Remove 'chandra_xcentroid.sh' (replaced by calc_centroid.py)

1 files changed, 0 insertions, 332 deletions

diff --git a/scripts/chandra_xcentroid.sh b/scripts/chandra_xcentroid.sh
deleted file mode 100755
index 856a863..0000000
--- a/scripts/chandra_xcentroid.sh
+++ /dev/null
@@ -1,332 +0,0 @@
-#!/bin/sh
-#
-###########################################################
-## get the coord of the X-ray centroid 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="v3.2"
-UPDATED="2017-02-06"
-##
-## ChangeLogs:
-## v3.2, 2017-02-06, Aaron LI
-##   * Generate skyfov if no previous skyfov found
-## v3.1, 2015-11-08, Aaron LI
-##   * Use previously generated skyfov instead to make a new one without asol
-## v3.0, 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'
-##   * Removed section of 'dmstat.par' deletion
-## v2.1, 2013/10/12, Weitian LI
-##   add support for extract center coordinates from 'point' and 'circle' regs
-## v2.0, 2013/01/22, Weitian LI
-##   aconvolve switch
-##   add iterations for better accuracy
-## 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 $0` evt=<evt_cl> reg=<reg> [ asol=<asol> chip=<chip> ] [ conv=yes|No ]\n"
-        printf "\nversion:\n"
-        printf "${VERSION}, ${UPDATED}\n"
-        exit ${ERR_USG}
-        ;;
-esac
-## usage, help }}}
-
-## check ciao init & solve confilt with heasoft {{{
-if [ -z "${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"
-
-## ciao & heasoft }}}
-
-## default parameters {{{
-# critical offset (in pixel)
-OFFSET_CRIC=10
-# energy range: 700-2000 eV
-E_RANGE="700:2000"
-# 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 2> /dev/null | head -n 1`"
-# default region file
-DFT_REG="`\ls sbprofile.reg rspec.reg 2> /dev/null | head -n 1`"
-# iteration step, ~150 arcsec, ~50 arcsec
-R_STP1=300
-R_STP2=100
-## 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 ${ERR_ASOL}
-    # fi
-    ASOL="NO"
-    printf "## asol file not supplied !\n"
-fi
-printf "## use asol file: \`${ASOL}'\n"
-
-# region file (optional)
-if [ -r "${reg}" ]; then
-    REG=${reg}
-elif [ -r "${DFT_REG}" ]; then
-    REG=${DFT_REG}
-else
-    read -p "region file: " REG
-    if [ ! -r "${REG}" ]; then
-        printf "ERROR: cannot access given \`${REG}' region file\n"
-        exit ${ERR_REG}
-    fi
-fi
-printf "## use reg file: \`${REG}'\n"
-# get centroid from the regionnn file
-CNTRD_X2=`\grep -iE '(point|circle|pie|annulus)' ${REG} | head -n 1 | tr -d 'a-zA-Z()' | awk -F',' '{ print $1 }'`
-CNTRD_Y2=`\grep -iE '(point|circle|pie|annulus)' ${REG} | head -n 1 | tr -d 'a-zA-Z()' | awk -F',' '{ print $2 }'`
-printf "## center from given regfile: (${CNTRD_X2},${CNTRD_Y2})\n"
-
-
-# convolve (optional)
-if [ -z "${conv}" ]; then
-    CONV="NO"
-else
-    case "${conv}" in
-        [yY]*)
-            CONV="YES"
-            printf "## apply \`aconvolve' !\n"
-            ;;
-        *)
-            CONV="NO"
-            ;;
-    esac
-fi
-
-# determine chip
-if [ ! -z "${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 aconvolve skyfov"
-
-# 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 {{{
-# Try to use previously generated `skyfov'
-SKYFOV=`\ls *skyfov*.fits 2>/dev/null | head -n 1`
-if [ -z "${SKYFOV}" ]; then
-    # Generate skyfov
-    SKYFOV="skyfov.fits"
-    punlearn skyfov
-    skyfov infile="${EVT}" outfile="${SKYFOV}" aspect="${ASOL}"
-    printf "Generated skyfov: ${SKYFOV}\n"
-else
-    printf "Use previously generated skyfov: ${SKYFOV}\n"
-fi
-
-# generate image
-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="${IMG}" clobber=yes
-
-# aconvolve
-if [ "${CONV}" = "YES" ]; then
-    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
-else
-    IMG_ACONV=${IMG}
-fi
-
-# tmp analysis region
-TMP_REG="_tmp_centroid.reg"
-[ -r "${TMP_REG}" ] && rm -f ${TMP_REG}
-echo "circle(${CNTRD_X2},${CNTRD_Y2},${R_STP1})" > ${TMP_REG}
-
-# dmstat to find the centroid
-printf "\`dmstat' to find the centroid ...\n"
-# step1
-printf "  region size ${R_STP1}pix: "
-for i in `seq 1 5`; do
-    printf "#$i ... "
-    punlearn dmstat
-    dmstat infile="${IMG_ACONV}[sky=region(${TMP_REG})]" centroid=yes verbose=0
-    CNTRD_X=`pget dmstat out_cntrd_phys | cut -d',' -f1`
-    CNTRD_Y=`pget dmstat out_cntrd_phys | cut -d',' -f2`
-    # printf "\n${CNTRD_X},${CNTRD_Y}\n"
-    echo "circle(${CNTRD_X},${CNTRD_Y},${R_STP1})" > ${TMP_REG}
-done
-printf " done\n"
-   echo "circle(${CNTRD_X},${CNTRD_Y},${R_STP2})" >${TMP_REG}
-# step2
-printf "  region size ${R_STP2}pix: "
-for i in `seq 1 5`; do
-    printf "#$i ... "
-    punlearn dmstat
-    dmstat infile="${IMG_ACONV}[sky=region(${TMP_REG})]" centroid=yes verbose=0
-    CNTRD_X=`pget dmstat out_cntrd_phys | cut -d',' -f1`
-    CNTRD_Y=`pget dmstat out_cntrd_phys | cut -d',' -f2`
-    # printf "\n${CNTRD_X},${CNTRD_Y}\n"
-    echo "circle(${CNTRD_X},${CNTRD_Y},${R_STP2})" > ${TMP_REG}
-done
-printf " done\n"
-
-# calc offset vs. given
-OFFSET=`echo "scale=5; sqrt((${CNTRD_X}-${CNTRD_X2})^2 + (${CNTRD_Y}-${CNTRD_Y2})^2)" | bc -l`
-
-# output
-CNTRD_PHY_REG="centroid_phy.reg"
-[ -e "${CNTRD_PHY_REG}" ] && mv -f ${CNTRD_PHY_REG} ${CNTRD_PHY_REG}_bak
-echo "point(${CNTRD_X},${CNTRD_Y})" > ${CNTRD_PHY_REG}
-
-# dmcoords to convert (x,y) to (ra,dec)
-if [ -r "${ASOL}" ]; then
-    printf "\`dmcoords' to convert (x,y) to (ra,dec) ...\n"
-    punlearn dmcoords
-    dmcoords infile="${EVT}" asolfile="${ASOL}" option=sky x=${CNTRD_X} y=${CNTRD_Y}
-    CNTRD_RA=`pget dmcoords ra`
-    CNTRD_DEC=`pget dmcoords dec`
-    CNTRD_WCS_REG="centroid_wcs.reg"
-    [ -e "${CNTRD_WCS_REG}" ] && mv -f ${CNTRD_WCS_REG} ${CNTRD_WCS_REG}_bak
-    echo "point(${CNTRD_RA},${CNTRD_DEC})" > ${CNTRD_WCS_REG}
-    ## from region
-    punlearn dmcoords
-    dmcoords infile="${EVT}" asolfile="${ASOL}" option=sky x=${CNTRD_X2} y=${CNTRD_Y2}
-    CNTRD_RA2=`pget dmcoords ra`
-    CNTRD_DEC2=`pget dmcoords dec`
-fi
-
-printf "\n"
-printf "++++++++++++++++++++++++++++++++++++++++++++\n"
-printf "X-ray centroid coordinates:\n"
-printf "via dmstat:\n"
-printf "  (X,Y):      (${CNTRD_X},${CNTRD_Y})\n"
-if [ -r "${ASOL}" ]; then
-    printf "  (RA,DEC):   (${CNTRD_RA},${CNTRD_DEC})\n"
-fi
-printf "via region:\n"
-printf "  (X2,Y2):    (${CNTRD_X2},${CNTRD_Y2})\n"
-if [ -r "${ASOL}" ]; then
-    printf "  (RA2,DEC2): (${CNTRD_RA2},${CNTRD_DEC2})\n"
-fi
-printf "offset (unit pixel):\n"
-printf "  offset:     ${OFFSET}\n"
-if [ `echo "${OFFSET} > ${OFFSET_CRIC}" | bc -l` -eq 1 ]; then
-    printf "*****************************\n"
-    printf "*** WARNING: large offset ***\n"
-fi
-printf "++++++++++++++++++++++++++++++++++++++++++++\n"
-## main }}}
-
-exit 0