Changeset 5624

Timestamp:

Jul 5, 2023 3:06:01 PM (5 months ago)

Author:

toby

Message:

add interpolation to PDF background subtraction when # of points dont agree

Files:

• Tutorials/CWCombined/Combined refinement.htm (modified) (3 diffs)
• Tutorials/CWNeutron/Neutron CW Powder Data.htm (modified) (1 diff)
• Tutorials/LabData/Laboratory X.htm (modified) (2 diffs)
• Tutorials/TOF-CW Joint Refinement/TOF combined XN Rietveld refinement in GSAS.htm (modified) (1 diff)
• trunk/GSASIIpwd.py (modified) (1 diff)
• trunk/GSASIIpwdGUI.py (modified) (1 diff)

Tutorials/CWCombined/Combined refinement.htm

@@ -2005 +2005 @@
 the extension). The refinement will finish with Rwp~18% for the neutron data
 and Rwp~41% for the X-ray pattern. Now look closely at the fit. The plot should
-be in q and with just one pattern selected (use ‘<b style='mso-bidi-font-weight:
+be in Q and with just one pattern selected (use ‘<b style='mso-bidi-font-weight:
 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>q</span></b>’
@@ -2021 +2021 @@
 src="Combined%20refinement_files/image026.png" v:shapes="Picture_x0020_20"><![endif]></span></p>
 
-<p class=MsoNormal><span class=GramE>but</span> are shifted to lower q in the
+<p class=MsoNormal><span class=GramE>but</span> are shifted to lower Q in the
 neutron pattern.</p>
 
@@ -2036 +2036 @@
 <h2>Step 5. Select some parameters and 2<sup>nd</sup> Rietveld refinement</h2>
 
-<p class=MsoNormal>To improve the refinement you should first select the <b
+<p class=MsoNormal>To improve the refinement you should first select
+the checkbox to <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:

Tutorials/CWNeutron/Neutron CW Powder Data.htm

@@ -2080 +2080 @@
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b>
-flags. Next go to <b style='mso-bidi-font-weight:normal'><span
+flags (these are the checkboxes next to GSAS-II parameters). Next go to <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b>.</p>

Tutorials/LabData/Laboratory X.htm

@@ -1821 +1821 @@
 focusing circle. <b style='mso-bidi-font-weight:normal'>Important</b>: this is
 the most likely reason for peaks displacement errors in laboratory data, not
-the zero point. The lattice parameter flag is on the <b style='mso-bidi-font-weight:
+the zero point. The lattice parameter flag (this is the checkbox next to the
+lattice parameters determines if the lattice parameters will be
+refined and is called the refinement flag) is on the <b style='mso-bidi-font-weight:
 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>General</span></b>
@@ -1839 +1841 @@
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
 minor-latin'>GSAS-II data tree</span></b>. Go to both places and set those
-flags; make sure that the <b style='mso-bidi-font-weight:normal'><span
+flags (checkboxes); make sure that the <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin'>Diffractometer type</span></b> is <b

Tutorials/TOF-CW Joint Refinement/TOF combined XN Rietveld refinement in GSAS.htm

@@ -1585 +1585 @@
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin'>Phase fraction</span></b> check box so it
-will be refined. We want these values and refinement flags to be used for the
+will be refined. We want these values and refinement flags (checkboxes
+used to determine the parameters that will be varied) to be used for the
 two neutron TOF patterns as well. Do <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;

trunk/GSASIIpwd.py

@@ -313 +313 @@
     IofQ[1] = np.array([I[Ibeg:Ifin] for I in IofQ[1]])
     if data['Sample Bkg.']['Name']:
-        IofQ[1][1] += xydata['Sample Bkg.'][1][1][Ibeg:Ifin]*data['Sample Bkg.']['Mult']
+        try:   # fails if background differs in number of points
+            IofQ[1][1] += xydata['Sample Bkg.'][1][1][Ibeg:Ifin]*data['Sample Bkg.']['Mult']
+        except ValueError:
+            print("Interpolating Sample background since points don't match")
+            interpF = si.interp1d(xydata['Sample Bkg.'][1][0],xydata['Sample Bkg.'][1][1],
+                                  fill_value='extrapolate')
+            IofQ[1][1] += interpF(IofQ[1][0]) * data['Sample Bkg.']['Mult']
     if data['Container']['Name']:
         xycontainer = xydata['Container'][1][1]*data['Container']['Mult']
         if data['Container Bkg.']['Name']:
-            xycontainer += xydata['Container Bkg.'][1][1][Ibeg:Ifin]*data['Container Bkg.']['Mult']
-        IofQ[1][1] += xycontainer[Ibeg:Ifin]
+            try:
+                xycontainer += xydata['Container Bkg.'][1][1][Ibeg:Ifin]*data['Container Bkg.']['Mult']
+            except ValueError:
+                print('Number of points do not agree between Container and Container Bkg.')
+                return
+        try:   # fails if background differs in number of points
+            IofQ[1][1] += xycontainer[Ibeg:Ifin]
+        except ValueError:
+            print("Interpolating Container background since points don't match")
+            interpF = si.interp1d(xydata['Container'][1][0],xycontainer,fill_value='extrapolate')
+            IofQ[1][1] += interpF(IofQ[1][0])
+        
     data['IofQmin'] = IofQ[1][1][-1]
     IofQ[1][1] -= data.get('Flat Bkg',0.)

trunk/GSASIIpwdGUI.py

@@ -7697 +7697 @@
     inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,powId,'Instrument Parameters'))[0]
     auxPlot = G2pwd.CalcPDF(data,inst,Xlimits,xydata)
-    data['I(Q)'] = xydata['IofQ']
-    data['S(Q)'] = xydata['SofQ']
-    data['F(Q)'] = xydata['FofQ']
-    data['G(R)'] = xydata['GofR']
-    data['g(r)'] = xydata['gofr']
-    return auxPlot
+    try:
+        data['I(Q)'] = xydata['IofQ']
+        data['S(Q)'] = xydata['SofQ']
+        data['F(Q)'] = xydata['FofQ']
+        data['G(R)'] = xydata['GofR']
+        data['g(r)'] = xydata['gofr']
+        return auxPlot
+    except:   # PDF Calc aborted
+        pass
 
 def OptimizePDF(G2frame,data,showFit=True,maxCycles=5):