Index: trunk/psModules/src/camera/pmFPAMosaic.c
===================================================================
--- trunk/psModules/src/camera/pmFPAMosaic.c	(revision 21363)
+++ trunk/psModules/src/camera/pmFPAMosaic.c	(revision 25383)
@@ -740,5 +740,5 @@
 static bool chipMosaic(psImage **mosaicImage, // The mosaic image, to be returned
                        psImage **mosaicMask, // The mosaic mask, to be returned
-                       psImage **mosaicVariances, // The mosaic variances, to be returned
+                       psImage **mosaicVariance, // The mosaic variance, to be returned
                        int *xBinChip, int *yBinChip, // The binning in x and y, to be returned
                        const pmChip *chip, // Chip to mosaic
@@ -749,5 +749,5 @@
     assert(mosaicImage);
     assert(mosaicMask);
-    assert(mosaicVariances);
+    assert(mosaicVariance);
     assert(xBinChip);
     assert(yBinChip);
@@ -826,5 +826,5 @@
     if (allGood) {
         *mosaicImage = imageMosaic(images, xFlip, yFlip, xBin, yBin, *xBinChip, *yBinChip, x0, y0, BLANK_VALUE);
-        *mosaicVariances = imageMosaic(variances, xFlip, yFlip, xBin, yBin, *xBinChip, *yBinChip, x0, y0, BLANK_VALUE);
+        *mosaicVariance = imageMosaic(variances, xFlip, yFlip, xBin, yBin, *xBinChip, *yBinChip, x0, y0, BLANK_VALUE);
         *mosaicMask = imageMosaic(masks, xFlip, yFlip, xBin, yBin, *xBinChip, *yBinChip, x0, y0, blank);
     }
@@ -847,5 +847,5 @@
 static bool fpaMosaic(psImage **mosaicImage, // The mosaic image, to be returned
                       psImage **mosaicMask, // The mosaic mask, to be returned
-                      psImage **mosaicVariances, // The mosaic variances, to be returned
+                      psImage **mosaicVariance, // The mosaic variance, to be returned
                       int *xBinFPA, int *yBinFPA, // The binning in x and y, to be returned
                       const pmFPA *fpa,  // FPA to mosaic
@@ -857,5 +857,5 @@
     assert(mosaicImage);
     assert(mosaicMask);
-    assert(mosaicVariances);
+    assert(mosaicVariance);
     assert(xBinFPA);
     assert(yBinFPA);
@@ -960,5 +960,5 @@
     if (allGood) {
         *mosaicImage = imageMosaic(images, xFlip, yFlip, xBin, yBin, *xBinFPA, *yBinFPA, x0, y0, BLANK_VALUE);
-        *mosaicVariances = imageMosaic(variances, xFlip, yFlip, xBin, yBin, *xBinFPA, *yBinFPA, x0, y0, BLANK_VALUE);
+        *mosaicVariance = imageMosaic(variances, xFlip, yFlip, xBin, yBin, *xBinFPA, *yBinFPA, x0, y0, BLANK_VALUE);
         *mosaicMask = imageMosaic(masks, xFlip, yFlip, xBin, yBin, *xBinFPA, *yBinFPA, x0, y0, blank);
     }
@@ -1025,5 +1025,5 @@
     psImage *mosaicImage   = NULL;      // The mosaic image
     psImage *mosaicMask    = NULL;      // The mosaic mask
-    psImage *mosaicVariances = NULL;      // The mosaic variances
+    psImage *mosaicVariance = NULL;      // The mosaic variances
 
     // Find the HDU
@@ -1052,6 +1052,6 @@
         }
         if (hdu->variances) {
-            mosaicVariances = psImageSubset(hdu->variances->data[0], bounds);
-            if (!mosaicVariances) {
+            mosaicVariance = psImageSubset(hdu->variances->data[0], bounds);
+            if (!mosaicVariance) {
                 psError(PS_ERR_UNKNOWN, false, "Unable to select variance pixels.\n");
                 return false;
@@ -1061,5 +1061,5 @@
         // Case 2 --- we need to mosaic by cut and paste
         psTrace("psModules.camera", 1, "Case 2 mosaicking: cut and paste.\n");
-        if (!chipMosaic(&mosaicImage, &mosaicMask, &mosaicVariances, &xBin, &yBin, source, targetCell, blank)) {
+        if (!chipMosaic(&mosaicImage, &mosaicMask, &mosaicVariance, &xBin, &yBin, source, targetCell, blank)) {
             psError(PS_ERR_UNKNOWN, false, "Unable to mosaic cells.\n");
             return false;
@@ -1069,4 +1069,5 @@
     }
     psTrace("psModules.camera", 1, "xBin,yBin: %d,%d\n", xBin, yBin);
+
 
     // Set the concepts for the target cell
@@ -1090,9 +1091,31 @@
     target->parent->concepts = psMetadataCopy(target->parent->concepts, source->parent->concepts); // FPA lvl
 
+    // Average the covariances
+    psList *covariances = psListAlloc(NULL); // Input covariance matrices
+    for (int i = 0; i < source->cells->n; i++) {
+        pmCell *cell = source->cells->data[i]; // Cell of interest
+        if (!cell || !cell->data_exists) {
+            continue;
+        }
+        pmReadout *ro = cell->readouts->data[0]; // Readout of interest
+        if (!ro || !ro->covariance) {
+            continue;
+        }
+        psListAdd(covariances, PS_LIST_TAIL, ro->covariance);
+    }
+    psKernel *mosaicCovariance = NULL;  // Covariance for mosaic
+    if (psListLength(covariances) > 0) {
+        psArray *covarArray = psListToArray(covariances); // Array with covariances
+        mosaicCovariance = psImageCovarianceAverage(covarArray);
+        psFree(covarArray);
+    }
+    psFree(covariances);
+
     // Now make a new readout to go in the target cell
     pmReadout *newReadout = pmReadoutAlloc(targetCell); // New readout
     newReadout->image  = mosaicImage;
     newReadout->mask   = mosaicMask;
-    newReadout->variance = mosaicVariances;
+    newReadout->variance = mosaicVariance;
+    newReadout->covariance = mosaicCovariance;
     psFree(newReadout);                 // Drop reference
 
@@ -1334,4 +1357,32 @@
     target->concepts = psMetadataCopy(target->concepts, source->concepts);
 
+    // Average the covariances
+    psList *covariances = psListAlloc(NULL); // Input covariance matrices
+    for (int i = 0; i < covariances->n; i++) {
+        pmChip *chip = chips->data[i];  // Chip of interest
+        if (!chip || !chip->data_exists) {
+            continue;
+        }
+        psArray *cells = chip->cells;   // Cells in chip
+        for (long j = 0; j < cells->n; j++) {
+            pmCell *cell = cells->data[i]; // Cell of interest
+            if (!cell || !cell->data_exists) {
+                continue;
+            }
+            pmReadout *ro = cell->readouts->data[0]; // Readout of interest
+            if (!ro || !ro->covariance) {
+                continue;
+            }
+            psListAdd(covariances, PS_LIST_TAIL, ro->covariance);
+        }
+    }
+    psKernel *mosaicCovariances = NULL; // Covariance for mosaic
+    if (psListLength(covariances) > 0) {
+        psArray *covarArray = psListToArray(covariances); // Array with covariances
+        mosaicCovariances = psImageCovarianceAverage(covarArray);
+        psFree(covarArray);
+    }
+    psFree(covariances);
+
     // Now make a new readout to go in the new cell
     pmReadout *newReadout = pmReadoutAlloc(targetCell); // New readout
@@ -1339,4 +1390,5 @@
     newReadout->mask   = mosaicMask;
     newReadout->variance = mosaicVariances;
+    newReadout->covariance = mosaicCovariances;
     psFree(newReadout);                 // Drop reference