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Diffstat (limited to 'scripts/chandra_update_xpeak2.sh')
| -rwxr-xr-x | scripts/chandra_update_xpeak2.sh | 311 |
1 files changed, 311 insertions, 0 deletions
diff --git a/scripts/chandra_update_xpeak2.sh b/scripts/chandra_update_xpeak2.sh new file mode 100755 index 0000000..d8cab0c --- /dev/null +++ b/scripts/chandra_update_xpeak2.sh @@ -0,0 +1,311 @@ +#!/bin/sh +# +unalias -a +export LC_COLLATE=C +## +## Take the `X-ray centroid' coordinate from region `sbprofile.reg' +## as the start location, then search for X-ray peak in a circle region +## of radius ${SEARCH_RADIUS} pixels centered on the X-ray centroid. +## After that the found X-ray peak is convert from physical coordinate to +## WCS coordinate and added/updated to the INFO json file. +## +## Note: The image on which the X-ray peak is to be searched is generated +## as following: +## (1) cleaned event file (c7, c0-3) +## (2) filter energy (${E_RANGE}) +## (3) smooth with aconvolve +## +## Based on `chandra_update_xpeak.sh' +## +## Weitian LI <liweitianux@gmail.com> +## Created: 2015-11-22 +## +VERSION="v1.0" +UPDATED="2015-11-20" +## +## ChangeLogs: +## + +## error code {{{ +ERR_USG=1 +ERR_DIR=11 +ERR_EVT=12 +ERR_BKG=13 +ERR_REG=14 +ERR_INFO=15 +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, help {{{ +case "$1" in + -[hH]*|--[hH]*) + printf "usage:\n" + printf " `basename $0` evt=<evt_file> reg=<sbp_reg> basedir=<base_dir> info=<INFO.json> conv=<YES|no> update=<YES|no>\n" + printf "\nversion:\n" + printf "${VERSION}, ${UPDATED}\n" + exit ${ERR_USG} + ;; +esac +## usage, help }}} + +## default parameters {{{ +# default circle radius within which to search the X-ray peak +SEARCH_RADIUS=100 +# critical offset (in pixel) +OFFSET_CRIC=20 + +# energy range: 700-2000 eV +E_RANGE="700:2000" +# default `event file' which used to match `blanksky' files +DFT_EVT="`\ls evt2*c7*_clean.fits evt2*c0-3*_clean.fits 2> /dev/null`" +# default dir which contains `asols, asol.lis, ...' files +DFT_BASEDIR=".." +# default `radial region file' to extract surface brightness +DFT_SBP_REG="`\ls sbprofile.reg rspec.reg 2> /dev/null | head -n 1`" + +## howto find files in `basedir' +# default `asol.lis pattern' +DFT_ASOLIS_PAT="acis*asol?.lis" +# default INFO.json pattern +DFT_INFO_PAT="*_INFO.json" + +# aconvolve parameters +ACONV_KERNELSPEC="lib:gaus(2,3,1,3,3)" +ACONV_METHOD="fft" +## 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}" +## check CIAO }}} + +## parameters {{{ +# process cmdline args using `getopt_keyval' +getopt_keyval "$@" + +# check given parameters +# check evt file +if [ -r "${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=${DFT_SBP_REG} +else + read -p "> surface brighness radial region file: " SBP_REG + if [ ! -r "${SBP_REG}" ]; then + printf "ERROR: cannot access given \`${SBP_REG}' region file\n" + exit ${ERR_REG} + fi +fi +printf "## use reg file(s): \`${SBP_REG}'\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" | ${TOLOG} +# check INFO.json file +if [ ! -z "${info}" ] && [ -r "${BASEDIR}/${info}" ]; then + INFO_JSON="${info}" +elif [ "`\ls ${BASEDIR}/${DFT_INFO_PAT} | wc -l`" -eq 1 ]; then + INFO_JSON=`( cd ${BASEDIR} && \ls ${DFT_INFO_PAT} )` +else + read -p "> info json file: " INFO_JSON + if ! [ -r "${BASEDIR}/${INFO_JSON}" ]; then + printf "ERROR: cannot access given \`${BASEDIR}/${INFO_JSON}' file\n" + exit ${ERR_INFO} + fi +fi +INFO_JSON=`readlink -f ${BASEDIR}/${INFO_JSON}` +printf "## use info json file: \`${INFO_JSON}'\n" +# update flag: whether to update xcentroid in the info.json file +if [ ! -z "${update}" ]; then + case "${update}" in + [nN][oO]|[fF]*) + F_UPDATE="NO" + ;; + *) + F_UPDATE="YES" + ;; + esac +else + F_UPDATE="YES" +fi + +# convolve (optional) +if [ -z "${conv}" ]; then + CONV="YES" +else + case "${conv}" in + [nN]*) + CONV="NO" + printf "## Do NOT apply \`aconvolve' !\n" + ;; + *) + CONV="YES" + printf "## apply \`aconvolve'\n" + ;; + esac +fi +## parameters }}} + +## prepare parameter files (pfiles) {{{ +CIAO_TOOLS="dmcopy dmstat aconvolve dmcoords" + +# 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 }}} + +## main process {{{ +# Use previously generated `skyfov' +SKYFOV=`\ls *skyfov*.fits 2>/dev/null | head -n 1` + +# Extract chip(s) from evt filename +CHIP=`echo "${EVT}" | sed 's/^.*_c\(7\|0-3\)_.*$/\1/' | tr '-' ':'` + +# generate image +IMG="img_c`echo ${CHIP} | tr ':' '-'`_e`echo ${E_RANGE} | tr ':' '-'`.fits" +if [ -r "${IMG}" ]; then + printf "use previously generated image: \`${IMG}'\n" +else + printf "generate image: \`${IMG}' ...\n" + punlearn dmcopy + dmcopy infile="${EVT_DEFLARE}[sky=region(${SKYFOV}[ccd_id=${CHIP}])][energy=${E_RANGE}][bin sky=::1]" outfile="${IMG}" clobber=yes +fi + +# aconvolve +if [ "${CONV}" = "YES" ]; then + IMG_ACONV="${IMG%.fits}_aconv.fits" + #if [ -r "${IMG_ACONV}" ]; then + # printf "use previously convolved image: \`${IMG_ACONV}'\n" + #else + printf "\`aconvolve' to smooth img: \`${IMG_ACONV}' ...\n" + printf "## aconvolve: kernelspec=\"${ACONV_KERNELSPEC}\" method=\"${ACONV_METHOD}\"\n" + punlearn aconvolve + aconvolve infile="${IMG}" outfile="${IMG_ACONV}" kernelspec="${ACONV_KERNELSPEC}" method="${ACONV_METHOD}" clobber=yes + #fi +else + IMG_ACONV=${IMG} +fi + +# Get X-ray centroid coordinate from sbp region +printf "get (x,y) from ${SBP_REG}\n" +CNTRD_X=`\grep -iE '(pie|annulus)' ${SBP_REG} | head -n 1 | awk -F',' '{ print $1 }' | tr -d 'a-zA-Z() '` +CNTRD_Y=`\grep -iE '(pie|annulus)' ${SBP_REG} | head -n 1 | awk -F',' '{ print $2 }' | tr -d 'a-zA-Z() '` + +SEARCH_REGION="circle(${CNTRD_X},${CNTRD_Y},${SEARCH_RADIUS})" +# dmstat to find the maximum location +printf "\`dmstat' to find the peak ...\n" +punlearn dmstat +dmstat infile="${IMG_ACONV}[sky=${SEARCH_REGION}]" verbose=0 +PEAK_X=`pget dmstat out_max_loc | cut -d',' -f1` +PEAK_Y=`pget dmstat out_max_loc | cut -d',' -f2` + +# asolis +ASOLIS=`( cd ${BASEDIR} && \ls ${DFT_ASOLIS_PAT} 2> /dev/null )` + +# Use "dmcoords" to convert (x,y) to (ra,dec) +printf "\`dmcoords' to convert (x,y) to (ra,dec) ...\n" +punlearn dmcoords +dmcoords infile="${EVT}" asolfile="@${BASEDIR}/${ASOLIS}" option=sky x=${PEAK_X} y=${PEAK_Y} +PEAK_RA=`pget dmcoords ra` +PEAK_DEC=`pget dmcoords dec` + +# Calculate the offset between peak and centroid coordinate +OFFSET=`echo "scale=5; sqrt((${PEAK_X}-${CNTRD_X})^2 + (${PEAK_Y}-${CNTRD_Y})^2)" | bc -l` + +printf "## X-ray centroid (x,y): (${CNTRD_X},${CNTRD_Y})\n" +printf "## X-ray peak (x,y): (${PEAK_X},${PEAK_Y})\n" +printf "## X-ray peak (ra,dec): (${PEAK_RA},${PEAK_DEC})\n" +printf "## Offset (pixel): ${OFFSET}\n" +if [ `echo "${OFFSET} > ${OFFSET_CRIC}" | bc -l` -eq 1 ]; then + printf "*** WARNING: large offset (> ${OFFSET_CRIC}) ***\n" +fi + +# Output X-ray peak coordinate to a region file +PEAK_PHY_REG="peak2_phy.reg" +[ -e "${PEAK_PHY_REG}" ] && mv -f ${PEAK_PHY_REG} ${PEAK_PHY_REG}_bak +echo "point(${PEAK_X},${PEAK_Y})" > ${PEAK_PHY_REG} +PEAK_WCS_REG="peak2_wcs.reg" +[ -e "${PEAK_WCS_REG}" ] && mv -f ${PEAK_WCS_REG} ${PEAK_WCS_REG}_bak +echo "point(${PEAK_RA},${PEAK_DEC})" > ${PEAK_WCS_REG} + +if [ "${F_UPDATE}" = "YES" ]; then + cp -f ${INFO_JSON} ${INFO_JSON}_bak + printf "update/add X-ray peak coordinate to info.json ...\n" + if \grep -qE 'XPEAK2_(RA|DEC)' ${INFO_JSON}; then + printf "update ...\n" + sed -i'' "s/XPEAK2_RA.*$/XPEAK2_RA\":\ \"${PEAK_RA}\",/" ${INFO_JSON} + sed -i'' "s/XPEAK2_DEC.*$/XPEAK2_DEC\":\ \"${PEAK_DEC}\",/" ${INFO_JSON} + sed -i'' "s/XPEAK2_XCNTRD_dist.*$/XPEAK2_XCNTRD_dist\ (pix)\":\ \"${OFFSET}\",/" ${INFO_JSON} + else + printf "add ...\n" + sed -i'' "/\"Dec\.\"/ a\ +\ \ \ \ \"XPEAK2_XCNTRD_dist\ (pix)\": \"${OFFSET}\"," ${INFO_JSON} + sed -i'' "/\"Dec\.\"/ a\ +\ \ \ \ \"XPEAK2_DEC\": \"${PEAK_DEC}\"," ${INFO_JSON} + sed -i'' "/\"Dec\.\"/ a\ +\ \ \ \ \"XPEAK2_RA\": \"${PEAK_RA}\"," ${INFO_JSON} + fi +fi +## main }}} + +exit 0 + |