Updated scripts and added some files

* Updated 'ciao_calc_csb.sh', 'ciao_calc_ct.sh'
* Added 'make_infojson.sh' for wjy's data
* Added some files:
  - fitting_mass.conf
  - fitting_sbp.conf
  - wang2012_param.txt

7 files changed, 232 insertions, 46 deletions

diff --git a/files/fitting_mass.conf b/files/fitting_mass.conf
new file mode 100644
index 0000000..4c2d3ca
--- /dev/null
+++ b/files/fitting_mass.conf
@@ -0,0 +1,7 @@
+t_profile           wang2012
+t_data_file         tcl_temp_profile.txt
+t_param_file        wang2012_param.txt
+sbp_cfg             fitting_sbp.conf
+nh                  0.
+abund               0.
+radius_sbp_file     sbprofile.txt
diff --git a/files/fitting_sbp.conf b/files/fitting_sbp.conf
new file mode 100644
index 0000000..39c6a2b
--- /dev/null
+++ b/files/fitting_sbp.conf
@@ -0,0 +1,13 @@
+radius_file     radius_sbp.txt
+sbp_file        flux_sbp.txt
+
+cfunc_file      coolfunc_calc_data.txt
+T_file          t_profile_dump.qdp
+
+n0              0.005
+rc              30
+beta            0.7
+bkg             0.0
+
+cm_per_pixel    
+z               
diff --git a/files/wang2012_param.txt b/files/wang2012_param.txt
new file mode 100644
index 0000000..1137704
--- /dev/null
+++ b/files/wang2012_param.txt
@@ -0,0 +1,7 @@
+A       5.0         1.0     500     T
+n       5.0         0.1     10      T
+xi      0.3         0.1     1.0     T
+a2      2000        1.0     1e+05   T
+a3      1000        100     3000    T
+beta    0.5         0.1     1.0     T
+T0      2.0         1.0     5.0     T
diff --git a/scripts/ciao_calc_csb.sh b/scripts/ciao_calc_csb.sh
index 92741b1..c50c908 100755
--- a/scripts/ciao_calc_csb.sh
+++ b/scripts/ciao_calc_csb.sh
@@ -21,16 +21,6 @@ ERR_Z=21
 ERR_CNT=22
 ## }}}
 
-## cosmology claculator {{{
-## write the path of cosmo claculator here
-BASE_PATH=`dirname $0`
-COSMO_CALC=`which cosmo_calc`
-if [ -z "${COSMO_CALC}" ] || [ ! -x  ${COSMO_CALC} ] ; then 
-    printf "ERROR: ${COSMO_CALC} neither executable nor specified\n"
-    exit ${ERR_CALC}
-fi
-## }}}
-
 ## usage, help {{{
 case "$1" in
     -[hH]*|--[hH]*)
@@ -42,6 +32,16 @@ case "$1" in
 esac
 ## usage, help }}}
 
+## cosmology claculator {{{
+## write the path of cosmo claculator here
+BASE_PATH=`dirname $0`
+COSMO_CALC="`which cosmo_calc calc_distance 2>/dev/null | head -n 1`"
+if [ -z "${COSMO_CALC}" ] || [ ! -x  ${COSMO_CALC} ] ; then 
+    printf "ERROR: ${COSMO_CALC} neither executable nor specified\n"
+    exit ${ERR_CALC}
+fi
+## }}}
+
 ## default parameters {{{
 # default basedir relative to 'spc/profile'
 DFT_BASEDIR="../.."
@@ -81,13 +81,13 @@ getopt_keyval() {
 getopt_keyval "$@"
 
 # basedir
-if [ -d "${basedir}" ] && ls ${basedir}/*repro_evt2.fits > /dev/null 2>&1; then
+if [ -d "${basedir}" ]; then
     BASEDIR=${basedir}
-elif [ -d "${DFT_BASEDIR}" ] && ls ${DFT_BASEDIR}/*repro_evt2.fits > /dev/null 2>&1; then
+elif [ -d "${DFT_BASEDIR}" ]; then
     BASEDIR=${DFT_BASEDIR}
 else
     read -p "> basedir (contains info json): " BASEDIR
-    if [ ! -d "${BASEDIR}" ] || ! ls ${BASEDIR}/*repro_evt2.fits >/dev/null 2>&1; then
+    if [ ! -d "${BASEDIR}" ]; then
         printf "ERROR: given \`${BASEDIR}' invalid!\n"
         exit ${ERR_DIR}
     fi
@@ -159,7 +159,7 @@ Z=`grep -i '"redshift"' ${JSON_FILE} | awk -F':' '{ print $2 }' | tr -d ' ,'`
 R500=`grep '"R500.*kpc' ${JSON_FILE} | awk -F':' '{ print $2 }' | tr -d ' ,'`
 OBS_ID=`grep '"Obs.*ID' ${JSON_FILE} | awk -F':' '{ print $2 }' | tr -d ' ,'`
 OBJ_NAME=`grep '"Source\ Name' ${JSON_FILE} | awk -F':' '{ print $2 }' | sed -e 's/\ *"//' -e 's/"\ *,$//'`
-CT=`grep '"Cooling_time' ${JSON_FILE} | awk -F':' '{ print $2 }' | tr -d ' ,'`
+#CT=`grep '"Cooling_time' ${JSON_FILE} | awk -F':' '{ print $2 }' | tr -d ' ,'`
 
 cd ${IMG_DIR}
 printf "entered img directory\n"
@@ -172,8 +172,9 @@ if [ `echo "${Z} < 0.3" | bc -l` -eq 1 ]; then
 #    exit ${ERR_Z}
 fi
 
-KPC_PER_PIXEL=`${COSMO_CALC} ${Z} | grep 'kpc/pixel' | awk '{ print $3 }'`
-RC_PIX=`echo "scale=2; 0.048 * ${R500} / ${KPC_PER_PIXEL}" | bc -l`
+#KPC_PER_PIX=`${COSMO_CALC} ${Z} | grep 'kpc/pixel' | awk '{ print $3 }'`
+KPC_PER_PIX=`${COSMO_CALC} ${Z} | grep 'kpc.*pix' | tr -d 'a-zA-Z_#=(),:/ '`
+RC_PIX=`echo "scale=2; 0.048 * ${R500} / ${KPC_PER_PIX}" | bc -l`
 # test counts_in_0.048R500<500?
 RC_REG="pie(${X},${Y},0,${RC_PIX},0,360)"
 punlearn dmlist
@@ -189,8 +190,8 @@ fi
 TMP_REG="_tmp_csb.reg"
 TMP_S="_tmp_csb.fits"
 
-R1=`echo "scale=2;  40 / ${KPC_PER_PIXEL}" | bc -l`
-R2=`echo "scale=2; 400 / ${KPC_PER_PIXEL}" | bc -l` 
+R1=`echo "scale=2;  40 / ${KPC_PER_PIX}" | bc -l`
+R2=`echo "scale=2; 400 / ${KPC_PER_PIX}" | bc -l` 
 cat > ${TMP_REG} << _EOF_
 pie(${X},${Y},0,${R1},0,360)
 pie(${X},${Y},0,${R2},0,360)
@@ -227,8 +228,8 @@ printf "S1=${S1}, S2=${S2} (sur_flux)\n" | tee -a ${CSB_RES}
 printf "C_sb: ${CSB}\n" | tee -a ${CSB_RES}
 [ "x${F_WZ}" = "xtrue" ] && printf "${WZ}\n" | tee -a ${CSB_RES}
 [ "x${F_WC}" = "xtrue" ] && printf "${WC}\n" | tee -a ${CSB_RES}
-printf "# OBS_ID,OBJ_NAME,Z,R500,RC_PIX,CNT_RC,CT,R1_PIX,R2_PIX,S1,S2,CSB,WZ,WC,WR\n" | tee -a ${CSB_RES}
-printf "# $OBS_ID,$OBJ_NAME,$Z,$R500,$RC_PIX,$CNT_RC,$CT,$R1,$R2,$S1,$S2,$CSB,$WZ,$WC,$WR\n\n" | tee -a ${CSB_RES}
+printf "# OBS_ID,OBJ_NAME,Z,R500,RC_PIX,CNT_RC,R1_PIX,R2_PIX,S1,S2,CSB,WZ,WC,WR\n" | tee -a ${CSB_RES}
+printf "# $OBS_ID,$OBJ_NAME,$Z,$R500,$RC_PIX,$CNT_RC,$R1,$R2,$S1,$S2,$CSB,$WZ,$WC,$WR\n\n" | tee -a ${CSB_RES}
 ## main }}}
 
 exit 0
diff --git a/scripts/ciao_calc_ct.sh b/scripts/ciao_calc_ct.sh
index 6fb1d79..926c785 100755
--- a/scripts/ciao_calc_ct.sh
+++ b/scripts/ciao_calc_ct.sh
@@ -19,18 +19,6 @@ export LC_COLLATE=C
 ##   2014/06/18: 'cooling_time2.sh' -> 'ciao_calc_ct.sh'
 ###########################################################
 
-## comology calculator {{{
-## XXX: MODIFY THIS TO YOUR OWN CASE
-## and make sure this `calc' is executable
-## NOTES: use `$HOME' instead of `~' in path
-BASE_PATH=`dirname $0`
-COSCALC="`which cosmo_calc calc_distance | head -n 1`"
-if [ -z "${COSCALC}" ] || [ ! -x ${COSCALC} ]; then
-    printf "ERROR: \`COSCALC: ${COSCALC}' neither specified nor executable\n"
-    exit 255
-fi
-## }}}
-
 ## about, used in `usage' {{{
 VERSION="v1.1"
 UPDATE="2012-08-26"
@@ -57,7 +45,7 @@ ERR_UNI=61
 case "$1" in
     -[hH]*|--[hH]*)
         printf "usage:\n"
-        printf "    `basename $0` evt=<evt2_clean> r500=<r500_kpc> 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 "    `basename $0` basedir=<repro_dir> evt=<evt2_clean> r500=<r500_kpc> regin=<input_reg> regout=<output_reg> bkgd=<blank_evt | lbkg_reg | bkg_spec> nh=<nH> z=<redshift> arf=<warf_file> rmf=<wrmf_file> [ grpcmd=<grppha_cmd> log=<log_file> ]\n"
         printf "\nversion:\n"
         printf "${VERSION}, ${UPDATE}\n"
         exit ${ERR_USG}
@@ -65,6 +53,18 @@ case "$1" in
 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
+BASE_PATH=`dirname $0`
+COSCALC="`which cosmo_calc calc_distance 2>/dev/null | head -n 1`"
+if [ -z "${COSCALC}" ] || [ ! -x ${COSCALC} ]; then
+    printf "ERROR: \`COSCALC: ${COSCALC}' neither specified nor executable\n"
+    exit 255
+fi
+## }}}
+
 ## default parameters {{{
 # default `event file' which used to match `blanksky' files
 #DFT_EVT="_NOT_EXIST_"
@@ -208,6 +208,7 @@ if [ -d "${basedir}" ]; then
 else
     BASEDIR=${DFT_BASEDIR}
 fi
+# json file
 if [ ! -z "${json}" ] && [ -r "${BASEDIR}/${json}" ]; then
     JSON_FILE="${BASEDIR}/${json}"
 elif [ `ls ${BASEDIR}/${DFT_JSON_PAT} 2> /dev/null | wc -l` -eq 1 ]; then
diff --git a/scripts/ciao_r500avgt_v3.sh b/scripts/ciao_r500avgt_v3.sh
index 3c9be08..9a8dffd 100755
--- a/scripts/ciao_r500avgt_v3.sh
+++ b/scripts/ciao_r500avgt_v3.sh
@@ -34,19 +34,6 @@ export LC_COLLATE=C
 ##   modify for new process
 ###########################################################
 
-## comology calculator {{{
-## XXX: MODIFY THIS TO YOUR OWN CASE
-## and make sure this `calc' is executable
-## NOTES: use `$HOME' instead of `~' in path
-COSCALC="`which cosmo_calc calc_distance | head -n 1`"
-# COSCALC="_path_to_calc_distance_"
-# COSCALC="$HOME/bin/mass/calc_distance"
-if [ -z "${COSCALC}" ] || [ ! -x ${COSCALC} ]; then
-    printf "ERROR: \`COSCALC: ${COSCALC}' neither specified nor executable\n"
-    exit 255
-fi
-## }}}
-
 ## about, used in `usage' {{{
 VERSION="v3.0"
 UPDATE="2013-02-09"
@@ -82,6 +69,19 @@ case "$1" in
 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_"
diff --git a/scripts/make_infojson.sh b/scripts/make_infojson.sh
new file mode 100755
index 0000000..34f9f7c
--- /dev/null
+++ b/scripts/make_infojson.sh
@@ -0,0 +1,157 @@
+#!/bin/sh
+#
+# This script is used to make a bare '_INFO.json' file
+# placed under directory 'repro/',
+# thus scripts 'ciao_calc_ct.sh' and 'ciao_calc_csb.sh'
+# can get required information from this file.
+#
+# Run this script in directory 'repro/'.
+#
+# Weitian LI <liweitianux@gmail.com>
+# 2014/06/24
+#
+
+## usage, help {{{
+case "$1" in
+    -[hH]*|--[hH]*)
+        printf "usage:\n"
+        printf "    `basename $0` evtdir=<evt_dir> spcdir=<spc_dir> imgdir=<img_dir> massdir=<mass_dir> json=<info_json>\n"
+        printf "NOTE: run this script in dir 'repro/'\n"
+        exit 1
+        ;;
+esac
+## usage, help }}}
+
+## default parameters {{{
+# basedir: . (run this script under basedir)
+BASEDIR=`pwd -P`
+#
+## directory structure of wjy's data
+# default evtdir relative to 'basedir'
+DFT_EVTDIR="../evt2/evt"
+# default spcdir relative to 'basedir'
+DFT_SPCDIR="../evt2/spc/profile"
+# default imgdir relative to 'basedir'
+DFT_IMGDIR="../evt2/img"
+# default massdir relative to 'basedir'
+DFT_MASSDIR="../evt2/mass"
+## }}}
+
+## 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 ${keyval}
+        shift                           # shift, process next one
+    done
+}
+## functions }}}
+
+## parameters {{{
+# process cmdline args using `getopt_keyval'
+getopt_keyval "$@"
+
+# evt dir
+if [ ! -z "${evtdir}" ] && [ -d "${BASEDIR}/${evtdir}" ]; then
+    EVT_DIR=`( cd ${BASEDIR}/${evtdir} && pwd -P )`
+elif [ -d "${BASEDIR}/${DFT_EVTDIR}" ]; then
+    EVT_DIR=`( cd ${BASEDIR}/${DFT_EVTDIR} && pwd -P )`
+else
+    read -p "> evt dir (relative to basedir): " EVT_DIR
+    if [ ! -d "${BASEDIR}/${EVT_DIR}" ]; then
+        printf "ERROR: given \`${EVT_DIR}' invalid\n"
+        exit 20
+    else
+        EVT_DIR="${BASEDIR}/${EVT_DIR}"
+    fi
+fi
+printf "## use evtdir: \`${EVT_DIR}'\n"
+
+# spc dir
+if [ ! -z "${spcdir}" ] && [ -d "${BASEDIR}/${spcdir}" ]; then
+    SPC_DIR=`( cd ${BASEDIR}/${spcdir} && pwd -P )`
+elif [ -d "${BASEDIR}/${DFT_SPCDIR}" ]; then
+    SPC_DIR=`( cd ${BASEDIR}/${DFT_SPCDIR} && pwd -P )`
+else
+    read -p "> spc dir (relative to basedir): " SPC_DIR
+    if [ ! -d "${BASEDIR}/${SPC_DIR}" ]; then
+        printf "ERROR: given \`${SPC_DIR}' invalid\n"
+        exit 21
+    else
+        SPC_DIR="${BASEDIR}/${SPC_DIR}"
+    fi
+fi
+printf "## use spcdir: \`${SPC_DIR}'\n"
+
+# img dir
+if [ ! -z "${imgdir}" ] && [ -d "${BASEDIR}/${imgdir}" ]; then
+    IMG_DIR=`( cd ${BASEDIR}/${imgdir} && pwd -P )`
+elif [ -d "${BASEDIR}/${DFT_IMGDIR}" ]; then
+    IMG_DIR=`( cd ${BASEDIR}/${DFT_IMGDIR} && pwd -P )`
+else
+    read -p "> img dir (relative to basedir): " IMG_DIR
+    if [ ! -d "${BASEDIR}/${IMG_DIR}" ]; then
+        printf "ERROR: given \`${IMG_DIR}' invalid\n"
+        exit 22
+    else
+        IMG_DIR="${BASEDIR}/${IMG_DIR}"
+    fi
+fi
+printf "## use imgdir: \`${IMG_DIR}'\n"
+
+# mass dir
+if [ ! -z "${massdir}" ] && [ -d "${BASEDIR}/${massdir}" ]; then
+    MASS_DIR=`( cd ${BASEDIR}/${massdir} && pwd -P )`
+elif [ -d "${BASEDIR}/${DFT_MASSDIR}" ]; then
+    MASS_DIR=`( cd ${BASEDIR}/${DFT_MASSDIR} && pwd -P )`
+else
+    read -p "> mass dir (relative to basedir): " MASS_DIR
+    if [ ! -d "${BASEDIR}/${MASS_DIR}" ]; then
+        printf "ERROR: given \`${MASS_DIR}' invalid\n"
+        exit 22
+    else
+        MASS_DIR="${BASEDIR}/${MASS_DIR}"
+    fi
+fi
+printf "## use massdir: \`${MASS_DIR}'\n"
+## }}}
+
+# set files
+EVT2_CLEAN=`readlink -f ${EVT_DIR}/evt2*_clean*.fits | head -n 1`
+MASS_SBP_CFG=`readlink -f ${MASS_DIR}/source.cfg`
+MASS_RES=`readlink -f ${MASS_DIR}/final_result*.txt`
+SPC_CFG=`readlink -f ${IMG_DIR}/spc_fit.cfg`
+
+# get needed data
+punlearn dmkeypar
+OBSID=`dmkeypar "${EVT2_CLEAN}" OBS_ID echo=yes`
+NAME=`dmkeypar "${EVT2_CLEAN}" OBJECT echo=yes`
+Z=`grep -E '^z\s+' ${MASS_SBP_CFG} | awk '{ print $2 }'`
+NH=`grep -E '^nh\s+' ${SPC_CFG} | awk '{ print $2 }'`
+R500=`grep -E '^r500=' ${MASS_RES} | awk '{ print $2 }'`
+
+# generate info json file
+if [ ! -z "${json}" ]; then
+    JSON_FILE="${json}"
+else
+    JSON_FILE="oi${OBSID}_INFO.json"
+fi
+printf "## info json_filename: \`${JSON_FILE}'\n"
+
+cat > ${JSON_FILE} << _EOF_
+{
+    "Obs. ID": ${OBSID},
+    "Source Name": "${NAME}",
+    "nH (10^22 cm^-2)": ${NH},
+    "redshift": ${Z},
+    "R500 (kpc)": ${R500},
+    "Comment": "Bare info json file created by `basename $0`"
+},
+_EOF_
+