Index: trunk/Ohana/src/opihi/cmd.data/Makefile
===================================================================
--- trunk/Ohana/src/opihi/cmd.data/Makefile	(revision 6249)
+++ trunk/Ohana/src/opihi/cmd.data/Makefile	(revision 6642)
@@ -68,4 +68,5 @@
 $(SDIR)/mset.$(ARCH).o		\
 $(SDIR)/peak.$(ARCH).o		\
+$(SDIR)/periodogram.$(ARCH).o	\
 $(SDIR)/plot.$(ARCH).o		\
 $(SDIR)/dot.$(ARCH).o		\
Index: trunk/Ohana/src/opihi/cmd.data/init.c
===================================================================
--- trunk/Ohana/src/opihi/cmd.data/init.c	(revision 6249)
+++ trunk/Ohana/src/opihi/cmd.data/init.c	(revision 6642)
@@ -53,4 +53,5 @@
 int mset             PROTO((int, char **));
 int peak             PROTO((int, char **));
+int periodogram      PROTO((int, char **));
 int plot             PROTO((int, char **));
 int dot              PROTO((int, char **));
@@ -160,4 +161,5 @@
   {"mset",    	   mset,	     "insert a vector in a matrix"},
   {"peak",	   peak,	     "find vector peak in range"},
+  {"periodogram",  periodogram,	     "measure periods in unevenly sampled data"},
   {"plot",    	   plot,	     "plot a pair of vectors"},
   {"dot",    	   dot,	             "plot a single point"},
Index: trunk/Ohana/src/opihi/cmd.data/peak.c
===================================================================
--- trunk/Ohana/src/opihi/cmd.data/peak.c	(revision 6249)
+++ trunk/Ohana/src/opihi/cmd.data/peak.c	(revision 6642)
@@ -3,11 +3,17 @@
 int peak (int argc, char **argv) {
   
-  int i, imax;
+  int i, N, imax, QUIET;
   double start, end, xmax, ymax;
   float *X, *Y;
   Vector *vecx, *vecy;
 
-  if (argc != 5) {
-    fprintf (stderr, "USAGE: peak <x> <y> start end\n");
+  QUIET = FALSE;
+  if ((N = get_argument (argc, argv, "-q"))) {
+    QUIET = TRUE;
+    remove_argument (N, &argc, argv);
+  }
+
+  if ((argc != 5) && (argc != 3)) {
+    fprintf (stderr, "USAGE: peak <x> <y> [start end]\n");
     return (FALSE);
   }
@@ -16,6 +22,11 @@
   if ((vecy = SelectVector (argv[2], OLDVECTOR, TRUE)) == NULL) return (FALSE);
 
-  start = atof (argv[3]);
-  end   = atof (argv[4]);
+  if (argc == 5) {
+    start = atof (argv[3]);
+    end   = atof (argv[4]);
+  } else {
+    start = vecx[0].elements[0];
+    end   = vecx[0].elements[vecx[0].Nelements - 1];
+  }
 
   X = vecx[0].elements;
@@ -39,7 +50,6 @@
   set_variable ("peaknum", imax);
 
-  fprintf (stderr, "peak %f @ %f (%d)\n", ymax, xmax, imax);
+  if (!QUIET) fprintf (GetOutfile(), "peak %f @ %f (%d)\n", ymax, xmax, imax);
 
   return (TRUE);
 }
-
Index: trunk/Ohana/src/opihi/cmd.data/periodogram.c
===================================================================
--- trunk/Ohana/src/opihi/cmd.data/periodogram.c	(revision 6642)
+++ trunk/Ohana/src/opihi/cmd.data/periodogram.c	(revision 6642)
@@ -0,0 +1,114 @@
+# include "data.h"
+
+int periodogram (int argc, char **argv) {
+  
+  int i, N, Npt, Np, NP, VERBOSE;
+  float *tv, *fv;
+  float minP, maxP, minT, maxT, dTime;
+  float mean, var, w, tau, P, Pc, Ps, Po;
+  float C, S, cs, sn, cs2, sn2, ratio;
+  Vector *time, *flux, *power, *period;
+
+  VERBOSE = FALSE;
+  if ((N = get_argument (argc, argv, "-v"))) {
+    VERBOSE = TRUE;
+    remove_argument (N, &argc, argv);
+  }
+
+  if (argc != 7) {
+    fprintf (stderr, "USAGE: periodogram (time) (flux) (minP) (maxP) (period) (power)\n");
+    return (FALSE);
+  }
+  
+  if ((time = SelectVector (argv[1], OLDVECTOR, TRUE)) == NULL) return (FALSE);
+  if ((flux = SelectVector (argv[2], OLDVECTOR, TRUE)) == NULL) return (FALSE);
+  minP = atof(argv[3]);
+  maxP = atof(argv[4]);
+  if ((period = SelectVector (argv[5], ANYVECTOR, TRUE)) == NULL) return (FALSE);
+  if ((power = SelectVector (argv[6], ANYVECTOR, TRUE)) == NULL) return (FALSE);
+
+  /* find the max baseline, mean, and variance */
+  minT = maxT = time[0].elements[0];
+  Npt = time[0].Nelements;
+  tv = time[0].elements;
+  fv = flux[0].elements;
+  mean = var = 0;
+  for (i = 0; i < Npt; i++, tv++, fv++) {
+    minT = MIN (minT, *tv);
+    maxT = MAX (maxT, *tv);
+    mean += *fv;
+  }
+  mean = mean / Npt;
+  fv = flux[0].elements;
+  for (i = 0; i < Npt; i++, fv++) {
+    var += SQ(*fv - mean);
+  }
+  var = var / (Npt - 1);
+
+  if (VERBOSE) fprintf (stderr, "mean: %f, var: %f, minT: %f, maxT: %f\n", mean, var, minT, maxT);
+
+  dTime = maxT - minT;
+  if (dTime == 0) {
+    fprintf (stderr, "ERROR: time range is zero\n");
+    return (FALSE);
+  }
+
+  Np = 0;
+  NP = 100;
+  REALLOCATE (power[0].elements, float, NP);
+  REALLOCATE (period[0].elements, float, NP);
+
+  P = minP;
+  while (P < maxP) {
+    w = 2*M_PI/P;
+    
+    /* find the period offset tau  */
+    tv = time[0].elements;
+    cs = sn = 0;
+    for (i = 0; i < Npt; i++, tv++) {
+      cs += cos (*tv*w*2);
+      sn += sin (*tv*2*2);
+    }
+    tau = 0.5*atan2 (sn, cs) / w;
+      
+    /* find the power at this period */
+    tv = time[0].elements;
+    fv = flux[0].elements;
+    cs = sn = cs2 = sn2 = 0;
+    for (i = 0; i < Npt; i++, tv++, fv++) {
+      C = cos (w*(*tv-tau));
+      S = sin (w*(*tv-tau));
+      // C = cos (w**tv);
+      // S = sin (w**tv);
+      cs += (*fv - mean) * C;
+      sn += (*fv - mean) * S;
+      cs2 += SQ(C);
+      sn2 += SQ(S);
+    }
+    Pc = SQ(cs) / cs2;
+    Ps = SQ(sn) / sn2;
+    Po = (Pc + Ps) / (2*var);
+
+    power[0].elements[Np] = Po;
+    period[0].elements[Np] = P;
+    Np ++;
+    if (Np >= NP) {
+      NP += 100;
+      REALLOCATE (power[0].elements, float, NP);
+      REALLOCATE (period[0].elements, float, NP);
+    }
+
+    ratio = 1 + 0.1*P/dTime;
+
+    if (VERBOSE) fprintf (stderr, "tau: %f, P: %f, ratio: %f, dTime: %f, nextP: %f\n", tau, P, ratio, dTime, P*ratio);
+
+    P *= ratio;
+  }
+
+  power[0].Nelements = Np;
+  period[0].Nelements = Np;
+  REALLOCATE (power[0].elements, float, Np);
+  REALLOCATE (period[0].elements, float, Np);
+ 
+  return (TRUE);
+}
Index: trunk/Ohana/src/opihi/cmd.data/test/peak.sh
===================================================================
--- trunk/Ohana/src/opihi/cmd.data/test/peak.sh	(revision 6642)
+++ trunk/Ohana/src/opihi/cmd.data/test/peak.sh	(revision 6642)
@@ -0,0 +1,75 @@
+
+list tests
+ test1
+ test2
+ test3
+end
+
+# test using full range
+macro test1
+ $PASS = 1
+ break -auto off
+
+ create x 0 100
+ set y = zero (x)
+ y[50] = 1
+
+ peak -q x y 0 100
+
+ if ($peakpos != 50)
+   $PASS = 0
+ end
+ if ($peaknum != 51)
+   $PASS = 0
+ end
+ if ($peakval != 1)
+   $PASS = 0
+ end
+end
+
+# test using auto range
+macro test2
+ $PASS = 1
+ break -auto off
+
+ create x 0 100
+ set y = zero (x)
+ y[50] = 1
+
+ peak -q x y 
+
+ if ($peakpos != 50)
+   $PASS = 0
+ end
+ if ($peaknum != 51)
+   $PASS = 0
+ end
+ if ($peakval != 1)
+   $PASS = 0
+ end
+end
+
+# test using constrained range
+macro test3
+ $PASS = 1
+ break -auto off
+
+ create x 0 100
+ set y = zero (x)
+ y[60] = 2
+ y[50] = 1
+ y[40] = 2
+
+ peak -q x y 45 55
+
+ if ($peakpos != 50)
+   $PASS = 0
+ end
+ if ($peaknum != 51)
+   $PASS = 0
+ end
+ if ($peakval != 1)
+   $PASS = 0
+ end
+end
+
Index: trunk/Ohana/src/opihi/cmd.data/test/periodogram.sh
===================================================================
--- trunk/Ohana/src/opihi/cmd.data/test/periodogram.sh	(revision 6642)
+++ trunk/Ohana/src/opihi/cmd.data/test/periodogram.sh	(revision 6642)
@@ -0,0 +1,100 @@
+
+list tests
+ test1
+ test2
+ test3
+end
+
+# test using even samples
+macro test1
+ $PASS = 1
+ break -auto off
+
+ local P PI
+ $PI = 3.14159265359
+ $P  = 15.0
+
+ create t 0 100
+ set f = sin(2*$PI*t/$P)
+ periodogram t f 5 50 period power
+
+ peak -q period power
+
+ if (abs ($peakpos - $P) > 0.5)
+   $PASS = 0
+ end
+end
+
+# test using random samples
+macro test2
+ $PASS = 1
+ break -auto off
+
+ local P PI
+ $PI = 3.14159265359
+ $P  = 15.0
+
+ create x 0 100
+ set t = 100 * rnd(x) 
+ set f = sin(2*$PI*t/$P)
+ periodogram t f 5 50 period power
+
+ # lim -n 0 t f; clear; box; plot -x 2 -pt 2 t f
+ # lim -n 1 period power; clear; box; plot period power
+
+ peak -q period power
+
+ if (abs ($peakpos - $P) > 0.5)
+   $PASS = 0
+ end
+end
+
+# test using random samples, higher frequency
+macro test3
+ $PASS = 1
+ break -auto off
+
+ local P PI
+ $PI = 3.14159265359
+ $P  = 2.0
+
+ create x 0 100
+ set t = 100 * rnd(x) 
+ set f = sin(2*$PI*t/$P)
+
+ periodogram t f 1 10 period power
+
+ # lim -n 0 t f; clear; box; plot -x 2 -pt 2 t f
+ # lim -n 1 period power; clear; box; plot period power
+
+ peak -q period power
+
+ if (abs ($peakpos - $P) > 0.05)
+   $PASS = 0
+ end
+end
+
+# test using random samples, offset start
+macro test4
+ $PASS = 1
+ break -auto off
+
+ local P PI
+ $PI = 3.14159265359
+ $P  = 15.0
+
+ create x 500 800
+ set t = 300 * rnd(x) + 500
+ set f = sin(2*$PI*t/$P)
+
+ periodogram t f 2 30 period power
+
+  lim -n 0 t f; clear; box; plot -x 2 -pt 2 t f
+  lim -n 1 period power; clear; box; plot period power
+
+ peak -q period power
+
+ if (abs ($peakpos - $P) > 0.05)
+   $PASS = 0
+ end
+end
Index: trunk/Ohana/src/opihi/cmd.data/write_vectors.c
===================================================================
--- trunk/Ohana/src/opihi/cmd.data/write_vectors.c	(revision 6249)
+++ trunk/Ohana/src/opihi/cmd.data/write_vectors.c	(revision 6642)
@@ -41,4 +41,5 @@
   for (i = 0; i < Nvec; i++) {
     if ((vec[i] = SelectVector (argv[i + 2], OLDVECTOR, FALSE)) == NULL) {
+      fprintf (stderr, "unknown vector %s\n", argv[i+2]);
       fprintf (stderr, "USAGE: write (file) vector vector ...\n");
       free (vec);