Index: trunk/magic/remove/src/streaksio.c
===================================================================
--- trunk/magic/remove/src/streaksio.c	(revision 24728)
+++ 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);
+    }
+}