Remove chandra_update_xpeak2.sh

1 files changed, 0 insertions, 311 deletions

diff --git a/scripts/chandra_update_xpeak2.sh b/scripts/chandra_update_xpeak2.sh
deleted file mode 100755
index 6ab6d8c..0000000
--- a/scripts/chandra_update_xpeak2.sh
+++ /dev/null
@@ -1,311 +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 ${SEARCH_RADIUS} pixels centered on the X-ray centroid.
-## After that the found X-ray peak is convert from physical coordinate to
-## WCS coordinate and added/updated to the INFO json file.
-##
-## Note: The image on which the X-ray peak is to be searched is generated
-## as following:
-##     (1) cleaned event file (c7, c0-3)
-##     (2) filter energy (${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="${EVT}[sky=region(${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
-