Updated ciao_calc_ct.sh, ciao_expcorr.sh, ciao_r500avgt.sh, ciao_sbp.sh

ciao_r500avgt.sh, ciao_calc_ct.sh:
  Updated to also find '.rmf' & '.arf' files in addition to '.wrmf'
  & '.warf'.
ciao_sbp.sh:
  Skip skyfov generation if already exists
  Renamed parameter 'aspec' to 'aspect'
ciao_expcorr.sh
  Added 'aspect' parameter for skyfov to fix the 'FoV shift bug'

4 files changed, 78 insertions, 76 deletions

diff --git a/scripts/ciao_calc_ct.sh b/scripts/ciao_calc_ct.sh
index 926c785..5f76ed5 100755
--- a/scripts/ciao_calc_ct.sh
+++ b/scripts/ciao_calc_ct.sh
@@ -16,12 +16,16 @@ export LC_COLLATE=C
 
 ###########################################################
 ## ChangeLogs
-##   2014/06/18: 'cooling_time2.sh' -> 'ciao_calc_ct.sh'
+## v1.1, 2014/06/18
+##   'cooling_time2.sh' -> 'ciao_calc_ct.sh'
+## v1.2, 2015/05/27, Weitian LI
+##   update 'DFT_ARF' & 'DFT_RMF' to find '*.arf' & '*.rmf' files
+##   (specextract only use .arf & .rmf extensions since revision 2014-12)
 ###########################################################
 
 ## about, used in `usage' {{{
-VERSION="v1.1"
-UPDATE="2012-08-26"
+VERSION="v1.2"
+UPDATE="2015-05-27"
 ## about }}}
 
 ## error code {{{
@@ -45,7 +49,7 @@ ERR_UNI=61
 case "$1" in
     -[hH]*|--[hH]*)
         printf "usage:\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 "    `basename $0` basedir=<repro_dir> evt=<evt2_clean> r500=<r500_kpc> regin=<input_reg> regout=<output_reg> bkgd=<blank_evt | lbkg_reg | bkg_spec> nh=<nH> z=<redshift> arf=<arf_file> rmf=<rmf_file> [ grpcmd=<grppha_cmd> log=<log_file> ]\n"
         printf "\nversion:\n"
         printf "${VERSION}, ${UPDATE}\n"
         exit ${ERR_USG}
@@ -81,8 +85,8 @@ DFT_REG_IN="rspec.reg"
 # default output region file (0.1-0.5 r500 region)
 DFT_REG_OUT="cooling.reg"
 # default ARF/RMF, the one of the outmost region
-DFT_ARF="`ls r1_*.warf 2> /dev/null`"
-DFT_RMF="`ls r1_*.wrmf 2> /dev/null`"
+DFT_ARF="`ls r1_*.warf r1_*.arf 2> /dev/null`"
+DFT_RMF="`ls r1_*.wrmf r1_*.rmf 2> /dev/null`"
 
 # default `group command' for `grppha'
 #DFT_GRP_CMD="group 1 128 2 129 256 4 257 512 8 513 1024 16"
diff --git a/scripts/ciao_expcorr.sh b/scripts/ciao_expcorr.sh
index c72973f..c1d7905 100755
--- a/scripts/ciao_expcorr.sh
+++ b/scripts/ciao_expcorr.sh
@@ -1,36 +1,32 @@
 #!/bin/sh
-#
-unalias -a
-export LC_COLLATE=C
-###########################################################
-## 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 ##
-##                                                       ##
-## LIweitiaNux <liweitianux@gmail.com>                   ##
-## August 16, 2012                                       ##
-###########################################################
-
-###########################################################
+##
+## 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
+UPDATED="2014/10/30"
+##
 ## ChangeLogs:
+## 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, LIweitiaNux
 ##   set `ardlib' before process `merge_all'
 ## v1.1, 2012-08-21, LIweitiaNux
 ##   fix a bug with `sed'
-###########################################################
+##
 
-## about, used in `usage' {{{
-VERSION="v2.0"
-UPDATE="2014-07-29"
-## about }}}
+unalias -a
+export LC_COLLATE=C
 
 ## error code {{{
 ERR_USG=1
@@ -54,8 +50,8 @@ 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}, ${UPDATE}\n"
+        printf "\nupdated:\n"
+        printf "${UPDATED}\n"
         exit ${ERR_USG}
         ;;
 esac
@@ -300,11 +296,8 @@ make_instmap_weights outfile="${SPEC_WGT}" \
 ## spectral weights }}}
 
 ## generate `skyfov'
-# XXX: omit `aspec', NOT provide `asol' file
-# otherwise the size of evt_img NOT match the `expmap'
 printf "generate skyfov ...\n"
-SKYFOV="_skyfov.fits"
-[ -e "${SKYFOV}" ] && rm -fv ${SKYFOV}
+SKYFOV="skyfov.fits"
 punlearn skyfov
 skyfov infile="${EVT}" outfile="${SKYFOV}" aspect="@${ASOLIS}" clobber=yes
 
@@ -348,7 +341,8 @@ if `which merge_all >/dev/null 2>&1`; then
     ## 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
-        ln -sv ${BASEDIR}/${f} .
+        asol=`basename ${f}`
+        ln -svf ${BASEDIR}/${asol} .
     done
     
     printf "use \`merge_all' to generate \`exposure map' ONLY ...\n"
diff --git a/scripts/ciao_r500avgt.sh b/scripts/ciao_r500avgt.sh
index 9a8dffd..3318bb4 100755
--- a/scripts/ciao_r500avgt.sh
+++ b/scripts/ciao_r500avgt.sh
@@ -32,11 +32,14 @@ export LC_COLLATE=C
 ##   change `DFT_GRP_CMD' to `group 1 128 4 ...'
 ## v3.0, 2013/02/09, LIweitiaNux
 ##   modify for new process
+## v3.1, 2015/05/27, Weitian LI
+##   update 'DFT_ARF' & 'DFT_RMF' to find '*.arf' & '*.rmf' files
+##   (specextract only use .arf & .rmf extensions since revision 2014-12)
 ###########################################################
 
 ## about, used in `usage' {{{
-VERSION="v3.0"
-UPDATE="2013-02-09"
+VERSION="v3.1"
+UPDATE="2015-05-27"
 ## about }}}
 
 ## error code {{{
@@ -61,7 +64,7 @@ ERR_UNI=61
 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 "    `basename $0` evt=<evt2_clean> r500=<r500_kpc> basedir=<basedir> info=<info_json> inner=<inner_val> outer=<outer_val> regin=<input_reg> regout=<output_reg> bkgd=<blank_evt|lbkg_reg|bkg_spec> nh=<nH> z=<redshift> arf=<arf_file> rmf=<rmf_file> [ grpcmd=<grppha_cmd> log=<log_file> ]\n"
         printf "\nversion:\n"
         printf "${VERSION}, ${UPDATE}\n"
         exit ${ERR_USG}
@@ -97,8 +100,8 @@ DFT_REG_IN="rspec.reg"
 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`"
+DFT_ARF="`ls -1 r?_*.warf r?_*.arf 2> /dev/null | tail -n 1`"
+DFT_RMF="`ls -1 r?_*.wrmf r?_*.rmf 2> /dev/null | tail -n 1`"
 
 # default `group command' for `grppha'
 DFT_GRP_CMD="group min 25"
diff --git a/scripts/ciao_sbp.sh b/scripts/ciao_sbp.sh
index 9c4963c..ef636ca 100755
--- a/scripts/ciao_sbp.sh
+++ b/scripts/ciao_sbp.sh
@@ -1,35 +1,34 @@
 #!/bin/sh
-#
-unalias -a
-export LC_COLLATE=C
-###########################################################
-## 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 ##
-##                                                       ##
-## LIweitiaNux <liweitianux@gmail.com>                   ##
-## August 16, 2012                                       ##
-###########################################################
-
-###########################################################
-## Changes:
+##
+## Extract `surface brighness profile'
+##
+## NOTES:
+## * Only ACIS-I (chip: 0-3) and ACIS-S (chip: 7) supported
+##
+## Weitian LI <liweitianux@gmail.com>
+## Created: 2012/08/16
+UPDATED="2015/03/29"
+##
+## ChangeLogs:
+## 2015/03/29, Weitian LI
+##   * Skip skyfov generation if it already exists.
+##   * Rename parameter 'aspec' to 'aspect' to match with 'skyfov'
+## 2015/03/06, Weitian LI
+##   * Updated this document of the script.
+##   * Added 'SKIP SINGLE' to the generated QDP of SBP file.
 ## v3.1: 2013/02/01, Zhenghao ZHU
 ##   removes the region in ccd gap of ACIS_I 
 ##   removes the region in the area of point source
 ##   need asol file to prevent offset 
-###########################################################
+##
+
+unalias -a
+export LC_COLLATE=C
 
 SCRIPT_PATH=`readlink -f $0`
 SCRIPT_DIR=`dirname ${SCRIPT_PATH}`
 CCDGAP_SCRIPT="chandra_ccdgap_rect.py"
 
-## about, used in `usage' {{{
-VERSION="v3.1"
-UPDATE="2013-02-01"
-## about }}}
-
 ## error code {{{
 ERR_USG=1
 ERR_DIR=11
@@ -52,9 +51,9 @@ ERR_CIAO=100
 case "$1" in
     -[hH]*|--[hH]*)
         printf "usage:\n"
-        printf "    `basename $0` evt_e=<evt_e_file> reg=<sbp_reg> expmap=<exp_map> cellreg=<cell_reg> aspec=<asol_file> [bkg=<bkg> log=<logfile> ]\n"
-        printf "\nversion:\n"
-        printf "${VERSION}, ${UPDATE}\n"
+        printf "    `basename $0` evt_e=<evt_e_file> reg=<sbp_reg> expmap=<exp_map> cellreg=<cell_reg> aspect=<asol_file> [bkg=<bkg> log=<logfile> ]\n"
+        printf "\nupdated:\n"
+        printf "${UPDATED}\n"
         exit ${ERR_USG}
         ;;
 esac
@@ -76,7 +75,7 @@ DFT_SBP_REG="sbprofile.reg"
 # defalut pointsource region file 
 DFT_CELL_REG="`ls celld*.reg 2> /dev/null`"
 # defalut asol file
-DFT_ASOL_FILE="`ls pcad*asol*fits 2> /dev/null`"
+DFT_ASOL_FILE="`ls -1 pcad*asol*fits 2> /dev/null`"
 
 # default `log file'
 DFT_LOGFILE="sbp_`date '+%Y%m%d'`.log"
@@ -193,8 +192,8 @@ else
 fi
 printf "## use cell reg file(s): \`${CELL_REG}'\n" | ${TOLOG}
 # check asol file
-if [ -r "${aspec}" ]; then
-    ASOL_FILE="${aspec}"
+if [ -r "${aspect}" ]; then
+    ASOL_FILE="${aspect}"
 elif [ -r "${DFT_ASOL_FILE}" ] ; then
     ASOL_FILE="${DFT_ASOL_FILE}"
 else
@@ -249,12 +248,12 @@ fi
 ## main process {{{
 
 ## generate `skyfov'
-# XXX: omit `aspec', NOT provide `asol' file
-# otherwise the size of evt_img NOT match the `expmap'
-printf "generate skyfov ...\n"
-SKYFOV="_skyfov.fits"
-punlearn skyfov
-skyfov infile="${EVT_E}" outfile="${SKYFOV}" aspec="${ASOL_FILE}" clobber=yes
+SKYFOV="skyfov.fits"
+if [ ! -r "${SKYFOV}" ]; then
+    printf "generate skyfov ...\n"
+    punlearn skyfov
+    skyfov infile="${EVT_E}" outfile="${SKYFOV}" aspect="${ASOL_FILE}" clobber=yes
+fi
 
 ## get CCD fov regions {{{
 printf "make regions for CCD ...\n"
@@ -498,6 +497,8 @@ cp -fv ${SBP_TXT} ${SBP_QDP}
 sed -i'' 's/#/!/g' ${SBP_QDP}
 # add QDP commands
 sed -i'' '1 i\
+SKIP SINGLE' ${SBP_QDP}
+sed -i'' '1 i\
 READ SERR 1 2' ${SBP_QDP}
 sed -i'' '2 i\
 LABEL Y "Surface Flux (photons/cm\\u2\\d/pixel\\u2\\d/s)"' ${SBP_QDP}