Running DAOPHOT from a script

This quite a straightforward problem in shell scripting, although there are one or two things specific to DAOPHOT to watch out for. Here is a C-shell script which does a FIND on all files called pic*.sdf in a directory, writing output to pic*.coo text files. It uses shell variables interpolated into a `here document' as the input to the program.

#!/bin/csh

#  Start up DAOPHOT.
      daostart

#  Get rid of any junk files which DAOPHOT has left lying around.
      rm -f *jnk.sdf

#  Loop over the files we're interested in.
      foreach file ( pic*.sdf )

#  Get filename without the .sdf extension.
         set fileroot = $file:r

#  Write filename to screen.
         echo "***"
         echo "*** Processing file $file ***"
         echo "***"

#  If an old version of the output file exists, delete it.
         rm -f $fileroot.coo

#  Run DAOPHOT with the appropriate commands.
         daophot <<__DAOPHOT-END__
ATTACH $fileroot
FIND
1,1
$fileroot
Y
EXIT
__DAOPHOT-END__

#  Get rid of scratch file that DAOPHOT has written.
         rm ${fileroot}jnk.sdf

#  End of loop.
      end

• The rm -f $fileroot.coo is there as a safeguard: if the .coo file exists when FIND runs, then DAOPHOT gives an extra prompt to ask whether you want to overwrite it, and if this happened here the rest of the commands in the file would get out of step and DAOPHOT would get terribly confused. If the .coo file doesn't exist, then no harm is done.

• DAOPHOT is keen on generating files with names *jnk.sdf. It's important at the start of this script to ensure that there are none lying around, so that they don't get picked up by the pic*.sdf list which we're looping over. If you haven't run the script before in this directory, then the rm -f *jnk.sdf will not be necessary, but it doesn't hurt anyway. The rm ${fileroot}jnk.sdf later on is just to prevent too much disk space being taken up with rubbish.

• The commands in the here document (and the delimiter line at the end) must not be indented, since DAOPHOT is fussy about leading spaces.

• If source /star/etc/cshrc is not in your .cshrc file, you would need to source it here, or replace the daostart line with source /star/bin/daophot/daophot.csh.

• If you're capturing the output of the script to a log file, you might want to set WA=0 (or do a NOMONITOR) to keep the size down a bit.