Changeset 1248 for trunk

Timestamp:

Mar 13, 2014 2:16:20 PM (11 years ago)

Author:

vondreele

Message:

add setscale for SASD data
don't square the 1/cos(2-theta) correction to integrated intensities in ImageIntegrate?
scale SASD error bars by Scale
replace ':' with ';' in BkPk? parameter names
fix bug of missing Residuals in LS Refine

Location:

trunk

Files:

• GSASIIgrid.py (modified) (3 diffs)
• GSASIIimage.py (modified) (1 diff)
• GSASIIplot.py (modified) (1 diff)
• GSASIIpwd.py (modified) (2 diffs)
• GSASIIpwdGUI.py (modified) (4 diffs)
• GSASIIsasd.py (modified) (2 diffs)
• GSASIIstrIO.py (modified) (2 diffs)
• GSASIIstrMain.py (modified) (2 diffs)
• GSASIIstrMath.py (modified) (1 diff)

trunk/GSASIIgrid.py ¶

@@ -106 +106 @@
 
 [ wxID_BACKCOPY,wxID_LIMITCOPY,wxID_SAMPLECOPY, wxID_BACKFLAGCOPY, wxID_SAMPLEFLAGCOPY,
-    wxID_SAMPLESAVE, wxID_SAMPLELOAD,wxID_ADDEXCLREGION,
-] = [wx.NewId() for item in range(8)]
+    wxID_SAMPLESAVE, wxID_SAMPLELOAD,wxID_ADDEXCLREGION,wxID_SETSCALE,
+] = [wx.NewId() for item in range(9)]
 
 [ wxID_INSTPRMRESET,wxID_CHANGEWAVETYPE,wxID_INSTCOPY, wxID_INSTFLAGCOPY, wxID_INSTLOAD,
@@ -2473 +2473 @@
         self.SampleEdit = wx.Menu(title='')
         self.SampleMenu.Append(menu=self.SampleEdit, title='Command')
+        self.SetScale = self.SampleEdit.Append(id=wxID_SETSCALE, kind=wx.ITEM_NORMAL,text='Set scale',
+            help='Set scale by matching to another histogram')
         self.SampleEdit.Append(id=wxID_SAMPLELOAD, kind=wx.ITEM_NORMAL,text='Load',
             help='Load sample parameters from file')
@@ -2482 +2484 @@
             help='Copy sample parameter refinement flags to other histograms')
         self.PostfillDataMenu()
+        self.SetScale.Enable(False)
 
         # PDR / Peak List

trunk/GSASIIimage.py ¶

@@ -879 +879 @@
     else:
         H1 = LRazm
-    H0 /= npcosd(H2[:-1])           #**2?
+    H0 /= npcosd(H2[:-1])           #**2? I don't think so, **1 is right for powders
     if data['Oblique'][1]:
         H0 /= G2pwd.Oblique(data['Oblique'][0],H2[:-1])

trunk/GSASIIplot.py ¶

@@ -903 +903 @@
                         Plot.set_yscale("log",nonposy='mask')
                         if G2frame.ErrorBars:
-                            Plot.errorbar(X,Y,yerr=np.sqrt(1./(Pattern[0]['wtFactor']*xye[2])),
+                            Plot.errorbar(X,Y,yerr=Sample['Scale'][0]*np.sqrt(1./(Pattern[0]['wtFactor']*xye[2])),
                                 ecolor=colors[N%6],picker=3.,clip_on=False)
                         else:

trunk/GSASIIpwd.py ¶

@@ -581 +581 @@
     while True:
         try:
-            pkP = parmDict[pfx+'BkPkpos:'+str(iD)]
-            pkI = parmDict[pfx+'BkPkint:'+str(iD)]
-            pkS = parmDict[pfx+'BkPksig:'+str(iD)]
-            pkG = parmDict[pfx+'BkPkgam:'+str(iD)]
+            pkP = parmDict[pfx+'BkPkpos;'+str(iD)]
+            pkI = parmDict[pfx+'BkPkint;'+str(iD)]
+            pkS = parmDict[pfx+'BkPksig;'+str(iD)]
+            pkG = parmDict[pfx+'BkPkgam;'+str(iD)]
             shl = 0.002
             Wd,fmin,fmax = getWidthsCW(pkP,pkS,pkG,shl)
@@ -675 +675 @@
     while True:
         try:
-            pkP = parmDict[pfx+'BkPkpos:'+str(iD)]
-            pkI = parmDict[pfx+'BkPkint:'+str(iD)]
-            pkS = parmDict[pfx+'BkPksig:'+str(iD)]
-            pkG = parmDict[pfx+'BkPkgam:'+str(iD)]
+            pkP = parmDict[pfx+'BkPkpos;'+str(iD)]
+            pkI = parmDict[pfx+'BkPkint;'+str(iD)]
+            pkS = parmDict[pfx+'BkPksig;'+str(iD)]
+            pkG = parmDict[pfx+'BkPkgam;'+str(iD)]
             shl = 0.002
             Wd,fmin,fmax = getWidthsCW(pkP,pkS,pkG,shl)

trunk/GSASIIpwdGUI.py ¶

@@ -1129 +1129 @@
     data tree item.
     '''
+                                                        
     def SetCopyNames(histName,addNames=[]):
         copyNames = ['Scale',]
@@ -1166 +1167 @@
         finally:
             dlg.Destroy()
-                                                        
+            
     def OnSampleLoad(event):
         '''Loads sample parameters from a G2 .samprm file
@@ -1195 +1196 @@
             dlg.Destroy()
     
+    def OnSetScale(event):
+        histList = []
+        item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
+        while item:
+            name = G2frame.PatternTree.GetItemText(item)
+            if 'SASD' in name and name != histName:
+                histList.append(name)
+            item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
+        if not len(histList):      #nothing to copy to!
+            return
+        dlg = wx.SingleChoiceDialog(G2frame,'Select reference histogram for scaling',
+            'Reference histogram',histList)
+        try:
+            if dlg.ShowModal() == wx.ID_OK:
+                sel = dlg.GetSelection()
+                refHist = histList[sel]
+        finally:
+            dlg.Destroy()
+        Limits = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Limits'))
+        Profile = G2frame.PatternTree.GetItemPyData(G2frame.PatternId)[1]
+        Data = [Profile,Limits,data]
+        refId = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,refHist)
+        refSample = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,refId, 'Sample Parameters'))
+        refLimits = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,refId, 'Limits'))
+        refProfile = G2frame.PatternTree.GetItemPyData(refId)[1]
+        refData = [refProfile,refLimits,refSample]
+        G2sasd.SetScale(Data,refData)
+        UpdateSampleGrid(G2frame,data)       
+        G2plt.PlotPatterns(G2frame,plotType='SASD',newPlot=True)
+        
     def OnSampleCopy(event):
         histType,copyNames = SetCopyNames(histName,
@@ -1327 +1358 @@
     G2gd.SetDataMenuBar(G2frame,G2frame.dataFrame.SampleMenu)
     G2frame.dataFrame.SetLabel('Sample Parameters')
+    G2frame.Bind(wx.EVT_MENU, OnSetScale, id=G2gd.wxID_SETSCALE)
     G2frame.Bind(wx.EVT_MENU, OnSampleCopy, id=G2gd.wxID_SAMPLECOPY)
     G2frame.Bind(wx.EVT_MENU, OnSampleFlagCopy, id=G2gd.wxID_SAMPLEFLAGCOPY)
     G2frame.Bind(wx.EVT_MENU, OnSampleSave, id=G2gd.wxID_SAMPLESAVE)
     G2frame.Bind(wx.EVT_MENU, OnSampleLoad, id=G2gd.wxID_SAMPLELOAD)
+    if 'SASD' in histName:
+        G2frame.dataFrame.SetScale.Enable(True)
     if not G2frame.dataFrame.GetStatusBar():
         Status = G2frame.dataFrame.CreateStatusBar()    

trunk/GSASIIsasd.py ¶

@@ -689 +689 @@
 if __name__ == '__main__':
     tests()
+    
+###############################################################################
+#### SASD Utilities
+###############################################################################
+
+def SetScale(Data,refData):
+    Profile,Limits,Sample = Data
+    refProfile,refLimits,refSample = refData
+    x,y = Profile[:2]
+    rx,ry = refProfile[:2]
+    Beg = np.max([rx[0],x[0],Limits[1][0],refLimits[1][0]])
+    Fin = np.min([rx[-1],x[-1],Limits[1][1],refLimits[1][1]])
+    iBeg = np.searchsorted(x,Beg)
+    iFin = np.searchsorted(x,Fin)
+    sum = np.sum(y[iBeg:iFin])
+    refsum = np.sum(np.interp(x[iBeg:iFin],rx,ry,0,0))
+    Sample['Scale'][0] = refSample['Scale'][0]*refsum/sum
     
 ###############################################################################
@@ -722 +739 @@
         Ic[Ibeg:Ifin] = Back[0]
     Gmat = G_matrix(Q[Ibeg:Ifin],Bins,Contrast,shapes[Shape][0],shapes[Shape][1],args=Parms)
-    chisq,BinMag,Ic[Ibeg:Ifin] = MaxEnt_SB(Io[Ibeg:Ifin]-Back[0],1./np.sqrt(wtFactor*wt[Ibeg:Ifin]),BinsBack,
+    chisq,BinMag,Ic[Ibeg:Ifin] = MaxEnt_SB(Sample['Scale'][0]*Io[Ibeg:Ifin]-Back[0],
+        Sample['Scale'][0]/np.sqrt(wtFactor*wt[Ibeg:Ifin]),BinsBack,
         data['Size']['MaxEnt']['Niter'],Gmat,report=True)
     print ' Final chi^2: %.3f'%(chisq)

trunk/GSASIIstrIO.py ¶

@@ -2190 +2190 @@
         peakList = []
         for i in range(DebyePeaks['nPeaks']):
-            peakNames = [':'+str(hId)+':BkPkpos:'+str(i),':'+str(hId)+ \
-                ':BkPkint:'+str(i),':'+str(hId)+':BkPksig:'+str(i),':'+str(hId)+':BkPkgam:'+str(i)]
+            peakNames = [':'+str(hId)+':BkPkpos;'+str(i),':'+str(hId)+ \
+                ':BkPkint;'+str(i),':'+str(hId)+':BkPksig;'+str(i),':'+str(hId)+':BkPkgam;'+str(i)]
             peakDict.update(dict(zip(peakNames,DebyePeaks['peaksList'][i][::2])))
             peakList += zip(peakNames,DebyePeaks['peaksList'][i][1::2])
@@ -2404 +2404 @@
         if DebyePeaks['nPeaks']:
             for i in range(DebyePeaks['nPeaks']):
-                names = [pfx+'BkPkpos:'+str(i),pfx+'BkPkint:'+str(i),
-                    pfx+'BkPksig:'+str(i),pfx+'BkPkgam:'+str(i)]
+                names = [pfx+'BkPkpos;'+str(i),pfx+'BkPkint;'+str(i),
+                    pfx+'BkPksig;'+str(i),pfx+'BkPkgam;'+str(i)]
                 for j,name in enumerate(names):
                     DebyePeaks['peaksList'][i][2*j] = parmDict[name]

trunk/GSASIIstrMain.py ¶

@@ -105 +105 @@
                         del(varyList[ipvt-1])
                         break
-        G2stMth.GetFobsSq(Histograms,Phases,parmDict,calcControls)
+    G2stMth.GetFobsSq(Histograms,Phases,parmDict,calcControls)
     return Rvals,result,covMatrix,sig
 
@@ -169 +169 @@
     Rvals,result,covMatrix,sig = RefineCore(Controls,Histograms,Phases,restraintDict,
         rigidbodyDict,parmDict,varyList,calcControls,pawleyLookup,ifPrint,printFile,dlg)
-        
     sigDict = dict(zip(varyList,sig))
     newCellDict = G2stMth.GetNewCellParms(parmDict,varyList)

trunk/GSASIIstrMath.py ¶

@@ -1497 +1497 @@
     for name in varylist:
         if 'BkPk' in name:
-            id = int(name.split(':')[-1])
-            parm = name[:int(name.rindex(':'))]
+            id = int(name.split(';')[-1])
+            parm = name[:int(name.rindex(';'))]
             ip = names.index(parm)
             dMdv[varylist.index(name)] = dMdpk[4*id+ip]