#!/bin/sh # unalias -a export LC_COLLATE=C ########################################################### ## based on `ciao_r500avgt' ## ## for calculating the `cooling time ' ## ## within (0.-0.048 r500) region ## ## ## ## Junhua Gu ## ## August 22, 2012 ## ## ## ## LIweitiaNux ## ## 2013/04/28 ## ########################################################### ########################################################### ## ChangeLogs ## v1.1, 2014/06/18 ## 'cooling_time2.sh' -> 'ciao_calc_ct.sh' ## v1.2, 2015/05/27, Weitian LI ## update 'DFT_ARF' & 'DFT_RMF' to find '*.arf' & '*.rmf' files ## (specextract only use .arf & .rmf extensions since revision 2014-12) ########################################################### ## about, used in `usage' {{{ VERSION="v1.2" UPDATE="2015-05-27" ## about }}} ## error code {{{ ERR_USG=1 ERR_DIR=11 ERR_EVT=12 ERR_BKG=13 ERR_REG=14 ERR_ASOL=21 ERR_BPIX=22 ERR_PBK=23 ERR_MSK=24 ERR_BKGTY=31 ERR_SPEC=32 ERR_ARF=51 ERR_RMF=52 ERR_UNI=61 ## error code }}} ## usage, help {{{ case "$1" in -[hH]*|--[hH]*) printf "usage:\n" printf " `basename $0` basedir= evt= r500= regin= regout= bkgd= nh= z= arf= rmf= [ grpcmd= log= ]\n" printf "\nversion:\n" printf "${VERSION}, ${UPDATE}\n" exit ${ERR_USG} ;; esac ## usage, help }}} ## comology calculator {{{ ## XXX: MODIFY THIS TO YOUR OWN CASE ## and make sure this `calc' is executable ## NOTES: use `$HOME' instead of `~' in path BASE_PATH=`dirname $0` COSCALC="`which cosmo_calc calc_distance 2>/dev/null | head -n 1`" if [ -z "${COSCALC}" ] || [ ! -x ${COSCALC} ]; then printf "ERROR: \`COSCALC: ${COSCALC}' neither specified nor executable\n" exit 255 fi ## }}} ## default parameters {{{ # default `event file' which used to match `blanksky' files #DFT_EVT="_NOT_EXIST_" DFT_EVT="`ls evt2*_clean.fits 2> /dev/null`" # default `bkgd', use `bkgcorr_blanksky*' corrected bkg spectrum DFT_BKGD="`ls bkgcorr_blanksky_*.pi 2> /dev/null`" # default basedir DFT_BASEDIR="../.." # default info_json pattern DFT_JSON_PAT="*_INFO.json" # default `radial region file' #DFT_REG_IN="_NOT_EXIST_" DFT_REG_IN="rspec.reg" # default output region file (0.1-0.5 r500 region) DFT_REG_OUT="cooling.reg" # default ARF/RMF, the one of the outmost region DFT_ARF="`ls r1_*.warf r1_*.arf 2> /dev/null`" DFT_RMF="`ls r1_*.wrmf r1_*.rmf 2> /dev/null`" # default `group command' for `grppha' #DFT_GRP_CMD="group 1 128 2 129 256 4 257 512 8 513 1024 16" DFT_GRP_CMD="group min 20" # default `log file' DFT_LOGFILE="cooling_`date '+%Y%m%d'`.log" INNER=0.0 OUTER=0.048 CT_RES="cooling_results.txt" # default output xspec scripts XSPEC_SCRIPT="xspec_cooling.xcm" # deproj xspec script, generated by `deproj_spectra' # from which get `nh' and `redshift' XSPEC_DEPROJ="xspec_deproj.xcm" ## default parameters }}} ## functions {{{ # process commandline arguments # cmdline arg format: `KEY=VALUE' getopt_keyval() { until [ -z "$1" ] do key=${1%%=*} # extract key val=${1#*=} # extract value keyval="${key}=\"${val}\"" echo "## getopt: eval '${keyval}'" eval ${keyval} shift # shift, process next one done } ## background renormalization (BACKSCAL) {{{ # renorm background according to particle background # energy range: 9.5-12.0 keV (channel: 651-822) CH_LOW=651 CH_HI=822 pb_flux() { punlearn dmstat COUNTS=`dmstat "$1[channel=${CH_LOW}:${CH_HI}][cols COUNTS]" | grep -i 'sum:' | awk '{ print $2 }'` punlearn dmkeypar EXPTIME=`dmkeypar $1 EXPOSURE echo=yes` BACK=`dmkeypar $1 BACKSCAL echo=yes` # fix `scientific notation' bug for `bc' EXPTIME_B=`echo ${EXPTIME} | sed 's/[eE]/\*10\^/' | sed 's/+//'` BACK_B=`echo "( ${BACK} )" | sed 's/[eE]/\*10\^/' | sed 's/+//'` PB_FLUX=`echo "scale = 16; ${COUNTS} / ${EXPTIME_B} / ${BACK_B}" | bc -l` echo ${PB_FLUX} } bkg_renorm() { # $1: src spectrum, $2: back spectrum PBFLUX_SRC=`pb_flux $1` PBFLUX_BKG=`pb_flux $2` BACK_OLD=`dmkeypar $2 BACKSCAL echo=yes` BACK_OLD_B=`echo "( ${BACK_OLD} )" | sed 's/[eE]/\*10\^/' | sed 's/+//'` BACK_NEW=`echo "scale = 16; ${BACK_OLD_B} * ${PBFLUX_BKG} / ${PBFLUX_SRC}" | bc -l` printf "\`$2': BACKSCAL:\n" printf " ${BACK_OLD} --> ${BACK_NEW}\n" punlearn dmhedit dmhedit infile=$2 filelist=none operation=add \ key=BACKSCAL value=${BACK_NEW} comment="old value: ${BACK_OLD}" } ## bkg renorm }}} ## functions end }}} ## parameters {{{ # process cmdline args using `getopt_keyval' getopt_keyval "$@" ## check log parameters {{{ if [ ! -z "${log}" ]; then LOGFILE="${log}" else LOGFILE=${DFT_LOGFILE} fi printf "## use logfile: \`${LOGFILE}'\n" [ -e "${LOGFILE}" ] && mv -fv ${LOGFILE} ${LOGFILE}_bak TOLOG="tee -a ${LOGFILE}" echo "process script: `basename $0`" >> ${LOGFILE} echo "process date: `date`" >> ${LOGFILE} ## log }}} # check given parameters # process `nh' and `redshift' {{{ if [ ! -r "${XSPEC_DEPROJ}" ]; then printf "## the script \`${XSPEC_DEPROJ}' generated by \`deproj_spectra' NOT found\n" | ${TOLOG} printf "## please supply the value of \`nh' and \`redshift' manully\n" | ${TOLOG} read -p "> value of nh: " N_H read -p "> value of redshift: " REDSHIFT else # get `nh' and `redshift' from xspec script LN=`grep -n 'projct\*wabs\*apec' ${XSPEC_DEPROJ} | tail -n 1 | cut -d':' -f1` # calc the line number of which contains `nh' LN_NH=`expr ${LN} + 4` NH_XCM=`head -n ${LN_NH} ${XSPEC_DEPROJ} | tail -n 1 | awk '{ print $1 }'` # calc the line number of `redshift' LN_RS=`expr ${LN} + 7` RS_XCM=`head -n ${LN_RS} ${XSPEC_DEPROJ} | tail -n 1 | awk '{ print $1 }'` printf "## get value of nh: \`${NH_XCM}' (from \`${XSPEC_DEPROJ}')\n" | ${TOLOG} printf "## get value of redshift: \`${RS_XCM}' (from \`${XSPEC_DEPROJ}')\n" | ${TOLOG} ## if `nh' and `redshift' supplied in cmdline, then use them if [ ! -z "${nh}" ]; then N_H=${nh} else N_H=${NH_XCM} fi # redshift if [ ! -z "${z}" ]; then REDSHIFT=${z} else REDSHIFT=${RS_XCM} fi fi printf "## use nH: ${N_H}\n" | ${TOLOG} printf "## use redshift: ${REDSHIFT}\n" | ${TOLOG} # nh & redshift }}} # check basedir & json file if [ -d "${basedir}" ]; then BASEDIR=${basedir} else BASEDIR=${DFT_BASEDIR} fi # json file if [ ! -z "${json}" ] && [ -r "${BASEDIR}/${json}" ]; then JSON_FILE="${BASEDIR}/${json}" elif [ `ls ${BASEDIR}/${DFT_JSON_PAT} 2> /dev/null | wc -l` -eq 1 ]; then JSON_FILE=`ls ${BASEDIR}/${DFT_JSON_PAT}` else read -p "> JSON_file: " JSON_FILE if [ ! -r "${JSON_FILE}" ]; then printf "ERROR: cannot access given \`${JSON_FILE}'\n" exit ${ERR_JSON} fi fi printf "## use json_file: \`${JSON_FILE}'\n" | ${TOLOG} # process `r500' {{{ R500_RAW=`grep '"R500.*kpc' ${JSON_FILE} | sed 's/.*"R500.*":\ //' | sed 's/\ *,$//'` if [ ! -z "${r500}" ]; then R500_RAW=${r500} fi if [ -z "${R500_RAW}" ]; then printf "## input R500 followed with unit, e.g.: 800kpc, 400pix\n" read -p "> value of \`R500' (in pixel/kpc): " R500_RAW fi R500_VAL=`echo "${R500_RAW}" | tr -d 'a-zA-Z, '` R500_UNI=`echo "${R500_RAW}" | tr -d '0-9, '` printf "## get \`R500': ${R500_VAL} in unit \`${R500_UNI}'\n" | ${TOLOG} # if in kpc, convert to pix case "${R500_UNI}" in [pP]*) printf "## units in \`pixel', conversion not needed\n" | ${TOLOG} R500_PIX_B=`echo ${R500_VAL} | sed 's/[eE]/\*10\^/' | sed 's/+//'` ;; *) printf "## units in \`kpc', convert to \`Chandra pixel'\n" | ${TOLOG} KPC_PER_PIX=`${COSCALC} ${REDSHIFT} | grep 'kpc.*pix' | tr -d 'a-zA-Z_#=(),:/ '` # convert scientific notation for `bc' KPC_PER_PIX_B=`echo ${KPC_PER_PIX} | sed 's/[eE]/\*10\^/' | sed 's/+//'` printf "## calculated \`kpc/pixel': ${KPC_PER_PIX_B}\n" R500_VAL_B=`echo ${R500_VAL} | sed 's/[eE]/\*10\^/' | sed 's/+//'` R500_PIX_B=`echo "scale = 4; ${R500_VAL_B} / ( ${KPC_PER_PIX_B} )" | bc -l` ;; esac # calc (inner-outer R500) R_IN=`echo "scale = 4; ${INNER} * ${R500_PIX_B}" | bc -l` R_OUT=`echo "scale = 4; ${OUTER} * ${R500_PIX_B}" | bc -l` printf "## R500 in units pixel: ${R500_PIX_B}\n" | ${TOLOG} printf "## (${INNER}-${OUTER} R500) range in pixel: ${R_IN} - ${R_OUT}\n" | ${TOLOG} # r500 }}} # check evt file if [ -r "${evt}" ]; then EVT=${evt} elif [ -r "${DFT_EVT}" ]; then EVT=${DFT_EVT} else read -p "> clean evt2 file: " EVT if [ ! -r "${EVT}" ]; then printf "ERROR: cannot access given \`${EVT}' evt file\n" exit ${ERR_EVT} fi fi printf "## use evt file: \`${EVT}'\n" | ${TOLOG} # input and output region files {{{ if [ -r "${regin}" ]; then REG_IN="${regin}" elif [ -r "${DFT_REG_IN}" ]; then REG_IN=${DFT_REG_IN} else read -p "> previous used radial spec regfile: " REG_IN if [ ! -r "${REG_IN}" ]; then printf "ERROR: cannot access given \`${REG_IN}' region file\n" exit ${ERR_REG} fi fi printf "## use previous regfile: \`${REG_IN}'\n" | ${TOLOG} if [ ! -z "${regout}" ]; then REG_OUT="${regout}" else REG_OUT=${DFT_REG_OUT} fi [ -e "${REG_OUT}" ] && mv -fv ${REG_OUT} ${REG_OUT}_bak printf "## set output regfile (0.1-0.5 r500 region): \`${REG_OUT}'\n" | ${TOLOG} # get center position from `regin' # only consider `pie' or `annulus'-shaped region TMP_REG=`grep -iE '(pie|annulus)' ${REG_IN} | head -n 1` XC=`echo ${TMP_REG} | tr -d ' ' | awk -F'[(),]' '{ print $2 }'` YC=`echo ${TMP_REG} | tr -d ' ' | awk -F'[(),]' '{ print $3 }'` printf "## get center coord: (${XC},${YC})\n" | ${TOLOG} # region files }}} # check given bkgd, determine background {{{ if [ -r "${bkgd}" ]; then BKGD=${bkgd} elif [ -r "${DFT_BKGD}" ]; then BKGD=${DFT_BKGD} else read -p "> background (blanksky_evt | lbkg_reg | bkg_spec): " BKGD if [ ! -r "${BKGD}" ]; then printf "ERROR: cannot access given \`${BKGD}'\n" exit ${ERR_BKG} fi fi printf "## use bkgd: \`${BKGD}'\n" | ${TOLOG} # determine bkg type: blanksky, lbkg_reg, bkg_spec ? # according to file type first: text / FITS # if FITS, then get values of `HDUCLAS1' and `OBJECT' if file -bL ${BKGD} | grep -qi 'text'; then printf "## given \`${BKGD}' is a \`text file'\n" printf "## use it as local bkg region file\n" printf "## use *LOCAL BKG SPEC*\n" | ${TOLOG} # just set flags, extract spectrum later USE_LBKG_REG=YES USE_BLANKSKY=NO USE_BKG_SPEC=NO elif file -bL ${BKGD} | grep -qi 'FITS'; then printf "## given \`${BKGD}' is a \`FITS file'\n" # get FITS header keyword HDUCLAS1=`dmkeypar ${BKGD} HDUCLAS1 echo=yes` if [ "${HDUCLAS1}" = "EVENTS" ]; then # event file printf "## given file is \`event'\n" # check if `blanksky' or `stowed bkg' BKG_OBJ=`dmkeypar ${BKGD} OBJECT echo=yes` if [ "${BKG_OBJ}" = "BACKGROUND DATASET" ] || [ "${BKG_OBJ}" = "ACIS STOWED" ]; then # valid bkg evt file printf "## given FITS file is a valid bkgrnd file\n" printf "## use *BLANKSKY*\n" | ${TOLOG} USE_BLANKSKY=YES USE_LBKG_REG=NO USE_BKG_SPEC=NO # specify `BLANKSKY' BLANKSKY=${BKGD} else # invalid bkg evt file printf "ERROR: invalid bkg evt file given\n" exit ${ERR_BKGTY} fi elif [ "${HDUCLAS1}" = "SPECTRUM" ]; then # spectrum file printf "## given file is \`spectrum'\n" printf "## use *BKG SPECTRUM*\n" | ${TOLOG} USE_BKG_SPEC=YES USE_BLANKSKY=NO USE_LBKG_REG=NO # specify `BKG_SPEC' BKG_SPEC=${BKGD} else # other type printf "ERROR: other type FITS given\n" exit ${ERR_BKGTY} fi else printf "ERROR: given \`${BKGD}' type UNKNOWN\n" exit ${ERR_BKGTY} fi # bkgd }}} # check `arf' and `rmf' {{{ if [ -r "${arf}" ]; then ARF=${arf} elif [ -r "${DFT_ARF}" ]; then ARF=${DFT_ARF} else read -p "> provide the ARF to use: " ARF if [ ! -r "${ARF}" ]; then printf "ERROR: cannot access given \`${ARF}'\n" exit ${ERR_ARF} fi fi printf "## use ARF: \`${ARF}'\n" | ${TOLOG} # rmf if [ -r "${rmf}" ]; then RMF=${rmf} elif [ -r "${DFT_RMF}" ]; then RMF=${DFT_RMF} else read -p "> provide the RMF to use: " RMF if [ ! -r "${RMF}" ]; then printf "ERROR: cannot access given \`${RMF}'\n" exit ${ERR_RMF} fi fi printf "## use RMF: \`${RMF}'\n" | ${TOLOG} # arf & rmf }}} # check given `grpcmd' if [ ! -z "${grpcmd}" ]; then GRP_CMD="${grpcmd}" else GRP_CMD="${DFT_GRP_CMD}" fi printf "## use grppha cmd: \`${GRP_CMD}'\n" | ${TOLOG} ## parameters }}} ################################################## #### main ## D_A #D_A_CM=`${COSCALC} ${REDSHIFT} | grep '^d_a_cm' | awk '{ print $2 }'` D_A_CM=`${COSCALC} ${REDSHIFT} | grep -i 'd_a.*cm' | awk -F'=' '{ print $2 }' | awk '{ print $1 }'` printf "D_A_CM(${REDSHIFT})= ${D_A_CM}\n" ## region related {{{ ## generate the needed region file printf "generate the output region file ...\n" cat > ${REG_OUT} << _EOF_ # Region file format: CIAO version 1.0 pie(${XC},${YC},${R_IN},${R_OUT},0,360) _EOF_ ## open the evt file to verify or modify printf "## check the generated pie region ...\n" printf "## if modified, save with the same name \`${REG_OUT}' (overwrite)\n" ds9 ${EVT} -regions ${REG_OUT} -cmap sls -bin factor 4 ## check the (modified) region (pie region end angle) printf "check the above region (for pie region end angle) ...\n" INVALID=`grep -i 'pie' ${REG_OUT} | awk -F'[,()]' '$7 > 360'` if [ "x${INVALID}" != "x" ]; then printf "*** WARNING: there are pie regions' END_ANGLE > 360\n" | ${TOLOG} printf "*** will to fix ...\n" mv -fv ${REG_OUT} ${REG_OUT}_tmp # using `awk' to fix awk -F'[,()]' '{ if ($7 > 360) { printf "%s(%.2f,%.2f,%.2f,%.2f,%.2f,%.2f)\n", $1,$2,$3,$4,$5,$6,($7-360) } else { print $0 } }' ${REG_OUT}_tmp > ${REG_OUT} rm -f ${REG_OUT}_tmp fi ## region related }}} ## generate spectrum {{{ # check counts punlearn dmlist CNT_RC=`dmlist infile="${EVT}[sky=region(${REG_OUT})][energy=700:7000]" opt=block | grep 'EVENTS' | awk '{ print $8 }'` if [ ${CNT_RC} -lt 500 ]; then F_WC=true WC="LOW_COUNTS" printf "*** WARNING: counts_in_0.048R500=${CNT_RC} < 500 ***\n" fi # object printf "extract object spectrum \`${AVGT_SPEC}' ...\n" AVGT_SPEC="${REG_OUT%.reg}.pi" AVGT_SPEC_GRP="${AVGT_SPEC%.pi}_grp.pi" punlearn dmextract dmextract infile="${EVT}[sky=region(${REG_OUT})][bin PI]" \ outfile="${AVGT_SPEC}" wmap="[bin det=8]" clobber=yes # group spectrum printf "group object spectrum ...\n" grppha infile="${AVGT_SPEC}" outfile="${AVGT_SPEC_GRP}" \ comm="${GRP_CMD} & exit" clobber=yes > /dev/null # background printf "generate the background spectrum ...\n" AVGT_BKG="${AVGT_SPEC%.pi}_bkg.pi" if [ "${USE_BLANKSKY}" = "YES" ]; then # use blanksky as background file printf "extract spectrum from blanksky ...\n" punlearn dmextract dmextract infile="${BLANKSKY}[sky=region(${REG_OUT})][bin PI]" \ outfile=${AVGT_BKG} wmap="[bin det=8]" clobber=yes elif [ "${USE_LBKG_REG}" = "YES" ]; then printf "extract local background ...\n" punlearn dmextract dmextract infile="${EVT}[sky=region(${BKGD})][bin PI]" \ outfile=${AVGT_BKG} wmap="[bin det=8]" clobber=yes elif [ "${USE_BKG_SPEC}" = "YES" ]; then printf "copy specified background spectrum ...\n" cp -fv ${BKG_SPEC} ${AVGT_BKG} fi printf "renormalize the background ...\n" bkg_renorm ${AVGT_SPEC} ${AVGT_BKG} ## spectrum }}} ## generate XSPEC script {{{ printf "generate a XSPEC script ...\n" [ -e "${XSPEC_SCRIPT}" ] && mv -fv ${XSPEC_SCRIPT} ${XSPEC_SCRIPT}_bak cat > ${XSPEC_SCRIPT} << _EOF_ ## XSPEC script ## spectrum analysis to get the average temperatue with (0-0.048 R500) ## ## generated by: \``basename $0`' ## date: \``date`' ## # xspec settings statistic chi abund grsa query yes # data data ${AVGT_SPEC_GRP} response ${RMF} arf ${ARF} backgrnd ${AVGT_BKG} # fitting range ignore bad ignore 0.0-0.7,7.0-** # plot related setplot energy method leven 10 0.01 xsect bcmc cosmo 70 0 0.73 xset delta 0.01 systematic 0 # model model wabs*apec ${N_H} -0.001 0 0 100000 1e+06 1.0 0.01 0.008 0.008 64 64 0.4 0.001 0 0 5 5 ${REDSHIFT} -0.01 -0.999 -0.999 10 10 0.0 0.01 0 0 1e+24 1e+24 ## xspec script end proc calc_cooling_time {} { set rout ${R_OUT} set d_a_cm ${D_A_CM} fit 1000 tclout param 4 set z [ lindex \$xspec_tclout 0 ] tclout param 2 set T [ lindex \$xspec_tclout 0 ] tclout param 5 set norm [ lindex \$xspec_tclout 0 ] newpar 1 0 dummyrsp .001 100 flux .001 100 tclout flux set flux [ lindex \$xspec_tclout 0 ] puts "flux(0.01-100kev): \$flux" set rout_cm [ expr \$rout*.492/3600/180*3.14159*\$d_a_cm ] set V [ expr 4./3.*3.14159*\$rout_cm*\$rout_cm*\$rout_cm ] set nenh [ expr \$norm*1E14*4*3.14159*\$d_a_cm*\$d_a_cm*(1+\$z)*(1+\$z)*(1+\$z)*(1+\$z)/\$V ] set d_l_cm [ expr \$d_a_cm*(1+\$z)*(1+\$z) ] set ne_np_ratio 1.2 set ne [ expr sqrt(\$nenh*\$ne_np_ratio) ] set lx [ expr \$flux*4*3.14159*\$d_l_cm*\$d_l_cm ] set kb 1.602E-9 set ct [ expr 3./2.*(\$ne+\$ne/\$ne_np_ratio)*\$kb*\$T*\$V/\$lx ] set ct_gyr [ expr \$ct/(3600*24*365.25*1E9) ] puts "Cooling_time= \$ct_gyr Gyr" } fit 1000 calc_cooling_time tclexit _EOF_ ## xspec script }}} ## invoke xspec to calc if [ "x${F_WC}" = "xtrue" ]; then printf "\n*** WC: LOW_COUNTS ***\n" printf "*** WARNING: counts_in_0.048R500=${CNT_RC} < 500 ***\n" else [ -e "${CT_RES}" ] && mv -f ${CT_RES} ${CT_RES}_bak printf "invoking XSPEC to calculate cooling time ...\n" xspec - ${XSPEC_SCRIPT} | tee ${CT_RES} OBS_ID=`grep '"Obs.*ID' ${JSON_FILE} | awk -F':' '{ print $2 }' | tr -d ' ,'` OBJ_NAME=`grep '"Source\ Name' ${JSON_FILE} | awk -F':' '{ print $2 }' | sed -e 's/\ *"//' -e 's/"\ *,$//'` CT=`grep -i '^Cooling_time' ${CT_RES} | awk '{ print $2 }'` printf "\n" | tee -a ${CT_RES} printf "# OBS_ID,OBJ_NAME,CT_gyr\n" | tee -a ${CT_RES} printf "# $OBS_ID,$OBJ_NAME,$CT\n" | tee -a ${CT_RES} fi exit 0