                     QV = G2mth.AVdeg2Q(A,VX)
                     Q = drawingData['Quaternion']

trunk/GSASIIplot.py

@@ -2536 +2536 @@
                 panel = G2frame.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
                 names = [child.GetName() for child in panel]
-                panel[names.index('viewPoint')].SetValue('%.3f, %.3f, %.3f'%(VP[0],VP[1],VP[2]))
+                panel[names.index('viewPoint')].SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
                 
     def SetViewDirText(VD):
@@ -2544 +2544 @@
                 panel = G2frame.dataDisplay.GetPage(page).GetChildren()[0].GetChildren()
                 names = [child.GetName() for child in panel]
-                panel[names.index('viewDir')].SetValue('%.3f, %.3f, %.3f'%(VD[0],VD[1],VD[2]))
+                panel[names.index('viewDir')].SetValue('%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]))
                 
     def SetMapPeaksText(mapPeaks):