fix to 'ciao_expcorr.sh' & removed versions in filenames

1 files changed, 539 insertions, 0 deletions

diff --git a/scripts/ciao_r500avgt.sh b/scripts/ciao_r500avgt.sh
new file mode 100755
index 0000000..9a8dffd
--- /dev/null
+++ b/scripts/ciao_r500avgt.sh
@@ -0,0 +1,539 @@
+#!/bin/sh
+#
+unalias -a
+export LC_COLLATE=C
+###########################################################
+## script to extract spectrum and prepare needed files   ##
+## for calculating the `average temperature'             ##
+## within (0.1-0.5 r500) region                          ##
+##                                                       ##
+## NOTE:                                                 ##
+## 1) r500 default in unit `pixel', if in `kpc',         ##
+## then `redshift z' and `calculator' are needed.        ##
+## 2) `background process' is same as `deproj_spectra'   ##
+## which supports `spectrum', `local' and `blanksky'     ##
+## 3) ARF/RMF files either provided or use the ARF/RMF   ##
+## of the outmost region                                 ##
+##                                                       ##
+## LIweitiaNux <liweitianux@gmail.com>                   ##
+## August 22, 2012                                       ##
+###########################################################
+
+###########################################################
+## ChangeLogs
+## v1.1, 2012/08/26, LIweitiaNux
+##   modify `KPC_PER_PIX', able to use the newest version `calc_distance'
+## v1.2, 2012/08/26, LIweitiaNux
+##   fix a bug with `DFT_BKGD'
+## v2.0, 2012/09/04, LIweitiaNux
+##   add parameter `inner' and `outer' to adjust the region range
+##   modify parameter `r500' to take `kpc' as the default unit
+## v2.1, 2012/10/05, LIweitiaNux
+##   change `DFT_GRP_CMD' to `group 1 128 4 ...'
+## v3.0, 2013/02/09, LIweitiaNux
+##   modify for new process
+###########################################################
+
+## about, used in `usage' {{{
+VERSION="v3.0"
+UPDATE="2013-02-09"
+## about }}}
+
+## error code {{{
+ERR_USG=1
+ERR_DIR=11
+ERR_EVT=12
+ERR_BKG=13
+ERR_REG=14
+ERR_JSON=15
+ERR_ASOL=21
+ERR_BPIX=22
+ERR_PBK=23
+ERR_MSK=24
+ERR_BKGTY=31
+ERR_SPEC=32
+ERR_ARF=51
+ERR_RMF=52
+ERR_UNI=61
+## error code }}}
+
+## usage, help {{{
+case "$1" in
+    -[hH]*|--[hH]*)
+        printf "usage:\n"
+        printf "    `basename $0` evt=<evt2_clean> r500=<r500_kpc> basedir=<basedir> info=<info_json> inner=<inner_val> outer=<outer_val> regin=<input_reg> regout=<output_reg> bkgd=<blank_evt|lbkg_reg|bkg_spec> nh=<nH> z=<redshift> arf=<warf_file> rmf=<wrmf_file> [ grpcmd=<grppha_cmd> log=<log_file> ]\n"
+        printf "\nversion:\n"
+        printf "${VERSION}, ${UPDATE}\n"
+        exit ${ERR_USG}
+        ;;
+esac
+## usage, help }}}
+
+## comology calculator {{{
+## XXX: MODIFY THIS TO YOUR OWN CASE
+## and make sure this `calc' is executable
+## NOTES: use `$HOME' instead of `~' in path
+COSCALC="`which cosmo_calc calc_distance 2>/dev/null | head -n 1`"
+# COSCALC="_path_to_calc_distance_"
+# COSCALC="$HOME/bin/mass/calc_distance"
+if [ -z "${COSCALC}" ] || [ ! -x ${COSCALC} ]; then
+    printf "ERROR: \`COSCALC: ${COSCALC}' neither specified nor executable\n"
+    exit 255
+fi
+## }}}
+
+## 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 `bkgd', use `bkgcorr_blanksky*' corrected bkg spectrum
+DFT_BKGD="`ls bkgcorr_blanksky_*.pi 2> /dev/null`"
+# default basedir
+DFT_BASEDIR="../.."
+# default `radial region file'
+#DFT_REG_IN="_NOT_EXIST_"
+DFT_REG_IN="rspec.reg"
+# default region range (0.1-0.5 R500)
+DFT_INNER="0.1"
+DFT_OUTER="0.5"
+# default ARF/RMF, the one of the outmost region
+DFT_ARF="`ls -1 r?_*.warf 2> /dev/null | tail -n 1`"
+DFT_RMF="`ls -1 r?_*.wrmf 2> /dev/null | tail -n 1`"
+
+# default `group command' for `grppha'
+DFT_GRP_CMD="group min 25"
+#DFT_GRP_CMD="group 1 128 2 129 256 4 257 512 8 513 1024 16"
+#DFT_GRP_CMD="group 1 128 4 129 256 8 257 512 16 513 1024 32"
+# default `log file'
+DFT_LOGFILE="r500avgt_`date '+%Y%m%d%H'`.log"
+
+# default JSON pattern
+DFT_JSON_PAT="*_INFO.json"
+## 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
+}
+
+## background renormalization (BACKSCAL) {{{
+# renorm background according to particle background
+# energy range: 9.5-12.0 keV (channel: 651-822)
+CH_LOW=651
+CH_HI=822
+pb_flux() {
+    punlearn dmstat
+    COUNTS=`dmstat "$1[channel=${CH_LOW}:${CH_HI}][cols COUNTS]" | grep -i 'sum:' | awk '{ print $2 }'`
+    punlearn dmkeypar
+    EXPTIME=`dmkeypar $1 EXPOSURE echo=yes`
+    BACK=`dmkeypar $1 BACKSCAL echo=yes`
+    # fix `scientific notation' bug for `bc'
+    EXPTIME_B=`echo ${EXPTIME} | sed 's/[eE]/\*10\^/' | sed 's/+//'`
+    BACK_B=`echo "( ${BACK} )" | sed 's/[eE]/\*10\^/' | sed 's/+//'`
+    PB_FLUX=`echo "scale = 16; ${COUNTS} / ${EXPTIME_B} / ${BACK_B}" | bc -l`
+    echo ${PB_FLUX}
+}
+
+bkg_renorm() {
+    # $1: src spectrum, $2: back spectrum
+    PBFLUX_SRC=`pb_flux $1`
+    PBFLUX_BKG=`pb_flux $2`
+    BACK_OLD=`dmkeypar $2 BACKSCAL echo=yes`
+    BACK_OLD_B=`echo "( ${BACK_OLD} )" | sed 's/[eE]/\*10\^/' | sed 's/+//'`
+    BACK_NEW=`echo "scale = 16; ${BACK_OLD_B} * ${PBFLUX_BKG} / ${PBFLUX_SRC}" | bc -l`
+    printf "\`$2': BACKSCAL:\n"
+    printf "    ${BACK_OLD} --> ${BACK_NEW}\n"
+    punlearn dmhedit
+    dmhedit infile=$2 filelist=none operation=add \
+        key=BACKSCAL value=${BACK_NEW} comment="old value: ${BACK_OLD}"
+}
+## bkg renorm }}}
+## functions end }}}
+
+## parameters {{{
+# process cmdline args using `getopt_keyval'
+getopt_keyval "$@"
+
+## 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`" >> ${LOGFILE}
+## log }}}
+
+# check given parameters
+if [ -d "${basedir}" ]; then
+    BASEDIR=${basedir}
+else
+    BASEDIR=${DFT_BASEDIR}
+fi
+if [ ! -z "${json}" ] && [ -r "${BASEDIR}/${json}" ]; then
+    JSON_FILE="${BASEDIR}/${json}"
+elif ls ${BASEDIR}/${DFT_JSON_PAT} > /dev/null 2>&1; then
+    JSON_FILE=`ls ${BASEDIR}/${DFT_JSON_PAT}`
+else
+    read -p "> JSON_file: " JSON_FILE
+    if [ ! -r "${JSON_FILE}" ]; then
+        printf "ERROR: cannot access given \`${JSON_FILE}'\n"
+        exit ${ERR_JSON}
+    fi
+fi
+printf "## use json_file: \`${JSON_FILE}'\n" | ${TOLOG}
+
+# process `nh' and `redshift' {{{
+NH_JSON=`grep '"nH' ${JSON_FILE} | sed 's/.*"nH.*":\ //' | sed 's/\ *,$//'`
+Z_JSON=`grep '"redshift' ${JSON_FILE} | sed 's/.*"redshift.*":\ //' | sed 's/\ *,$//'`
+printf "## get nh: \`${NH_JSON}' (from \`${JSON_FILE}')\n" | ${TOLOG}
+printf "## get redshift: \`${Z_JSON}' (from \`${JSON_FILE}')\n" | ${TOLOG}
+## if `nh' and `redshift' supplied in cmdline, then use them
+if [ ! -z "${nh}" ]; then
+    N_H=${nh}
+else
+    N_H=${NH_JSON}
+fi
+# redshift
+if  [ ! -z "${z}" ]; then
+    REDSHIFT=${z}
+else
+    REDSHIFT=${Z_JSON}
+fi
+printf "## use nH: ${N_H}\n" | ${TOLOG}
+printf "## use redshift: ${REDSHIFT}\n" | ${TOLOG}
+# nh & redshift }}}
+
+# region range {{{
+if [ ! -z "${inner}" ]; then
+    INNER="${inner}"
+else
+    INNER=${DFT_INNER}
+fi
+if [ ! -z "${outer}" ]; then
+    OUTER="${outer}"
+else
+    OUTER=${DFT_OUTER}
+fi
+printf "## region range: (${INNER} - ${OUTER} R500)\n" | ${TOLOG}
+# range }}}
+
+# process `r500' {{{
+R500_RAW=`grep '"R500.*kpc' ${JSON_FILE} | sed 's/.*"R500.*":\ //' | sed 's/\ *,$//'`
+if [ ! -z "${r500}" ]; then
+    R500_RAW=${r500}
+fi
+if [ -z "${R500_RAW}" ]; then
+    printf "## input R500 followed with unit, e.g.: 800kpc, 400pix\n"
+    read -p "> value of \`R500' (in pixel/kpc): " R500_RAW
+fi
+R500_VAL=`echo "${R500_RAW}" | tr -d 'a-zA-Z, '`
+R500_UNI=`echo "${R500_RAW}" | tr -d '0-9, '`
+printf "## get \`R500': ${R500_VAL} in unit \`${R500_UNI}'\n" | ${TOLOG}
+
+# if in kpc, convert to pix
+case "${R500_UNI}" in
+    [pP]*)
+        printf "## units in \`pixel', conversion not needed\n" | ${TOLOG}
+        R500_PIX_B=`echo ${R500_VAL} | sed 's/[eE]/\*10\^/' | sed 's/+//'`
+        ;;
+    *)
+        printf "## units in \`kpc', convert to \`Chandra pixel'\n" | ${TOLOG}
+        KPC_PER_PIX=`${COSCALC} ${REDSHIFT} | grep 'kpc.*pix' | tr -d 'a-zA-Z_#=(),:/ '`
+        # convert scientific notation for `bc'
+        KPC_PER_PIX_B=`echo ${KPC_PER_PIX} | sed 's/[eE]/\*10\^/' | sed 's/+//'`
+        printf "## calculated \`kpc/pixel': ${KPC_PER_PIX_B}\n"
+        R500_VAL_B=`echo ${R500_VAL} | sed 's/[eE]/\*10\^/' | sed 's/+//'`
+        R500_PIX_B=`echo "scale = 4; ${R500_VAL_B} / ( ${KPC_PER_PIX_B} )" | bc -l`
+        ;;
+esac
+# calc (inner-outer R500)
+R_IN=`echo "scale = 4; ${INNER} * ${R500_PIX_B}" | bc -l`
+R_OUT=`echo "scale = 4; ${OUTER} * ${R500_PIX_B}" | bc -l`
+printf "## R500 in units pixel: ${R500_PIX_B}\n" | ${TOLOG}
+printf "## (${INNER}-${OUTER} R500) range in pixel: ${R_IN} - ${R_OUT}\n" | ${TOLOG}
+# r500 }}}
+
+# check evt file
+if [ -r "${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" | ${TOLOG}
+
+# input and output region files {{{
+if [ -r "${regin}" ]; then
+    REG_IN="${regin}"
+elif [ -r "${DFT_REG_IN}" ]; then
+    REG_IN=${DFT_REG_IN}
+else
+    read -p "> previous used radial spec regfile: " REG_IN
+    if [ ! -r "${REG_IN}" ]; then
+        printf "ERROR: cannot access given \`${REG_IN}' region file\n"
+        exit ${ERR_REG}
+    fi
+fi
+printf "## use previous regfile: \`${REG_IN}'\n" | ${TOLOG}
+if [ ! -z "${regout}" ]; then
+    REG_OUT="${regout}"
+else
+    REG_OUT="r500avgt_${INNER}-${OUTER}.reg"
+fi
+[ -e "${REG_OUT}" ] && mv -fv ${REG_OUT} ${REG_OUT}_bak
+printf "## set output regfile: \`${REG_OUT}'\n" | ${TOLOG}
+
+# get center position from `regin'
+# only consider `pie' or `annulus'-shaped region
+TMP_REG=`grep -iE '(pie|annulus)' ${REG_IN} | head -n 1`
+XC=`echo ${TMP_REG} | tr -d 'a-zA-Z() ' | awk -F',' '{ print $1 }'`
+YC=`echo ${TMP_REG} | tr -d 'a-zA-Z() ' | awk -F',' '{ print $2 }'`
+printf "## get center coord: (${XC},${YC})\n" | ${TOLOG}
+# region files }}}
+
+# check given bkgd, determine background {{{
+if [ -r "${bkgd}" ]; then
+    BKGD=${bkgd}
+elif [ -r "${DFT_BKGD}" ]; then
+    BKGD=${DFT_BKGD}
+else
+    read -p "> background (blanksky_evt | lbkg_reg | bkg_spec): " BKGD
+    if [ ! -r "${BKGD}" ]; then
+        printf "ERROR: cannot access given \`${BKGD}'\n"
+        exit ${ERR_BKG}
+    fi
+fi
+printf "## use bkgd: \`${BKGD}'\n" | ${TOLOG}
+# determine bkg type: blanksky, lbkg_reg, bkg_spec ?
+# according to file type first: text / FITS
+# if FITS, then get values of `HDUCLAS1' and `OBJECT'
+if file -bL ${BKGD} | grep -qi 'text'; then
+    printf "## given \`${BKGD}' is a \`text file'\n"
+    printf "##   use it as local bkg region file\n"
+    printf "##   use *LOCAL BKG SPEC*\n" | ${TOLOG}
+    # just set flags, extract spectrum later
+    USE_LBKG_REG=YES
+    USE_BLANKSKY=NO
+    USE_BKG_SPEC=NO
+elif file -bL ${BKGD} | grep -qi 'FITS'; then
+    printf "## given \`${BKGD}' is a \`FITS file'\n"
+    # get FITS header keyword
+    HDUCLAS1=`dmkeypar ${BKGD} HDUCLAS1 echo=yes`
+    if [ "${HDUCLAS1}" = "EVENTS" ]; then
+        # event file
+        printf "##   given file is \`event'\n"
+        # check if `blanksky' or `stowed bkg'
+        BKG_OBJ=`dmkeypar ${BKGD} OBJECT echo=yes`
+        if [ "${BKG_OBJ}" = "BACKGROUND DATASET" ] || [ "${BKG_OBJ}" = "ACIS STOWED" ]; then
+            # valid bkg evt file
+            printf "##   given FITS file is a valid bkgrnd file\n"
+            printf "##   use *BLANKSKY*\n" | ${TOLOG}
+            USE_BLANKSKY=YES
+            USE_LBKG_REG=NO
+            USE_BKG_SPEC=NO
+            # specify `BLANKSKY'
+            BLANKSKY=${BKGD}
+        else
+            # invalid bkg evt file
+            printf "ERROR: invalid bkg evt file given\n"
+            exit ${ERR_BKGTY}
+        fi
+    elif [ "${HDUCLAS1}" = "SPECTRUM" ]; then
+        # spectrum file
+        printf "##   given file is \`spectrum'\n"
+        printf "##   use *BKG SPECTRUM*\n" | ${TOLOG}
+        USE_BKG_SPEC=YES
+        USE_BLANKSKY=NO
+        USE_LBKG_REG=NO
+        # specify `BKG_SPEC'
+        BKG_SPEC=${BKGD}
+    else
+        # other type
+        printf "ERROR: other type FITS given\n"
+        exit ${ERR_BKGTY}
+    fi
+else
+    printf "ERROR: given \`${BKGD}' type UNKNOWN\n"
+    exit ${ERR_BKGTY}
+fi
+# bkgd }}}
+
+# check `arf' and `rmf' {{{
+if [ -r "${arf}" ]; then
+    ARF=${arf}
+elif [ -r "${DFT_ARF}" ]; then
+    ARF=${DFT_ARF}
+else
+    read -p "> provide the ARF to use: " ARF
+    if [ ! -r "${ARF}" ]; then
+        printf "ERROR: cannot access given \`${ARF}'\n"
+        exit ${ERR_ARF}
+    fi
+fi
+printf "## use ARF: \`${ARF}'\n" | ${TOLOG}
+# rmf
+if [ -r "${rmf}" ]; then
+    RMF=${rmf}
+elif [ -r "${DFT_RMF}" ]; then
+    RMF=${DFT_RMF}
+else
+    read -p "> provide the RMF to use: " RMF
+    if [ ! -r "${RMF}" ]; then
+        printf "ERROR: cannot access given \`${RMF}'\n"
+        exit ${ERR_RMF}
+    fi
+fi
+printf "## use RMF: \`${RMF}'\n" | ${TOLOG}
+# arf & rmf }}}
+
+# check given `grpcmd'
+if [ ! -z "${grpcmd}" ]; then
+    GRP_CMD="${grpcmd}"
+else
+    GRP_CMD="${DFT_GRP_CMD}"
+fi
+printf "## use grppha cmd: \`${GRP_CMD}'\n" | ${TOLOG}
+## parameters }}}
+
+##################################################
+#### main
+## region related {{{
+## generate the needed region file
+printf "generate the output region file ...\n"
+cat > ${REG_OUT} << _EOF_
+# Region file format: CIAO version 1.0
+pie(${XC},${YC},${R_IN},${R_OUT},0,360)
+_EOF_
+
+## open the evt file to verify or modify
+printf "## check the generated pie region ...\n"
+printf "## if modified, save with the same name \`${REG_OUT}' (overwrite)\n"
+ds9 ${EVT} -region ${REG_OUT}
+
+## check the (modified) region (pie region end angle)
+printf "check the above region (for pie region end angle) ...\n"
+INVALID=`grep -i 'pie' ${REG_OUT} | awk -F'[,()]' '$7 > 360'`
+if [ "x${INVALID}" != "x" ]; then
+    printf "*** WARNING: there are pie regions' END_ANGLE > 360\n" | ${TOLOG}
+    printf "*** will to fix ...\n"
+    mv -fv ${REG_OUT} ${REG_OUT}_tmp
+    # using `awk' to fix
+    awk -F'[,()]' '{
+        if ($7 > 360) {
+            printf "%s(%.2f,%.2f,%.2f,%.2f,%.2f,%.2f)\n", $1,$2,$3,$4,$5,$6,($7-360)
+        }
+        else {
+            print $0
+        }
+    }' ${REG_OUT}_tmp > ${REG_OUT}
+    rm -f ${REG_OUT}_tmp
+fi
+## region related }}}
+
+## generate spectrum {{{
+# object
+AVGT_SPEC="${REG_OUT%.reg}.pi"
+AVGT_SPEC_GRP="${AVGT_SPEC%.pi}_grp.pi"
+printf "extract object spectrum \`${AVGT_SPEC}' ...\n"
+punlearn dmextract
+dmextract infile="${EVT}[sky=region(${REG_OUT})][bin PI]" \
+    outfile="${AVGT_SPEC}" wmap="[bin det=8]" clobber=yes
+# group spectrum
+printf "group object spectrum ...\n"
+grppha infile="${AVGT_SPEC}" outfile="${AVGT_SPEC_GRP}" \
+    comm="${GRP_CMD} & exit" clobber=yes > /dev/null
+
+# background
+printf "generate the background spectrum ...\n"
+AVGT_BKG="${AVGT_SPEC%.pi}_bkg.pi"
+if [ "${USE_BLANKSKY}" = "YES" ]; then
+    # use blanksky as background file
+    printf "extract spectrum from blanksky ...\n"
+    punlearn dmextract
+    dmextract infile="${BLANKSKY}[sky=region(${REG_OUT})][bin PI]" \
+        outfile=${AVGT_BKG} wmap="[bin det=8]" clobber=yes
+elif [ "${USE_LBKG_REG}" = "YES" ]; then
+    printf "extract local background ...\n"
+    punlearn dmextract
+    dmextract infile="${EVT}[sky=region(${BKGD})][bin PI]" \
+        outfile=${AVGT_BKG} wmap="[bin det=8]" clobber=yes
+elif [ "${USE_BKG_SPEC}" = "YES" ]; then
+    printf "copy specified background spectrum ...\n"
+    cp -fv ${BKG_SPEC} ${AVGT_BKG}
+fi
+
+printf "renormalize the background ...\n"
+bkg_renorm ${AVGT_SPEC} ${AVGT_BKG}
+
+## spectrum }}}
+
+## generate XSPEC script {{{
+printf "generate a XSPEC script ...\n"
+# default output xspec scripts
+XSPEC_SCRIPT="xspec_${REG_OUT%.reg}.xcm"
+[ -e "${XSPEC_SCRIPT}" ] && mv -fv ${XSPEC_SCRIPT} ${XSPEC_SCRIPT}_bak
+cat > ${XSPEC_SCRIPT} << _EOF_
+## XSPEC script
+## spectrum analysis to get the average temperatue with (0.1-0.5 R500)
+##
+## generated by: \``basename $0`'
+## date: \``date`'
+##
+
+# xspec settings
+statistic chi
+abund grsa
+query yes
+
+# data
+data ${AVGT_SPEC_GRP}
+response ${RMF}
+arf ${ARF}
+backgrnd ${AVGT_BKG}
+
+# fitting range
+ignore bad
+ignore 0.0-0.7,7.0-**
+
+# plot related
+setplot energy
+
+method leven 10 0.01
+xsect bcmc
+cosmo 70 0 0.73
+xset delta 0.01
+systematic 0
+
+# model
+model wabs*apec
+         ${N_H}     -0.001          0          0     100000      1e+06
+            1.0       0.01      0.008      0.008         64         64
+            0.4      0.001          0          0          5          5
+    ${REDSHIFT}      -0.01     -0.999     -0.999         10         10
+            0.0       0.01          0          0      1e+24      1e+24
+
+## xspec script end
+_EOF_
+## xspec script }}}
+
+exit 0
+