troughfinder/do_it_all_template.sh at master · des-science/troughfinder · GitHub

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#!/bin/bash
# one script to rule them all, to be run from within the script with config options ...

ncores=2

if [ "$do_tracers" == "1" ]
then

if [ "$sysweight" != "" ]
then
  sysweight="$base/data/$sysweight"
fi

##########################
 echo "(1.1) convert Eli's redMaGiC mask to healpix mask map"
 mkdir -p lenses
 cd lenses

 if [ "$incremental" == "0" ]
 then
   rm -f mask_zcut_*.fits
 fi
 for i in "${countredshift_max[@]}"
 do
   if [ ! -f mask_zcut_$i.fits ]
   then
     echo $helpers/mkhealpixmask $base/data/$mask mask_zcut_$i.fits $i ${mask_hpixcol} ${mask_fracgood} ${mask_zmax} ${mask_nside} ${sysweight}
     $helpers/mkhealpixmask $base/data/$mask mask_zcut_$i.fits $i ${mask_hpixcol} ${mask_fracgood} ${mask_zmax} ${mask_nside} ${sysweight}
   fi
 done
 cd ..
##########################


##########################
 echo "(1.2) convert tracer catalog to txt file"
 cd lenses
 for(( i=0; i<${#countredshift_min[@]}; ++i ))
 do
   lowz=${countredshift_min[$i]}
   highz=${countredshift_max[$i]}

   if [ "$incremental" == "0" ]
   then
     rm -f tracers_${lowz}_${highz}.txt
   fi

   if [ ! -f tracers_${lowz}_${highz}.txt ]
   then
     echo $helpers/cut_mask_z $base/data/$tracers $tracers_racol $tracers_deccol $tracers_zcol $lowz $highz mask_zcut_$highz.fits
     $helpers/cut_mask_z $base/data/$tracers $tracers_racol $tracers_deccol $tracers_zcol $lowz $highz mask_zcut_$highz.fits > tracers_${lowz}_${highz}.txt
   fi
 done

 cd ..
##########################

##########################
 echo "(1.3) convert tracer catalog to healpix map"
 cd lenses
 for(( i=0; i<${#countredshift_min[@]}; ++i ))
 do
   lowz=${countredshift_min[$i]}
   highz=${countredshift_max[$i]}

   if [ "$incremental" == "0" ]
   then
     rm -f tracers_${lowz}_${highz}.fits
   fi

   if [ ! -f tracers_${lowz}_${highz}.fits ]
   then
      echo $helpers/count_in_trough tracers_${lowz}_${highz}.txt 0 tracers_${lowz}_${highz}.fits
      $helpers/count_in_trough tracers_${lowz}_${highz}.txt 0 tracers_${lowz}_${highz}.fits
   fi
 done

 cd ..
##########################

##########################
 echo "(1.4) create jackknife patches"
 cd lenses

 if [ "$incremental" == "0" ]
 then
     rm -f jackknife.fits
 fi

 if [ ! -f jackknife.fits ]
 then
      $helpers/healpix_resample.py mask_zcut_${jackkniferedshift_max}.fits 512 tmp.fits
      $helpers/mkjackknife.py tmp.fits $npatch tmppatches.fits
      $helpers/healpix_resample.py tmppatches.fits ${trough_nside} jackknife.fits
      rm -f tmp.fits tmppatches.fits
 fi
 cd ..
##########################

fi


if [ "$do_counts" == "1" ]
then

##########################
 echo "(2.1) generate count healpix map from tracer catalog"
 cd lenses
 for theta in $countradii
 do
  for(( i=0; i<${#countredshift_min[@]}; ++i ))
  do
    lowz=${countredshift_min[$i]}
    highz=${countredshift_max[$i]}

    if [ "$incremental" == "0" ]
    then
      rm -f trough_${theta}_${lowz}_${highz}_count.fits
    fi

    if [ ! -f trough_${theta}_${lowz}_${highz}_count.fits ]
    then
      echo $helpers/count_in_trough tracers_${lowz}_${highz}.txt $theta trough_${theta}_${lowz}_${highz}_count.fits
      $helpers/count_in_trough tracers_${lowz}_${highz}.txt $theta trough_${theta}_${lowz}_${highz}_count.fits
    fi
  done
 done
 cd ..
##########################


##########################
 echo "(2.2) generate trough-averaged z-cut mask healpix map"
 cd lenses
 for theta in $countradii
 do
  if [ "$incremental" == "0" ]
  then
    rm -f trough_${theta}_*_mask.fits
  fi

  for(( i=0; i<${#countredshift_min[@]}; ++i ))
  do
    highz=${countredshift_max[$i]}

    if [ ! -f trough_${theta}_${highz}_mask.fits ]
    then
      echo $helpers/mask_trough mask_zcut_$highz.fits $theta trough_${theta}_${highz}_mask.fits ${trough_nside}
      $helpers/mask_trough mask_zcut_${highz}.fits $theta trough_${theta}_${highz}_mask.fits ${trough_nside}
    fi
  done
 done
 cd ..
##########################


##########################
 echo "(2.3) generate trough maps"
 cd lenses
 for theta in $countradii
 do
  for(( i=0; i<${#countredshift_min[@]}; ++i ))
  do
    lowz=${countredshift_min[$i]}
    highz=${countredshift_max[$i]}

    if [ "$incremental" == "0" ]
    then
      rm -f trough_${theta}_${lowz}_${highz}_map*.fits
    fi

    if [ ! -f trough_${theta}_${lowz}_${highz}_0.fits ]
    then
      echo $helpers/troughfinder trough_${theta}_${lowz}_${highz}_count.fits trough_${theta}_${highz}_mask.fits ${count_maxmaskfrac} trough_${theta}_${lowz}_${highz} $countpercentiles
      $helpers/troughfinder trough_${theta}_${lowz}_${highz}_count.fits trough_${theta}_${highz}_mask.fits ${count_maxmaskfrac} trough_${theta}_${lowz}_${highz} $countpercentiles &> trough_${theta}_${lowz}_${highz}.log
    fi
  done
 done
 cd ..
##########################

##########################
 echo "(2.4) calculate p(N) statistics"
 mkdir -p pofn
 mkdir -p pofn_jackknife
 cd pofn

 if [ "$incremental" == "0" ]
 then
     rm -f pofn_*.tab
 fi

 for theta in $countradii
 do
  for(( i=0; i<${#countredshift_min[@]}; ++i ))
  do
    lowz=${countredshift_min[$i]}
    highz=${countredshift_max[$i]}

    if [ ! -s pofn_${theta}_${lowz}_${highz}.tab ]
    then
      $helpers/pofn_bernoulli_jackknife ../lenses/trough_${theta}_${lowz}_${highz}_count.fits ../lenses/trough_${theta}_${highz}_mask.fits \
                                             ../lenses/jackknife.fits ${count_maxmaskfrac} ../pofn_jackknife/pofn_${theta}_${lowz}_${highz} > pofn_${theta}_${lowz}_${highz}.tab
    fi
  done
 done

 cd ..
##########################

fi