07_OLD_extract_RVs.sh

#!/bin/bash
#
# Pull RV information out of tarballs and raw spectra.
#
# Rob Siverd
# Created:      2018-04-17
# Last updated: 2018-10-09
#--------------------------------------------------------------------------
#**************************************************************************
#--------------------------------------------------------------------------

## Default options:
debug=0 ; clobber=0 ; force=0 ; timer=0 ; vlevel=0
script_version="0.03"
this_prog="${0##*/}"
#shopt -s nullglob
# Propagate errors through pipelines: set -o pipefail
# Exit if uninitialized variable used (set -u): set -o nounset
# Exit in case of nonzero status (set -e): set -o errexit

## Program options:
#save_file=""
#shuffle=0
#confirmed=0

## Standard scratch files/dirs:
tmp_name="$(date +%Y%m%d.%H%M%S).$$.$(whoami)"
tmp_root="/tmp"
[ -d /dev/shm ] && [ -w /dev/shm ] && tmp_root="/dev/shm"
tmp_dir="$tmp_root"
#tmp_dir="$tmp_root/$tmp_name"
#mkdir -p $tmp_dir
foo="$tmp_dir/foo_$$.txt"
bar="$tmp_dir/bar_$$.txt"
baz="$tmp_dir/baz_$$.fits"
qux="$tmp_dir/qux_$$.fits"
jnk="$foo $bar $baz $qux"  # working copy
def_jnk="$jnk"             # original set
dir_cleanup='(echo -e "\nAutomatic clean up ... " ; cmde "rm -vrf $tmp_dir")'
jnk_cleanup='for X in $jnk ; do [ -f $X ] && cmde "rm -vf $X" ; done'
trap "$jnk_cleanup" EXIT
##trap '[ -d $tmp_dir ] && cmde "rm -vrf $tmp_dir"' EXIT
#trap "[ -d $tmp_dir ] && $dir_cleanup" EXIT
#trap "[ -d $tmp_dir ] && $dir_cleanup ; $jnk_cleanup" EXIT
#trap 'oops=$? ; echo ; exit $oops' HUP INT TERM

## Required programs:
declare -a need_exec
need_exec+=( awk cat extract-specproc-RVs FuncDef iltk sed tr )
#need_exec+=( shuf shuffle sort ) # for randomization
for need in ${need_exec[*]}; do
   if ! ( /usr/bin/which $need >& /dev/null ); then
      echo "Error:  can't find '$need' in PATH !!" >&2
      exit 1
   fi
done

## Helper function definitions:
fd_args="--argchk --colors --cmde --echo"
#fd_args+=" --Critical"
fd_args+=" --rowwrite"
#fd_args+=" --timers"
fd_args+=" --warnings"
FuncDef $fd_args >/dev/null || exit $?
eval "$(FuncDef $fd_args)"  || exit $?

## Check for arguments:
usage () { 
   Recho "\nSyntax: $this_prog --START\n\n"
   #Recho "\nSyntax: $this_prog arg1\n\n"
}
if [ "$1" != "--START" ]; then
#if [ -z "$1" ]; then
   usage >&2
   exit 1
fi

##**************************************************************************##
##==========================================================================##
##--------------------------------------------------------------------------##

## Load config:
cmde "source config.sh"

##--------------------------------------------------------------------------##
## Extract data:
for object in `cat $object_list`; do
   echo "-------------------------------------------"
   obs_list="$meta_dir/tb_list_$object.txt"
   obs_data="$meta_dir/spectra_$object.txt"
   cmde "grep $object $recent_all_img_hdrs > tmp.txt"
   cmde "iltk -Lr $recent_cln_tarballs -c tmp.txt -o $obs_list"
   cmde "extract-specproc-RVs $obs_list -co $obs_data"
done
rm tmp.txt


##--------------------------------------------------------------------------##
## Clean up:
#[ -d $tmp_dir ] && [ -O $tmp_dir ] && rm -rf $tmp_dir
#[ -f $foo ] && rm -f $foo
#[ -f $bar ] && rm -f $bar
#[ -f $baz ] && rm -f $baz
#[ -f $qux ] && rm -f $qux
exit 0

######################################################################
# CHANGELOG (02_extract_RVs.sh):
#---------------------------------------------------------------------
#
#  2018-05-07:
#     -- Increased script_version to 0.02.
#     -- Now pull from 'clean' data files (blacklisted files removed).
#
#  2018-04-17:
#     -- Increased script_version to 0.01.
#     -- First created 02_extract_RVs.sh.
#