Index: branches/pap/ppStack/src/ppStackReject.c
===================================================================
--- branches/pap/ppStack/src/ppStackReject.c	(revision 25950)
+++ branches/pap/ppStack/src/ppStackReject.c	(revision 25964)
@@ -23,5 +23,4 @@
 
     int num = options->num;             // Number of inputs
-    options->rejected = psArrayAlloc(num);
 
     psMetadata *recipe = psMetadataLookupMetadata(NULL, config->recipes, PPSTACK_RECIPE); // ppStack recipe
@@ -53,4 +52,5 @@
         psThreadJob *job = psThreadJobAlloc("PPSTACK_INSPECT"); // Job to start
         psArrayAdd(job->args, 1, options->inspect);
+        psArrayAdd(job->args, 1, options->rejected);
         PS_ARRAY_ADD_SCALAR(job->args, i, PS_TYPE_S32);
         if (!psThreadJobAddPending(job)) {
@@ -92,15 +92,11 @@
 #endif
 
-        psPixels *reject = pmStackReject(options->inspect->data[i], options->numCols, options->numRows,
-                                         threshold, poorFrac, stride, options->regions->data[i],
-                                         options->kernels->data[i]); // Rejected pixels
-
 #ifdef TESTING
         {
-            psImage *mask = psPixelsToMask(NULL, reject,
+            psImage *mask = psPixelsToMask(NULL, options->rejected->data[i],
                                            psRegionSet(0, options->numCols - 1, 0, options->numRows - 1),
                                            0xff); // Mask image
             psString name = NULL;           // Name of image
-            psStringAppend(&name, "reject_%03d.fits", i);
+            psStringAppend(&name, "pre_reject_%03d.fits", i);
             pmStackVisualPlotTestImage(mask, name);
             psFits *fits = psFitsOpen(name, "w");
@@ -111,4 +107,8 @@
         }
 #endif
+
+        psPixels *reject = pmStackReject(options->inspect->data[i], options->numCols, options->numRows,
+                                         threshold, poorFrac, stride, options->regions->data[i],
+                                         options->kernels->data[i]); // Rejected pixels
 
         psFree(options->inspect->data[i]);
@@ -127,5 +127,4 @@
                           "exceeds limit (%.3f)", i, frac, imageRej);
                 psFree(reject);
-                // reject == NULL means reject image completely
                 reject = NULL;
                 options->inputMask->data.PS_TYPE_VECTOR_MASK_DATA[i] |= PPSTACK_MASK_BAD;
@@ -134,6 +133,25 @@
         }
 
-        // Images without a list of rejected pixels (the list may be empty) are rejected completely
-        options->rejected->data[i] = reject;
+        if (reject) {
+            // Add to list of pixels already rejected
+            reject = psPixelsConcatenate(reject, options->rejected->data[i]);
+            options->rejected->data[i] = psPixelsDuplicates(options->rejected->data[i], reject);
+        }
+
+#ifdef TESTING
+        {
+            psImage *mask = psPixelsToMask(NULL, options->rejected->data[i],
+                                           psRegionSet(0, options->numCols - 1, 0, options->numRows - 1),
+                                           0xff); // Mask image
+            psString name = NULL;           // Name of image
+            psStringAppend(&name, "reject_%03d.fits", i);
+            pmStackVisualPlotTestImage(mask, name);
+            psFits *fits = psFitsOpen(name, "w");
+            psFree(name);
+            psFitsWriteImage(fits, NULL, mask, 0, NULL);
+            psFree(mask);
+            psFitsClose(fits);
+        }
+#endif
 
         if (options->stats) {
@@ -143,4 +161,6 @@
                              "Number of pixels rejected", reject ? reject->n : 0);
         }
+
+        psFree(reject);
         psLogMsg("ppStack", PS_LOG_INFO, "Time to perform rejection on image %d: %f sec", i,
                  psTimerClear("PPSTACK_REJECT"));