Index: /branches/eam_branches/ipp-20111122/Ohana/src/opihi/cmd.astro/specpairfit.c
===================================================================
--- /branches/eam_branches/ipp-20111122/Ohana/src/opihi/cmd.astro/specpairfit.c	(revision 32864)
+++ /branches/eam_branches/ipp-20111122/Ohana/src/opihi/cmd.astro/specpairfit.c	(revision 32865)
@@ -9,6 +9,6 @@
 
   if ((flux1  = SelectVector (argv[1], OLDVECTOR, TRUE)) == NULL) goto escape;
-  if ((flux2  = SelectVector (argv[2], OLDVECTOR, TRUE)) == NULL) goto escape;
-  if ((dflux1 = SelectVector (argv[3], OLDVECTOR, TRUE)) == NULL) goto escape;
+  if ((dflux1 = SelectVector (argv[2], OLDVECTOR, TRUE)) == NULL) goto escape;
+  if ((flux2  = SelectVector (argv[3], OLDVECTOR, TRUE)) == NULL) goto escape;
   if ((dflux2 = SelectVector (argv[4], OLDVECTOR, TRUE)) == NULL) goto escape;
   if ((window = SelectVector (argv[5], OLDVECTOR, TRUE)) == NULL) goto escape;
@@ -37,5 +37,5 @@
     if ((mask & window->elements.Int[i]) == 0) continue;
     double weight = 1.0 / (SQ(dflux1->elements.Flt[i]) + SQ(dflux2->elements.Flt[i]));
-    chisq += (flux1->elements.Flt[i] - Ao * flux2->elements.Flt[i]) * weight;
+    chisq += SQ(flux1->elements.Flt[i] - Ao * flux2->elements.Flt[i]) * weight;
     Ndof ++;
   }
@@ -43,5 +43,9 @@
   double chisqNu = chisq / Ndof;
 
-  fprintf (stderr, "Ao: %f +/- %f, chisq_nu : %f for %d dof\n", Ao, dA, chisqNu, Ndof);
+  // fprintf (stderr, "Ao: %f +/- %f, chisq: %f, chisq_nu : %f for %d dof\n", Ao, dA, chisq, chisqNu, Ndof);
+  set_variable ("Ao", Ao);
+  set_variable ("dA", dA);
+  set_variable ("Xv", chisqNu);
+  set_variable ("Nd", Ndof);
   return (TRUE);
   
@@ -54,6 +58,2 @@
   return FALSE;
 }
-
-
-
-