diff options
| -rw-r--r-- | README.md | 1 | ||||
| -rwxr-xr-x | scripts/ciao_bkg_spectra_v4.sh | 11 | ||||
| -rwxr-xr-x | scripts/ciao_deproj_spectra_v8.sh | 16 | ||||
| -rwxr-xr-x | scripts/ciao_expcorr_only.sh | 75 | ||||
| -rwxr-xr-x | scripts/ciao_expcorr_sbp_v4.sh | 233 |
5 files changed, 308 insertions, 28 deletions
@@ -4,6 +4,7 @@ README.md Install/Compile --------------- +needs `libgsl-dev' (1) mass_profile $ cd mass_profile $ make clean diff --git a/scripts/ciao_bkg_spectra_v4.sh b/scripts/ciao_bkg_spectra_v4.sh index bc40151..b4dbbbd 100755 --- a/scripts/ciao_bkg_spectra_v4.sh +++ b/scripts/ciao_bkg_spectra_v4.sh @@ -31,6 +31,8 @@ export LC_COLLATE=C # (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' {{{ @@ -307,11 +309,18 @@ for reg_i in ${REGLIST}; do # NO background response files # NO background spectrum (generate by self) # NO spectrum grouping (group by self using `grppha') + # 'pbkfile' parameter deprecated in CIAO-4.6 + if `pget specextract pbkfile >/dev/null 2>&1`; then + P_PBKFILE="pbkfile='${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}" \ - pbkfile="${PBK}" mskfile="${MSK}" badpixfile="${BPIX}" \ + ${P_PBKFILE} mskfile="${MSK}" badpixfile="${BPIX}" \ weight=yes correct=no bkgresp=no \ energy="0.3:11.0:0.01" channel="1:1024:1" \ combine=no binarfwmap=2 \ diff --git a/scripts/ciao_deproj_spectra_v8.sh b/scripts/ciao_deproj_spectra_v8.sh index 3818a44..abebc7c 100755 --- a/scripts/ciao_deproj_spectra_v8.sh +++ b/scripts/ciao_deproj_spectra_v8.sh @@ -39,6 +39,10 @@ export LC_COLLATE=C ## v8, 2012/08/14, LIweitiaNux ## use `cmdline' args instead of `cfg file' ## add `logging' function +## v8.1, 2014/07/29, Weitian LI +## fix variable 'ABUND=grsa' +## v8.2, 2014/07/29, Weitian LI +## fix 'pbkfile' parameters for CIAO-4.6 ########################################################### ## about, used in `usage' {{{ @@ -88,6 +92,9 @@ DFT_BPIX_PAT="acis*repro*bpix?.fits" DFT_PBK_PAT="acis*pbk?.fits" # default `msk file pattern' DFT_MSK_PAT="acis*msk?.fits" + +## abundance standard +ABUND="grsa" ## default parameters }}} ## error code {{{ @@ -416,10 +423,17 @@ for i in `seq ${LINES}`; do # NO background response files # NO background spectrum (generate by self) # NO spectrum grouping (group by self using `grppha') + # 'pbkfile' parameter deprecated in CIAO-4.6 + if `pget specextract pbkfile >/dev/null 2>&1`; then + P_PBKFILE="pbkfile='${PBK}'" + else + P_PBKFILE="" + fi + # punlearn specextract specextract infile="${EVT}[sky=region(${REG_CIAO})]" \ outroot="r${i}_${ROOTNAME}" bkgfile="" asp="@${ASOLIS}" \ - pbkfile="${PBK}" mskfile="${MSK}" badpixfile="${BPIX}" \ + ${P_PBKFILE} mskfile="${MSK}" badpixfile="${BPIX}" \ weight=yes correct=no bkgresp=no \ energy="0.3:11.0:0.01" channel="1:1024:1" \ combine=no binarfwmap=2 \ diff --git a/scripts/ciao_expcorr_only.sh b/scripts/ciao_expcorr_only.sh index 526540d..1321382 100755 --- a/scripts/ciao_expcorr_only.sh +++ b/scripts/ciao_expcorr_only.sh @@ -5,7 +5,7 @@ export LC_COLLATE=C ########################################################### ## make `image' from `evt file' ## ## make `spectral weight' using `make_instmap_weights' ## -## use `merge_all' to generating `exposure map' ## +## use `fluximage' to generating `exposure map' ## ## make `exposure-corrected' image ## ## and extract `surface brighness profile' ## ## ## @@ -23,6 +23,8 @@ export LC_COLLATE=C ## fix a bug with `sed' ## v1.2, 2012-08-21, LIweitiaNux ## set `ardlib' before process `merge_all' +## v2.0, 2014/07/29, Weitian LI +## `merge_all' deprecated, use `fluximage' if possible ########################################################### ## about, used in `usage' {{{ @@ -81,6 +83,8 @@ DFT_LOGFILE="expcorr_sbp_`date '+%Y%m%d'`.log" DFT_ASOLIS_PAT="acis*asol?.lis" # default `bad pixel filename pattern' DFT_BPIX_PAT="acis*repro*bpix?.fits" +# default `msk file pattern' +DFT_MSK_PAT="acis*msk?.fits" ## default parameters }}} ## functions {{{ @@ -233,11 +237,6 @@ if [ -z "${ASOLIS}" ]; then exit ${ERR_ASOL} fi printf "## use asolis: \`${ASOLIS}'\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 - ln -sv ${BASEDIR}/${f} . -done # check badpixel file BPIX=`ls -1 ${BASEDIR}/${DFT_BPIX_PAT} | head -n 1` if [ -z "${BPIX}" ]; then @@ -245,6 +244,13 @@ if [ -z "${BPIX}" ]; then 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" | ${TOLOG} ## check files }}} ## determine ACIS type {{{ @@ -328,29 +334,46 @@ get_sky_limits image="${IMG_ORIG}" XYGRID=`pget get_sky_limits xygrid` printf "## get \`xygrid': \`${XYGRID}'\n" | ${TOLOG} -## for simplicity, use `merge_all' to generating `exposure map' {{{ -## set `ardlib' again to make sure the matched bpix file specified -printf "set \`ardlib' again for \`merge_all' ...\n" -punlearn ardlib -acis_set_ardlib badpixfile="${BPIX}" - -printf "use \`merge_all' to generate \`exposure map' ONLY ...\n" EXPMAP="expmap_${ROOTNAME}.fits" -punlearn merge_all -merge_all evtfile="${EVT_E}" asol="@${ASOLIS}" \ - chip="${CCD}" xygrid="${XYGRID}" \ - energy="${SPEC_WGT}" expmap="${EXPMAP}" \ - dtffile="" refcoord="" merged="" expcorr="" \ - clobber=yes -## `merge_all' }}} - -## apply exposure correction -printf "use \`dmimgcalc' to apply \`exposure correction' ...\n" IMG_EXPCORR="img_expcorr_${ROOTNAME}.fits" -punlearn dmimgcalc -dmimgcalc infile="${IMG_ORIG}" infile2="${EXPMAP}" \ - outfile="${IMG_EXPCORR}" operation=div clobber=yes +if `which merge_all >/dev/null 2>&1`; then + # merge_all available + printf "merge_all ...\n" + ## set `ardlib' again to make sure the matched bpix file specified + printf "set \`ardlib' again for \`merge_all' ...\n" + punlearn ardlib + acis_set_ardlib badpixfile="${BPIX}" + + ## 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 + ln -sv ${BASEDIR}/${f} . + 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="${IMG_EXPCORR}" operation=div clobber=yes +else + # `merge_all' deprecated and not available + ## use 'fluximage' to generate `exposure map' and apply exposure correction + printf "fluximage ...\n" + punlearn fluximage + fluximage infile="${EVT_E}" outroot="${ROOTNAME}" \ + binsize=1 bands="${SPEC_WGT}" xygrid="${XYGRID}" \ + asol="@${ASOLIS}" badpixfile="${BPIX}" \ + maskfile="${MSK}" clobber=yes verbose=2 +fi ## main }}} diff --git a/scripts/ciao_expcorr_sbp_v4.sh b/scripts/ciao_expcorr_sbp_v4.sh new file mode 100755 index 0000000..861c6dd --- /dev/null +++ b/scripts/ciao_expcorr_sbp_v4.sh @@ -0,0 +1,233 @@ +#!/bin/sh +unalias -a +export LC_COLLATE=C + +##################################################################### +## make exposure map and exposure-corrected image +## extract surface brightness profile (revoke 'ciao_sbp_v3.1.sh') +## +## ChangeLogs: +## v4, 2013/10/12, LIweitiaNux +## split out the 'generate regions' parts -> 'ciao_genreg_v1.sh' +## v3, 2013/05/03, LIweitiaNux +## add parameter 'ds9' to check the centroid and regions +##################################################################### + +SCRIPT_PATH=`readlink -f $0` +SCRIPT_DIR=`dirname ${SCRIPT_PATH}` +EXPCORR_SCRIPT="ciao_expcorr_only.sh" +EXTRACT_SBP_SCRIPT="ciao_sbp_v3.1.sh" + +## about, used in `usage' {{{ +VERSION="v4" +UPDATE="2013-10-12" +## about }}} + +## err 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 +## error code }}} + +## usage {{{ +case "$1" in + -[hH]*|--[hH]*) + printf "usage:\n" + printf " `basename $0` evt=<evt2_clean> sbp_reg=<sbprofile.reg> nh=<nh> z=<redshift> temp=<avg_temp> abund=<avg_abund> cellreg=<celld_reg> expcorr=<yes|no>\n" + printf "\nversion:\n" + printf "${VERSION}, ${UPDATE}\n" + exit ${ERR_USG} + ;; +esac +## usage }}} + +## default parameters {{{ +## clean evt2 file +DFT_EVT=`ls evt2*_clean.fits 2> /dev/null` +## the repro dir +DFT_BASEDIR=".." + +## xcentroid region +DFT_SBP_REG="sbprofile.reg" + +## log file +DFT_LOGFILE="expcorr_sbp_`date '+%Y%m%d'`.log" + +## cell region +DFT_CELL_REG=`ls celld*.reg 2> /dev/null` + +## background spectra +DFT_BKGD=`ls bkgcorr_bl*.pi 2> /dev/null` +## default parameters }}} + +## functions {{{ +getopt_keyval() { + until [ -z "$1" ] + do + key=${1%%=*} # extract key + val=${1#*=} # extract value + keyval="${key}=\"${val}\"" + echo "## getopt: eval '${keyval}'" + eval ${keyval} + shift # shift, process next one + done +} +## functions }}} + +## check ciao init and set path to solve conflit with heasoft {{{ +if [ -z "${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: ${PATH}\n" +## check ciao&heasoft}}} + +## parameters {{{ +getopt_keyval "$@" + +##log file +LOGFILE="not_exist" + +##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 ${ERR_EVT} + fi +fi + +##check ori sbp region +if [ -r "${sbp_reg}" ]; then + SBP_REG="${sbp_reg}" +elif [ -r "${DFT_SBP_REG}" ] ;then + SBP_REG="${DFT_SBP_REG}" +else + read -p "sbp region file: " SBP_REG + if [ ! -r "${SBP_REG}" ]; then + printf "ERROR: cannot access given \`${SBP}' sbp region file\n" + exit ${ERR_REG} + fi +fi + +## nh z temp abund +if [ -z "${nh}" ]; then + read -p "> value of nH: " N_H +else + N_H=${nh} +fi +if [ -z "${z}" ]; then + read -p "> value of redshift: " REDSHIFT +else + REDSHIFT=${z} +fi +if [ -z "${temp}" ]; then + read -p "> object average temperature: " TEMP +else + TEMP=${temp} +fi +if [ -z "${abund}" ]; then + read -p "> object average abundance: " ABUND +else + ABUND=${abund} +fi +# check give basedir +if [ -d "${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 ${BASEDIR} | sed 's/\/*$//'` + +# point source region +if [ -r "${cellreg}" ]; then + CELL_REG=${cellreg} +elif [ -r "${DFT_CELL_REG}" ]; then + CELL_REG=${DFT_CELL_REG} +else + read -p ">point source region file: " CELL_REG + if [ ! -d ${CELL_REG} ] ; then + printf " ERROR no point source region\n" + exit ${ERR_REG} + fi +fi + +## expcorr: flag to determine whether to process expcorr +if [ ! -z "${expcorr}" ]; then + case "${expcorr}" in + [nN][oO]|[fF]*) + F_EXPCORR="NO" + ;; + *) + F_EXPCORR="YES" + ;; + esac +else + F_EXPCORR="YES" +fi +## parameters }}} + +if [ "${F_EXPCORR}" = "NO" ]; then + printf "################################\n" + printf "### SKIP EXPOSURE CORRECTION ###\n" + printf "################################\n\n" +else + printf "======== EXPOSURE CORRECTION =======\n" + CMD="${SCRIPT_DIR}/${EXPCORR_SCRIPT} evt=${EVT} basedir=${BASEDIR} nh=${N_H} z=${REDSHIFT} temp=${TEMP} abund=${ABUND}" + printf "CMD: ${CMD}\n" + ${SCRIPT_DIR}/${EXPCORR_SCRIPT} evt=${EVT} basedir=${BASEDIR} nh=${N_H} z=${REDSHIFT} temp=${TEMP} abund=${ABUND} + printf "======== EXPOSURE CORRECTION FINISHED =======\n\n" +fi + +EXPMAP=`ls expmap*e700-7000*fits 2> /dev/null` +EVT_E=`ls evt*e700-7000*fits 2> /dev/null` + +printf "======== EXTRACT SBP =======\n" +CMD="${SCRIPT_DIR}/${EXTRACT_SBP_SCRIPT} evt_e=${EVT_E} reg=${SBP_REG} expmap=${EXPMAP} cellreg=${CELL_REG}" +printf "CMD: ${CMD}\n" +${SCRIPT_DIR}/${EXTRACT_SBP_SCRIPT} evt_e=${EVT_E} reg=${SBP_REG} expmap=${EXPMAP} cellreg=${CELL_REG} +printf "======== EXTRACT SBP FINISHED =======\n\n" + +#generate a cfg file for specextract +[ -e "spc_fit.cfg" ] && mv -fv spc_fit.cfg spc_fit.cfg_bak +cat > spc_fit.cfg << _EOF_ +nh ${N_H} +z ${REDSHIFT} +basedir ../.. +bkgd ../${BKGD} +_EOF_ + +#link for sbp2.dat radius.dat sbp3.dat +ln -svf radius_sbp.txt radius.dat +ln -svf flux_sbp.txt sbp2.dat +ln -svf sbprofile.txt sbp3.dat + +exit 0 + |