Index: trunk/magic/remove/src/streaksio.c
===================================================================
--- trunk/magic/remove/src/streaksio.c	(revision 24761)
+++ trunk/magic/remove/src/streaksio.c	(revision 24853)
@@ -9,4 +9,9 @@
 
 static nebServer *ourNebServer = NULL;
+
+// Assumptions about the file structure of non-raw files
+// The 'image' for each file (image, mask weight) is contained in the first
+// extension. 
+
 
 // open the files required for streaks procesing.
@@ -285,4 +290,6 @@
         // copy header from fpu
         sfile->header = (psMetadata*) psMemIncrRefCounter(sfile->pmfile->fpa->hdu->header);
+
+        sfile->nHDU = psFitsGetSize(sfile->pmfile->fits);
 
         return sfile;
@@ -1198,2 +1205,59 @@
     *maskMask = ~convPoor;
 }
+
+static void
+doCopyExtraExtensions(streakFiles *sf, sFile *in, sFile *out)
+{
+    for (int extnum = sf->extnum; extnum < in->nHDU; extnum++) {
+        moveExt(in, extnum);
+        readImage(in, extnum, sf->stage, false);
+
+        if (SFILE_IS_IMAGE(in)) {
+            // Turn off compression (code adapted from pmFPAWrite)
+#ifdef SAVE_AND_RESTORE_COMPRESSION
+            int bitpix = out->fits->options ? out->fits->options->bitpix : 0; // Desired bits per pixel
+            psFitsCompression *compress = psFitsCompressionGet(out->fits); // Current compression options
+#endif
+            if (!psFitsSetCompression(out->fits, PS_FITS_COMPRESS_NONE, NULL, 0, 0, 0)) {
+                psError(PM_ERR_UNKNOWN, false, "failed to turn off compression for extension %d\n", extnum);
+                streaksExit("", PS_EXIT_UNKNOWN_ERROR);
+            }
+#ifdef SAVE_AND_RESTORE_COMPRESSION
+            if (out->fits->options) {
+                out->fits->options->bitpix = 0;
+            }
+            if (!psFitsWriteImage(out->fits, in->header, in->image, 0, in->extname)) {
+                psError(PM_ERR_UNKNOWN, false, "failed to write image for extension %d\n", extnum);
+                streaksExit("", PS_EXIT_UNKNOWN_ERROR);
+            }
+            if (out->fits->options) {
+                out->fits->options->bitpix = bitpix;
+            }
+            if (!psFitsCompressionApply(out->fits, compress)) {
+                psError(PM_ERR_UNKNOWN, false, "failed to rest compression image for extension %d\n", extnum);
+                streaksExit("", PS_EXIT_UNKNOWN_ERROR);
+            }
+#endif
+        } else {
+            copyTable(out, in, extnum);
+        }
+    }
+}
+
+void
+copyExtraExtensions(streakFiles *sf)
+{
+    // XXX: Bad assumption, the begining of the mask and weight files have the same structure as the image
+    // So we are currently at the image portion
+    sf->extnum = sf->inImage->nHDU;
+
+    if (sf->inWeight && sf->outWeight) {
+        doCopyExtraExtensions(sf, sf->inWeight, sf->outWeight);
+    }
+    if (sf->inMask && sf->outMask) {
+        doCopyExtraExtensions(sf, sf->inMask, sf->outMask);
+    }
+    if (sf->inChMask && sf->outChMask) {
+        doCopyExtraExtensions(sf, sf->inChMask, sf->outChMask);
+    }
+}
Index: trunk/magic/remove/src/streaksio.h
===================================================================
--- trunk/magic/remove/src/streaksio.h	(revision 24761)
+++ trunk/magic/remove/src/streaksio.h	(revision 24853)
@@ -17,4 +17,5 @@
 void setupImageRefs(sFile *out, sFile *recoveryOut, sFile *in, int extnum, bool exciseAll);
 void strkGetMaskValues(streakFiles *sfiles, psU32 *maskStreak, psU32 *maskMask);
+void copyExtraExtensions(streakFiles *sfiles);
 
 void writeImage(sFile *sfile, psString extname, int extnum);
Index: trunk/magic/remove/src/streaksrelease.c
===================================================================
--- trunk/magic/remove/src/streaksrelease.c	(revision 24761)
+++ trunk/magic/remove/src/streaksrelease.c	(revision 24853)
@@ -67,4 +67,10 @@
         printf("time to process component %d: %f\n", sfiles->extnum, psTimerClear("PROCESS_COMPONENT"));
     } while (streakFilesNextExtension(sfiles));
+
+    // check the weight and mask files for extra extensions that might be in files
+    // (covariance matrix for example)
+    copyExtraExtensions(sfiles);
+
+
 
     psTimerStart("CLOSE_IMAGES");
Index: trunk/magic/remove/src/streaksremove.c
===================================================================
--- trunk/magic/remove/src/streaksremove.c	(revision 24761)
+++ trunk/magic/remove/src/streaksremove.c	(revision 24853)
@@ -198,7 +198,12 @@
     } while (streakFilesNextExtension(sfiles));
 
+
     psFree(streaks);
 
     psLogMsg("streaksremove", PS_LOG_INFO, "pixels: %ld streak pixels: %ld %4.2f%%\n", totalPixels, totalStreakPixels, 100. * totalStreakPixels / totalPixels);
+
+    // check the weight and mask files for extra extensions that might be in files
+    // (covariance matrix for example)
+    copyExtraExtensions(sfiles);
 
     // all done close the files. This is where the files are written so it can take a long time.