Changeset 429

Timestamp:

Nov 28, 2011 10:32:08 AM (12 years ago)

Author:

vondreele

Message:

set 'browser' as default help display
fix zero & zero offset to be consistent in peak fitting/indexing/cell refinement

Location:

trunk

Files:

• GSASIIgrid.py (modified) (1 diff)
• GSASIIindex.py (modified) (4 diffs)
• GSASIIpwd.py (modified) (4 diffs)
• GSASIIpwdGUI.py (modified) (19 diffs)
• GSASIIstruct.py (modified) (2 diffs)

trunk/GSASIIgrid.py

@@ -30 +30 @@
 htmlFrame = None
 helpMode = 'internal'    # need a global control to set this
-#helpMode = 'browser'    # need a global control to set this
+helpMode = 'browser'    # need a global control to set this
 htmlFirstUse = True
 

trunk/GSASIIindex.py

@@ -289 +289 @@
     return True,np.sum(errFit(result[0],ibrav,Peaks[7],Peaks[4:7],Pwr)**2),A,result
            
-def FitHKLZ(wave,ibrav,peaks,A,Z,Pwr):
-    
-    def errFit(values,ibrav,d,H,tth,wave,Pwr):
-        A = Values2A(ibrav,values[:-1])
-        Z = values[-1]
+def FitHKLZ(wave,ibrav,peaks,A,Z,Zref,Pwr):
+    
+    def errFit(values,ibrav,d,H,tth,wave,Zref,Pwr):
+        Zero = Z
+        if Zref:    
+            Zero = values[-1]
+        A = Values2A(ibrav,values[:6])
         Qo = 1./d**2
-        Qc = G2lat.calc_rDsqZ(H,A,Z,tth,wave)
+        Qc = G2lat.calc_rDsqZ(H,A,Zero,tth,wave)
         return (Qo-Qc)*d**Pwr
     
@@ -301 +303 @@
     
     values = A2values(ibrav,A)
-    values.append(Z)
-    result = so.leastsq(errFit,values,full_output=True,ftol=0.001,
-        args=(ibrav,Peaks[7],Peaks[4:7],Peaks[0],wave,Pwr))
-    A = Values2A(ibrav,result[0][:-1])
-    Z = result[0][-1]
-    
-    return True,np.sum(errFit(result[0],ibrav,Peaks[7],Peaks[4:7],Peaks[0],wave,Pwr)**2),A,Z,result
+    if Zref:
+        values.append(Z)
+    result = so.leastsq(errFit,values,full_output=True,ftol=0.0001,factor=0.001,
+        args=(ibrav,Peaks[7],Peaks[4:7],Peaks[0],wave,Zref,Pwr))
+    A = Values2A(ibrav,result[0][:6])
+    if Zref:
+        Z = result[0][-1]
+    
+    return True,np.sum(errFit(result[0],ibrav,Peaks[7],Peaks[4:7],Peaks[0],wave,Zref,Pwr)**2),A,Z,result
                
 def rotOrthoA(A):
@@ -349 +353 @@
     return peaks[0][7]
     
-def refinePeaksZ(peaks,wave,ibrav,A,Zero):
+def refinePeaksZ(peaks,wave,ibrav,A,Zero,ZeroRef):
     dmin = getDmin(peaks)
-    OK,smin,Aref,Z,result = FitHKLZ(wave,ibrav,peaks,A,Zero,2)
+    OK,smin,Aref,Z,result = FitHKLZ(wave,ibrav,peaks,A,Zero,ZeroRef,0)
     Peaks = np.array(peaks).T
     H = Peaks[4:7]
     Peaks[8] = 1./np.sqrt(G2lat.calc_rDsqZ(H,Aref,Z,Peaks[0],wave))
-    peaks = Peaks.T
-    
+    peaks = Peaks.T    
     HKL = G2lat.GenHBravais(dmin,ibrav,Aref)
     M20,X20 = calc_M20(peaks,HKL)
@@ -501 +504 @@
     Nobs = len(peaks)
     wave = inst[1]
-    if len(inst) > 10:
-        zero = inst[3]
-    else:
-        zero = inst[2]
-    print "%s %8.5f %6.3f" % ('wavelength, zero =',wave,zero)
+    zero,ncno = controls[1:3]
+    ncMax = Nobs*ncno
     print "%s %8.3f %8.3f" % ('lattice parameter range = ',amin,amax)
-    ifzero,maxzero,ncno = controls[:3]
-    ncMax = Nobs*ncno
-    print "%s %d %s %d %s %d" % ('change zero =',ifzero,'Nc/No max =',ncno,' Max Nc =',ncno*Nobs)
+    print "%s %8.5f %s %.4f %s %d %s %d" % ('Wavelength =',wave,'Zero =',zero,'Nc/No max =',ncno,' Max Nc =',ncno*Nobs)
     cells = []
     for ibrav in range(14):

trunk/GSASIIpwd.py

@@ -730 +730 @@
         try:
             pos = parmDict['pos'+str(iPeak)]
+            theta = (pos-parmDict['Zero'])/2.0
             intens = parmDict['int'+str(iPeak)]
             sigName = 'sig'+str(iPeak)
@@ -735 +736 @@
                 sig = parmDict[sigName]
             else:
-                sig = U*tand(pos/2.0)**2+V*tand(pos/2.0)+W
+                sig = U*tand(theta)**2+V*tand(theta)+W
             sig = max(sig,0.001)          #avoid neg sigma
             gamName = 'gam'+str(iPeak)
@@ -741 +742 @@
                 gam = parmDict[gamName]
             else:
-                gam = X/cosd(pos/2.0)+Y*tand(pos/2.0)
+                gam = X/cosd(theta)+Y*tand(theta)
             gam = max(gam,0.001)             #avoid neg gamma
             Wd,fmin,fmax = getWidths(pos,sig,gam,shl)
@@ -792 +793 @@
         try:
             pos = parmDict['pos'+str(iPeak)]
+            theta = (pos-parmDict['Zero'])/2.0
             intens = parmDict['int'+str(iPeak)]
             sigName = 'sig'+str(iPeak)
-            tanth = tand(pos/2.0)
-            costh = cosd(pos/2.0)
+            tanth = tand(theta)
+            costh = cosd(theta)
             if sigName in varyList:
                 sig = parmDict[sigName]

trunk/GSASIIpwdGUI.py

@@ -619 +619 @@
                     instSizer.Add((5,5),0)
             for item in ['Zero','Polariz.']:
-                fmt = '%10.3f'
+                fmt = '%10.4f'
                 Fmt = ' %s: ('+fmt+')'
                 if item in insDef:
@@ -850 +850 @@
 def UpdateIndexPeaksGrid(self, data):
     IndexId = G2gd.GetPatternTreeItemId(self,self.PatternId, 'Index Peak List')
+    inst = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))
+    Inst = dict(zip(inst[3],inst[1]))
+    try:
+        wave = Inst['Lam']
+    except KeyError:
+        wave = Inst['Lam1']
     
     def RefreshIndexPeaksGrid(event):
@@ -867 +873 @@
         peaks = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Peak List'))
         for peak in peaks:
-            dsp = inst[1]/(2.0*sind(peak[0]/2.0))
+            dsp = wave/(2.0*sind((peak[0]-Inst['Zero'])/2.0))
             data.append([peak[0],peak[2],True,False,0,0,0,dsp,0.0])
         self.PatternTree.SetItemPyData(IndexId,data)
@@ -899 +905 @@
         self.dataFrame.SetMenuBar(self.dataFrame.IndPeaksMenu)
         self.Bind(wx.EVT_MENU, OnReload, id=G2gd.wxID_INDXRELOAD)
-    inst = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1]
     self.dataFrame.IndexPeaks.Enable(False)
     self.IndexPeaksTable = []
@@ -916 +921 @@
                     G2indx.IndexPeaks(data,self.HKL)
                     for hkl in self.HKL:
-                        hkl.append(2.0*asind(inst[1]/(2.*hkl[3])))             
+                        hkl.append(2.0*asind(wave/(2.*hkl[3]))+Inst['Zero'])             
     rowLabels = []
     for i in range(len(data)): rowLabels.append(str(i+1))
@@ -946 +951 @@
     spaceGroups = ['F m 3 m','I m 3 m','P m 3 m','R -3 H','P 6/m m m','I 4/m m m',
         'P 4/m m m','F m m m','I m m m','C m m m','P m m m','C 2/m','P 2/m','P -1']
+    inst = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))
+    Inst = dict(zip(inst[3],inst[1]))
+    if 'Lam' in Inst:
+        wave = Inst['Lam']
+    else:
+        wave = Inst['Lam1']
         
     def SetLattice(controls):
@@ -984 +995 @@
     def OnZero(event):
         try:
-            Zero = min(0.1,max(-0.1,float(zero.GetValue())))
+            Zero = min(5.0,max(-5.0,float(zero.GetValue())))
         except ValueError:
             Zero = 0.0
@@ -1051 +1062 @@
         A = G2lat.cell2A(cell)
         ibrav = bravaisSymb.index(controls[5])
-        inst = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Instrument Parameters'))
-        inst = dict(zip(inst[3],inst[1]))
-        if 'Lam' in inst:
-            wave = inst['Lam']
-        else:
-            wave = inst['Lam1']
         dmin = wave/(2.0*sind(limits[1]/2.0))
         self.HKL = G2lat.GenHBravais(dmin,ibrav,A)
         for hkl in self.HKL:
-            hkl.append(2.0*asind(wave/(2.*hkl[3]))+controls[1])             
+            hkl.append(2.0*asind(wave/(2.*hkl[3]))+controls[1]+Inst['Zero'])             
         if 'PKS' in self.PatternTree.GetItemText(self.PatternId):
             G2plt.PlotPowderLines(self)
@@ -1118 +1123 @@
             return        
         print 'Refine cell'
-        inst = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Instrument Parameters'))[1]
         controls,bravais,cells,dmin = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Unit Cells List'))
         cell = controls[6:12]
@@ -1126 +1130 @@
         self.HKL = G2lat.GenHBravais(dmin,ibrav,A)
         G2indx.IndexPeaks(peaks,self.HKL)
-        if controls[0]:
-            Lhkl,M20,X20,Aref,Zero = G2indx.refinePeaksZ(peaks,inst[1],ibrav,A,controls[1])            
-            controls[1] = Zero
-        else:
-            Lhkl,M20,X20,Aref = G2indx.refinePeaks(peaks,ibrav,A)
+        Lhkl,M20,X20,Aref,Zero = G2indx.refinePeaksZ(peaks,wave,ibrav,A,controls[1],controls[0])            
+        controls[1] = Zero
         controls[6:12] = G2lat.A2cell(Aref)
         controls[12] = G2lat.calc_V(Aref)
@@ -1145 +1146 @@
         cellPrint(ibrav,Aref)
         for hkl in self.HKL:
-            hkl.append(2.0*asind(inst[1]/(2.*hkl[3]))+controls[1])             
+            hkl.append(2.0*asind(wave/(2.*hkl[3]))+controls[1]+Inst['Zero'])             
         if 'PKS' in self.PatternTree.GetItemText(self.PatternId):
             G2plt.PlotPowderLines(self)
@@ -1153 +1154 @@
     def IndexPeaks(event):
         PatternId = self.PatternId    
-#        peaks = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Index Peak List'))
-#        if not peaks:
-#            self.ErrorDialog('No peaks!', 'Nothing to index!')
-#            return
-        inst = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PatternId, 'Instrument Parameters'))[1]
         print 'Peak Indexing'
         try:
@@ -1170 +1166 @@
         self.dataFrame.CopyCell.Enable(False)
         self.dataFrame.RefineCell.Enable(False)
-        OK,dmin,cells = G2indx.DoIndexPeaks(peaks,inst,controls,bravais)
+        OK,dmin,cells = G2indx.DoIndexPeaks(peaks,inst[1],controls,bravais)
         if OK:
             data = [controls,bravais,cells,dmin]
@@ -1179 +1175 @@
                 self.HKL = G2lat.GenHBravais(dmin,bestCell[2],G2lat.cell2A(bestCell[3:9]))
                 for hkl in self.HKL:
-                    hkl.append(2.0*asind(inst[1]/(2.*hkl[3])))             
+                    hkl.append(2.0*asind(wave/(2.*hkl[3]))+controls[1]+Inst['Zero'])             
                 if 'PKS' in self.PatternTree.GetItemText(self.PatternId):
                     G2plt.PlotPowderLines(self)
@@ -1204 +1200 @@
                 self.HKL = G2lat.GenHBravais(dmin,ibrav,A)
                 for hkl in self.HKL:
-                    hkl.append(2.0*asind(inst[1]/(2.*hkl[3])))
+                    hkl.append(2.0*asind(wave/(2.*hkl[3]))+controls[1]+Inst['Zero'])             
                 if 'PKS' in self.PatternTree.GetItemText(self.PatternId):
                     G2plt.PlotPowderLines(self)
@@ -1250 +1246 @@
         controls.append(G2lat.calc_V(G2lat.cell2A(controls[6:12])))
     self.PatternTree.SetItemPyData(UnitCellsId,data)            #update with volume
-    inst = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.PatternId, 'Instrument Parameters'))[1]
     bravaisNames = ['Cubic-F','Cubic-I','Cubic-P','Trigonal-R','Trigonal/Hexagonal-P',
         'Tetragonal-I','Tetragonal-P','Orthorhombic-F','Orthorhombic-I','Orthorhombic-C',
@@ -1330 +1325 @@
     zeroVar.Bind(wx.EVT_CHECKBOX,OnZeroVar)
     littleSizer.Add(zeroVar,0,wx.ALIGN_CENTER_VERTICAL)
-    hklShow = wx.Button(self.dataDisplay,label="  Show hkl positions")
+    hklShow = wx.Button(self.dataDisplay,label="Show refined hkl positions + Zero offset")
     hklShow.Bind(wx.EVT_BUTTON,OnHklShow)
     littleSizer.Add(hklShow,0,wx.ALIGN_CENTER_VERTICAL)
@@ -1365 +1360 @@
         else:
             topSize[1] += 200
-    self.dataFrame.setSizePosLeft(topSize)
-    
+    self.dataFrame.setSizePosLeft(topSize)    
     
     if cells:
@@ -1389 +1383 @@
                 self.HKL = G2lat.GenHBravais(dmin,cell[2],A)
                 for hkl in self.HKL:
-                    hkl.append(2.0*asind(inst[1]/(2.*hkl[3])))
+                    hkl.append(2.0*asind(wave/(2.*hkl[3]))+controls[1]+Inst['Zero'])             
             table.append(row)
         UnitCellsTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)

trunk/GSASIIstruct.py

@@ -1111 +1111 @@
                     continue
                 if 'C' in inst['Type']:
-                    pos = 2.0*asind(wave/(2.0*d))
+                    pos = 2.0*asind(wave/(2.0*d))+Zero
                     if limits[0] < pos < limits[1]:
                         refList.append([h,k,l,mul,d,pos,0.0,0.0,0.0,0.0,0.0,Uniq,phi,0.0])
@@ -1973 +1973 @@
     dsq = 1./G2lat.calc_rDsq2(np.array([h,k,l]),G)
     d = np.sqrt(dsq)
+
     refl[4] = d
     pos = 2.0*asind(wave/(2.0*d))+parmDict[hfx+'Zero']