Add scripts/ciao_fill_sources.sh

1 files changed, 182 insertions, 0 deletions

diff --git a/scripts/ciao_fill_sources.sh b/scripts/ciao_fill_sources.sh
new file mode 100755
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+++ b/scripts/ciao_fill_sources.sh
@@ -0,0 +1,182 @@
+#!/bin/sh
+#
+# Fill the detected source regions by sampling from their surrounding
+# regions, using CIAO `roi' and `dmfilth'.
+# NOTE: The `dmfilth' only operates on the FITS image, NOT event table.
+#
+# References:
+# [1] An Image of Diffuse Emission - CIAO
+#     http://cxc.harvard.edu/ciao/threads/diffuse_emission/
+#
+#
+# Aaron LI
+# Created: 2016-04-11
+UPDATED="2016-04-11"
+
+
+usage() {
+    echo "usage:"
+    echo "    `basename $0` evt=<evt.fits> outfile=<filled_img> erange=<elow:ehigh> reg=<sources.reg> repro=<repro_dir_relapath>"
+    echo ""
+    echo "version: ${UPDATED}"
+}
+
+# process commandline arguments of 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
+    unset _key _val _keyval
+}
+
+# set CIAO pfiles
+# syntax: set_pfiles tool1 tool2 ...
+set_pfiles() {
+    while [ ! -z "$1" ]; do
+        _tool="$1"
+        shift
+        _pfile=`paccess ${_tool}`
+        [ -n "${_pfile}" ] && punlearn ${_tool} && cp -Lvf ${_pfile} .
+    done
+    # Modify environment variable 'PFILES' to use local pfiles first
+    export PFILES="./:${PFILES}"
+    unset _tool _pfile
+}
+
+# set arguments/variables
+# syntax: set_variable VAR_NAME default_value cmdline_value
+set_variable() {
+    _var="$1"
+    _default="$2"
+    _cmd="$3"
+    if [ ! -z "${_cmd}" ]; then
+        _value="${_cmd}"
+    elif [ ! -z "${_default}" ]; then
+        _value="${_default}"
+    else
+        echo "ERROR: variable '${_var}' get none value"
+        exit 11
+    fi
+    eval "${_var}=${_value}"
+    unset _var _default _cmd _value
+}
+
+# syntax: set_variable VAR_NAME default_ls_pattern cmdline_value
+set_variable_pattern() {
+    _default_pat="$2"
+    if [ `\ls ${_default_pat} 2>/dev/null | wc -l` -eq 0 ]; then
+        echo "ERROR: ls pattern '${_default_pat}' not found"
+        exit 21
+    elif [ `\ls ${_default_pat} 2>/dev/null | wc -l` -eq 1 ]; then
+        _default="`\ls ${_default_pat} 2>/dev/null`"
+        set_variable "$1" "${_default}" "$3"
+    else
+        echo "ERROR: ls pattern '${_default_pat}' found more than 1 values"
+        exit 22
+    fi
+    unset _default_pat _default
+}
+
+# determine the ACIS type: whether "S" or "I"
+get_acis_type() {
+    punlearn dmkeypar
+    _detnam=`dmkeypar "$1" DETNAM echo=yes`
+    if echo "${_detnam}" | \grep -q 'ACIS-0123'; then
+        echo "I"
+    elif echo "${_detnam}" | \grep -q 'ACIS-[0-6]*7'; then
+        echo "S"
+    else
+        printf "ERROR: unknown detector type: ${DETNAM}\n"
+        exit 31
+    fi
+    unset _detnam
+}
+
+
+case "$1" in
+    -[hH]*|--[hH]*)
+        usage
+        exit 1
+        ;;
+esac
+
+# arguments
+getopt_keyval "$@"
+set_variable_pattern EVT "evt2_c7_clean.fits evt2_c0-3_clean.fits" ${evt}
+set_variable ERANGE "700:7000" ${erange}
+ROOTNAME="${EVT%_clean.fits}_e`echo ${ERANGE} | tr ':' '-'`"
+ROOTNAME="${ROOTNAME#evt2_}"
+set_variable OUTFILE "img_${ROOTNAME}_fill.fits" ${outfile}
+set_variable_pattern REG "celld_evt2_c7.reg celld_evt2_c0-3.reg" ${reg}
+set_variable REPRO ".." ${repro}
+
+set_pfiles dmcopy dmkeypar dmmakereg roi dmfilth
+
+# FoV
+ln -svf ${REPRO}/acisf*_fov1.fits .
+FOV=`\ls acisf*_fov1.fits`
+
+# Filter energy
+EVT_E="evt2_${ROOTNAME}.fits"
+if [ ! -e "${EVT_E}" ]; then
+    echo "Filter by energy range ..."
+    punlearn dmcopy
+    dmcopy infile="${EVT}[energy=${ERANGE}]" outfile=${EVT_E}
+fi
+
+# Make image
+IMG="img_${ROOTNAME}.fits"
+if [ ! -e "${IMG}" ]; then
+    echo "Make FITS image ..."
+    ACIS_TYPE=`get_acis_type ${EVT_E}`
+    if [ "${ACIS_TYPE}" = "I" ]; then
+        CCD=0:3
+    else
+        CCD=7
+    fi
+    punlearn dmcopy
+    dmcopy infile="${EVT_E}[sky=region(${FOV}[ccd_id=${CCD}])][bin sky=1]" \
+        outfile=${IMG}
+fi
+
+# Convert ASCII region to FITS format
+echo "Convert region to FITS format ..."
+REG_FITS="${REG%.reg}.fits"
+punlearn dmmakereg
+dmmakereg region="region(${REG})" outfile="${REG_FITS}" clobber=yes
+
+# Determine the background regions for each source
+echo "Determine the background regions for each source ..."
+ROI_TMP_DIR="_tmp_roi"
+[ -d "${ROI_TMP_DIR}" ] && rm -rf ${ROI_TMP_DIR}
+mkdir ${ROI_TMP_DIR}
+punlearn roi
+roi infile="${REG_FITS}" outsrcfile="${ROI_TMP_DIR}/src_%d.fits" \
+    fovregion="region(${FOV})" streakregion="" bkgfactor=0.5 \
+    radiusmode=mul bkgradius=3 clobber=yes
+
+# Combine all the background regions
+echo "Combine all regions ..."
+REG_FILL_ROOT="fill"
+REG_FILL_SRC="${REG_FILL_ROOT}.src.reg"
+REG_FILL_BKG="${REG_FILL_ROOT}.bg.reg"
+REG_FILL_BKG2="${REG_FILL_ROOT}.bg.fits"
+splitroi "${ROI_TMP_DIR}/src_*.fits" ${REG_FILL_ROOT}
+punlearn dmmakereg
+dmmakereg region="region(${REG_FILL_BKG})" \
+    outfile=${REG_FILL_BKG2} clobber=yes
+
+# Fill the source regions using `dmfilth'
+echo "Fill the source regions ..."
+punlearn dmfilth
+dmfilth infile=${IMG} outfile=${OUTFILE} method=POISSON \
+    srclist="@${REG_FILL_SRC}" bkglist="@${REG_FILL_BKG}" clobber=yes
+
+rm -rf ${ROI_TMP_DIR}
+