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Diffstat (limited to 'scripts/ciao_r500avgt.sh')
| -rwxr-xr-x | scripts/ciao_r500avgt.sh | 539 |
1 files changed, 539 insertions, 0 deletions
diff --git a/scripts/ciao_r500avgt.sh b/scripts/ciao_r500avgt.sh new file mode 100755 index 0000000..9a8dffd --- /dev/null +++ b/scripts/ciao_r500avgt.sh @@ -0,0 +1,539 @@ +#!/bin/sh +# +unalias -a +export LC_COLLATE=C +########################################################### +## script to extract spectrum and prepare needed files ## +## for calculating the `average temperature' ## +## within (0.1-0.5 r500) region ## +## ## +## NOTE: ## +## 1) r500 default in unit `pixel', if in `kpc', ## +## then `redshift z' and `calculator' are needed. ## +## 2) `background process' is same as `deproj_spectra' ## +## which supports `spectrum', `local' and `blanksky' ## +## 3) ARF/RMF files either provided or use the ARF/RMF ## +## of the outmost region ## +## ## +## LIweitiaNux <liweitianux@gmail.com> ## +## August 22, 2012 ## +########################################################### + +########################################################### +## ChangeLogs +## v1.1, 2012/08/26, LIweitiaNux +## modify `KPC_PER_PIX', able to use the newest version `calc_distance' +## v1.2, 2012/08/26, LIweitiaNux +## fix a bug with `DFT_BKGD' +## v2.0, 2012/09/04, LIweitiaNux +## add parameter `inner' and `outer' to adjust the region range +## modify parameter `r500' to take `kpc' as the default unit +## v2.1, 2012/10/05, LIweitiaNux +## change `DFT_GRP_CMD' to `group 1 128 4 ...' +## v3.0, 2013/02/09, LIweitiaNux +## modify for new process +########################################################### + +## about, used in `usage' {{{ +VERSION="v3.0" +UPDATE="2013-02-09" +## about }}} + +## error code {{{ +ERR_USG=1 +ERR_DIR=11 +ERR_EVT=12 +ERR_BKG=13 +ERR_REG=14 +ERR_JSON=15 +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 $0` evt=<evt2_clean> r500=<r500_kpc> basedir=<basedir> info=<info_json> inner=<inner_val> outer=<outer_val> regin=<input_reg> regout=<output_reg> bkgd=<blank_evt|lbkg_reg|bkg_spec> nh=<nH> z=<redshift> arf=<warf_file> rmf=<wrmf_file> [ grpcmd=<grppha_cmd> log=<log_file> ]\n" + printf "\nversion:\n" + printf "${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 +COSCALC="`which cosmo_calc calc_distance 2>/dev/null | head -n 1`" +# COSCALC="_path_to_calc_distance_" +# COSCALC="$HOME/bin/mass/calc_distance" +if [ -z "${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 `radial region file' +#DFT_REG_IN="_NOT_EXIST_" +DFT_REG_IN="rspec.reg" +# default region range (0.1-0.5 R500) +DFT_INNER="0.1" +DFT_OUTER="0.5" +# default ARF/RMF, the one of the outmost region +DFT_ARF="`ls -1 r?_*.warf 2> /dev/null | tail -n 1`" +DFT_RMF="`ls -1 r?_*.wrmf 2> /dev/null | tail -n 1`" + +# default `group command' for `grppha' +DFT_GRP_CMD="group min 25" +#DFT_GRP_CMD="group 1 128 2 129 256 4 257 512 8 513 1024 16" +#DFT_GRP_CMD="group 1 128 4 129 256 8 257 512 16 513 1024 32" +# default `log file' +DFT_LOGFILE="r500avgt_`date '+%Y%m%d%H'`.log" + +# default JSON pattern +DFT_JSON_PAT="*_INFO.json" +## 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`" >> ${LOGFILE} +## log }}} + +# check given parameters +if [ -d "${basedir}" ]; then + BASEDIR=${basedir} +else + BASEDIR=${DFT_BASEDIR} +fi +if [ ! -z "${json}" ] && [ -r "${BASEDIR}/${json}" ]; then + JSON_FILE="${BASEDIR}/${json}" +elif ls ${BASEDIR}/${DFT_JSON_PAT} > /dev/null 2>&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 `nh' and `redshift' {{{ +NH_JSON=`grep '"nH' ${JSON_FILE} | sed 's/.*"nH.*":\ //' | sed 's/\ *,$//'` +Z_JSON=`grep '"redshift' ${JSON_FILE} | sed 's/.*"redshift.*":\ //' | sed 's/\ *,$//'` +printf "## get nh: \`${NH_JSON}' (from \`${JSON_FILE}')\n" | ${TOLOG} +printf "## get redshift: \`${Z_JSON}' (from \`${JSON_FILE}')\n" | ${TOLOG} +## if `nh' and `redshift' supplied in cmdline, then use them +if [ ! -z "${nh}" ]; then + N_H=${nh} +else + N_H=${NH_JSON} +fi +# redshift +if [ ! -z "${z}" ]; then + REDSHIFT=${z} +else + REDSHIFT=${Z_JSON} +fi +printf "## use nH: ${N_H}\n" | ${TOLOG} +printf "## use redshift: ${REDSHIFT}\n" | ${TOLOG} +# nh & redshift }}} + +# region range {{{ +if [ ! -z "${inner}" ]; then + INNER="${inner}" +else + INNER=${DFT_INNER} +fi +if [ ! -z "${outer}" ]; then + OUTER="${outer}" +else + OUTER=${DFT_OUTER} +fi +printf "## region range: (${INNER} - ${OUTER} R500)\n" | ${TOLOG} +# range }}} + +# 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="${regout}" +else + REG_OUT="r500avgt_${INNER}-${OUTER}.reg" +fi +[ -e "${REG_OUT}" ] && mv -fv ${REG_OUT} ${REG_OUT}_bak +printf "## set output regfile: \`${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 'a-zA-Z() ' | awk -F',' '{ print $1 }'` +YC=`echo ${TMP_REG} | tr -d 'a-zA-Z() ' | awk -F',' '{ print $2 }'` +printf "## get center coord: (${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 +## 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} -region ${REG_OUT} + +## 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 ${REG_OUT}_tmp +fi +## region related }}} + +## generate spectrum {{{ +# object +AVGT_SPEC="${REG_OUT%.reg}.pi" +AVGT_SPEC_GRP="${AVGT_SPEC%.pi}_grp.pi" +printf "extract object spectrum \`${AVGT_SPEC}' ...\n" +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} ${AVGT_BKG} + +## spectrum }}} + +## generate XSPEC script {{{ +printf "generate a XSPEC script ...\n" +# default output xspec scripts +XSPEC_SCRIPT="xspec_${REG_OUT%.reg}.xcm" +[ -e "${XSPEC_SCRIPT}" ] && mv -fv ${XSPEC_SCRIPT} ${XSPEC_SCRIPT}_bak +cat > ${XSPEC_SCRIPT} << _EOF_ +## XSPEC script +## spectrum analysis to get the average temperatue with (0.1-0.5 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 +_EOF_ +## xspec script }}} + +exit 0 + |