Changeset 3070

Timestamp:

Sep 13, 2017 8:53:49 AM (6 years ago)

Author:

vondreele

Message:

implement use of background pattern for PWDR data.
Used for plot & peak fitting; not Rietveld refinement
fix background parm copy issue - needed deepcopy

Location:

trunk

Files:

• GSASIIplot.py (modified) (5 diffs)
• GSASIIpwd.py (modified) (4 diffs)
• GSASIIpwdGUI.py (modified) (8 diffs)

trunk/GSASIIplot.py

@@ -1971 +1971 @@
         Pattern.append(G2frame.GPXtree.GetItemText(PatternId))
         PlotList = [Pattern,]
+        Pattern[0]['BackFile'] =  G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Background'))[1].get('background PWDR',['',-1.0])
         Parms,Parms2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,
             G2frame.PatternId, 'Instrument Parameters'))
@@ -1994 +1995 @@
                 Ymax = max(Pattern[1][1])
                 Pattern[0].update({'Offset':[0.0,0.0],'delOffset':0.02*Ymax,'refOffset':-0.1*Ymax,'refDelt':0.1*Ymax,})
+            Pattern[0]['BackFile'] =  G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Background'))[1].get('background PWDR',['',-1.0])
             PlotList.append(Pattern)
             ParmList.append(G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,
@@ -2003 +2005 @@
     for Pattern in PlotList:
         xye = Pattern[1]
+        bxye = G2pdG.GetFileBackground(G2frame,xye,Pattern)
         if xye[1] is None: continue
-        if Ymax is None: Ymax = max(xye[1])
-        Ymax = max(Ymax,max(xye[1]))
+        if Ymax is None: Ymax = max(xye[1]+bxye)
+        Ymax = max(Ymax,max(xye[1]+bxye))
     if Ymax is None: return # nothing to plot
     offsetX = Pattern[0]['Offset'][1]
@@ -2062 +2065 @@
         LimitId = 0
         if Pattern[1] is None: continue # skip over uncomputed simulations
-        xye = ma.array(ma.getdata(Pattern[1]))
+#        xye = ma.array(ma.getdata(Pattern[1]))
+        xye = np.array(ma.getdata(Pattern[1]))
+        bxye = G2pdG.GetFileBackground(G2frame,xye,Pattern)
         if PickId:
             ifpicked = Pattern[2] == G2frame.GPXtree.GetItemText(PatternId)
@@ -2081 +2086 @@
             if G2frame.plotStyle['sqrtPlot']:
                 olderr = np.seterr(invalid='ignore') #get around sqrt(-ve) error
-                Y = np.where(xye[1]>=0.,np.sqrt(xye[1]),-np.sqrt(-xye[1]))
+                Y = np.where(xye[1]+bxye>=0.,np.sqrt(xye[1]+bxye),-np.sqrt(-xye[1]-bxye))
                 np.seterr(invalid=olderr['invalid'])
             else:
-                Y = xye[1]+offsetY*N*Ymax/100.0
+                Y = xye[1]+bxye+offsetY*N*Ymax/100.0
         elif plottype in ['SASD','REFD']:
             if plottype == 'SASD':

trunk/GSASIIpwd.py

@@ -1501 +1501 @@
     return True
             
-def DoPeakFit(FitPgm,Peaks,Background,Limits,Inst,Inst2,data,prevVaryList=[],oneCycle=False,controls=None,dlg=None):
+def DoPeakFit(FitPgm,Peaks,Background,Limits,Inst,Inst2,data,fixback,prevVaryList=[],oneCycle=False,controls=None,dlg=None):
     '''Called to perform a peak fit, refining the selected items in the peak
     table as well as selected items in the background.
@@ -1519 +1519 @@
       data[1] is the y-values, data[2] are weight values, data[3], [4] and [5] are
       calc, background and difference intensities, respectively. 
+    :param array fixback: fixed background values
     :param list prevVaryList: Used in sequential refinements to override the
       variable list. Defaults as an empty list.
@@ -1801 +1802 @@
         badVary = []
         result = so.leastsq(errPeakProfile,values,Dfun=devPeakProfile,full_output=True,ftol=Ftol,col_deriv=True,
-               args=(x[xBeg:xFin],y[xBeg:xFin],w[xBeg:xFin],dataType,parmDict,varyList,bakType,dlg))
+               args=(x[xBeg:xFin],(y+fixback)[xBeg:xFin],w[xBeg:xFin],dataType,parmDict,varyList,bakType,dlg))
         ncyc = int(result[2]['nfev']/2)
         runtime = time.time()-begin    
         chisq = np.sum(result[2]['fvec']**2)
         Values2Dict(parmDict, varyList, result[0])
-        Rvals['Rwp'] = np.sqrt(chisq/np.sum(w[xBeg:xFin]*y[xBeg:xFin]**2))*100.      #to %
+        Rvals['Rwp'] = np.sqrt(chisq/np.sum(w[xBeg:xFin]*(y+fixback)[xBeg:xFin]**2))*100.      #to %
         Rvals['GOF'] = chisq/(xFin-xBeg-len(varyList))       #reduced chi^2
         print 'Number of function calls:',result[2]['nfev'],' Number of observations: ',xFin-xBeg,' Number of parameters: ',len(varyList)
@@ -1834 +1835 @@
     yb[xBeg:xFin] = getBackground('',parmDict,bakType,dataType,x[xBeg:xFin])[0]
     yc[xBeg:xFin] = getPeakProfile(dataType,parmDict,x[xBeg:xFin],varyList,bakType)
-    yd[xBeg:xFin] = y[xBeg:xFin]-yc[xBeg:xFin]
+    yd[xBeg:xFin] = (y+fixback)[xBeg:xFin]-yc[xBeg:xFin]
     GetBackgroundParms(parmDict,Background)
     if bakVary: BackgroundPrint(Background,sigDict)

trunk/GSASIIpwdGUI.py

@@ -138 +138 @@
 ##### Setup routines
 ################################################################################
+
+def GetFileBackground(G2frame,xye,Pattern):
+    backfile,mult = Pattern[0]['BackFile']
+    bxye = np.zeros(len(xye[1]))
+    if backfile:
+        bxye = mult*G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root,backfile))[1][1]
+    return bxye
     
 def IsHistogramInAnyPhase(G2frame,histoName):
@@ -426 +433 @@
         limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Limits'))[1]
         inst,inst2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Instrument Parameters'))
-        profile = G2frame.GPXtree.GetItemPyData(PatternId)[1]
+        Pattern = G2frame.GPXtree.GetItemPyData(PatternId)
+        profile = Pattern[1]
+        bxye = GetFileBackground(G2frame,profile,Pattern)
         x0 = profile[0]
         iBeg = np.searchsorted(x0,limits[0])
         iFin = np.searchsorted(x0,limits[1])
         x = x0[iBeg:iFin]
-        y0 = profile[1][iBeg:iFin]
+        y0 = (profile[1]+bxye)[iBeg:iFin]
         ysig = 1.0*np.std(y0)
         offset = [-1,1]
@@ -567 +576 @@
                 limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Limits'))[1]
                 inst,inst2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Instrument Parameters'))
-                data = G2frame.GPXtree.GetItemPyData(PatternId)[1]
+                Pattern = G2frame.GPXtree.GetItemPyData(PatternId)
+                data = Pattern[1]
+                fixback = GetFileBackground(G2frame,data,Pattern)
                 peaks['sigDict'],result,sig,Rvals,varyList,parmDict,fullvaryList,badVary = G2pwd.DoPeakFit(FitPgm,peaks['peaks'],
-                    background,limits,inst,inst2,data,prevVaryList,oneCycle,controls)
+                    background,limits,inst,inst2,data,fixback,prevVaryList,oneCycle,controls)
                 if len(result[0]) != len(fullvaryList):
                     dlg.Destroy()
@@ -611 +622 @@
         limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Limits'))[1]
         inst,inst2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Instrument Parameters'))
-        data = G2frame.GPXtree.GetItemPyData(PatternId)[1]
+        Pattern = G2frame.GPXtree.GetItemPyData(PatternId)
+        data = Pattern[1]
+        bxye = GetFileBackground(G2frame,data,Pattern)
         dlg = wx.ProgressDialog('Residual','Peak fit Rwp = ',101.0, 
             style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_REMAINING_TIME|wx.PD_CAN_ABORT)
@@ -620 +633 @@
             dlg.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5))
         try:
-            peaks['sigDict'] = G2pwd.DoPeakFit(FitPgm,peaks['peaks'],background,limits,inst,inst2,data,[],oneCycle,controls,dlg)[0]
+            peaks['sigDict'] = G2pwd.DoPeakFit(FitPgm,peaks['peaks'],background,limits,inst,inst2,data,bxye,[],oneCycle,controls,dlg)[0]
         finally:
             print 'finished'
@@ -933 +946 @@
             Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
             G2frame.GPXtree.SetItemPyData(
-                G2gd.GetGPXtreeItemId(G2frame,Id,'Background'),copy.copy(data))
+                G2gd.GetGPXtreeItemId(G2frame,Id,'Background'),copy.deepcopy(data))
 
     def OnBkgFit(event):
@@ -1231 +1244 @@
             peaksSizer.Add(peaksGrid)        
         return peaksSizer
+    
+    def BackFileSizer():
+        
+        def OnBackPWDR(event):
+            data[1]['background PWDR'][0] = back.GetValue()
+            G2plt.PlotPatterns(G2frame,plotType='PWDR')
+        
+        fileSizer = wx.BoxSizer(wx.VERTICAL)
+        fileSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Fixed background file:'),0,WACV)
+        if 'background PWDR' not in data[1]:
+            data[1]['background PWDR'] = ['',-1.]
+        backSizer = wx.BoxSizer(wx.HORIZONTAL)
+        Choices = ['',]+G2gd.GetGPXtreeDataNames(G2frame,['PWDR',])
+        Source = G2frame.GPXtree.GetItemText(G2frame.PatternId)
+        Choices.pop(Choices.index(Source))
+        back = wx.ComboBox(parent=G2frame.dataWindow,value=data[1]['background PWDR'][0],choices=Choices,
+            style=wx.CB_READONLY|wx.CB_DROPDOWN)
+        back.Bind(wx.EVT_COMBOBOX,OnBackPWDR)
+        backSizer.Add(back)
+        backSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' multiplier'),0,WACV)
+        backMult = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data[1]['background PWDR'],1,nDig=(10,3))
+        backSizer.Add(backMult,0,WACV)
+        fileSizer.Add(backSizer)
+        return fileSizer
 
     # UpdateBackground execution starts here
@@ -1254 +1291 @@
     mainSizer.Add((0,5),0)
     mainSizer.Add(PeaksSizer())
+    mainSizer.Add((0,5),0)
+    mainSizer.Add(BackFileSizer())
     G2frame.dataWindow.SetDataSize()