Remove 'scripts/ciao_expcorr.sh'

Replaced by 'calc_spectral_weights.py' and 'make_expmap.py'

1 files changed, 0 insertions, 414 deletions

diff --git a/scripts/ciao_expcorr.sh b/scripts/ciao_expcorr.sh
deleted file mode 100755
index 3215056..0000000
--- a/scripts/ciao_expcorr.sh
+++ /dev/null
@@ -1,414 +0,0 @@
-#!/bin/sh
-##
-## This script performs exposure correction to images, and
-## finally produce the exposure-corrected image.
-##
-## * make `image' from `evt file'
-## * make `spectral weight' using `make_instmap_weights'
-## * use `fluximage' to generating `exposure map'
-## * make `exposure-corrected' image
-## * and extract `surface brighness profile'
-##
-## NOTES:
-## only ACIS-I (chip: 0-3) and ACIS-S (chip: 7) supported
-## `merge_all' conflict with Heasoft's `pget' etc. tools
-##
-## Weitian LI
-## 2012/08/16
-##
-VERSION="v3.0"
-UPDATED="2015/06/03"
-##
-## ChangeLogs:
-## v3.1, 2015/06/04, Aaron LI
-##   * Added check for 'fluximage' parameter 'xygrid' before to use.
-##     'fluximage' of version before '15Oct2012' does not have parameter
-##     'xygrid' and dose not support spectral weights with parameter 'bands'.
-## v3.0, 2015/06/03, Aaron LI
-##   * Changed to use 'fluximage' by default, and fallback to 'merge_all'
-##   * Copy needed pfiles to current working directory, and
-##     set environment variable $PFILES to use these first.
-##   * Replaced 'grep' with '\grep', 'ls' with '\ls'
-## v2.1, 2014/10/30, Weitian LI
-##   Add 'aspect' parameter for 'skyfov' to fix the 'FoV shift bug'
-## v2.0, 2014/07/29, Weitian LI
-##   `merge_all' deprecated, use `fluximage' if possible
-## v1.2, 2012/08/21, Weitian LI
-##   set `ardlib' before process `merge_all'
-## v1.1, 2012/08/21, Weitian LI
-##   fix a bug with `sed'
-##
-
-unalias -a
-export LC_COLLATE=C
-
-## 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
-ERR_ENG=42
-ERR_CIAO=100
-ERR_TOOL=110
-## error code }}}
-
-## usage, help {{{
-case "$1" in
-    -[hH]*|--[hH]*)
-        printf "usage:\n"
-        printf "    `basename $0` evt=<evt_file> energy=<e_start:e_end:e_width> basedir=<base_dir> nh=<nH> z=<redshift> temp=<avg_temperature> abund=<avg_abund> [ logfile=<log_file> ]\n"
-        printf "\nversion:\n"
-        printf "    ${VERSION}, ${UPDATED}\n"
-        exit ${ERR_USG}
-        ;;
-esac
-## usage, help }}}
-
-## default parameters {{{
-# default `event file' which used to match `blanksky' files
-#DFT_EVT="_NOT_EXIST_"
-DFT_EVT="`\ls evt2*_clean.fits 2> /dev/null`"
-# default dir which contains `asols, asol.lis, ...' files
-# DFT_BASEDIR="_NOT_EXIST_"
-DFT_BASEDIR=".."
-# default `radial region file' to extract surface brightness
-DFT_SBP_REG="_NOT_EXIST_"
-#DFT_SBP_REG="sbprofile.reg"
-# default `energy band' applying to `images' analysis
-# format: `E_START:E_END:E_WIDTH'
-DFT_ENERGY="700:7000:100"
-
-# default `log file'
-DFT_LOGFILE="expcorr_sbp_`date '+%Y%m%d'`.log"
-
-## howto find files in `basedir'
-# default `asol.lis pattern'
-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 {{{
-# 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}"
-printf "## PATH: ${PATH}\n"
-## check CIAO }}}
-
-## parameters {{{
-# process cmdline args using `getopt_keyval'
-getopt_keyval "$@"
-
-## check log parameters {{{
-if [ ! -z "${log}" ]; then
-    LOGFILE="${log}"
-else
-    LOGFILE=${DFT_LOGFILE}
-fi
-printf "## use logfile: \`${LOGFILE}'\n"
-[ -e "${LOGFILE}" ] && mv -fv ${LOGFILE} ${LOGFILE}_bak
-TOLOG="tee -a ${LOGFILE}"
-echo "process script: `basename $0`" >> ${LOGFILE}
-echo "process date: `date`" >> ${LOGFILE}
-## log }}}
-
-# check given parameters
-# check evt file
-if [ -r "${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=${DFT_SBP_REG}
-fi
-printf "## use reg file(s): \`${SBP_REG}'\n" | ${TOLOG}
-## check given `energy' {{{
-if [ ! -z "${energy}" ]; then
-    ENERGY="${energy}"
-else
-    ENERGY="${DFT_ENERGY}"
-fi
-# split energy variable
-ENG_N=`echo ${ENERGY} | awk -F':' '{ print NF }'`
-if [ ${ENG_N} -eq 1 ]; then
-    E_START=`echo ${DFT_ENERGY} | awk -F':' '{ print $1 }'`
-    E_END=`echo ${DFT_ENERGY} | awk -F':' '{ print $2 }'`
-    E_WIDTH=${ENERGY}
-elif [ ${ENG_N} -eq 2 ]; then
-    E_START=`echo ${ENERGY} | awk -F':' '{ print $1 }'`
-    E_END=`echo ${ENERGY} | awk -F':' '{ print $2 }'`
-    E_WIDTH=`echo ${DFT_ENERGY} | awk -F':' '{ print $3 }'`
-elif [ ${ENG_N} -eq 3 ]; then
-    E_START=`echo ${ENERGY} | awk -F':' '{ print $1 }'`
-    E_END=`echo ${ENERGY} | awk -F':' '{ print $2 }'`
-    E_WIDTH=`echo ${ENERGY} | awk -F':' '{ print $3 }'`
-else
-    printf "ERROR: invalid energy: \`${ENERGY}'\n"
-    exit ${ERR_ENG}
-fi
-ENG_RANGE="${E_START}:${E_END}"
-printf "## use energy range: \`${ENG_RANGE}' eV\n" | ${TOLOG}
-printf "## use energy width: \`${E_WIDTH}' eV\n" | ${TOLOG}
-## parse energy }}}
-# parameters (nH, z, avg_temp, avg_abund) used to calculate {{{
-# `spectral weights' for `mkinstmap'
-# check given nH
-if [ -z "${nh}" ]; then
-    read -p "> value of nH: " N_H
-else
-    N_H=${nh}
-fi
-printf "## use nH: ${N_H}\n" | ${TOLOG}
-# check given redshift
-if [ -z "${z}" ]; then
-    read -p "> value of redshift: " REDSHIFT
-else
-    REDSHIFT=${z}
-fi
-printf "## use redshift: ${REDSHIFT}\n" | ${TOLOG}
-# check given temperature
-if [ -z "${temp}" ]; then
-    read -p "> object average temperature: " TEMP
-else
-    TEMP=${temp}
-fi
-printf "## use temperature: ${TEMP}\n" | ${TOLOG}
-# check given abundance
-if [ -z "${abund}" ]; then
-    read -p "> object average abundance: " ABUND
-else
-    ABUND=${abund}
-fi
-printf "## use abundance: ${ABUND}\n" | ${TOLOG}
-# `spectral weights' parameters }}}
-# check given dir
-if [ -d "${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}
-## parameters }}}
-
-## prepare parameter files (pfiles) {{{
-CIAO_TOOLS="dmkeypar dmcopy dmhedit dmimgcalc ardlib make_instmap_weights skyfov get_sky_limits fluximage merge_all"
-
-# 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 }}}
-
-## check files in `basedir' {{{
-# check asol files
-ASOLIS=`\ls -1 ${BASEDIR}/${DFT_ASOLIS_PAT} | head -n 1`
-if [ -z "${ASOLIS}" ]; then
-    printf "ERROR: cannot find \"${DFT_ASOLIS_PAT}\" in dir \`${BASEDIR}'\n"
-    exit ${ERR_ASOL}
-fi
-printf "## use asolis: \`${ASOLIS}'\n"
-# check badpixel file
-BPIX=`\ls -1 ${BASEDIR}/${DFT_BPIX_PAT} | head -n 1`
-if [ -z "${BPIX}" ]; then
-    printf "ERROR: cannot find \"${DFT_BPIX_PAT}\" in dir \`${BASEDIR}'\n"
-    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 {{{
-# consistent with `ciao_procevt'
-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"
-    CCD="0:3"
-    NEW_DETNAM="ACIS-0123"
-    ROOTNAME="c0-3_e${E_START}-${E_END}"
-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"
-    CCD="7"
-    NEW_DETNAM="ACIS-7"
-    ROOTNAME="c7_e${E_START}-${E_END}"
-else
-    printf "ERROR: unknown detector type: ${DETNAM}\n"
-    exit ${ERR_DET}
-fi
-## ACIS type }}}
-
-## main process {{{
-## set `ardlib' at first
-printf "set \`ardlib' first ...\n"
-punlearn ardlib
-acis_set_ardlib badpixfile="${BPIX}"
-
-## generate `spectral weights' for `instrumental map' {{{
-printf "generate \`spectral weights' for making instrumental map ...\n"
-SPEC_WGT="instmap_weights.txt"
-# convert `eV' to `keV'
-EMIN=`echo ${E_START} | awk '{ print $1/1000 }'`
-EMAX=`echo ${E_END} | awk '{ print $1/1000 }'`
-EWIDTH=`echo ${E_WIDTH} | awk '{ print $1/1000 }'`
-punlearn make_instmap_weights
-make_instmap_weights outfile="${SPEC_WGT}" \
-    model="xswabs.gal*xsapec.ap" \
-    paramvals="gal.nh=${N_H};ap.kt=${TEMP};ap.abundanc=${ABUND};ap.redshift=${REDSHIFT}" \
-    emin="${EMIN}" emax="${EMAX}" ewidth="${EWIDTH}" \
-    abund="grsa" clobber=yes
-## spectral weights }}}
-
-## generate `skyfov'
-printf "generate skyfov ...\n"
-SKYFOV="skyfov.fits"
-punlearn skyfov
-skyfov infile="${EVT}" outfile="${SKYFOV}" aspect="@${ASOLIS}" clobber=yes
-
-## filter by energy band & make image
-printf "filter out events in energy band: \`${ENG_RANGE}' ...\n"
-EVT_E="evt2_${ROOTNAME}.fits"
-if [ ! -r "${EVT_E}" ]; then
-    punlearn dmcopy
-    dmcopy infile="${EVT}[energy=${E_START}:${E_END}]" outfile="${EVT_E}" clobber=yes
-fi
-
-printf "make image ...\n"
-IMG_ORIG="img_${ROOTNAME}.fits"
-punlearn dmcopy
-dmcopy infile="${EVT_E}[sky=region(${SKYFOV}[ccd_id=${CCD}])][bin sky=1]" \
-    outfile="${IMG_ORIG}" clobber=yes
-
-## modify `DETNAM' of image
-printf "modify keyword \`DETNAM' of image -> \`${NEW_DETNAM}'\n"
-punlearn dmhedit
-dmhedit infile="${IMG_ORIG}" filelist=none operation=add \
-    key=DETNAM value="${NEW_DETNAM}"
-
-## get `xygrid' for image
-punlearn get_sky_limits
-get_sky_limits image="${IMG_ORIG}"
-XYGRID=`pget get_sky_limits xygrid`
-printf "## get \`xygrid': \`${XYGRID}'\n" | ${TOLOG}
-
-EXPMAP="expmap_${ROOTNAME}.fits"
-IMG_EXPCORR="img_expcorr_${ROOTNAME}.fits"
-
-# Check whether fluximage is capable to make exposure correction for us
-# version after '15Oct2012' supports 'xygrid' and spectral weights file.
-if `pget fluximage xygrid >/dev/null 2>&1`; then
-    USE_FLUXIMAGE="YES"
-else
-    # 'fluximage' do not support 'xygrid' parameter and spectral weights.
-    # fallback to use 'merge_all'
-    USE_FLUXIMAGE="NO"
-fi
-
-if [ "${USE_FLUXIMAGE}" = "YES" ]; then
-    ## 'fluximage' is available, use it by default
-    ## use 'fluximage' to generate `exposure map' and apply exposure correction
-    printf "use fluximage to generate expmap and apply correction ...\n"
-    punlearn fluximage
-    fluximage infile="${EVT_E}" outroot="${ROOTNAME}" \
-        binsize=1 bands="${SPEC_WGT}" xygrid="${XYGRID}" \
-        asol="@${ASOLIS}" badpixfile="${BPIX}" \
-        maskfile="${MSK}" clobber=yes
-    ## make symbolic links
-    # clipped counts image
-    ln -svf ${ROOTNAME}*band*thresh.img ${IMG_ORIG%.fits}_thresh.fits
-    # clipped exposure map
-    ln -svf ${ROOTNAME}*band*thresh.expmap ${EXPMAP}
-    # exposure-corrected image
-    ln -svf ${ROOTNAME}*band*flux.img ${IMG_EXPCORR}
-else
-    # 'merge_all' is available, fallback to this
-    printf "fallback to merge_all ...\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
-        asol=`basename ${f}`
-        ln -svf ${BASEDIR}/${asol} .
-    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
-fi
-
-## main }}}
-
-exit 0
-