Index: trunk/pstamp/scripts/pstamp_job_run.pl
===================================================================
--- trunk/pstamp/scripts/pstamp_job_run.pl	(revision 33512)
+++ trunk/pstamp/scripts/pstamp_job_run.pl	(revision 35398)
@@ -113,4 +113,5 @@
 
     if ($stage eq "raw") {
+        # zap options that don't apply to raw stage
         $options &= ~($PSTAMP_SELECT_MASK | $PSTAMP_SELECT_VARIANCE); 
     }
@@ -136,4 +137,22 @@
         $argString .= " -astrom $params->{astrom}";
         push @file_list, $params->{astrom};
+    }
+
+    if ($options & $PSTAMP_SELECT_SOURCES) {
+        # Extract sources from astrometry file if provided. This will be the smf for chip stage
+        # or the skycal cmf for stacks
+        if ($params->{astrom}) {
+            $argString .= " -write_cmf";
+            if ($stage eq 'stack') {
+                # Set psphot recipe to STACKPHOT so that the extended source paramters will
+                # be copied from the cmf file.
+                $argString .= " -recipe PSPHOT STACKPHOT"
+            }
+        } elsif ($params->{cmf}) {
+            $argString .= " -write_cmf";
+            push @file_list, $params->{cmf};
+        } else {
+            print "Could not find suitable sources file will not write cmf\n";
+        }
     }
 
@@ -254,7 +273,8 @@
                            $PSTAMP_SELECT_MASK     => "mk.fits",
                            $PSTAMP_SELECT_VARIANCE => "wt.fits",
+                           $PSTAMP_SELECT_SOURCES  => "cmf",
                            $PSTAMP_SELECT_JPEG     => "jpg");
 
-        my $output_mask = $options & ($PSTAMP_SELECT_IMAGE | $PSTAMP_SELECT_MASK | $PSTAMP_SELECT_VARIANCE | $PSTAMP_SELECT_JPEG);
+        my $output_mask = $options & ($PSTAMP_SELECT_IMAGE | $PSTAMP_SELECT_MASK | $PSTAMP_SELECT_VARIANCE | $PSTAMP_SELECT_JPEG | $PSTAMP_SELECT_SOURCES);
 
         foreach my $key (keys (%extensions)) {
@@ -400,8 +420,8 @@
         my $pattern_file = $params->{pattern} if ($options & $PSTAMP_SELECT_BACKMDL);
         my $cmf_file;
-        if ($stage ne 'chip') {
-            # we don't ship chip stage cmf files because they may not be censored
-            $cmf_file = $params->{cmf} if ($options & $PSTAMP_SELECT_CMF);
-        }
+#        if ($stage ne 'chip') {
+#            # we don't ship chip stage cmf files because they may not be censored
+#            $cmf_file = $params->{cmf} if ($options & $PSTAMP_SELECT_CMF);
+#        }
 
         my $outdir = dirname($output_base);