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| -rwxr-xr-x | scripts/ciao_expcorr.sh | 414 |
1 files changed, 0 insertions, 414 deletions
diff --git a/scripts/ciao_expcorr.sh b/scripts/ciao_expcorr.sh deleted file mode 100755 index 3215056..0000000 --- a/scripts/ciao_expcorr.sh +++ /dev/null @@ -1,414 +0,0 @@ -#!/bin/sh -## -## This script performs exposure correction to images, and -## finally produce the exposure-corrected image. -## -## * make `image' from `evt file' -## * make `spectral weight' using `make_instmap_weights' -## * use `fluximage' to generating `exposure map' -## * make `exposure-corrected' image -## * and extract `surface brighness profile' -## -## NOTES: -## only ACIS-I (chip: 0-3) and ACIS-S (chip: 7) supported -## `merge_all' conflict with Heasoft's `pget' etc. tools -## -## Weitian LI -## 2012/08/16 -## -VERSION="v3.0" -UPDATED="2015/06/03" -## -## ChangeLogs: -## v3.1, 2015/06/04, Aaron LI -## * Added check for 'fluximage' parameter 'xygrid' before to use. -## 'fluximage' of version before '15Oct2012' does not have parameter -## 'xygrid' and dose not support spectral weights with parameter 'bands'. -## v3.0, 2015/06/03, Aaron LI -## * Changed to use 'fluximage' by default, and fallback to 'merge_all' -## * Copy needed pfiles to current working directory, and -## set environment variable $PFILES to use these first. -## * Replaced 'grep' with '\grep', 'ls' with '\ls' -## v2.1, 2014/10/30, Weitian LI -## Add 'aspect' parameter for 'skyfov' to fix the 'FoV shift bug' -## v2.0, 2014/07/29, Weitian LI -## `merge_all' deprecated, use `fluximage' if possible -## v1.2, 2012/08/21, Weitian LI -## set `ardlib' before process `merge_all' -## v1.1, 2012/08/21, Weitian LI -## fix a bug with `sed' -## - -unalias -a -export LC_COLLATE=C - -## 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_DET=41 -ERR_ENG=42 -ERR_CIAO=100 -ERR_TOOL=110 -## error code }}} - -## usage, help {{{ -case "$1" in - -[hH]*|--[hH]*) - printf "usage:\n" - printf " `basename $0` evt=<evt_file> energy=<e_start:e_end:e_width> basedir=<base_dir> nh=<nH> z=<redshift> temp=<avg_temperature> abund=<avg_abund> [ logfile=<log_file> ]\n" - printf "\nversion:\n" - printf " ${VERSION}, ${UPDATED}\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 2> /dev/null`" -# default dir which contains `asols, asol.lis, ...' files -# DFT_BASEDIR="_NOT_EXIST_" -DFT_BASEDIR=".." -# default `radial region file' to extract surface brightness -DFT_SBP_REG="_NOT_EXIST_" -#DFT_SBP_REG="sbprofile.reg" -# default `energy band' applying to `images' analysis -# format: `E_START:E_END:E_WIDTH' -DFT_ENERGY="700:7000:100" - -# default `log file' -DFT_LOGFILE="expcorr_sbp_`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 `msk file pattern' -DFT_MSK_PAT="acis*msk?.fits" -## 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 ${keyval} - shift # shift, process next one - done -} -## functions }}} - -## check CIAO init {{{ -if [ -z "${ASCDS_INSTALL}" ]; then - printf "ERROR: CIAO NOT initialized\n" - exit ${ERR_CIAO} -fi - -## XXX: heasoft's `pget' etc. tools conflict with some CIAO tools -printf "set \$PATH to avoid conflicts between HEAsoft and CIAO\n" -export PATH="${ASCDS_BIN}:${ASCDS_CONTRIB}:${PATH}" -printf "## PATH: ${PATH}\n" -## check CIAO }}} - -## parameters {{{ -# process cmdline args using `getopt_keyval' -getopt_keyval "$@" - -## 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" | ${TOLOG} -# check given region file(s) -if [ -r "${reg}" ]; then - SBP_REG="${reg}" -elif [ -r "${DFT_SBP_REG}" ]; then - SBP_REG=${DFT_SBP_REG} -fi -printf "## use reg file(s): \`${SBP_REG}'\n" | ${TOLOG} -## check given `energy' {{{ -if [ ! -z "${energy}" ]; then - ENERGY="${energy}" -else - ENERGY="${DFT_ENERGY}" -fi -# split energy variable -ENG_N=`echo ${ENERGY} | awk -F':' '{ print NF }'` -if [ ${ENG_N} -eq 1 ]; then - E_START=`echo ${DFT_ENERGY} | awk -F':' '{ print $1 }'` - E_END=`echo ${DFT_ENERGY} | awk -F':' '{ print $2 }'` - E_WIDTH=${ENERGY} -elif [ ${ENG_N} -eq 2 ]; then - E_START=`echo ${ENERGY} | awk -F':' '{ print $1 }'` - E_END=`echo ${ENERGY} | awk -F':' '{ print $2 }'` - E_WIDTH=`echo ${DFT_ENERGY} | awk -F':' '{ print $3 }'` -elif [ ${ENG_N} -eq 3 ]; then - E_START=`echo ${ENERGY} | awk -F':' '{ print $1 }'` - E_END=`echo ${ENERGY} | awk -F':' '{ print $2 }'` - E_WIDTH=`echo ${ENERGY} | awk -F':' '{ print $3 }'` -else - printf "ERROR: invalid energy: \`${ENERGY}'\n" - exit ${ERR_ENG} -fi -ENG_RANGE="${E_START}:${E_END}" -printf "## use energy range: \`${ENG_RANGE}' eV\n" | ${TOLOG} -printf "## use energy width: \`${E_WIDTH}' eV\n" | ${TOLOG} -## parse energy }}} -# parameters (nH, z, avg_temp, avg_abund) used to calculate {{{ -# `spectral weights' for `mkinstmap' -# check given nH -if [ -z "${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" | ${TOLOG} -# check given temperature -if [ -z "${temp}" ]; then - read -p "> object average temperature: " TEMP -else - TEMP=${temp} -fi -printf "## use temperature: ${TEMP}\n" | ${TOLOG} -# check given abundance -if [ -z "${abund}" ]; then - read -p "> object average abundance: " ABUND -else - ABUND=${abund} -fi -printf "## use abundance: ${ABUND}\n" | ${TOLOG} -# `spectral weights' parameters }}} -# check given dir -if [ -d "${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} -## parameters }}} - -## prepare parameter files (pfiles) {{{ -CIAO_TOOLS="dmkeypar dmcopy dmhedit dmimgcalc ardlib make_instmap_weights skyfov get_sky_limits fluximage merge_all" - -# Copy necessary pfiles for localized usage -for tool in ${CIAO_TOOLS}; do - pfile=`paccess ${tool}` - [ -n "${pfile}" ] && punlearn ${tool} && cp -Lvf ${pfile} . -done - -# Modify environment variable 'PFILES' to use local pfiles first -export PFILES="./:${PFILES}" -## pfiles }}} - -## check files in `basedir' {{{ -# check asol 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" -# 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 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 ${ERR_MSK} -fi -printf "## use msk file: \`${MSK}'\n" | ${TOLOG} -## check files }}} - -## determine ACIS type {{{ -# consistent with `ciao_procevt' -punlearn dmkeypar -DETNAM=`dmkeypar ${EVT} DETNAM echo=yes` -if echo ${DETNAM} | \grep -q 'ACIS-0123'; then - printf "## \`DETNAM' (${DETNAM}) has chips 0123\n" - printf "## ACIS-I\n" - ACIS_TYPE="ACIS-I" - CCD="0:3" - NEW_DETNAM="ACIS-0123" - ROOTNAME="c0-3_e${E_START}-${E_END}" -elif echo ${DETNAM} | \grep -q 'ACIS-[0-6]*7'; then - printf "## \`DETNAM' (${DETNAM}) has chip 7\n" - printf "## ACIS-S\n" - ACIS_TYPE="ACIS-S" - CCD="7" - NEW_DETNAM="ACIS-7" - ROOTNAME="c7_e${E_START}-${E_END}" -else - printf "ERROR: unknown detector type: ${DETNAM}\n" - exit ${ERR_DET} -fi -## ACIS type }}} - -## main process {{{ -## set `ardlib' at first -printf "set \`ardlib' first ...\n" -punlearn ardlib -acis_set_ardlib badpixfile="${BPIX}" - -## generate `spectral weights' for `instrumental map' {{{ -printf "generate \`spectral weights' for making instrumental map ...\n" -SPEC_WGT="instmap_weights.txt" -# convert `eV' to `keV' -EMIN=`echo ${E_START} | awk '{ print $1/1000 }'` -EMAX=`echo ${E_END} | awk '{ print $1/1000 }'` -EWIDTH=`echo ${E_WIDTH} | awk '{ print $1/1000 }'` -punlearn make_instmap_weights -make_instmap_weights outfile="${SPEC_WGT}" \ - model="xswabs.gal*xsapec.ap" \ - paramvals="gal.nh=${N_H};ap.kt=${TEMP};ap.abundanc=${ABUND};ap.redshift=${REDSHIFT}" \ - emin="${EMIN}" emax="${EMAX}" ewidth="${EWIDTH}" \ - abund="grsa" clobber=yes -## spectral weights }}} - -## generate `skyfov' -printf "generate skyfov ...\n" -SKYFOV="skyfov.fits" -punlearn skyfov -skyfov infile="${EVT}" outfile="${SKYFOV}" aspect="@${ASOLIS}" clobber=yes - -## filter by energy band & make image -printf "filter out events in energy band: \`${ENG_RANGE}' ...\n" -EVT_E="evt2_${ROOTNAME}.fits" -if [ ! -r "${EVT_E}" ]; then - punlearn dmcopy - dmcopy infile="${EVT}[energy=${E_START}:${E_END}]" outfile="${EVT_E}" clobber=yes -fi - -printf "make image ...\n" -IMG_ORIG="img_${ROOTNAME}.fits" -punlearn dmcopy -dmcopy infile="${EVT_E}[sky=region(${SKYFOV}[ccd_id=${CCD}])][bin sky=1]" \ - outfile="${IMG_ORIG}" clobber=yes - -## modify `DETNAM' of image -printf "modify keyword \`DETNAM' of image -> \`${NEW_DETNAM}'\n" -punlearn dmhedit -dmhedit infile="${IMG_ORIG}" filelist=none operation=add \ - key=DETNAM value="${NEW_DETNAM}" - -## get `xygrid' for image -punlearn get_sky_limits -get_sky_limits image="${IMG_ORIG}" -XYGRID=`pget get_sky_limits xygrid` -printf "## get \`xygrid': \`${XYGRID}'\n" | ${TOLOG} - -EXPMAP="expmap_${ROOTNAME}.fits" -IMG_EXPCORR="img_expcorr_${ROOTNAME}.fits" - -# Check whether fluximage is capable to make exposure correction for us -# version after '15Oct2012' supports 'xygrid' and spectral weights file. -if `pget fluximage xygrid >/dev/null 2>&1`; then - USE_FLUXIMAGE="YES" -else - # 'fluximage' do not support 'xygrid' parameter and spectral weights. - # fallback to use 'merge_all' - USE_FLUXIMAGE="NO" -fi - -if [ "${USE_FLUXIMAGE}" = "YES" ]; then - ## 'fluximage' is available, use it by default - ## use 'fluximage' to generate `exposure map' and apply exposure correction - printf "use fluximage to generate expmap and apply correction ...\n" - punlearn fluximage - fluximage infile="${EVT_E}" outroot="${ROOTNAME}" \ - binsize=1 bands="${SPEC_WGT}" xygrid="${XYGRID}" \ - asol="@${ASOLIS}" badpixfile="${BPIX}" \ - maskfile="${MSK}" clobber=yes - ## make symbolic links - # clipped counts image - ln -svf ${ROOTNAME}*band*thresh.img ${IMG_ORIG%.fits}_thresh.fits - # clipped exposure map - ln -svf ${ROOTNAME}*band*thresh.expmap ${EXPMAP} - # exposure-corrected image - ln -svf ${ROOTNAME}*band*flux.img ${IMG_EXPCORR} -else - # 'merge_all' is available, fallback to this - printf "fallback to merge_all ...\n" - ## XXX: `merge_all' needs `asol files' in working directory - printf "link asol files into currect dir (\`merge_all' needed) ...\n" - for f in `cat ${ASOLIS}`; do - asol=`basename ${f}` - ln -svf ${BASEDIR}/${asol} . - done - - printf "use \`merge_all' to generate \`exposure map' ONLY ...\n" - punlearn merge_all - merge_all evtfile="${EVT_E}" asol="@${ASOLIS}" \ - chip="${CCD}" xygrid="${XYGRID}" \ - energy="${SPEC_WGT}" expmap="${EXPMAP}" \ - dtffile="" refcoord="" merged="" expcorr="" \ - clobber=yes - - ## apply exposure correction - printf "use \`dmimgcalc' to apply \`exposure correction' ...\n" - punlearn dmimgcalc - dmimgcalc infile="${IMG_ORIG}" infile2="${EXPMAP}" \ - outfile="${IMG_EXPCORR}" operation=div clobber=yes -fi - -## main }}} - -exit 0 - |