Index: branches/pap/ppStack/src/ppStackReadout.c
===================================================================
--- branches/pap/ppStack/src/ppStackReadout.c	(revision 25924)
+++ branches/pap/ppStack/src/ppStackReadout.c	(revision 25964)
@@ -25,11 +25,9 @@
     psVector *addVariance = options->matchChi2; // Additional variance when rejecting
 
-    psArray *inspect = ppStackReadoutInitial(config, outRO, thread->readouts, mask,
-                                             weightings, addVariance);
-
-    job->results = inspect;
+    job->results = ppStackReadoutInitial(config, outRO, thread->readouts, mask,
+                                         weightings, addVariance);
     thread->busy = false;
 
-    return inspect ? true : false;
+    return job->results ? true : false;
 }
 
@@ -43,7 +41,6 @@
     ppStackOptions *options = args->data[2]; // Options
     pmConfig *config = args->data[3];   // Configuration
-    bool full = PS_SCALAR_VALUE(args->data[4], U8); // Combine full image?
-    bool safety = PS_SCALAR_VALUE(args->data[5], U8);    // Safety switch on?
-    bool normalise = PS_SCALAR_VALUE(args->data[6], U8); // Normalise images?
+    bool safety = PS_SCALAR_VALUE(args->data[4], U8);    // Safety switch on?
+    bool normalise = PS_SCALAR_VALUE(args->data[5], U8); // Normalise images?
 
     psVector *mask = options->inputMask; // Mask for inputs
@@ -54,5 +51,5 @@
 
     bool status = ppStackReadoutFinal(config, target, thread->readouts, mask, rejected,
-                                      weightings, addVariance, full, safety, norm); // Status of operation
+                                      weightings, addVariance, safety, norm); // Status of operation
 
     thread->busy = false;
@@ -67,24 +64,35 @@
 
     psArray *args = job->args;  // Input arguments
-    psArray *inspect = args->data[0]; // Array of pixel arrays
-    int index = PS_SCALAR_VALUE(args->data[1], S32); // Index of interest
-
-    psArray *inputs = inspect->data[index]; // Array of interest
-    psPixels *output = NULL;    // Output pixel list
-    for (int i = 0; i < inputs->n; i++) {
-        psPixels *input = inputs->data[i]; // Input pixel list
-        if (!input || input->n == 0) {
-            continue;
-        }
-        output = psPixelsConcatenate(output, input);
-    }
-
-    if (!output) {
-        // If there are no pixels to inspect, then just fake it
-        output = psPixelsAllocEmpty(0);
-    }
-
-    psFree(inputs);
-    inspect->data[index] = output;
+    psArray *inspects = args->data[0]; // Array of pixel arrays
+    psArray *rejects = args->data[1];  // Array of pixel arrays
+    int index = PS_SCALAR_VALUE(args->data[2], S32); // Index of interest
+
+    psArray *inInspects = inspects->data[index]; // Array of interest
+    psArray *inRejects = rejects->data[index]; // Array of interest
+    psAssert(inInspects->n == inRejects->n, "Size should be the same");
+    psPixels *outInspect = NULL, *outReject = NULL; // Output pixel lists
+    for (int i = 0; i < inInspects->n; i++) {
+        psPixels *inInspect = inInspects->data[i]; // Input pixel list
+        if (inInspect && inInspect->n > 0) {
+            outInspect = psPixelsConcatenate(outInspect, inInspect);
+        }
+        psPixels *inReject = inRejects->data[i]; // Input pixel list
+        if (inReject && inReject->n > 0) {
+            outReject = psPixelsConcatenate(outReject, inReject);
+        }
+    }
+
+    // If there are no pixels to inspect, then just fake it
+    if (!outInspect) {
+        outInspect = psPixelsAllocEmpty(0);
+    }
+    if (!outReject) {
+        outReject = psPixelsAllocEmpty(0);
+    }
+
+    psFree(inspects->data[index]);
+    inspects->data[index] = outInspect;
+    psFree(rejects->data[index]);
+    rejects->data[index] = outReject;
 
     return true;
@@ -154,5 +162,5 @@
 
     if (!pmStackCombine(outRO, stack, maskVal | maskBad, maskBad, kernelSize, iter,
-                        combineRej, combineSys, combineDiscard, true, useVariance, safe, false)) {
+                        combineRej, combineSys, combineDiscard, useVariance, safe, false)) {
         psError(PS_ERR_UNKNOWN, false, "Unable to combine input readouts with rejection.");
         psFree(stack);
@@ -160,6 +168,7 @@
     }
 
-    // Save list of pixels to inspect
+    // Save lists of pixels
     psArray *inspect = psArrayAlloc(num); // List of pixels to inspect
+    psArray *reject = psArrayAlloc(num);  // List of pixels rejected
     for (int i = 0; i < num; i++) {
         pmStackData *data = stack->data[i]; // Data for this image
@@ -172,4 +181,5 @@
         }
         inspect->data[i] = psMemIncrRefCounter(data->inspect);
+        reject->data[i] = psMemIncrRefCounter(data->reject);
     }
     psFree(stack);
@@ -177,5 +187,9 @@
     sectionNum++;
 
-    return inspect;
+    psArray *results = psArrayAlloc(2); // Array of results
+    results->data[0] = inspect;
+    results->data[1] = reject;
+
+    return results;
 }
 
@@ -184,5 +198,5 @@
 bool ppStackReadoutFinal(const pmConfig *config, pmReadout *outRO, const psArray *readouts,
                          const psVector *mask, const psArray *rejected, const psVector *weightings,
-                         const psVector *addVariance, bool full, bool safety, const psVector *norm)
+                         const psVector *addVariance, bool safety, const psVector *norm)
 {
     assert(config);
@@ -225,10 +239,6 @@
     for (int i = 0; i < num; i++) {
         pmReadout *ro = readouts->data[i];
-        if (mask->data.U8[i] & (PPSTACK_MASK_REJECT | PPSTACK_MASK_BAD)) {
-            // Image completely rejected since previous combination
-            full = true;
-            continue;
-        } else if (mask->data.U8[i]) {
-            // Image completely rejected before original combination
+        if (mask->data.U8[i]) {
+            // Image completely rejected
             continue;
         }
@@ -262,7 +272,6 @@
     }
 
-    if (!pmStackCombine(outRO, stack, maskVal | maskBad, maskBad, 0,
-                        iter, combineRej, combineSys, combineDiscard,
-                        full, useVariance, safe, !rejected)) {
+    if (!pmStackCombine(outRO, stack, maskVal | maskBad, maskBad, 0, iter, combineRej,
+                        combineSys, combineDiscard, useVariance, safe, !rejected)) {
         psError(PS_ERR_UNKNOWN, false, "Unable to combine input readouts.");
         psFree(stack);