Index: trunk/psphot/src/pmFootprintsAssignPeaks.c
===================================================================
--- trunk/psphot/src/pmFootprintsAssignPeaks.c	(revision 17443)
+++ trunk/psphot/src/pmFootprintsAssignPeaks.c	(revision 17516)
@@ -8,5 +8,5 @@
 psErrorCode
 pmFootprintsAssignPeaks(psArray *footprints,	// the pmFootprints
-			  const psArray *peaks) { // the pmPeaks
+			const psArray *peaks) { // the pmPeaks
     assert (footprints != NULL);
     assert (footprints->n == 0 || pmFootprintTest(footprints->data[0]));
@@ -54,18 +54,61 @@
     
     psFree(ids);
-    //
+
     // Make sure that peaks within each footprint are sorted and unique
-    //
     for (int i = 0; i < footprints->n; i++) {
+	
 	pmFootprint *fp = footprints->data[i];
+
+	// XXX are we allowed to have peak-less footprints??
+	if (!fp->peaks->n) continue;
+
         fp->peaks = psArraySort(fp->peaks, pmPeakSortBySN);
 
-	for (int j = 1; j < fp->peaks->n; j++) { // check for duplicates
-	    if (fp->peaks->data[j] == fp->peaks->data[j-1]) {
-		(void)psArrayRemoveIndex(fp->peaks, j);
-		j--;			// we moved everything down one
+	// XXX EAM : the algorithm below should be much faster than using psArrayRemove if
+	// the number of peaks in the footprint is large, or if there are no duplicates.
+	// if we have a lot of small-number peak arrays with duplicates, this may be
+	// slower.
+
+	// track the number of good peaks in the footprint
+	int nGood = 1;
+
+	// check for duplicates
+	// on first pass, we set the index to NULL if peak is a duplicate
+	// XXX EAM : this can leave behind duplicates of the same S/N
+	// (if sorted list has A, B, A, B ...)
+	for (int j = 1; j < fp->peaks->n; j++) { 
+	    if (fp->peaks->data[j] == fp->peaks->data[nGood]) {
+		// everything on the array has its own mem reference; free and drop this one
+		psFree (fp->peaks->data[j]);
+		fp->peaks->data[j] = NULL;
+	    } else {
+		nGood ++;
 	    }
 	}
+
+	// no deleted peaks, go to next footprint
+	if (nGood == fp->peaks->n) continue;
+
+	int nKeep = 0;
+
+	psArray *goodPeaks = psArrayAlloc (nGood);
+	// on second pass, save the good peaks
+	for (int j = 0; j < fp->peaks->n; j++) { // check for duplicates
+	    if (fp->peaks->data[j] == NULL) continue;
+	    // transfer the data (NULL to avoid double free)
+	    // this is only slightly sleazy
+	    goodPeaks->data[nKeep] = fp->peaks->data[j];
+	    fp->peaks->data[j] = NULL;
+	    nKeep ++;
+	}
+	psAssert (nGood == nKeep, "mis-counted nKeep or nGood");
+
+	// free the old (now NULL-filled) array
+	psFree (fp->peaks);
+	fp->peaks = goodPeaks;
     }
+
+    // (void)psArrayRemoveIndex(fp->peaks, j);
+
 
     return PS_ERR_NONE;