diff options
Diffstat (limited to 'scripts/ciao_bkg_spectra.sh')
| -rwxr-xr-x | scripts/ciao_bkg_spectra.sh | 425 |
1 files changed, 425 insertions, 0 deletions
diff --git a/scripts/ciao_bkg_spectra.sh b/scripts/ciao_bkg_spectra.sh new file mode 100755 index 0000000..b4dbbbd --- /dev/null +++ b/scripts/ciao_bkg_spectra.sh @@ -0,0 +1,425 @@ +#!/bin/sh - +# +trap date INT +unalias -a +export GREP_OPTIONS="" +export LC_COLLATE=C +########################################################### +## extract background spectra from src and blanksky ## +## renormalization the blank spectrum ## +## ## +## Ref: Chandra spectrum analysis ## +## http://cxc.harvard.edu/ciao/threads/extended/ ## +## Ref: specextract ## +## http://cxc.harvard.edu/ciao/ahelp/specextract.html ## +## Ref: CIAO v4.4 region bugs ## +## http://cxc.harvard.edu/ciao/bugs/regions.html#bug-12187 +## ## +## LIweitiaNux, July 24, 2012 ## +########################################################### + +########################################################### +# ChangeLogs: +# v3, 2012/08/09 +# fix `scientific notation' for `bc' +# change `spec group' method to `min 15' +# v4, 2012/08/13 +# add `clobber=yes' +# improve error code +# improve cmdline arguements +# provide a flexible way to pass parameters +# (through cmdline which similar to CIAO, +# and default filename match patterns) +# add simple `logging' function +# v4.1, 2014/07/29, Weitian LI +# fix 'pbkfile' parameters for CIAO-4.6 +########################################################### + +## about, used in `usage' {{{ +VERSION="v4" +UPDATE="2012-08-14" +## about }}} + +## usage, help {{{ +case "$1" in + -[hH]*|--[hH]*) + printf "usage:\n" + printf " `basename $0` evt=<evt2_clean> reg=<reglist> blank=<blanksky_evt> basedir=<base_dir> nh=<nH> z=<redshift> [ grpcmd=<grppha_cmd> log=<log_file> ]\n" + printf "\nversion:\n" + printf "${VERSION}, ${UPDATE}\n" + exit ${ERR_USG} + ;; +esac +## usage, help }}} + +## default parameters {{{ +# default `event file' which used to match `blanksky' files +#DFT_EVT="_NOT_EXIST_" +DFT_EVT="`ls evt2*_clean.fits`" +# default `blanksky file' +#DFT_BLANK="_NOT_EXIST_" +DFT_BLANK="`ls blanksky*.fits`" +# default dir which contains `asols, asol.lis, ...' files +#DFT_BASEDIR="_NOT_EXIST_" +DFT_BASEDIR=".." +# 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="bkg_spectra_`date '+%Y%m%d'`.log" + +## howto find files in `basedir' +# default `asol.lis pattern' +DFT_ASOLIS_PAT="acis*asol?.lis" +# default `bad pixel filename pattern' +DFT_BPIX_PAT="acis*repro*bpix?.fits" +# default `pbk file pattern' +DFT_PBK_PAT="acis*pbk?.fits" +# default `msk file pattern' +DFT_MSK_PAT="acis*msk?.fits" +## default parameters }}} + +## 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 +## error code }}} + +## 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`" >> ${LOGFILE} +## log }}} + +# check given parameters +# check evt file +if [ -r "${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" | ${TOLOG} +# check given region file(s) +if [ -z "${reg}" ]; then + read -p "> selected local bkg region file: " REGLIST +else + REGLIST="${reg}" +fi +REGLIST=`echo ${REGLIST} | tr ',' ' '` # use *space* to separate +printf "## use reg file(s): \`${REGLIST}'\n" | ${TOLOG} +# check given blanksky +if [ -r "${blank}" ]; then + BLANK=${blank} +elif [ -r "${DFT_BLANK}" ]; then + BLANK=${DFT_BLANK} +else + read -p "> matched blanksky evtfile: " BLANK + if [ ! -r "${BLANK}" ]; then + printf "ERROR: cannot acces given \`${BLANK}' blanksky file\n" + exit ${ERR_BKG} + fi +fi +# check given nH +if [ -z "${nh}" ]; then + read -p "> value of nH: " N_H +else + N_H=${nh} +fi +printf "## use nH: ${N_H}\n" | ${TOLOG} +# check given redshift +if [ -z "${z}" ]; then + read -p "> value of redshift: " REDSHIFT +else + REDSHIFT=${z} +fi +printf "## use redshift: ${REDSHIFT}\n" | ${TOLOG} +# check given dir +if [ -d "${basedir}" ]; then + BASEDIR=${basedir} +elif [ -d "${DFT_BASEDIR}" ]; then + BASEDIR=${DFT_BASEDIR} +else + read -p "> basedir (contains asol files): " BASEDIR + if [ ! -d "${BASEDIR}" ]; then + printf "ERROR: given \`${BASEDIR}' NOT a directory\n" + exit ${ERR_DIR} + fi +fi +# remove the trailing '/' +BASEDIR=`echo ${BASEDIR} | sed 's/\/*$//'` +printf "## use basedir: \`${BASEDIR}'\n" | ${TOLOG} +# check given `grpcmd' +if [ ! -z "${grpcmd}" ]; then + GRP_CMD="${grpcmd}" +else + GRP_CMD="${DFT_GRP_CMD}" +fi +printf "## use grppha cmd: \`${GRP_CMD}'\n" | ${TOLOG} +## parameters }}} + +## check needed files {{{ +# check reg file(s) +printf "check accessibility of reg file(s) ...\n" +for reg_f in ${REGLIST}; do + if [ ! -r "${reg_f}" ]; then + printf "ERROR: file \`${reg_f}' NOT accessiable\n" + exit ${ERR_REG} + fi +done +# check the validity of *pie* regions +printf "check pie reg validity ...\n" +INVALID=`cat ${REGLIST} | grep -i 'pie' | awk -F, '{ print $6 }' | tr -d ')' | awk '$1 > 360'` +if [ "x${INVALID}" != "x" ]; then + printf "WARNING: some pie region's END_ANGLE > 360\n" | ${TOLOG} + printf " CIAO v4.4 tools may run into trouble\n" +fi + +# check files in `basedir' +printf "check needed files in basedir \`${BASEDIR}' ...\n" +# check asolis files +ASOLIS=`ls -1 ${BASEDIR}/${DFT_ASOLIS_PAT} | head -n 1` +if [ -z "${ASOLIS}" ]; then + printf "ERROR: cannot find \"${DFT_ASOLIS_PAT}\" in dir \`${BASEDIR}'\n" + exit ${ERR_ASOL} +fi +printf "## use asolis: \`${ASOLIS}'\n" | ${TOLOG} +# check badpixel file +BPIX=`ls -1 ${BASEDIR}/${DFT_BPIX_PAT} | head -n 1` +if [ -z "${BPIX}" ]; then + printf "ERROR: cannot find \"${DFT_BPIX_PAT}\" in dir \`${BASEDIR}'\n" + exit ${ERR_BPIX} +fi +printf "## use badpixel: \`${BPIX}'\n" | ${TOLOG} +# check pbk file +PBK=`ls -1 ${BASEDIR}/${DFT_PBK_PAT} | head -n 1` +if [ -z "${PBK}" ]; then + printf "ERROR: cannot find \"${DFT_PBK_PAT}\" in dir \`${BASEDIR}'\n" + exit ${ERR_PBK} +fi +printf "## use pbk: \`${PBK}'\n" | ${TOLOG} +# check msk file +MSK=`ls -1 ${BASEDIR}/${DFT_MSK_PAT} | head -n 1` +if [ -z "${MSK}" ]; then + printf "ERROR: cannot find \"${DFT_MSK_PAT}\" in dir \`${BASEDIR}'\n" + exit ${ERR_MSK} +fi +printf "## use msk: \`${MSK}'\n" | ${TOLOG} +## check files }}} + +## main part {{{ +## use 'for' loop to process every region file +for reg_i in ${REGLIST}; do + printf "\n==============================\n" + printf "PROCESS REGION fle \`${reg_i}' ...\n" + + REG_TMP="_tmp.reg" + [ -f "${REG_TMP}" ] && rm -fv ${REG_TMP} # remove tmp files + cp -fv ${reg_i} ${REG_TMP} + # check the validity of *pie* regions {{{ + INVALID=`grep -i 'pie' ${REG_TMP} | awk -F, '{ print $6 }' | tr -d ')' | awk '$1 > 360'` + if [ "x${INVALID}" != "x" ]; then + printf "WARNING: fix for *pie* region in file \`${reg_i}'\n" + cat ${REG_TMP} + A_OLD=`echo ${INVALID} | sed 's/\./\\\./'` + A_NEW=`echo ${INVALID}-360 | bc -l | sed 's/\./\\\./'` + sed -i'' "s/${A_OLD}\ *)/${A_NEW})/" ${REG_TMP} + printf " --> " + cat ${REG_TMP} + fi + ## check pie region }}} + + LBKG_PI="${reg_i%.reg}.pi" + ## use `specextract' to extract local bkg spectrum {{{ + # NOTE: set `binarfwmap=2' to save the time for generating `ARF' + # I have tested that this bin factor has little impact on the results. + # NO background response files + # NO background spectrum (generate by self) + # NO spectrum grouping (group by self using `grppha') + # 'pbkfile' parameter deprecated in CIAO-4.6 + if `pget specextract pbkfile >/dev/null 2>&1`; then + P_PBKFILE="pbkfile='${PBK}'" + else + P_PBKFILE="" + fi + # + printf "use \`specextract' to generate spectra and response ...\n" + punlearn specextract + specextract infile="${EVT}[sky=region(${REG_TMP})]" \ + outroot=${LBKG_PI%.pi} bkgfile="" asp="@${ASOLIS}" \ + ${P_PBKFILE} mskfile="${MSK}" badpixfile="${BPIX}" \ + weight=yes correct=no bkgresp=no \ + energy="0.3:11.0:0.01" channel="1:1024:1" \ + combine=no binarfwmap=2 \ + grouptype=NONE binspec=NONE \ + verbose=2 clobber=yes + # `specextract' }}} + + ## generate the blanksky bkg spectrum {{{ + printf "generate the blanksky bkg spectrum ...\n" + BBKG_PI="blanksky_${LBKG_PI}" + punlearn dmextract + dmextract infile="${BLANK}[sky=region(${REG_TMP})][bin pi]" \ + outfile=${BBKG_PI} wmap="[bin det=8]" clobber=yes + ## blanksky bkg spectrum }}} + + ## bkg renormalization {{{ + printf "Renormalize background ...\n" + bkg_renorm ${LBKG_PI} ${BBKG_PI} + ## bkg renorm }}} + + ## group spectrum {{{ + printf "group spectrum using \`grppha'\n" + LBKG_GRP_PI="${LBKG_PI%.pi}_grp.pi" + grppha infile="${LBKG_PI}" outfile="${LBKG_GRP_PI}" \ + comm="${GRP_CMD} & exit" clobber=yes > /dev/null + ## group spectra }}} + + ## generate a script for XSPEC {{{ + XSPEC_XCM="xspec_${LBKG_PI%.pi}_model.xcm" + if [ -e ${XSPEC_XCM} ]; then + mv -fv ${XSPEC_XCM} ${XSPEC_XCM}_bak + fi + cat >> ${XSPEC_XCM} << _EOF_ +## xspec script +## analysis chandra acis background components +## xspec model: apec+apec+wabs*(pow+apec) +## +## generated by script \``basename $0`' +## `date` +## NOTES: needs XSPEC v12.x + +# settings +statistic chi +#weight churazov +abund grsa +query yes + +# data +data ${LBKG_GRP_PI} +response ${LBKG_PI%.pi}.wrmf +arf ${LBKG_PI%.pi}.warf +backgrnd ${BBKG_PI} + +# fitting range +ignore bad +ignore 0.0-0.4,8.0-** + +# plot related +setplot energy + +method leven 10 0.01 +xsect bcmc +cosmo 70 0 0.73 +xset delta 0.01 +systematic 0 + +# model +model apec + apec + wabs(powerlaw + apec) + 0.08 -0.01 0.008 0.008 64 64 + 1 -0.001 0 0 5 5 + 0 -0.01 -0.999 -0.999 10 10 + 0.0 0.01 -1 0 0 1 + 0.2 -0.01 0.008 0.008 64 64 + 1 -0.001 0 0 5 5 + 0 -0.01 -0.999 -0.999 10 10 + 0.0 0.01 -1 0 0 1 + ${N_H} -0.001 0 0 100000 1e+06 + 1.4 -0.01 -3 -2 9 10 + 0.0 0.01 -1 0 0 1 + 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 + +freeze 1 2 3 +freeze 5 6 7 +freeze 9 10 14 +thaw 12 13 +_EOF_ + ## XSPEC script }}} + +done # end 'for', `specextract' +## main part }}} + +# clean +printf "clean ...\n" +rm -f ${REG_TMP} + +printf "DONE\n" +########################################################### + +# vim: set ts=8 sw=4 tw=0 fenc=utf-8 ft=sh: # |