Index: /branches/eam_branches/ipp-20111122/Ohana/src/opihi/cmd.astro/Makefile
===================================================================
--- /branches/eam_branches/ipp-20111122/Ohana/src/opihi/cmd.astro/Makefile	(revision 32866)
+++ /branches/eam_branches/ipp-20111122/Ohana/src/opihi/cmd.astro/Makefile	(revision 32867)
@@ -58,4 +58,5 @@
 $(SRC)/spec.$(ARCH).o		   \
 $(SRC)/specpairfit.$(ARCH).o	   \
+$(SRC)/mkclusters.$(ARCH).o	   \
 $(SRC)/star.$(ARCH).o		   \
 $(SRC)/transform.$(ARCH).o         \
Index: /branches/eam_branches/ipp-20111122/Ohana/src/opihi/cmd.astro/init.c
===================================================================
--- /branches/eam_branches/ipp-20111122/Ohana/src/opihi/cmd.astro/init.c	(revision 32866)
+++ /branches/eam_branches/ipp-20111122/Ohana/src/opihi/cmd.astro/init.c	(revision 32867)
@@ -46,4 +46,5 @@
 int spec                    PROTO((int, char **));
 int specpairfit             PROTO((int, char **));
+int mkclusters              PROTO((int, char **));
 int star                    PROTO((int, char **));
 int times                   PROTO((int, char **));
@@ -95,4 +96,5 @@
   {1, "spec",        spec,         "extract a spectrum"},
   {1, "specpairfit", specpairfit,  "fit spectrum to another spectrum"},
+  {1, "mkclusters",  mkclusters,   "group spectra by distance"},
   {1, "star",        star,         "star stats at rough coords"},
   {1, "transform",   transform,    "geometric transformation of image"},
Index: /branches/eam_branches/ipp-20111122/Ohana/src/opihi/cmd.astro/mkclusters.c
===================================================================
--- /branches/eam_branches/ipp-20111122/Ohana/src/opihi/cmd.astro/mkclusters.c	(revision 32867)
+++ /branches/eam_branches/ipp-20111122/Ohana/src/opihi/cmd.astro/mkclusters.c	(revision 32867)
@@ -0,0 +1,208 @@
+# include "astro.h"
+
+typedef struct {
+  int *friend;;
+  float *dist;
+  int Ndist;
+  int NDIST;
+  int group;
+} Object;
+
+typedef struct {
+  int *entry;
+  int Nentry;
+  int NENTRY;
+} Group;
+
+static Group  *group = NULL;
+static int Ngroup = 0;
+static int NGROUP = 0;
+
+static Object *object = NULL;
+static int Nobject = 0;
+// static int NOBJECT = 0;
+
+void add_to_group (int Nobj, float scale) {
+
+  int j;
+
+  // fprintf (stderr, "add object %d to group %d\n", Nobj, Ngroup);
+
+  object[Nobj].group = Ngroup;
+
+  // add to this group
+  int N = group[Ngroup].Nentry;
+  group[Ngroup].entry[N] = Nobj;
+  group[Ngroup].Nentry ++;
+  CHECK_REALLOCATE (group[Ngroup].entry, int, group[Ngroup].NENTRY, group[Ngroup].Nentry, 100);
+
+  // add all friends of this object
+  for (j = 0; j < object[Nobj].Ndist; j++) {
+    if (object[Nobj].dist[j] > scale) continue;
+
+    int Nnew = object[Nobj].friend[j];
+
+    if (object[Nnew].group != -1) continue;
+
+    // found a friend : 
+    add_to_group (Nnew, scale);
+  }
+  return;
+}
+
+void sortvecset (opihi_flt *X, opihi_int *IDX1, opihi_int *IDX2, int N) {
+
+# define SWAPFUNC(A,B){ opihi_flt tmp; opihi_int itmp; \
+  tmp  = X[A];    X[A]    = X[B];    X[B]    = tmp; \
+  itmp = IDX1[A]; IDX1[A] = IDX1[B]; IDX1[B] = itmp; \
+  itmp = IDX2[A]; IDX2[A] = IDX2[B]; IDX2[B] = itmp; \
+}
+
+# define COMPARE(A,B)(X[A] < X[B])
+
+  OHANA_SORT (N, COMPARE, SWAPFUNC);
+
+# undef SWAPFUNC
+# undef COMPARE
+
+}
+
+int mkclusters (int argc, char **argv) {
+  
+  int i, j;
+  Vector *index1, *index2, *distance;
+
+  if (argc != 5) goto usage;
+
+  if ((index1   = SelectVector (argv[1], OLDVECTOR, TRUE)) == NULL) goto escape;
+  if ((index2   = SelectVector (argv[2], OLDVECTOR, TRUE)) == NULL) goto escape;
+  if ((distance = SelectVector (argv[3], OLDVECTOR, TRUE)) == NULL) goto escape;
+  float scale = atof (argv[4]);
+
+  // XXX enforce matching lengths on the three vectors
+
+  CastVector (index1, OPIHI_INT);
+  CastVector (index2, OPIHI_INT);
+
+  Nobject = 0;
+  for (i = 0; i < index1->Nelements; i++) {
+    Nobject = MAX (Nobject, index1->elements.Int[i]);
+    Nobject = MAX (Nobject, index2->elements.Int[i]);
+  }
+  Nobject ++;  // after the loop, Nobject has the value of the highest index, not the count
+
+  // allocate the list of Object -- these list the possible friends of the given object[i] 
+  ALLOCATE (object, Object, Nobject);
+  for (i = 0; i < Nobject; i++) {
+    ALLOCATE (object[i].friend, int, Nobject);
+    memset (object[i].friend, 0, Nobject*sizeof(int));
+    ALLOCATE (object[i].dist, float, Nobject);
+    memset (object[i].dist, 0, Nobject*sizeof(float));
+    object[i].NDIST = Nobject;
+    object[i].Ndist = 0;
+    object[i].group = -1; // unassigned
+  }
+
+  // generate the set of vectors of all distances for each entry
+  // the object seq number (object[i]) will be used to match the index1 and index2 values
+  for (i = 0; i < index1->Nelements; i++) {
+    int N, m;
+    N = index1->elements.Int[i];
+    if (N >= Nobject) abort();
+    m = object[N].Ndist;
+    object[N].friend[m] = index2->elements.Int[i];
+    object[N].dist[m] = distance->elements.Flt[i];
+    object[N].Ndist ++;
+    if (object[N].Ndist == object[N].NDIST) {
+      object[N].NDIST += 100;
+      REALLOCATE (object[N].dist, float, object[N].NDIST);
+      REALLOCATE (object[N].friend, int, object[N].NDIST);
+    }
+
+    N = index2->elements.Int[i];
+    if (N >= Nobject) abort();
+    m = object[N].Ndist;
+    object[N].friend[m] = index1->elements.Int[i];
+    object[N].dist[m] = distance->elements.Flt[i];
+    object[N].Ndist ++;
+    if (object[N].Ndist == object[N].NDIST) {
+      object[N].NDIST += 100;
+      REALLOCATE (object[N].dist, float, object[N].NDIST);
+      REALLOCATE (object[N].friend, int, object[N].NDIST);
+    }
+  }
+
+  // generate the set of groups. each group is a list of friends and their friends
+  Ngroup = 0;
+  NGROUP = Nobject;
+  ALLOCATE (group, Group, NGROUP);
+  for (i = 0; i < NGROUP; i++) {
+    group[i].Nentry = 0;
+    group[i].NENTRY = 100;
+    ALLOCATE (group[i].entry, int, group[i].NENTRY);
+  }
+
+  sortvecset (distance->elements.Flt, index1->elements.Int, index2->elements.Int, index2->Nelements);
+  
+  for (i = 0; i < distance->Nelements; i++) {
+    int Nnew;
+    int found;
+
+    if (distance->elements.Flt[i] > scale) continue;
+
+    found = FALSE;
+
+    Nnew = index1->elements.Int[i];
+    if (object[Nnew].group == -1) {
+      add_to_group (Nnew, scale);
+      // fprintf (stderr, "new group %d part 1 with %d elements\n", Ngroup, group[Ngroup].Nentry);
+      found = TRUE;
+    }
+
+    Nnew = index2->elements.Int[i];
+    if (object[Nnew].group == -1) {
+      add_to_group (Nnew, scale);
+      // fprintf (stderr, "new group %d part 1 with %d elements\n", Ngroup, group[Ngroup].Nentry);
+      found = TRUE;
+    }
+
+    if (found) {
+      fprintf (stderr, "group %d with %d elements\n", Ngroup, group[Ngroup].Nentry);
+      Ngroup ++;
+      if (Ngroup >= NGROUP) abort();
+    }
+  }
+
+  if (1) {
+    int Nmiss = 0;
+    for (i = 0; i < Nobject; i++) {
+      if (object[i].group > -1) continue;
+      Nmiss ++;
+      // fprintf (stderr, "object %d not assigned\n", i);
+      for (j = 0; FALSE && j < object[i].Ndist; j++) {
+	fprintf (stderr, "friend %d, dist %f\n", object[i].friend[j], object[i].dist[j]);
+      }
+    }
+    fprintf (stderr, "%d objects not assigned\n", Nmiss);
+  } 
+
+  return TRUE;
+  
+ escape: 
+  gprint (GP_ERR, "invalid vector\n");
+  return FALSE;
+  
+usage:
+  gprint (GP_ERR, "USAGE: mkclusters (index1) (index2) (distance) scale\n");
+  return FALSE;
+}
+
+/* this function takes 3 vectors: a set of distances and a pair of indicies identifying the end points.  
+   
+   the goal is to generate groups of the end points that are relatively closer.
+
+   note that the distances may not be Euclidean: nothing can be assumed about relationships between d(1,2), d(2,3), and d(1,3)
+
+   the indicies should be sequential.  the algorithm does not require it, but storage is much cleaner if it is
+
+*/
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 32866)
+++ /branches/eam_branches/ipp-20111122/Ohana/src/opihi/cmd.astro/specpairfit.c	(revision 32867)
@@ -14,4 +14,6 @@
   if ((window = SelectVector (argv[5], OLDVECTOR, TRUE)) == NULL) goto escape;
   
+  // XXX enforce matching lengths on the 6 vectors
+
   int mask = atoi (argv[6]);
   CastVector (window, OPIHI_INT);