Initial commit

Added files:
  * mass_profile: developed by Junhua GU, modified by Weitian LI
  * opt_utilities: developed by Junhua GU
  * tools/cosmo_calc: originated from 'calc_distance', modified
  * scripts: scripts used to process Chandra ACIS data
  * files: useful files used in processing
  * HOWTO_chandra_acis_process.txt
  * README.md

1 files changed, 416 insertions, 0 deletions

diff --git a/scripts/ciao_bkg_spectra_v4.sh b/scripts/ciao_bkg_spectra_v4.sh
new file mode 100755
index 0000000..bc40151
--- /dev/null
+++ b/scripts/ciao_bkg_spectra_v4.sh
@@ -0,0 +1,416 @@
+#!/bin/sh -
+#
+trap date INT
+unalias -a
+export GREP_OPTIONS=""
+export LC_COLLATE=C
+###########################################################
+## extract background spectra from src and blanksky      ##
+## renormalization the blank spectrum                    ##
+##                                                       ##
+## Ref: Chandra spectrum analysis                        ##
+## http://cxc.harvard.edu/ciao/threads/extended/         ##
+## Ref: specextract                                      ##
+## http://cxc.harvard.edu/ciao/ahelp/specextract.html    ##
+## Ref: CIAO v4.4 region bugs                            ##
+## http://cxc.harvard.edu/ciao/bugs/regions.html#bug-12187
+##                                                       ##
+## LIweitiaNux, July 24, 2012                            ##
+###########################################################
+
+###########################################################
+# ChangeLogs:
+# v3, 2012/08/09
+#   fix `scientific notation' for `bc'
+#   change `spec group' method to `min 15'
+# v4, 2012/08/13
+#   add `clobber=yes'
+#   improve error code
+#   improve cmdline arguements
+#   provide a flexible way to pass parameters
+#     (through cmdline which similar to CIAO,
+#     and default filename match patterns)
+#   add simple `logging' function
+###########################################################
+
+## about, used in `usage' {{{
+VERSION="v4"
+UPDATE="2012-08-14"
+## about }}}
+
+## usage, help {{{
+case "$1" in
+    -[hH]*|--[hH]*)
+        printf "usage:\n"
+        printf "    `basename $0` evt=<evt2_clean> reg=<reglist> blank=<blanksky_evt> basedir=<base_dir> nh=<nH> z=<redshift> [ grpcmd=<grppha_cmd> log=<log_file> ]\n"
+        printf "\nversion:\n"
+        printf "${VERSION}, ${UPDATE}\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`"
+# default `blanksky file'
+#DFT_BLANK="_NOT_EXIST_"
+DFT_BLANK="`ls blanksky*.fits`"
+# default dir which contains `asols, asol.lis, ...' files
+#DFT_BASEDIR="_NOT_EXIST_"
+DFT_BASEDIR=".."
+# default `group command' for `grppha'
+#DFT_GRP_CMD="group 1 128 2 129 256 4 257 512 8 513 1024 16"
+DFT_GRP_CMD="group min 20"
+# default `log file'
+DFT_LOGFILE="bkg_spectra_`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 `pbk file pattern'
+DFT_PBK_PAT="acis*pbk?.fits"
+# default `msk file pattern'
+DFT_MSK_PAT="acis*msk?.fits"
+## default parameters }}}
+
+## 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
+## error code }}}
+
+## 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`" >> ${LOGFILE}
+## log }}}
+
+# check given parameters
+# check evt file
+if [ -r "${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" | ${TOLOG}
+# check given region file(s)
+if [ -z "${reg}" ]; then
+    read -p "> selected local bkg region file: " REGLIST
+else
+    REGLIST="${reg}"
+fi
+REGLIST=`echo ${REGLIST} | tr ',' ' '`      # use *space* to separate
+printf "## use reg file(s): \`${REGLIST}'\n" | ${TOLOG}
+# check given blanksky
+if [ -r "${blank}" ]; then
+    BLANK=${blank}
+elif [ -r "${DFT_BLANK}" ]; then
+    BLANK=${DFT_BLANK}
+else
+    read -p "> matched blanksky evtfile: " BLANK
+    if [ ! -r "${BLANK}" ]; then
+        printf "ERROR: cannot acces given \`${BLANK}' blanksky file\n"
+        exit ${ERR_BKG}
+    fi
+fi
+# check given nH
+if [ -z "${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" | ${TOLOG}
+# check given dir
+if [ -d "${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" | ${TOLOG}
+# check given `grpcmd'
+if [ ! -z "${grpcmd}" ]; then
+    GRP_CMD="${grpcmd}"
+else
+    GRP_CMD="${DFT_GRP_CMD}"
+fi
+printf "## use grppha cmd: \`${GRP_CMD}'\n" | ${TOLOG}
+## parameters }}}
+
+## check needed files {{{
+# check reg file(s)
+printf "check accessibility of reg file(s) ...\n"
+for reg_f in ${REGLIST}; do
+    if [ ! -r "${reg_f}" ]; then
+        printf "ERROR: file \`${reg_f}' NOT accessiable\n"
+        exit ${ERR_REG}
+    fi
+done
+# check the validity of *pie* regions
+printf "check pie reg validity ...\n"
+INVALID=`cat ${REGLIST} | grep -i 'pie' | awk -F, '{ print $6 }' | tr -d ')' | awk '$1 > 360'`
+if [ "x${INVALID}" != "x" ]; then
+    printf "WARNING: some pie region's END_ANGLE > 360\n" | ${TOLOG}
+    printf "    CIAO v4.4 tools may run into trouble\n"
+fi
+
+# check files in `basedir'
+printf "check needed files in basedir \`${BASEDIR}' ...\n"
+# check asolis 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" | ${TOLOG}
+# 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 pbk file
+PBK=`ls -1 ${BASEDIR}/${DFT_PBK_PAT} | head -n 1`
+if [ -z "${PBK}" ]; then
+    printf "ERROR: cannot find \"${DFT_PBK_PAT}\" in dir \`${BASEDIR}'\n"
+    exit ${ERR_PBK}
+fi
+printf "## use pbk: \`${PBK}'\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 ${ERR_MSK}
+fi
+printf "## use msk: \`${MSK}'\n" | ${TOLOG}
+## check files }}}
+
+## main part {{{
+## use 'for' loop to process every region file
+for reg_i in ${REGLIST}; do
+    printf "\n==============================\n"
+    printf "PROCESS REGION fle \`${reg_i}' ...\n"
+
+    REG_TMP="_tmp.reg"
+    [ -f "${REG_TMP}" ] && rm -fv ${REG_TMP}         # remove tmp files
+    cp -fv ${reg_i} ${REG_TMP}
+    # check the validity of *pie* regions {{{
+    INVALID=`grep -i 'pie' ${REG_TMP} | awk -F, '{ print $6 }' | tr -d ')' | awk '$1 > 360'`
+    if [ "x${INVALID}" != "x" ]; then
+        printf "WARNING: fix for *pie* region in file \`${reg_i}'\n"
+        cat ${REG_TMP}
+        A_OLD=`echo ${INVALID} | sed 's/\./\\\./'`
+        A_NEW=`echo ${INVALID}-360 | bc -l | sed 's/\./\\\./'`
+        sed -i'' "s/${A_OLD}\ *)/${A_NEW})/" ${REG_TMP}
+        printf "    --> "
+        cat ${REG_TMP}
+    fi
+    ## check pie region }}}
+
+    LBKG_PI="${reg_i%.reg}.pi"
+    ## use `specextract' to extract local bkg spectrum {{{
+    # NOTE: set `binarfwmap=2' to save the time for generating `ARF'
+    # I have tested that this bin factor has little impact on the results.
+    # NO background response files
+    # NO background spectrum (generate by self)
+    # NO spectrum grouping (group by self using `grppha')
+    printf "use \`specextract' to generate spectra and response ...\n"
+    punlearn specextract
+    specextract infile="${EVT}[sky=region(${REG_TMP})]" \
+        outroot=${LBKG_PI%.pi} bkgfile="" asp="@${ASOLIS}" \
+        pbkfile="${PBK}" mskfile="${MSK}" badpixfile="${BPIX}" \
+        weight=yes correct=no bkgresp=no \
+        energy="0.3:11.0:0.01" channel="1:1024:1" \
+        combine=no binarfwmap=2 \
+        grouptype=NONE binspec=NONE \
+        verbose=2 clobber=yes
+    # `specextract' }}}
+
+    ## generate the blanksky bkg spectrum {{{
+    printf "generate the blanksky bkg spectrum ...\n"
+    BBKG_PI="blanksky_${LBKG_PI}"
+    punlearn dmextract
+    dmextract infile="${BLANK}[sky=region(${REG_TMP})][bin pi]" \
+        outfile=${BBKG_PI} wmap="[bin det=8]" clobber=yes
+    ## blanksky bkg spectrum }}}
+
+    ## bkg renormalization {{{
+    printf "Renormalize background ...\n"
+    bkg_renorm ${LBKG_PI} ${BBKG_PI}
+    ## bkg renorm }}}
+
+    ## group spectrum {{{
+    printf "group spectrum using \`grppha'\n"
+    LBKG_GRP_PI="${LBKG_PI%.pi}_grp.pi"
+    grppha infile="${LBKG_PI}" outfile="${LBKG_GRP_PI}" \
+        comm="${GRP_CMD} & exit" clobber=yes > /dev/null
+    ## group spectra }}}
+
+    ## generate a script for XSPEC {{{
+    XSPEC_XCM="xspec_${LBKG_PI%.pi}_model.xcm"
+    if [ -e ${XSPEC_XCM} ]; then
+        mv -fv ${XSPEC_XCM} ${XSPEC_XCM}_bak
+    fi
+    cat >> ${XSPEC_XCM} << _EOF_
+## xspec script
+## analysis chandra acis background components
+## xspec model: apec+apec+wabs*(pow+apec)
+##
+## generated by script \``basename $0`'
+## `date`
+## NOTES: needs XSPEC v12.x
+
+# settings
+statistic chi
+#weight churazov
+abund grsa
+query yes
+
+# data
+data ${LBKG_GRP_PI}
+response ${LBKG_PI%.pi}.wrmf
+arf ${LBKG_PI%.pi}.warf
+backgrnd ${BBKG_PI}
+
+# fitting range
+ignore bad
+ignore 0.0-0.4,8.0-**
+
+# plot related
+setplot energy
+
+method leven 10 0.01
+xsect bcmc
+cosmo 70 0 0.73
+xset delta 0.01
+systematic 0
+
+# model
+model  apec + apec + wabs(powerlaw + apec)
+           0.08      -0.01      0.008      0.008         64         64
+              1     -0.001          0          0          5          5
+              0      -0.01     -0.999     -0.999         10         10
+            0.0       0.01         -1          0          0          1
+            0.2      -0.01      0.008      0.008         64         64
+              1     -0.001          0          0          5          5
+              0      -0.01     -0.999     -0.999         10         10
+            0.0       0.01         -1          0          0          1
+         ${N_H}     -0.001          0          0     100000      1e+06
+            1.4      -0.01         -3         -2          9         10
+            0.0       0.01         -1          0          0          1
+            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
+
+freeze 1 2 3
+freeze 5 6 7
+freeze 9 10 14
+thaw 12 13
+_EOF_
+    ## XSPEC script }}}
+
+done  # end 'for', `specextract'
+## main part }}}
+
+# clean
+printf "clean ...\n"
+rm -f ${REG_TMP}
+
+printf "DONE\n"
+###########################################################
+
+# vim: set ts=8 sw=4 tw=0 fenc=utf-8 ft=sh: #