Index: trunk/psModules/src/camera/pmFPACopy.c
===================================================================
--- trunk/psModules/src/camera/pmFPACopy.c	(revision 24058)
+++ trunk/psModules/src/camera/pmFPACopy.c	(revision 24272)
@@ -242,4 +242,21 @@
         readoutCopyComponent(&targetReadout->variance, sourceReadout->variance, binning, xFlip, yFlip,
                              pixels);
+        // Copy covariance matrix: doesn't care about flips, etc.
+        if (sourceReadout->covariance) {
+            if (targetReadout->covariance) {
+                psFree(targetReadout->covariance);
+            }
+            targetReadout->covariance = psKernelCopy(sourceReadout->covariance);
+#if 0
+            if (binning) {
+                // XXX This isn't strictly correct, but we don't have a function that bins covariance matrices
+                // with unequal binning factors.
+                psKernel *covar = psImageCovarianceBin(PS_MAX(binning->nXbin, binning->nYbin),
+                                                       targetReadout->covariance);
+                psFree(targetReadout->covariance);
+                targetReadout->covariance = covar;
+            }
+#endif
+        }
 
         // Copy bias