diff options
| -rwxr-xr-x | scripts/chandra_update_xpeak.sh | 334 | ||||
| -rwxr-xr-x | scripts/chandra_xpeak_coord.sh | 236 |
2 files changed, 0 insertions, 570 deletions
diff --git a/scripts/chandra_update_xpeak.sh b/scripts/chandra_update_xpeak.sh deleted file mode 100755 index 080c4a9..0000000 --- a/scripts/chandra_update_xpeak.sh +++ /dev/null @@ -1,334 +0,0 @@ -#!/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 ${SEARCH_RADIUS} pixels centered on the X-ray centroid. -## After that the found X-ray peak is convert from physical coordinate to -## WCS coordinate and added/updated to the INFO json file. -## -## Note: The image on which the X-ray peak is to be searched is generated -## as following: -## (1) original event file (c7, c0-3) -## (2) filter flares (deflare) -## (3) filter energy (${E_RANGE}) -## (4) smooth with aconvolve -## -## Based on `chandra_update_xcentroid.sh' -## -## Weitian LI <liweitianux@gmail.com> -## Created: 2015-11-08 -## -VERSION="v1.3" -UPDATED="2015-11-22" -## -## ChangeLogs: -## 2015-11-08: -## * Also add offset to info json -## * Default to use aconvolve -## * Change Gaussian kernel from gaus(2,5,1,10,10) to gaus(2,3,1,3,3) -## 2015-11-20: -## * Re-arrange default parameters -## * Use previously generated image -## - -## 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 {{{ -CUR_DIR=`pwd -P` - -# Generate the defalred event file (without filtering out the point sources) -EVT_DIR=$(dirname $(readlink ${EVT})) -cd ${EVT_DIR} -EVT_ORIG="`\ls evt*c7*_orig.fits evt2*c0-3*_orig.fits 2>/dev/null`" -GTI="`\ls *bkg*.gti | head -n 1`" -printf "make a deflared evt (without filtering out point sources) ...\n" -EVT_DEFLARE="${EVT_ORIG%_orig.fits}_deflare.fits" -punlearn dmcopy -dmcopy infile="${EVT_ORIG}[@${GTI}]" outfile="${EVT_DEFLARE}" clobber=yes - -cd ${CUR_DIR} -ln -svf ${EVT_DIR}/${EVT_DEFLARE} . - -# 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 ${E_RANGE} | tr ':' '-'`_deflare.fits" -if [ -r "${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 (> ${OFFSET_CRIC}) ***\n" -fi - -# Output X-ray peak coordinate to a region file -PEAK_PHY_REG="peak_phy.reg" -[ -e "${PEAK_PHY_REG}" ] && mv -f ${PEAK_PHY_REG} ${PEAK_PHY_REG}_bak -echo "point(${PEAK_X},${PEAK_Y})" > ${PEAK_PHY_REG} -PEAK_WCS_REG="peak_wcs.reg" -[ -e "${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 'XPEAK_(RA|DEC)' ${INFO_JSON}; then - printf "update ...\n" - sed -i'' "s/XPEAK_RA.*$/XPEAK_RA\":\ \"${PEAK_RA}\",/" ${INFO_JSON} - sed -i'' "s/XPEAK_DEC.*$/XPEAK_DEC\":\ \"${PEAK_DEC}\",/" ${INFO_JSON} - sed -i'' "s/XPEAK_XCNTRD_dist.*$/XPEAK_XCNTRD_dist\ (pix)\":\ \"${OFFSET}\",/" ${INFO_JSON} - else - printf "add ...\n" - sed -i'' "/\"Dec\.\"/ a\ -\ \ \ \ \"XPEAK_XCNTRD_dist\ (pix)\": \"${OFFSET}\"," ${INFO_JSON} - sed -i'' "/\"Dec\.\"/ a\ -\ \ \ \ \"XPEAK_DEC\": \"${PEAK_DEC}\"," ${INFO_JSON} - sed -i'' "/\"Dec\.\"/ a\ -\ \ \ \ \"XPEAK_RA\": \"${PEAK_RA}\"," ${INFO_JSON} - fi -fi -## main }}} - -exit 0 - diff --git a/scripts/chandra_xpeak_coord.sh b/scripts/chandra_xpeak_coord.sh deleted file mode 100755 index beb2698..0000000 --- a/scripts/chandra_xpeak_coord.sh +++ /dev/null @@ -1,236 +0,0 @@ -#!/bin/sh -# -########################################################### -## get the coord of the X-ray peak in given evt file ## -## 1) given `evt_clean' file ## -## 2) `aconvolve' and then `dmstat' ## -## 3) `dmcoords' convert `sky x, y' to `ra, dec' ## -## ## -## NOTES: ## -## support ACIS-I(chip: 0-3) and ACIS-S(chip: 7) ## -## determine by check `DETNAM' for chip number ## -## if `DETNAM' has `0123', then `ACIS-I' ## -## if `DETNAM' has `7', then `ACIS-S' ## -## ## -## Weitian LI <liweitianux@gmail.com> ## -## 2012/11/08 ## -########################################################### -## -VERSION="v2.0" -UPDATED="2015/06/03" -## -## ChangeLogs: -## v2.0, 2015/06/03, Aaron LI -## * Copy needed pfiles to current working directory, and -## set environment variable $PFILES to use these first. -## * Replace 'grep' with '\grep', 'ls' with '\ls' -## v1.1, 2012/11/08, Weitian LI -## get x-ray peak coord from given region file -## - -## 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 -## error code }}} - -## usage, help {{{ -case "$1" in - -[hH]*|--[hH]*) - printf "usage:\n" - printf " `basename $0` evt=<evt_cl> asol=<asol> [ reg=<reg> chip=<chip> ]\n" - printf "\nversion:\n" - printf "${VERSION}, ${UPDATED}\n" - exit ${ERR_USG} - ;; -esac -## usage, help }}} - -## default parameters {{{ -# default `evt clean file' -DFT_EVT="`\ls evt*clean.fits *clean*evt*.fits 2> /dev/null | head -n 1`" -# default `asol file' -DFT_ASOL="`\ls ../pcadf*_asol1.fits pcadf*_asol1.fits 2> /dev/null | head -n 1`" -# default region file -DFT_REG="`\ls sbprofile.reg rspec.reg 2> /dev/null | head -n 1`" -## 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 ${keyval} - shift # shift, process next one - done -} -## functions }}} - -## parameters {{{ -# process cmdline args using `getopt_keyval' -getopt_keyval "$@" - -## check given parameters -# check evt file -if [ -r "${evt}" ]; then - EVT=${evt} -elif [ -r "${DFT_EVT}" ]; then - EVT=${DFT_EVT} -else - read -p "evt clean 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" - -# asol -if [ ! -z "${asol}" ]; then - ASOL=${asol} -elif [ -r "${DFT_ASOL}" ]; then - ASOL=${DFT_ASOL} -else - read -p "asol file: " ASOL - if ! [ -r "${ASOL}" ]; then - printf "ERROR: cannot access given \`${ASOL}' asol file\n" - exit ${ERR_ASOL} - fi -fi -printf "## use asol file: \`${ASOL}'\n" - -# region file (optional) -if [ ! -z "${reg}" ]; then - REG=${reg} -else - REG=${DFT_REG} -fi -printf "## use reg file: \`${REG}'\n" - -# determine chip -if [ ! -z "${chip}" ]; then - CHIP="${chip}" - printf "## use chip: \`${CHIP}'\n" -else - # determine chip by ACIS type - 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" - CHIP="0:3" - 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" - CHIP="7" - else - printf "ERROR: unknown detector type: ${DETNAM}\n" - exit ${ERR_DET} - fi -fi -## parameters }}} - -## prepare parameter files (pfiles) {{{ -CIAO_TOOLS="dmkeypar dmcopy dmstat dmcoords skyfov aconvolve" - -# 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 part {{{ -# generate `skyfov' -SKYFOV="_skyfov.fits" -printf "generate skyfov: \`${SKYFOV}' ...\n" -punlearn skyfov -skyfov infile="${EVT}" outfile="${SKYFOV}" clobber=yes - -# generate image -# energy range: 500-7000 eV -E_RANGE="500:7000" -IMG="img_c`echo ${CHIP} | tr ':' '-'`_e`echo ${E_RANGE} | tr ':' '-'`.fits" -printf "generate image: \`${IMG}' ...\n" -punlearn dmcopy -dmcopy infile="${EVT}[sky=region(${SKYFOV}[ccd_id=${CHIP}])][energy=${E_RANGE}][bin sky=::1]" outfile="${IMG}" clobber=yes - -# aconvolve -IMG_ACONV="${IMG%.fits}_aconv.fits" -KERNELSPEC="lib:gaus(2,5,1,10,10)" -METHOD="fft" -printf "\`aconvolve' to smooth img: \`${IMG_ACONV}' ...\n" -printf "## aconvolve: kernelspec=\"${KERNELSPEC}\" method=\"${METHOD}\"\n" -punlearn aconvolve -aconvolve infile="${IMG}" outfile="${IMG_ACONV}" kernelspec="${KERNELSPEC}" method="${METHOD}" clobber=yes - -# dmstat -printf "\`dmstat' to analyze the img ...\n" -punlearn dmstat -dmstat infile="${IMG_ACONV}" -MAX_X=`pget dmstat out_max_loc | cut -d',' -f1` -MAX_Y=`pget dmstat out_max_loc | cut -d',' -f2` -# dmcoords to convert (x,y) to (ra,dec) -printf "\`dmcoords' to convert (x,y) to (ra,dec) ...\n" -punlearn dmcoords -dmcoords infile="${EVT}" asolfile="${ASOL}" option=sky x=${MAX_X} y=${MAX_Y} -MAX_RA=`pget dmcoords ra` -MAX_DEC=`pget dmcoords dec` - -# output results -PHY_REG="peak_phy.reg" -WCS_REG="peak_wcs.reg" -[ -e "${PHY_REG}" ] && mv -f ${PHY_REG} ${PHY_REG}_bak -[ -e "${WCS_REG}" ] && mv -f ${WCS_REG} ${WCS_REG}_bak -echo "point(${MAX_X},${MAX_Y})" > ${PHY_REG} -echo "point(${MAX_RA},${MAX_DEC})" > ${WCS_REG} - -printf "\n" -printf "++++++++++++++++++++++++++++++++++++++++++++\n" -printf "X-ray peak coordinates:\n" -printf "via dmstat:\n" -printf " (X,Y): (${MAX_X},${MAX_Y})\n" -printf " (RA,DEC): (${MAX_RA},${MAX_DEC})\n" - -## region file based {{{ -if [ -r "${REG}" ]; then - MAX_X2=`\grep -iE '(pie|annulus)' ${REG} | head -n 1 | tr -d 'a-zA-Z()' | awk -F',' '{ print $1 }'` - MAX_Y2=`\grep -iE '(pie|annulus)' ${REG} | head -n 1 | tr -d 'a-zA-Z()' | awk -F',' '{ print $2 }'` - punlearn dmcoords - dmcoords infile="${EVT}" asolfile="${ASOL}" option=sky x=${MAX_X2} y=${MAX_Y2} - MAX_RA2=`pget dmcoords ra` - MAX_DEC2=`pget dmcoords dec` - # calc offset - OFFSET=`echo "scale=5; sqrt((${MAX_X}-${MAX_X2})^2 + (${MAX_Y}-${MAX_Y2})^2)" | bc -l` - - printf "via region:\n" - printf " (X2,Y2): (${MAX_X2},${MAX_Y2})\n" - printf " (RA2,DEC2): (${MAX_RA2},${MAX_DEC2})\n" - printf "offset (unit pixel):\n" - printf " offset: ${OFFSET}\n" -fi -## region file }}} -printf "++++++++++++++++++++++++++++++++++++++++++++\n" -## main }}} - -exit 0 - |