Index: branches/tap_branches/ppStack/src/ppStackThread.c
===================================================================
--- branches/tap_branches/ppStack/src/ppStackThread.c	(revision 25900)
+++ branches/tap_branches/ppStack/src/ppStackThread.c	(revision 27838)
@@ -56,5 +56,5 @@
 }
 
-ppStackThreadData *ppStackThreadDataSetup(const ppStackOptions *options, const pmConfig *config)
+ppStackThreadData *ppStackThreadDataSetup(const ppStackOptions *options, const pmConfig *config, bool conv)
 {
     psAssert(options, "Require options");
@@ -62,14 +62,22 @@
 
     const psArray *cells = options->cells; // Array of input cells
-    const psArray *imageNames = options->imageNames; // Names of images to read
-    const psArray *maskNames = options->maskNames; // Names of masks to read
-    const psArray *varianceNames = options->varianceNames; // Names of variance maps to read
-    const psArray *covariances = options->covariances; // Covariance matrices (already read)
+    const psArray *imageNames = conv ? options->convImages : options->origImages; // Names of images to read
+    const psArray *maskNames = conv ? options->convMasks : options->origMasks; // Names of masks to read
+    const psArray *varianceNames = conv ? options->convVariances : options->origVariances; // Variance names
+    const psArray *covariances = conv ? options->convCovars : options->origCovars; // Covariance matrices
 
     PS_ASSERT_ARRAY_NON_NULL(cells, NULL);
-    PS_ASSERT_ARRAYS_SIZE_EQUAL(cells, imageNames, NULL);
-    PS_ASSERT_ARRAYS_SIZE_EQUAL(cells, maskNames, NULL);
-    PS_ASSERT_ARRAYS_SIZE_EQUAL(cells, varianceNames, NULL);
-    PS_ASSERT_ARRAYS_SIZE_EQUAL(cells, covariances, NULL);
+    if (imageNames) {
+        PS_ASSERT_ARRAYS_SIZE_EQUAL(cells, imageNames, NULL);
+    }
+    if (maskNames) {
+        PS_ASSERT_ARRAYS_SIZE_EQUAL(cells, maskNames, NULL);
+    }
+    if (varianceNames) {
+        PS_ASSERT_ARRAYS_SIZE_EQUAL(cells, varianceNames, NULL);
+    }
+    if (covariances) {
+        PS_ASSERT_ARRAYS_SIZE_EQUAL(cells, covariances, NULL);
+    }
 
     ppStackThreadData *stack = psAlloc(sizeof(ppStackThreadData)); // Thread data, to return
@@ -87,19 +95,21 @@
             continue;
         }
-        // Resolved names
-        psString imageResolved = pmConfigConvertFilename(imageNames->data[i], config, false, false);
-        psString maskResolved = pmConfigConvertFilename(maskNames->data[i], config, false, false);
-        psString varianceResolved = pmConfigConvertFilename(varianceNames->data[i], config, false, false);
-        stack->imageFits->data[i] = psFitsOpen(imageResolved, "r");
-        stack->maskFits->data[i] = psFitsOpen(maskResolved, "r");
-        stack->varianceFits->data[i] = psFitsOpen(varianceResolved, "r");
-        psFree(imageResolved);
-        psFree(maskResolved);
-        psFree(varianceResolved);
-        if (!stack->imageFits->data[i] || !stack->maskFits->data[i] || !stack->varianceFits->data[i]) {
-            psError(PS_ERR_UNKNOWN, false, "Unable to open convolved files %s, %s, %s",
-                    (char*)imageNames->data[i], (char*)maskNames->data[i], (char*)varianceNames->data[i]);
-            return NULL;
-        }
+
+// Open an image
+#define IMAGE_OPEN(NAMES, FITS, INDEX)          \
+        if (NAMES) { \
+            psString resolved = pmConfigConvertFilename((NAMES)->data[INDEX], config, false, false); \
+            (FITS)->data[INDEX] = psFitsOpen(resolved, "r");                            \
+            if (!(FITS)->data[INDEX]) { \
+                psError(PPSTACK_ERR_IO, false, "Unable to open file %s", (char*)(NAMES)->data[INDEX]); \
+                psFree(resolved); \
+                return NULL; \
+            } \
+            psFree(resolved); \
+        }
+
+        IMAGE_OPEN(imageNames, stack->imageFits, i);
+        IMAGE_OPEN(maskNames, stack->maskFits, i);
+        IMAGE_OPEN(varianceNames, stack->varianceFits, i);
     }
 
@@ -116,5 +126,7 @@
             }
             pmReadout *ro = pmReadoutAlloc(cell); // Readout for thread
-            ro->covariance = psMemIncrRefCounter(covariances->data[j]);
+            if (covariances) {
+                ro->covariance = psMemIncrRefCounter(covariances->data[j]);
+            }
             readouts->data[j] = ro;
         }
@@ -140,10 +152,10 @@
     psMetadata *recipe = psMetadataLookupMetadata(NULL, config->recipes, PPSTACK_RECIPE); // Recipe
     if (!recipe) {
-        psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to find recipe %s", PPSTACK_RECIPE);
+        psError(PPSTACK_ERR_CONFIG, false, "Unable to find recipe %s", PPSTACK_RECIPE);
         return NULL;
     }
     int rows = psMetadataLookupS32(NULL, recipe, "ROWS"); // Number of rows to read per chunk
     if (rows <= 0) {
-        psError(PS_ERR_BAD_PARAMETER_VALUE, false, "ROWS is not set in the recipe.");
+        psError(PPSTACK_ERR_CONFIG, false, "ROWS is not set in the recipe.");
         return NULL;
     }
@@ -186,11 +198,12 @@
                 psFits *varianceFits = stack->varianceFits->data[i]; // FITS file for variance
 
-
-		int zMax = 0;
+                int zMax = 0;
                 bool keepReading = false;
-                if (pmReadoutMore(ro, imageFits, 0, &zMax, rows, config)) {
+
+                if (imageFits && pmReadoutMore(ro, imageFits, 0, &zMax, rows, config)) {
                     keepReading = true;
                     if (!pmReadoutReadChunk(ro, imageFits, 0, NULL, rows, overlap, config)) {
-                        psError(PS_ERR_IO, false, "Unable to read chunk %d for file PPSTACK.INPUT %d",
+                        psError(PPSTACK_ERR_IO, false,
+                                "Unable to read chunk %d for file PPSTACK.INPUT %d",
                                 numChunk, i);
                         *status = false;
@@ -199,8 +212,9 @@
                 }
 
-                if (pmReadoutMoreMask(ro, maskFits, 0, &zMax, rows, config)) {
+                if (maskFits && pmReadoutMoreMask(ro, maskFits, 0, &zMax, rows, config)) {
                     keepReading = true;
                     if (!pmReadoutReadChunkMask(ro, maskFits, 0, NULL, rows, overlap, config)) {
-                        psError(PS_ERR_IO, false, "Unable to read chunk %d for file PPSTACK.INPUT.MASK %d",
+                        psError(PPSTACK_ERR_IO, false,
+                                "Unable to read chunk %d for file PPSTACK.INPUT.MASK %d",
                                 numChunk, i);
                         *status = false;
@@ -209,8 +223,8 @@
                 }
 
-                if (pmReadoutMoreVariance(ro, varianceFits, 0, &zMax, rows, config)) {
+                if (varianceFits && pmReadoutMoreVariance(ro, varianceFits, 0, &zMax, rows, config)) {
                     keepReading = true;
                     if (!pmReadoutReadChunkVariance(ro, varianceFits, 0, NULL, rows, overlap, config)) {
-                        psError(PS_ERR_IO, false,
+                        psError(PPSTACK_ERR_IO, false,
                                 "Unable to read chunk %d for file PPSTACK.INPUT.VARIANCE %d",
                                 numChunk, i);
@@ -263,5 +277,5 @@
 
     {
-        psThreadTask *task = psThreadTaskAlloc("PPSTACK_INSPECT", 2);
+        psThreadTask *task = psThreadTaskAlloc("PPSTACK_INSPECT", 3);
         task->function = &ppStackInspect;
         psThreadTaskAdd(task);
@@ -270,5 +284,5 @@
 
     {
-        psThreadTask *task = psThreadTaskAlloc("PPSTACK_FINAL_COMBINE", 3);
+        psThreadTask *task = psThreadTaskAlloc("PPSTACK_FINAL_COMBINE", 6);
         task->function = &ppStackReadoutFinalThread;
         psThreadTaskAdd(task);