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SEdiff.sh
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SEdiff.sh
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#!/bin/bash
if [ $# -lt 1 ]; then
echo "usage: SEdiff.sh -E EXPNUM -r RNUM -p PNUM -n NITE -b BAND (i|r|g|Y|z|u) -S season (dpXX) [-c ccdlist] [-d destcache (scratch|persistent)] [-m SCHEMA (gw|wsdiff)] [-v diffimg_version] [-t] [-C] [-j] [-s] [-O] [-V SNVETO_NAME] [-T STARCAT_NAME] [-Y] [-F]"
exit 1
fi
OLDHOME=$HOME
export HOME=$PWD
DESTCACHE="persistent"
SCHEMA="gw"
DIFFIMG_VERSION="gw8" # can change this with parameter -v <diffimg_version>
ulimit -a
OVERWRITE=false
SKIPSE=false
CCDNUM_LIST=1,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,62
IFDHCP_OPT=""
DOCALIB="false"
FAILEDEXPS=""
FULLCOPY=false
STATBASE="https://fndcadoor.fnal.gov:2880/pnfs/fnal.gov/usr/des"
umask 002
#######################################
### Protection against dead nodes ###
if [ ! -f /cvmfs/fermilab.opensciencegrid.org/products/common/etc/setup ]; then
echo "Unable to find fermilab CVMFS repo setup file, so I assume the whole repo is missing."
echo "I will sleep for four hours to block the slot and then exit with an error."
sleep 14400
exit 1
fi
if [ ! -f /cvmfs/des.opensciencegrid.org/eeups/startupcachejob21i.sh ]; then
echo "Unable to find DES CVMFS repo startup file, so I assume the whole repo is missing."
echo "I will sleep for four hours to block the slot and then exit with an error."
sleep 14400
exit 1
fi
#######################################
### Protection against wrong StashCache version ###
if [ -n "${MIN_STASH_VERSION}" ]; then
echo "MIN_STASH_VERSION = $MIN_STASH_VERSION"
while [ $MIN_STASH_VERSION -gt $(attr -q -g revision /cvmfs/des.osgstorage.org) ]
do
echo "Revision of /cvmfs/des.osgstorage.org below minimum value of ${MIN_STASH_VER}. Sleeping 15 minutes to check next update."
sleep 900
done
else
echo "$MIN_STASH_VERSION not set. Continuing."
fi
####################
# get some worker node information
echo "Worker node information: `uname -a`"
OLDHOME=$HOME
export HOME=$PWD
# set environment
source /cvmfs/des.opensciencegrid.org/eeups/startupcachejob31i.sh
source /cvmfs/des.opensciencegrid.org/ncsa/centos7/finalcut/Y6A1+2/eups/desdm_eups_setup.sh
export EUPS_PATH=/cvmfs/des.opensciencegrid.org/ncsa/centos7/finalcut/Y6A1+2/eups/packages:/cvmfs/des.opensciencegrid.org/eeups/fnaleups:/cvmfs/des.opensciencegrid.org/2015_Q2/eeups/SL6/eups/packages
export IFDH_CP_MAXRETRIES=2
export IFDH_XROOTD_EXTRA="-f -N"
export XRD_REDIRECTLIMIT=255
#for IFDH
export EXPERIMENT=des
export IFDH_NO_PROXY=1
#export IFDH_TOKEN_ENABLE=1
#if [ "${GRID_USER}" = "desgw" ]; then
# export HTGETTOKENOPTS="--credkey=desgw/managedtokens/fifeutilgpvm01.fnal.gov" ;
#fi
export IFDH_GRIDFTP_EXTRA="-st 1800"
export XRD_REQUESTTIMEOUT=1200
# parse arguments and flags
ARGS="$@"
##### Don't forget to shift the args after you pull these out #####
while getopts "E:n:b:r:p:S:d:c:v:V:T:F:CjhsYOtm:" opt $ARGS
do case $opt in
E)
[[ $OPTARG =~ ^[0-9]+$ ]] || { echo "Error: exposure number must be an integer! You put $OPTARG" ; exit 1; }
EXPNUM=$OPTARG #TODO export?
shift 2
;;
n)
[[ $OPTARG =~ ^[0-9]+$ ]] || { echo "Error: Night must be an integer! You put $OPTARG" ; exit 1; }
NITE=$OPTARG #TODO export?
shift 2
;;
b)
case $OPTARG in
i|r|g|Y|z|u)
BAND=$OPTARG
shift 2
;;
*)
echo "Error: band option must be one of r,i,g,Y,z,u. You put $OPTARG."
exit 1
;;
esac
;;
r)
RNUM=$OPTARG #TODO export?
shift 2
;;
p)
PNUM=$OPTARG #TODO export?
shift 2
;;
S)
procnum=$OPTARG
shift 2
;;
j)
JUMPTOEXPCALIB=true
shift
;;
t)
TEMPLATE=true
shift
;;
V)
SNVETO_NAME=$OPTARG
shift 2
;;
T)
STARCAT_NAME=$OPTARG
shift 2
;;
C)
DOCALIB=true
shift
;;
s)
SINGLETHREAD=true
shift
;;
d) # add some checks here?
DESTCACHE=$OPTARG
shift 2
;;
m)
SCHEMA=$OPTARG
shift 2
;;
v)
DIFFIMG_VERSION=$OPTARG
shift 2
;;
F)
FULLCOPY=true
shift
;;
Y)
SPECIALY4=true
shift
;;
O)
OVERWRITE=true
shift
;;
h)
echo "usage: SEdiff.sh -E EXPNUM -r RNUM -p PNUM -n NITE -b BAND (i|r|g|Y|z|u) -S season (dpXX) [-c ccdlist] [-d destcache (scratch|persistent)] [-m SCHEMA (gw|wsdiff)] [-v diffimg_version] [-t] [-C] [-j] [-s] [-O] [-V SNVETO_NAME] [-T STARCAT_NAME] [-Y] [-F]"
exit 1
;;
c)
#TODO: does this work for a comma-separated list?
[[ $OPTARG =~ ^[0-9]+$ ]] || { echo "Error: CCD number must be an integer! You put $OPTARG" ; exit 1; }
[[ $OPTARG -lt 70 ]] || { echo "Error: the chip number must be less than 70. You entered $OPTARG." ; exit 1; }
if [ $OPTARG -gt 0 ]; then
CCDNUM_LIST=$OPTARG
shift 2
else
CCDNUM_LIST=$(echo $CCDNUM_LIST | awk -F "," '{print $'$((${PROCESS}+1))'}')
shift 2
fi
;;
:)
echo "Option -$OPTARG requires an argument."
exit 1
;;
esac
done
if [ "x$EXPNUM" = "x" ]; then echo "Exposure number not set; exiting." ; exit 1 ; fi
if [ "x$NITE" = "x" ]; then echo "NITE not set; exiting." ; exit 1 ; fi
if [ "x$BAND" = "x" ]; then echo "BAND not set; exiting." ; exit 1 ; fi
if [ "x$RNUM" = "x" ]; then echo "r number not set; exiting." ; exit 1 ; fi
if [ "x$PNUM" = "x" ]; then echo "p number not set; exiting." ; exit 1 ; fi
if [ "x$procnum" == "x" ]; then echo "season number not set (use -S option); exiting." ; exit 1 ; fi
if [ "x$CCDNUM_LIST" == "x" ]; then echo "CCD number not set; exiting."; exit 1 ; fi
rpnum="r${RNUM}p${PNUM}"
# tokenize ccd argument (in case of multiple comma-separated ccds)
ccdlist=(${CCDNUM_LIST//,/ })
PNFSPATH="/pnfs/des/${DESTCACHE}/${SCHEMA}/exp/${NITE}/${EXPNUM}"
STATPATH=${STATBASE}/${DESTCACHE}/${SCHEMA}/exp/${NITE}/${EXPNUM}
immaskfiles=""
psffiles=""
csvfiles=""
ccdsvfiles=""
dotoutfile=""
ccddotoutfile=""
# Check whether SE outputs and .out files exist with gfal-stat; computationally cheaper than ifdh ls.
statfile=D$(printf %08d ${EXPNUM})_${BAND}_$(printf %02d ${CCDNUM_LIST})_r${RNUM}p${PNUM}_immask.fits.fz
gfal-stat ${STATPATH}/${statfile} > /dev/null
if [ $? -eq 0 ]; then
immaskfiles="$immaskfiles ${PNFSPATH}/${statfile}"
else
echo "$statfile not already present on disk."
fi
statfile=D$(printf %08d ${EXPNUM})_${BAND}_$(printf %02d ${CCDNUM_LIST})_r${RNUM}p${PNUM}_fullcat.fits
gfal-stat ${STATPATH}/${statfile} > /dev/null
if [ $? -eq 0 ]; then
psffiles="$psffiles ${PNFSPATH}/${statfile}"
else
echo "$statfile not already present on disk."
fi
statfile=allZP_D$(printf %08d ${EXPNUM})_r${RNUM}p${PNUM}.csv
gfal-stat ${STATPATH}/${statfile} > /dev/null
if [ $? -eq 0 ]; then
csvfiles="$csvfiles ${PNFSPATH}/${statfile}"
else
echo "$statfile not already present on disk."
fi
statfile=D$(printf %08d ${EXPNUM})_r${RNUM}p${PNUM}_ZP.csv
gfal-stat ${STATPATH}/${statfile} > /dev/null
if [ $? -eq 0 ]; then
csvfiles="$csvfiles ${PNFSPATH}/${statfile}"
else
echo "$statfile not already present on disk."
fi
for csvfile in allZP_D$(printf %08d ${EXPNUM})_r${RNUM}p${PNUM}.csv Zero_D$(printf %08d ${EXPNUM})_$(printf %02d $CCDNUM_LIST)_r${RNUM}p${PNUM}.csv D$(printf %08d ${EXPNUM})_$(printf %02d $CCDNUM_LIST)_r${RNUM}p${PNUM}_ZP.csv
do
gfal-stat ${STATPATH}/${csvfile} > /dev/null && ccdcsvfiles="$ccdcsvfiles ${PNFSPATH}/${csvfile}"
done
statfile=${EXPNUM}.out
gfal-stat ${STATPATH}/${statfile} > /dev/null
if [ $? -eq 0 ]; then
dotoutfile=${PNFSPATH}/${statfile}
else
echo "$statfile not already present on disk."
fi
statfile=${EXPNUM}_$(printf %d ${ccdlist}).out
gfal-stat ${STATPATH}/${statfile} > /dev/null
if [ $? -eq 0 ]; then
ccddotoutfile=${PNFSPATH}/${statfile}
else
echo "$statfile not already present on disk."
fi
# get filenames
nimmask=`echo $immaskfiles | wc -w`
if [ $nimmask -ge 1 ]; then
npsf=`echo $psffiles | wc -w`
if [ $npsf -ge 1 ] || [ "$DOCALIB" == "false" ]; then
ncsv=`echo $csvfiles | wc -w`
if [ $ncsv -ge 2 ] || [ "$DOCALIB" == "false" ]; then
if [ "$OVERWRITE" == "false" ]; then
echo "All SE processing for $EXPNUM, r=$RNUM, p=$PNUM is complete. We will skip the SE step."
SKIPSE=true
else
echo "All files are present, but the -O option was given, so we are continuing on with the job."
fi
else
# we don't have the combined csv files for this exposure and rpnum. Let's check for the CCD-specific files now.
# If they are present,
nccdcsv=`echo $ccdcsvfiles | wc -w`
if [ $nccdcsv -ge 2 ]; then
if [ "$OVERWRITE" == "false" ]; then
echo "All SE processing for $EXPNUM, r=$RNUM, p=$PNUM is complete. We will skip the SE step."
SKIPSE=true
else
echo "All files are present, but the -O option was given, so we are continuing on with the job."
fi
else
echo "csv files not all present; continuing with the job."
fi
fi
else
echo "fullcat files not all present; continuing with the job."
fi
else
echo "immask files not all present; continuing with the job."
fi
# do SE processing
if [ "$SKIPSE" == "false" ] ; then # if statement allows SE to be skipped if SE is complete and the -O flag is not used
echo "***** BEGIN SE PROCESSING *****"
# flag for whether or not to do calibration (if the image isn't/is in the DES footprint)
if [ "$DOCALIB" == "true" ] ; then
echo "This SE job will include BLISS calib step."
else
echo "This SE job will use calib info from the DB."
filestorm="$psffiles $csvfiles"
if [ ! -z "${filestorm}" ]; then
ifdh rm $filestorm
fi
fi
ifdh cp -D /pnfs/des/resilient/gw/code/MySoft4_v2.tar.gz /pnfs/des/resilient/gw/code/test_mysql_libs.tar.gz ./ || { echo "Error copying input files. Exiting." ; exit 2 ; }
tar xzf ./MySoft4_v2.tar.gz
#NORA FIX
ifdh cp /pnfs/des/persistent/desgw/desdmLiby1e2.py ./
#cp ../desdmLiby1e2.py ./
#END NORA FIX
tar xzfm ./test_mysql_libs.tar.gz
chmod +x make_red_catlist.py expCalib-isaac-BBH.py expCalib-isaac-BNS.py getcorners.sh
rm -f confFile
# Automatically determine year and epoch based on exposure number
# NAME MINNITE MAXNITE MINEXPNUM MAXEXPNUM
# -------------------------------- -------- -------- ---------- ----------
# SVE1 20120911 20121228 133757 164457
# SVE2 20130104 20130228 165290 182695
# Y1E1 20130815 20131128 226353 258564
# Y1E2 20131129 20140209 258621 284018
# Y2E1 20140807 20141129 345031 382973
# Y2E2 20141205 20150518 383751 438346
# Y3 20150731 20160212 459984 516846
# Y4E1 666747
# Y7 666748 # Per Nikolay 2020-11-15, everything for Y5+ now using "Y7"
#######################################
# need to implement here handling of different "epochs" within the same year
# need lso the "if not special option to use Y4E1 numbers"
# note that we could use {filter:s}no61.head for sve1, sve2, and y1e1, but for consistency
# we are doing no2no61.head for everything as of now (2017-01-04)
# IMPORTANT NOTE: Be sure that all of the filenames below are in SINGLE QUOTES.
if [ "${SPECIALY4}" == "true" ]; then
YEAR=y4
EPOCH=e1
biasfile='D_n20151113t1123_c{ccd:>02s}_r2350p02_biascor.fits'
bpmfile='D_n20151113t1123_c{ccd:>02s}_r2400p01_bpm.fits'
dflatfile='D_n20151113t1123_{filter:s}_c{ccd:>02s}_r2350p02_norm-dflatcor.fits'
skytempfile='Y2T4_20150715t0315_{filter:s}_c{ccd:>02s}_r2404p01_skypca-tmpl.fits'
starflatfile='Y2A1_20150715t0315_{filter:s}_c{ccd:>02s}_r2360p01_starflat.fits'
headfile='f'$CCDNUM_LIST'.head'
pcaprefix='Y2T4_20150715t0315_{filter:s}_r2404p01_skypca-binned-fp.fits'
else
if [ $EXPNUM -lt 165290 ]; then
YEAR=sv
EPOCH=e1
biasfile='D_n20130115t0131_c{ccd:>02s}_r1788p01_biascor.fits'
bpmfile='D_n20130115t0130_c{ccd:>02s}_r1975p01_bpm.fits'
dflatfile='D_n20130115t0131_{filter:s}_c{ccd:>02s}_r1788p01_norm-dflatcor.fits'
skytempfile='Y2A1_20130101t0315_{filter:s}_c{ccd:>02s}_r1979p01_skypca-tmpl.fits'
starflatfile='Y2A1_20130101t0315_{filter:s}_c{ccd:>02s}_r1976p01_starflat.fits'
headfile='f'$CCDNUM_LIST'.head'
pcaprefix='Y2A1_20130101t0315_{filter:s}_r1979p01_skypca-binned-fp.fits'
elif [ $EXPNUM -lt 226353 ]; then
YEAR=sv
EPOCH=e1
biasfile='D_n20130115t0131_c{ccd:>02s}_r1788p01_biascor.fits'
bpmfile='D_n20130115t0130_c{ccd:>02s}_r1975p01_bpm.fits'
dflatfile='D_n20130115t0131_{filter:s}_c{ccd:>02s}_r1788p01_norm-dflatcor.fits'
skytempfile='Y2A1_20130101t0315_{filter:s}_c{ccd:>02s}_r1979p01_skypca-tmpl.fits'
starflatfile='Y2A1_20130101t0315_{filter:s}_c{ccd:>02s}_r1976p01_starflat.fits'
headfile='f'$CCDNUM_LIST'.head'
pcaprefix='Y2A1_20130101t0315_{filter:s}_r1979p01_skypca-binned-fp.fits'
elif [ $EXPNUM -lt 258564 ]; then
YEAR=y1
EPOCH=e1
biasfile='D_n20130916t0926_c{ccd:>02s}_r1999p06_biascor.fits'
bpmfile='D_n20130916t0926_c{ccd:>02s}_r2083p01_bpm.fits'
dflatfile='D_n20130916t0926_{filter:s}_c{ccd:>02s}_r1999p06_norm-dflatcor.fits'
skytempfile='Y2A1_20130801t1128_{filter:s}_c{ccd:>02s}_r2044p01_skypca-tmpl.fits'
starflatfile='Y2A1_20130801t1128_{filter:s}_c{ccd:>02s}_r2046p01_starflat.fits'
headfile='f'$CCDNUM_LIST'.head'
pcaprefix='Y2A1_20130801t1128_{filter:s}_r2044p01_skypca-binned-fp.fits'
elif [ $EXPNUM -lt 284391 ]; then
YEAR=y1
EPOCH=e2
biasfile='D_n20140117t0129_c{ccd:>02s}_r2045p01_biascor.fits'
bpmfile='D_n20140117t0129_c{ccd:>02s}_r2105p01_bpm.fits'
dflatfile='D_n20140117t0129_{filter:s}_c{ccd:>02s}_r2045p01_norm-dflatcor.fits'
skytempfile='Y2A1_20131129t0315_{filter:s}_c{ccd:>02s}_r2106p01_skypca-tmpl.fits'
starflatfile='Y2A1_20131129t0315_{filter:s}_c{ccd:>02s}_r2107p01_starflat.fits'
headfile='f'$CCDNUM_LIST'.head'
pcaprefix='binned-fp/Y2A1_20131129t0315_{filter:s}_r2106p01_skypca-binned-fp.fits'
elif [ $EXPNUM -le 383321 ]; then
YEAR=y2
EPOCH=e1
biasfile='D_n20141204t1209_c{ccd:>02s}_r1426p08_biascor.fits'
bpmfile='D_n20141020t1030_c{ccd:>02s}_r1474p01_bpm.fits'
dflatfile='D_n20141020t1030_{filter:s}_c{ccd:>02s}_r1471p01_norm-dflatcor.fits'
skytempfile='Y2A1_20140801t1130_{filter:s}_c{ccd:>02s}_r1635p01_skypca-tmpl.fits'
starflatfile='Y2A1_20140801t1130_{filter:s}_c{ccd:>02s}_r1637p01_starflat.fits'
headfile='f'$CCDNUM_LIST'.head'
pcaprefix='Y2A1_20140801t1130_{filter:s}_r1635p01_skypca-binned-fp.fits'
elif [ $EXPNUM -le 438444 ]; then
YEAR=y2
EPOCH=e2
biasfile='D_n20150105t0115_c{ccd:>02s}_r2050p02_biascor.fits'
bpmfile='D_n20150105t0115_c{ccd:>02s}_r2134p01_bpm.fits'
dflatfile='D_n20150105t0115_{filter:s}_c{ccd:>02s}_r2050p02_norm-dflatcor.fits'
skytempfile='Y2A1_20141205t0315_{filter:s}_c{ccd:>02s}_r2133p01_skypca-tmpl.fits'
starflatfile='Y2A1_20141205t0315_{filter:s}_c{ccd:>02s}_r2132p01_starflat.fits'
headfile='f'$CCDNUM_LIST'.head'
pcaprefix='Y2A1_20141205t0315_{filter:s}_r2133p01_skypca-binned-fp.fits'
elif [ $EXPNUM -le 519543 ]; then
YEAR=y3
EPOCH=e1
biasfile='D_n20151113t1123_c{ccd:>02s}_r2350p02_biascor.fits'
bpmfile='D_n20151113t1123_c{ccd:>02s}_r2359p01_bpm.fits'
dflatfile='D_n20151113t1123_{filter:s}_c{ccd:>02s}_r2350p02_norm-dflatcor.fits'
skytempfile='Y2A1_20150715t0315_{filter:s}_c{ccd:>02s}_r2361p01_skypca-tmpl.fits'
starflatfile='Y2A1_20150715t0315_{filter:s}_c{ccd:>02s}_r2360p01_starflat.fits'
headfile='f'$CCDNUM_LIST'.head'
pcaprefix='Y2A1_20150715t0315_{filter:s}_r2361p01_skypca-binned-fp.fits'
elif [ $EXPNUM -le 666747 ]; then
YEAR=y4
EPOCH=e1
biasfile='D_n20151113t1123_c{ccd:>02s}_r2350p02_biascor.fits'
bpmfile='D_n20151113t1123_c{ccd:>02s}_r2400p01_bpm.fits'
dflatfile='D_n20151113t1123_{filter:s}_c{ccd:>02s}_r2350p02_norm-dflatcor.fits'
skytempfile='Y2T4_20150715t0315_{filter:s}_c{ccd:>02s}_r2404p01_skypca-tmpl.fits'
starflatfile='Y2A1_20150715t0315_{filter:s}_c{ccd:>02s}_r2360p01_starflat.fits'
headfile='f'$CCDNUM_LIST'.head'
pcaprefix='Y2T4_20150715t0315_{filter:s}_r2404p01_skypca-binned-fp.fits'
else
YEAR=y7
EPOCH=''
biasfile='D_n20180913t0923_c{ccd:>02s}_r4033p02_biascor.fits'
bpmfile='D_n20180912t1105_c{ccd:>02s}_r3697p01_bpm.fits'
dflatfile='D_n20180913t0923_{filter:s}_c{ccd:>02s}_r4033p02_norm-dflatcor.fits'
skytempfile='Y6A1_20180908t1117_{filter:s}_c{ccd:>02s}_r4024p01_skypca-tmpl.fits'
starflatfile='Y6A1_20180908t1117_{filter:s}_c{ccd:>02s}_r3762p01_starflat.fits'
headfile='f'$CCDNUM_LIST'.head'
pcaprefix='binned-fp/Y6A1_20180908t1117_{filter:s}_r4024p01_skypca-binned-fp.fits'
fi
if [ "${BAND}" == "u" ]; then
YEAR=y2
EPOCH=e1
biasfile='D_n20141204t1209_c{ccd:>02s}_r1426p08_biascor.fits'
bpmfile='D_n20141020t1030_c{ccd:>02s}_r1474p01_bpm.fits'
dflatfile='D_n20141020t1030_{filter:s}_c{ccd:>02s}_r1471p01_norm-dflatcor.fits'
skytempfile='Y2A1_20140801t1130_{filter:s}_c{ccd:>02s}_r1635p02_skypca-tmpl.fits'
starflatfile='Y2A1_20140801t1130_{filter:s}_c{ccd:>02s}_r1637p01_starflat.fits'
headfile='f'$CCDNUM_LIST'.head'
pcaprefix='binned-fp/Y2A1_20140801t1130_{filter:s}_r1635p02_skypca-binned-fp.fits'
if [ $EXPNUM -gt 666747 ]; then
YEAR=y7u
EPOCH=''
biasfile='D_n20180913t0923_c{ccd:>02s}_r4033p02_biascor.fits'
bpmfile='D_n20180912t1105_c{ccd:>02s}_r3697p01_bpm.fits'
dflatfile='D_n20170201t0213_{filter:s}_c{ccd:>02s}_r2922p01_norm-dflatcor.fits'
skytempfile='Y6A1_20170104t190116_{filter:s}_c{ccd:>02s}_r4099p01_skypca-tmpl.fits'
starflatfile='Y2A1_20150715t0315_{filter:s}_c{ccd:>02s}_r2360p01_starflat.fits'
headfile='f'$CCDNUM_LIST'.head'
pcaprefix='binned-fp/Y6A1_20170104t190116_{filter:s}_r4099p01_skypca-binned-fp.fits'
fi
fi
fi
# IMPORTANT: test whether we are on a node where stashCache work properly.
# now, we test if /cvmfs/des.ogstorage.ord is available and works properly. If it does,
# use it for corr_dir and conf_dir
corr_dir=""
conf_dir=""
cat /cvmfs/des.osgstorage.org/pnfs/fnal.gov/usr/des/persistent/stash/test.stashdes.1M > /dev/null 2>&1
TEST_STASH=$?
if [ $TEST_STASH -eq 0 ]; then
corr_dir="/cvmfs/des.osgstorage.org/pnfs/fnal.gov/usr/des/persistent/stash/desdm/calib/"
conf_dir="/cvmfs/des.osgstorage.org/pnfs/fnal.gov/usr/des/persistent/stash/desdm/config/"
else
corr_dir="/pnfs/des/persistent/desdm/calib/"
conf_dir="/pnfs/des/persistent/stash/desdm/config/"
fi
# write to confFile
cat <<EOF >> confFile
[General]
nite: 20141229
expnum: 393047
filter: z
r: 04
p: 11
chiplist: $CCDNUM_LIST
data_dir: /pnfs/des/scratch/${SCHEMA}/dts/
corr_dir: $corr_dir
conf_dir: $conf_dir
exp_dir: /pnfs/des/${DESTCACHE}/${SCHEMA}/exp/
template: D{expnum:>08s}_{filter:s}_{ccd:>02s}_r{r:s}p{p:s}
exp_template: D{expnum:>08s}_{filter:s}_r{r:s}p{p:s}
year: $YEAR
yearb: y2
epoch: $EPOCH
epochb: e1
[crosstalk]
xtalk = DECam_20130606.xtalk
template = D{expnum:>08s}_{filter:s}_%02d_r{r:s}p{p:s}_xtalk.fits
replace = DES_header_update.20151120
[pixcorrect]
bias=$biasfile
bpm=$bpmfile
linearity = lin_tbl_v0.4.fits
bf = bfmodel_20150305.fits
flat=$dflatfile
[sextractor]
filter_name = sex.conv
filter_name2 = sex.conv
starnnw_name = sex.nnw
parameters_name = sex.param_scamp_psfex
parameters_name_psfex = sex.param_psfex
configfile = sexforscamp.config
parameters_name2 = sex.param.finalcut.20130702
configfile2 = sexgain.config
sexforpsfexconfigfile = sexforpsfex.config
[skyCombineFit]
################3 THIS IS WHAT SHOULD BE CHANGED FOR BINNED FP ################3
#pcafileprefix = pca_mini
pcafileprefix = $pcaprefix
[skysubtract]
pcfilename = $skytempfile
weight = sky
[scamp]
imagflags = 0x0700
flag_mask = 0x00fd
flag_astr = 0x0000
catalog_ref = GAIA-DR2
default_scamp = default2.scamp.20240701
head = $headfile
[starflat]
starflat = $starflatfile
[psfex]
#old version with PSFVAR_DEGREES 0
#configfile = configoutcat2.psfex
configfile = configse.psfex
EOF
sed -i -e "/^nite\:/ s/nite\:.*/nite\: ${NITE}/" -e "/^expnum\:/ s/expnum\:.*/expnum\: ${EXPNUM}/" -e "/^filter\:/ s/filter:.*/filter\: ${BAND}/" -e "/^r\:/ s/r:.*/r\: ${RNUM}/" -e "/^p\:/ s/p:.*/p\: ${PNUM}/" confFile
#setup -j finalcut Y6A1+2 -Z /cvmfs/des.opensciencegrid.org/2015_Q2/eeups/SL6/eups/packages
setup finalcut Y6A1+2
setup diffimg $DIFFIMG_VERSION
setup CoreUtils 1.0.1+0
setup wcstools 3.9.6+0
export PATH=${WCSTOOLS_DIR}/bin:${PATH}
setup -j ftools v6.17; export HEADAS=$FTOOLS_DIR
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${PWD}/usr/lib64/mysql
# in case single epoch processing was already done, skip that step
if [ "$JUMPTOEXPCALIB" == "true" ] ; then
echo "jumping to the calibration step..."
nfiles=`ls *_r${RNUM}p${PNUM}_fullcat.fits *_r${RNUM}p${PNUM}_immask.fits.fz | wc -l`
nccds=`grep chiplist confFile | awk -F ':' '{print $2}' | sed 's/,/ /g' | wc -w`
nccds2=`expr $nccds \* 2`
if [ $nfiles -ne $nccds2 ] ; then
echo "copying fits files from Dcache"
for c in $ccdlist; do
# copies all ccds
c=$(printf "%02d" $c)
filestocopy1=""
filestocopy2=""
gfal-stat ${STATBASE}/${DESTCACHE}/${SCHEMA}/exp/${NITE}/${EXPNUM}/D$(printf %08d ${EXPNUM})_${BAND}_${c}_r${RNUM}p${PNUM}_fullcat.fits > /dev/null 2>&1
if [ $? -eq 0 ]; then
filestocopy1="/pnfs/des/${DESTCACHE}/${SCHEMA}/exp/${NITE}/${EXPNUM}/D$(printf %08d ${EXPNUM})_${BAND}_${c}_r${RNUM}p${PNUM}_fullcat.fits"
else
echo "Error finding ${PNFSPATH}/D$(printf %08d ${EXPNUM})_${BAND}_${c}_r${RNUM}p${PNUM}_fullcat.fits"
fi
echo "filestocopy1: $filestocopy1"
gfal-stat ${STATBASE}/${DESTCACHE}/${SCHEMA}/exp/${NITE}/${EXPNUM}/D$(printf %08d ${EXPNUM})_${BAND}_${c}_r${RNUM}p${PNUM}_immask.fits.fz > /dev/null 2>&1
if [ $? -eq 0 ]; then
filestocopy2="/pnfs/des/${DESTCACHE}/${SCHEMA}/exp/${NITE}/${EXPNUM}/D$(printf %08d ${EXPNUM})_${BAND}_${c}_r${RNUM}p${PNUM}_immask.fits.fz"
else
echo "Error finding ${PNFSPATH}/D$(printf %08d ${EXPNUM})_${BAND}_${c}_r${RNUM}p${PNUM}_immask.fits.fz"
fi
echo "filestocopy2: $filestocopy2"
ifdh cp --force=xrootd -D $filestocopy1 $filestocopy2 .
done
for file in $(ls *_immask.fits.fz)
do
funpack -D $file
done
fi
else
if [ "$SINGLETHREAD" == "true" ] ; then
python run_desdmy1e2.py confFile
else
python run_SEproc.py confFile
fi
RESULT=$?
if [ $RESULT -ne 0 ] ; then
echo "ERROR: Main SE processing has exited abnormally with status $RESULT. The rest of the script will now terminate."
# cleanup if we are in a grid job (defined as having the GRID_USER environment variable set) to avoid potential timeouts on exit
if [ -n "$GRID_USER" ] ; then rm -f *.fits *.fits.fz *.ps *.psf *.xml full_1.cat *.head ; fi
exit
fi
fi
if [ "$DOCALIB" == "true" ]; then
#setup expCalib
#setup python 2.7.9+1
python ./make_red_catlist.py
echo "make_red_catlist.py finished with exit status $?"
# doing this unsetup bit seems to break the BLISS old script. Commenting out for now
# for prodlist in healpy astropy fitsio matplotlib six python ; do unsetup $prodlist ; done # some attempted version fixing
#touch bliss_test.log
ifdh cp /pnfs/des/persistent/desgw/expCalib-isaac-BBH.py ./expCalib-isaac-BBH.py
#cp ../BLISS-expCalib_Y3apass-old-Nora.py ./BLISS-expCalib_Y3apass-old.py
./expCalib-isaac-BBH.py --expnum $EXPNUM --reqnum $RNUM --attnum $PNUM --ccd $CCDNUM_LIST
RESULT=$?
echo "BLISS-expCalib_Y3pass-old.py exited with status $RESULT"
files2cp=`ls allZP*r${RNUM}*p${PNUM}*.csv Zero*r${RNUM}*p${PNUM}*.csv D*${EXPNUM}*_ZP.csv D*${EXPNUM}*CCDsvsZPs.png D*${EXPNUM}*NumClipstar.png D*${EXPNUM}*ZP.png`
if [ "x${files2cp}" = "x" ]; then
echo "Error, no calibration files to copy!"
else
ifdh cp --force=xrootd -D $files2cp /pnfs/des/${DESTCACHE}/${SCHEMA}/exp/${NITE}/${EXPNUM} || echo "ifdh cp of calibration csv and png files failed. There could be problems with Diffimg down the road when using this exposure."
fi
fi
du -sh .
# cleanup if we are in a grid job (defined as having the GRID_USER environment variable set) to avoid potential timeouts on exit
if [ -n "$GRID_USER" ] ; then rm -f *.fits *.fits.fz *.ps *.psf *.xml full_1.cat *.head ; fi
export HOME=$OLDHOME
fi # end the if statement that skips SE processing
# exit now if SE processing a template
if [ "$TEMPLATE" == "true" ]; then
echo "Finished SE processing template image; exiting before verifySE steps"
exit 0
fi
######## CODE FORMERLY IN verifySE.sh ##########
echo "***** BEGIN VERIFYSE *****"
export RNUM=$RNUM
export PNUM=$PNUM
export EXPNUM=$EXPNUM
export NITE=$NITE
# copy over the copy_pairs script so we know the templates
ifdh cp ${IFDHCP_OPT} -D /pnfs/des/${DESTCACHE}/${SCHEMA}/exp/${NITE}/${EXPNUM}/${procnum}/input_files/copy_pairs_for_${EXPNUM}.sh /pnfs/des/${DESTCACHE}/${SCHEMA}/exp/${NITE}/${EXPNUM}/WS_diff.list ./ || { echo "failed to copy WS_diff.list and copy_paris_for_${EXPNUM}.sh files" ; exit 2 ; } # do we want to exit here?
TEMPLATEPATHS=`cat copy_pairs_for_${EXPNUM}.sh | sed -r -e "s/ifdh\ cp\ (\-\-force=xrootd\ )?\-D\ //" -e "s/[0-9]{6,7}\.out//g" | sed -e 's/\$TOPDIR_WSTEMPLATES\/pairs\///'` ##AGTEST 6-->7
baseccddotout=$(basename $ccddotoutfile)
ifdh cp -D $dotoutfile $ccddotoutfile ./ || { echo "Failed to copy both combined .out file $dotoutfiles and CCD file ${ccddotoutfiles}. At least one is required. Exiting." ; exit 2 ; }
#AG change
if [ ! -s ${EXPNUM}.out ]; then
if [ -s $baseccddotout ]; then
cp ${baseccddotout} ${EXPNUM}.out || echo "Error copying ${baseccdotout}."
fi
fi
# if any of them failed remove them from WS_diff.list
echo "FAILEDEXPS = $FAILEDEXPS"
for failedexp in $FAILEDEXPS
do
echo "If FAILEDEXPS is empty, I shouldn't be getting here"
sed -i -e "s/${failedexp}//" ./WS_diff.list
OLDCOUNT=`awk '{print $1}' WS_diff.list`
NEWCOUNT=$((${OLDCOUNT}-1))
sed -i -e s/${OLDCOUNT}/${NEWCOUNT}/ WS_diff.list
done
# run make starcat and difference imaging ccd-by-ccd (in case of comma-separated ccd list)
# in most cases, this list will only be 1 ccd long (and the 1-ccd runs will be run in parallel)
for c in $ccdlist; do
c2=$(printf "%02d" $c)
######## CODE FORMERLY IN RUN_DIFFIMG_PIPELINE.sh ##########
### now we want to make the local directory structure by copying in
#copy some of the top dir list files and such
# .ini sets up database access (with passwords)
# WS_diff.list created by dagmaker
# run_inputs.tar.gz for each exposure number, copies over all the scripts in order to run
#### revised tar file 20180203
filestocopy="/pnfs/des/resilient/${SCHEMA}/db-tools/desservices.ini /pnfs/des/${DESTCACHE}/${SCHEMA}/exp/${NITE}/${EXPNUM}/WS_diff.list /pnfs/des/${DESTCACHE}/${SCHEMA}/exp/${NITE}/${EXPNUM}/${procnum}/${EXPNUM}_run_inputs.tar.gz"
ifdh cp ${IFDHCP_OPT} -D $filestocopy ./ || { echo "ifdh cp failed for SN_mon* and such" ; exit 1 ; }
tar zxf ${EXPNUM}_run_inputs.tar.gz
chmod 600 ${HOME}/desservices.ini
# set environment location
LOCDIR="${procnum}/${BAND}_`printf %02d $CCDNUM_LIST`"
# for backwards compatibility tar file copy stuff; not needed anymore
if [ ! -d ${procnum}/input_files ]; then
echo "${procnum}/input_files does not exist. This is probably an older input tar file. Create and copy from dCache."
inputfiles=$(ifdh ls /pnfs/des/${DESTCACHE}/${SCHEMA}/exp/${NITE}/${EXPNUM}/${procnum}/input_files/ )
for ifile in $inputfiles
do
basefile=`basename $ifile`
if [ "${basefile}" == "input_files" ] || [ -z "$basefile" ]; then
echo "skipping dir itself"
else
ifdh cp ${IFDHCP_OPT} -D /pnfs/des/${DESTCACHE}/${SCHEMA}/exp/${NITE}/${EXPNUM}/${procnum}/input_files/${basefile} ./${procnum}/input_files/ || exit 2
fi
done
fi
# make symlinks to these files
ln -s ${procnum}/input_files/* .
# make some local directories expected by the diffimg pipeline
mkdir ${LOCDIR}/headers ${LOCDIR}/ingest ${LOCDIR}/$(basename $(ifdh ls /pnfs/${DESTCACHE}/${SCHEMA}/exp/${NITE}/${EXPNUM}/${LOCDIR}/stamps* 0 | head -1))
ln -s ${LOCDIR}/ingest ${LOCDIR}/stamps* ${LOCDIR}/headers .
/cvmfs/grid.cern.ch/util/cvmfs-uptodate /cvmfs/des.opensciencegrid.org # make sure we have new version of cvmfs
# Setup
setup diffimg $DIFFIMG_VERSiON
setup CoreUtils 1.0.1+0
setup wcstools 3.9.6+0
setup -j easyaccess -Z /cvmfs/des.opensciencegrid.org/eeups/fnaleups
setup cxOracle
setup oracleclient
setup -j fitsio -Z /cvmfs/des.opensciencegrid.org/eeups/fnaleups
#setup -j astropy -Z /cvmfs/des.opensciencegrid.org/2015_Q2/eeups/SL6/eups/packages
#setup -j scipy -Z /cvmfs/des.opensciencegrid.org/2015_Q2/eeups/SL6/eups/packages
setup astropy
setup scipy
setup -j sep -Z /cvmfs/des.opensciencegrid.org/eeups/fnaleups
setup wcslib
setup cfitsio
setup cfitsio_shared
setup gsl
setup swarp
setup sextractor
setup scamp
setup psfex
setup gw_utils -Z /cvmfs/des.opensciencegrid.org/eeups/fnaleups
export PATH=$DIFFIMG_DIR/bin:$PATH
export WCS_INC=-I${WCSLIB_DIR}/include/wcslib
export SNANA_DIR=/cvmfs/des.opensciencegrid.org/eeups/fnaleups/Linux64/SNANA/v11_03e
setup -j ftools v6.17
setup extralibs
export HEADAS=$FTOOLS_DIR
export PATH=${WCSTOOLS_DIR}/bin:${PATH}
setup -j autoscan v3.2.1+0 -Z /cvmfs/des.opensciencegrid.org/eeups/fnaleups
setup -j joblib -Z /cvmfs/des.opensciencegrid.org/2015_Q2/eeups/SL6/eups/packages
setup -j scikitlearn -Z /cvmfs/des.opensciencegrid.org/2015_Q2/eeups/SL6/eups/packages
setup -j esutil -Z /cvmfs/des.opensciencegrid.org/eeups/fnaleups
# have to set the PFILES variable to be a local dir and not something in CVMFS
mkdir syspfiles
ln -s ${FTOOLS_DIR}/syspfiles/* ./syspfiles
export PFILES=${PWD}/syspfiles
echo "EUPS setup complete"
# setup lots more environment variables
export DES_SERVICES=${PWD}/desservices.ini
export DES_DB_SECTION=db-dessci
export DIFFIMG_HOST=FNAL
# use catalog dir in stashCache if StashCache works on this worker node. Otherwise fall back to regular CVMFS.
# try to read testfile in stashcache ; to check if StashCache is correct version and readable
STASHTEST=$( cat /cvmfs/des.osgstorage.org/stash/test.stashdes.1M > /dev/null 2>&1)
if [ $? -eq 0 ] && [ -d /cvmfs/des.osgstorage.org/stash/fnal/SNscampCatalog ]; then
export SCAMP_CATALOG_DIR=/cvmfs/des.osgstorage.org/stash/fnal/SNscampCatalog
else
export SCAMP_CATALOG_DIR=/cvmfs/des.opensciencegrid.org/fnal/SNscampCatalog
fi
export AUTOSCAN_PYTHON=$PYTHON_DIR/bin/python
export DES_ROOT=${PWD}/SNDATA_ROOT/INTERNAL/DES
export TOPDIR_SNFORCEPHOTO_IMAGES=${PWD}/data/DESSN_PIPELINE/SNFORCE/IMAGES
export TOPDIR_SNFORCEPHOTO_OUTPUT=${PWD}/data/DESSN_PIPELINE/SNFORCE/OUTPUT
export TOPDIR_DATAFILES_PUBLIC=${PWD}/data/DESSN_PIPELINE/SNFORCE/DATAFILES_TEST
export TOPDIR_WSTEMPLATES=${PWD}/WSTemplates
export TOPDIR_TEMPLATES=${PWD}/WSTemplates
export TOPDIR_SNTEMPLATES=${PWD}/SNTemplates
export TOPDIR_WSRUNS=${PWD}/data/WSruns
export TOPDIR_SNRUNS=${PWD}/data/SNruns
# these vars are for the make pair function that we pulled out of makeWSTemplates.sh
TOPDIR_WSDIFF=${TOPDIR_WSTEMPLATES}
echo "TOPDIR_WSDIFF $TOPDIR_WSDIFF"
DATADIR=${TOPDIR_WSDIFF}/data # DECam_XXXXXX directories
CORNERDIR=${TOPDIR_WSDIFF}/pairs # output XXXXXX.out and XXXXXX-YYYYYY.out
ETCDIR=${DIFFIMG_DIR}/etc # parameter files
CALDIR=${TOPDIR_WSDIFF}/relativeZP # relative zeropoints
MAKETEMPLDIR=${TOPDIR_WSDIFF}/makeTempl # templates are made in here
XY2SKY=${WCSTOOLS_DIR}/bin/xy2sky
AWK=/bin/awk
mkdir -p ${TOPDIR_SNFORCEPHOTO_IMAGES}
mkdir -p WSTemplates/data
mkdir SNTemplates
mkdir -p data/WSruns
mkdir -p data/SNruns
mkdir -p SNDATA_ROOT/INTERNAL/DES
mkdir -p ${TOPDIR_WSDIFF}/makeTempl
mkdir -p ${TOPDIR_WSDIFF}/pairs
mkdir -p ${TOPDIR_SNFORCEPHOTO_IMAGES}/${NITE} $DES_ROOT $TOPDIR_SNFORCEPHOTO_OUTPUT $TOPDIR_DATAFILES_PUBLIC
# now copy in the template files
# so now what we are going to do is copy in the .out files from the overlap_CCD part, and then use those to build the pairs, only
# copy in all possible template combinations for exposure, overlap
# overlap calculation is not done on per-ccd basis because it takes too long - instead it's faster to do all of them within this job
# copy files and symlink them
for overlapfile in $(cat ./${procnum}/input_files/copy_pairs_for_${EXPNUM}.sh)
do
if [[ $overlapfile =~ [0-9]{6,7}.out$ ]] ; then
filebase=$(basename $overlapfile)
if [ -s ${PWD}/overlap_outfiles/$filebase ]; then ln -s ${PWD}/overlap_outfiles/$filebase $TOPDIR_WSTEMPLATES/pairs/ ; fi
fi
done
if [ ! "$(ls -A $TOPDIR_WSTEMPLATES/pairs)" ]; then
echo "executing copy_pairs.sh at `date`"
source ./${procnum}/input_files/copy_pairs_for_${EXPNUM}.sh || echo "Error in copy_pairs_for_${EXPNUM}.sh. You may have problems with overlap calculation." # { echo "Error in copy_pairs_for_${EXPNUM}.sh. Exiting..." ; exit 2 ; }
fi
if [ -s ${EXPNUM}.out ] && [ -f ${EXPNUM}.out ] && [ ! "$(ls -A $TOPDIR_WSTEMPLATES/pairs/)" ]; then
cp ${EXPNUM}.out $TOPDIR_WSTEMPLATES/pairs/
fi
for templatedir in $TEMPLATEPATHS
do
tempexp=$(echo $templatedir | egrep -o "\/[0-9]{6,7}\/$" | tr -d "/") ##AGTEST
echo "Checking exposure $tempexp"
if [ ! -s $TOPDIR_WSTEMPLATES/pairs/${tempexp}.out ] ; then
dirfiles=$(ifdh ls $templatedir)
tempdotouts=""
for dirfile in $dirfiles
do
if [[ $dirfile == *.out ]]; then
tempdotouts="$tempdotouts $dirfile"
fi
done
ifdh cp -D $tempdotouts . || echo "Error copying .out files for $tempexp."
ccddots=$(ls ${tempexp}_[0-9]*.out 2>/dev/null)
if [ ! -z "${ccddots}" ] ; then
cat $ccddots > $TOPDIR_WSTEMPLATES/pairs/${tempexp}.out
fi
fi
done
#show output of copy
echo "contents of pairs directory:"
ls $TOPDIR_WSTEMPLATES/pairs/
echo "------"
################################
# create pairs of search and template images
################################
create_pairs() {
echo "start create_pairs at `date`"
tstart=`date +%s`
sexp=$EXPNUM
dtorad=`echo 45 | ${AWK} '{printf "%12.9f\n",atan2(1,1)/$1}'`
twopi=`echo 8 | ${AWK} '{printf "%12.9f\n",atan2(1,1)*$1}'`
echo "now in create_pairs: sexp = $sexp texp = $texp"
outpair=${CORNERDIR}/${sexp}-${texp}.out
outpairno=${CORNERDIR}/${sexp}-${texp}.no
rm -f ${outpair}
sexpfile=""
if [ -s ${sexp}_${CCDNUM_LIST}.out ]; then
sexpfile=${sexp}_${CCDNUM_LIST}.out
else
sexpfile=${CORNERDIR}/${sexp}.out
fi
sccd=`${AWK} '($3=='${CCDNUM_LIST}'){print $3}' $sexpfile | head -1`
# Search CCD RA Dec corner coordinates coverted to radians
info1=( `${AWK} '($3=='${CCDNUM_LIST}'){printf "%10.7f %10.7f %10.7f %10.7f %10.7f %10.7f %10.7f %10.7f\n",$4*"'"${dtorad}"'",$5*"'"${dtorad}"'",$6*"'"${dtorad}"'",$7*"'"${dtorad}"'",$8*"'"${dtorad}"'",$9*"'"${dtorad}"'",$10*"'"${dtorad}"'",$11*"'"${dtorad}"'"}' $sexpfile | head -1` )
rm -f tmp.tmp1
touch tmp.tmp1
j=1
while [[ $j -le 4 ]] # loop over 4 corners of the search image chip
do
thisa=`echo $j | ${AWK} '{print 2*($1-1)}'`
thisd=`echo $j | ${AWK} '{print 1+2*($1-1)}'`
a1=${info1[$thisa]}
d1=${info1[$thisd]}
# calculate angular distance (in degrees) of the 4 sides of each CCD
# ${texp}.out -> ${texp}.sides
(${AWK} '{printf "%11.8f %11.8f %11.8f %11.8f %11.8f %11.8f %11.8f %11.8f\n",$4*"'"${dtorad}"'",$5*"'"${dtorad}"'",$6*"'"${dtorad}"'",$7*"'"${dtorad}"'",$8*"'"${dtorad}"'",$9*"'"${dtorad}"'",$10*"'"${dtorad}"'",$11*"'"${dtorad}"'"}' ${CORNERDIR}/${texp}.out | ${AWK} '{printf "%10.8f %10.8f %10.8f %10.8f\n",sin($2)*sin($4)+cos($2)*cos($4)*cos($3-$1),sin($2)*sin($6)+cos($2)*cos($6)*cos($5-$1),sin($6)*sin($8)+cos($6)*cos($8)*cos($7-$5),sin($4)*sin($8)+cos($4)*cos($8)*cos($7-$3)}' | ${AWK} '{printf "%11.8f %11.8f %11.8f %11.8f\n",atan2(sqrt(1-$1*$1),$1),atan2(sqrt(1-$2*$2),$2),atan2(sqrt(1-$3*$3),$3),atan2(sqrt(1-$4*$4),$3)}' > ${texp}.sides) >& /dev/null
# calculate angular distance from a1 d1 to each corner of template image
# ${texp}.out -> ${texp}.dist
(${AWK} '{printf "%11.8f %11.8f %11.8f %11.8f %11.8f %11.8f %11.8f %11.8f %2d\n",$4*"'"${dtorad}"'",$5*"'"${dtorad}"'",$6*"'"${dtorad}"'",$7*"'"${dtorad}"'",$8*"'"${dtorad}"'",$9*"'"${dtorad}"'",$10*"'"${dtorad}"'",$11*"'"${dtorad}"'",$3}' ${CORNERDIR}/${texp}.out | ${AWK} '{printf "%10.8f %10.8f %10.8f %10.8f %2d\n",sin("'"${d1}"'")*sin($2)+cos("'"${d1}"'")*cos($2)*cos("'"${a1}"'"-$1),sin("'"${d1}"'")*sin($4)+cos("'"${d1}"'")*cos($4)*cos("'"${a1}"'"-$3),sin("'"${d1}"'")*sin($6)+cos("'"${d1}"'")*cos($6)*cos("'"${a1}"'"-$5),sin("'"${d1}"'")*sin($8)+cos("'"${d1}"'")*cos($8)*cos("'"${a1}"'"-$7),$9}' | ${AWK} '{printf "%11.8f %11.8f %11.8f %11.8f %2d\n",atan2(sqrt(1-$1*$1),$1),atan2(sqrt(1-$2*$2),$2),atan2(sqrt(1-$3*$3),$3),atan2(sqrt(1-$4*$4),$4),$5}' > ${texp}.dist) >& /dev/null
# protections for out-of-bounds results to cos/sin when image and template are exactly on top of each other
(paste ${texp}.sides ${texp}.dist | ${AWK} -v eps=0.00000001 '{printf "%11.8f %11.8f %11.8f %11.8f %2d\n",(cos($1)-cos($5)*cos($6))/(sin($5)*sin($6)+eps),(cos($2)-cos($5)*cos($7))/(sin($5)*sin($7)+eps),(cos($3)-cos($7)*cos($8))/(sin($7)*sin($8)+eps),(cos($4)-cos($6)*cos($8))/(sin($6)*sin($8)+eps),$9}' | while read one two three four five ; do eps=0.00000001 ; if [[ "$one" =~ ^[1-9] ]] ; then one=0.99999999 ; elif [[ "$one" =~ ^-[1-9] ]]; then one=-0.99999999 ; fi ; if [[ "$two" =~ ^[1-9] ]] ; then two=0.99999999 ; elif [[ "$two" =~ ^-[1-9] ]] ; then two=-0.99999999 ; fi ; if [[ "$three" =~ ^[1-9] ]] ; then three=0.99999999 ; elif [[ "$three" =~ ^-[1-9] ]] ; then three=-0.99999999 ; fi ; if [[ "$four" =~ ^[1-9] ]] ; then four=0.99999999 ; elif [[ "$four" =~ ^-[1-9] ]] ; then four=-0.99999999 ; fi ; echo $one $two $three $four $five ; done | ${AWK} '{printf "%11.8f %11.8f %11.8f %11.8f %2d\n",atan2(sqrt(1-$1*$1),$1),atan2(sqrt(1-$2*$2),$2),atan2(sqrt(1-$3*$3),$3),atan2(sqrt(1-$4*$4),$4),$5}' | ${AWK} '($1<10)&&($2<10)&&($3<10)&&($4<10)&&($1+$2+$3+$4>"'"${twopi}"'"*0.95){printf "%8d %2d %8d %2d\n","'"${sexp}"'","'"${sccd}"'","'"${texp}"'",$5}' >> tmp.tmp1) >& /dev/null
j=$[$j+1]
done # while j [[ ...
cat tmp.tmp1 | uniq > tmp.tmp2
mv tmp.tmp2 tmp.tmp1
n=`wc -l tmp.tmp1 | ${AWK} '{print $1}'`
if [[ $n -eq 1 ]]
then
${AWK} '(NR==1){printf "%8d %2d %8d %2d %2d\n",$1,$2,$3,'${n}',$4}' tmp.tmp1 >> ${outpair}
elif [[ $n -gt 1 ]]
then
${AWK} '(NR==1){printf "%8d %2d %8d %2d %2d",$1,$2,$3,'${n}',$4}' tmp.tmp1 >> ${outpair}
${AWK} '(NR>1){printf " %2d",$4}' tmp.tmp1 >> ${outpair}
echo hi | ${AWK} '{printf "\n"}' >> ${outpair}
fi
rm -f ${texp}.{sides,dist} tmp.tmp1
i=$[$i+1]
#done # sccd
# determine if there is an overlap
if [[ -f ${outpair} ]]
then
echo " ... has overlaps"
haspairs[$e]=1
else
echo " ... has NO overlaps"
touch ${outpairno}
haspairs[$e]=0
fi
e=$[$e+1]
echo "create_pairs done at `date`"
echo "create_pairs took $(( `date +%s` - $tstart )) seconds."
} # end create_pairs
# figure out how many out files we have and make the pairs (exclude the search exposure.out from this list)
dotoutfiles=$(ls ${TOPDIR_WSDIFF}/pairs/*.out | grep -v "${EXPNUM}-" )
echo $dotoutfiles
if [ -z "$dotoutfiles" ]; then
echo "Error, no .out files to make templates!!!"
fi
for idotoutfile in $dotoutfiles
do