NicerXti_a_products.sh

# _NicerXti_a_products
# _NicerXti_1_products
## xti products
if [[ $(declare --help | grep -c -o -E "\-g\s+create global variables") -eq 0 ]]; then
    My_Nicer_D=${My_Nicer_D:=$(pwd)}
else
    declare -g My_Nicer_D=${My_Nicer_D:=$(pwd)}
fi # 未定義時に代入
cd $My_Nicer_D
obs_dirs=($(find . -maxdepth 1 -type d -printf "%P\n" | grep ^[0-9] | sort))
for My_Nicer_ID in ${obs_dirs[@]}; do

    My_Nicer_Dir=$My_Nicer_D/$My_Nicer_ID
    if [[ ! -r $My_Nicer_Dir/xti/event_cl ]]; then continue; fi

    cd $My_Nicer_Dir/xti/event_cl

    _evt_tmps=($(find . -name "ni${My_Nicer_ID}_0mpu7_cl.evt*" -printf "%f\n"))
    evt_file=${_evt_tmps[-1]}

    rm -f nicerXti__*.fits
    cat <<EOF | bash
xselect
xsel
read events ${evt_file}
./
y
extract all
extract spectrum
save spectrum nicerXti__nongrp.fits
exit
n
EOF

    # arf, rmfをcopy
    _arf_files=($(find $CALDB/data/nicer/xti/cpf/arf/ -name "*.arf"))
    _rmf_files=($(find $CALDB/data/nicer/xti/cpf/rmf/ -name "*.rmf"))
    cp -f ${_arf_files[-1]} nicerXti__arf.fits
    cp -f ${_rmf_files[-1]} nicerXti__rmf.fits

    mkdir fit -p
    mv nicerXti__*.fits fit/

done
cd $My_Nicer_D
# _NicerXti_2_obtainBkg
## obtain bkg
if [[ $(declare --help | grep -c -o -E "\-g\s+create global variables") -eq 0 ]]; then
    My_Nicer_D=${My_Nicer_D:=$(pwd)}
else
    declare -g My_Nicer_D=${My_Nicer_D:=$(pwd)}
fi # 未定義時に代入
cd $My_Nicer_D

# nibackestimator
if [[ -x $(which nibkgestimator) ]]; then
    obs_dirs=($(find . -maxdepth 1 -type d -printf "%P\n" | grep ^[0-9] | sort))
    for My_Nicer_ID in ${obs_dirs[@]}; do

        My_Nicer_Dir=$My_Nicer_D/$My_Nicer_ID
        if [[ ! -r $My_Nicer_Dir/xti/event_cl/fit ]]; then continue; fi

        cd $My_Nicer_Dir/xti/event_cl/fit

        # toolの兼ね合いで名前を.phaに変更
        ln -nfs nicerXti__nongrp.fits ni${My_Nicer_ID}.pha
        rm -f ni${My_Nicer_ID}_bkg.pha

        # mkf3存在確認
        if [[ -f $My_Nicer_Dir/auxil/ni${My_Nicer_ID}.mkf3 ]]; then
            :
        elif [[ -f $My_Nicer_Dir/auxil/ni${My_Nicer_ID}.mkf2 ]]; then
            # mkf2からmkf3作成
            niaddkp $My_Nicer_Dir/auxil/ni${My_Nicer_ID}.mkf2
        elif [[ -f $My_Nicer_Dir/auxil/ni${My_Nicer_ID}.mkf.gz ]]; then
            # mkf -> mkf2
            niprefilter2 indir=${My_Nicer_Dir} infile=${My_Nicer_Dir}/auxil/ni${My_Nicer_ID}.mkf.gz outfile=${My_Nicer_Dir}/auxil/ni${My_Nicer_ID}.mkf2
            # mkf2 -> mkf3
            niaddkp $My_Nicer_Dir/auxil/ni${My_Nicer_ID}.mkf2
        else
            # mkfもないなら無理
            continue
        fi

        # bk作成
        nibkgestimator ni${My_Nicer_ID}.pha $My_Nicer_Dir/auxil/ni${My_Nicer_ID}.mkf3 --bkg_evt $CALDB/data/nicer/xti/pcf/30nov18targskc_enhanced.evt
        # 名前を調整
        #mv ni${My_Nicer_ID}.pha ni${My_Nicer_ID}_nongrp.fits
        mv ni${My_Nicer_ID}_bkg.pha nicerXti__esti_bkg.fits
    done
fi

# nibackgen3C50
# NIBACKGEN3C50_MODEL_PATH の判定
if [[ -x $(which nibackgen3C50) ]] && [[ -x ${NIBACKGEN3C50_MODEL_PATH} ]]; then
    ni3C50_bin_path=$(cd $(dirname $(readlink -f $(which nibackgen3C50))); pwd )
    ni3C50_bkg_path=${ni3C50_bin_path}/../
    obs_dirs=($(find . -maxdepth 1 -type d -printf "%P\n" | grep ^[0-9] | sort))
    for My_Nicer_ID in ${obs_dirs[@]}; do

        My_Nicer_Dir=$My_Nicer_D/$My_Nicer_ID
        if [[ ! -r $My_Nicer_Dir/xti/event_cl/fit ]]; then continue; fi

        cd $My_Nicer_Dir/xti/event_cl/fit

        #mkdir $My_Nicer_Dir/xti/out3C50 -p
        #mv $My_Nicer_Dir/xti/out3C50
        ln -nfs nicerXti__nongrp.fits nibackgen3C50_tot.pi
        rm nibackgen3C50_bkg.pi -f

        nibackgen3C50 rootdir=$My_Nicer_D obsid=$My_Nicer_ID bkgdir=${NIBACKGEN3C50_MODEL_PATH} #~/mylib/soft/nicer/nibackgen3C50/bg_model_3C50_RGv5

        #mv nibackgen3C50_tot.pi ni3C50_${My_Nicer_ID}_nongrp.fits
        mv nibackgen3C50_bkg.pi nicerXti__3C50_bkg.fits

    done
fi


cd $My_Nicer_D
# _NicerXti_3_editHeader
## edit header
if [[ $(declare --help | grep -c -o -E "\-g\s+create global variables") -eq 0 ]]; then
    My_Nicer_D=${My_Nicer_D:=$(pwd)}
else
    declare -g My_Nicer_D=${My_Nicer_D:=$(pwd)}
fi # 未定義時に代入
cd $My_Nicer_D

function _ObtainExtNum(){
    tmp_fits="$1"
    extName="${2:-SPECTRUM}"
    if [[ -n "${tmp_fits}" ]]; then
        _tmp_extNums=($(fkeyprint infile=$tmp_fits keynam=EXTNAME |
            grep -B 1 $extName |
            sed -r -n "s/^.*#\s*EXTENSION:\s*([0-9]+)\s*$/\1/p"))
    else
        _tmp_extNums=(0)
    fi
    echo ${_tmp_extNums[0]:-0}
}

obs_dirs=($(find . -maxdepth 1 -type d -printf "%P\n" | grep ^[0-9] | sort))
for My_Nicer_ID in ${obs_dirs[@]}; do

    My_Nicer_Dir=$My_Nicer_D/$My_Nicer_ID
    if [[ ! -r $My_Nicer_Dir/xti/event_cl/fit ]]; then continue; fi

    cd $My_Nicer_Dir/xti/event_cl/fit

    find . -name "nicerXti__*" |
        rename -f "s/nicerXti__/nicerXti_${My_Nicer_ID}_/"

    # bkgにあわせて2つにCOPY
    nongrp_name=nicerXti_${My_Nicer_ID}_nongrp.fits
    nongrpExtNum=$(_ObtainExtNum $nongrp_name SPECTRUM)

    declare -A tr_keys=(
        ["BACKFILE"]=nicerXti_${My_Nicer_ID}_3C50_bkg.fits
        ["RESPFILE"]=nicerXti_${My_Nicer_ID}_rmf.fits
        ["ANCRFILE"]=nicerXti_${My_Nicer_ID}_arf.fits)

    for key in ${!tr_keys[@]}; do
        fparkey value="${tr_keys[$key]}" \
            fitsfile="${nongrp_name}+${nongrpExtNum}" \
            keyword="${key}" add=yes
    done

done

cd $My_Nicer_D
# _NicerXti_4_grppha
## grppha
gnum=50 # arg
if [[ $(declare --help | grep -c -o -E "\-g\s+create global variables") -eq 0 ]]; then
    My_Nicer_D=${My_Nicer_D:=$(pwd)}
else
    declare -g My_Nicer_D=${My_Nicer_D:=$(pwd)}
fi # 未定義時に代入
cd $My_Nicer_D
obs_dirs=($(find . -maxdepth 1 -type d -printf "%P\n" | grep ^[0-9] | sort))
for My_Nicer_ID in ${obs_dirs[@]}; do

    My_Nicer_Dir=$My_Nicer_D/$My_Nicer_ID
    if [[ ! -r $My_Nicer_Dir/xti/event_cl/fit ]]; then continue; fi

    cd $My_Nicer_Dir/xti/event_cl/fit
    nongrp_name=nicerXti_${My_Nicer_ID}_nongrp.fits
    grp_name=nicerXti_${My_Nicer_ID}_grp${gnum}.fits
    rm $grp_name -f
    cat <<EOF | bash
grppha infile=$nongrp_name outfile=$grp_name
group min ${gnum}
exit !$grp_name
EOF

done
cd $My_Nicer_D
# _NicerXti_5_fitDirectory
## fitディレクトリにまとめ
FLAG_hardCopy=false # arg
FLAG_symbLink=false # arg
tmp_prefix="xrt_" # arg
if [[ $(declare --help | grep -c -o -E "\-g\s+create global variables") -eq 0 ]]; then
    My_Nicer_D=${My_Nicer_D:=$(pwd)}
else
    declare -g My_Nicer_D=${My_Nicer_D:=$(pwd)}
fi # 未定義時に代入
cd $My_Nicer_D
mkdir -p $My_Nicer_D/fit $My_Nicer_D/../fit
obs_dirs=($(find . -maxdepth 1 -type d -printf "%P\n" | grep ^[0-9] | sort))
for My_Nicer_ID in ${obs_dirs[@]}; do
    fit_path=$My_Nicer_D/$My_Nicer_ID/xti/event_cl/fit
    if [[ ${FLAG_symbLink:=false} == "true" ]]; then
        #find $fit_path -name "${tmp_prefix}*.*" \
        #    -type f -printf "%f\n" |
        #    xargs -n 1 -i rm -f $My_Nicer_D/fit/{}
        ln -nfs ${fit_path}/${tmp_prefix}* ${My_Nicer_D}/fit/
    else
        if [[ ! -d "$fit_path" ]]; then continue; fi
        find $fit_path -name "${tmp_prefix}*" | xargs -i cp {} ${My_Nicer_D}/fit/
        #cp -f $fit_path/${tmp_prefix}* ${My_Nicer_D}/fit/
    fi
done
if [[ ${FLAG_hardCopy:=false} == "true" ]]; then
    cp -f $My_Nicer_D/fit/${tmp_prefix}*.* $My_Nicer_D/../fit/
else
    # remove the files with the same name as new files
    #find $My_Nicer_D/fit/ -name "${tmp_prefix}*.*" \
    #    -type f -printf "%f\n" |
    #    xargs -n 1 -i rm -f $My_Nicer_D/../fit/{}
    # generate symbolic links
    ln -nfs $My_Nicer_D/fit/${tmp_prefix}*.* $My_Nicer_D/../fit/
fi
# remove broken symbolic links
find -L $My_Nicer_D/../fit/ -type l -delete