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 32849)
+++ /branches/eam_branches/ipp-20111122/Ohana/src/opihi/cmd.astro/specpairfit.c	(revision 32849)
@@ -0,0 +1,57 @@
+# include "astro.h"
+
+int specpairfit (int argc, char **argv) {
+  
+  Vector *flux1, *flux2, *dflux1, *dflux2, *window;
+
+  if (argc != 2) goto usage;
+
+  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 ((dflux2 = SelectVector (argv[4], OLDVECTOR, TRUE)) == NULL) goto escape;
+  if ((window = SelectVector (argv[5], OLDVECTOR, TRUE)) == NULL) goto escape;
+  
+  mask = atoi (argv[6]);
+
+  // minimize (flux1 - flux2*alpha) in window defined by mask
+  // note that the mask is a SELECTION mask not an EXCLUSION mask
+
+  double F12 = 0.0; 
+  double F22 = 0.0;
+  for (i = 0; i < flux1->Nelements; i++) {
+    if ((mask & window->elements.Int[i]) == 0) continue;
+    weight = 1.0 / (SQ(dflux1->elements.Flt[i]) + SQ(dflux2->elements.Flt[i]));
+    F12 += flux1->elements.Flt[i] * flux2->elements.Flt[i] * weight;
+    F22 += flux2->elements.Flt[i] * flux2->elements.Flt[i] * weight;
+  }
+
+  double Ao = F12 / F22;
+  double dA = sqrt(1.0 / F22);
+
+  int Ndof = -1; // 1 parameter fit
+  double chisq = 0.0;
+  for (i = 0; i < flux1->Nelements; i++) {
+    if ((mask & window->elements.Int[i]) == 0) continue;
+    weight = 1.0 / (SQ(dflux1->elements.Flt[i]) + SQ(dflux2->elements.Flt[i]));
+    chisq += (flux1->elements.Flt[i] - Ao * flux2->elements.Flt[i]) * weight;
+    Ndof ++;
+  }
+
+  double chisqNu = chisq / Ndof;
+
+  fprintf (stderr, "Ao: %f +/- %f, chisq_nu : %f for %d dof\n", Ao, dA, chisqNu, Ndof);
+  return (TRUE);
+  
+ escape: 
+  gprint (GP_ERR, "invalid vector\n");
+  return (FALSE);
+  
+usage:
+  gprint (GP_ERR, "USAGE: specpairfit (flux1) (dflux1) (flux2) (dflux2) (window) (mask) [options]\n");
+  return FALSE;
+}
+
+
+
+