#!/bin/csh -f
#
#      "do-jemx-science-analysis"
#
#  This script works for JEMX ISSW running on rev_2 data such as those
#  downloaded from Stockholm.
#
#    Version  2.0   2005-09-13/NJW   Include possibility of revised data (rev.002)
#                                    in archive in /lin6/data/arc/rev_2
#    Version  2.1   2007-01-18/NJW   Using OSA6.0
#    Version  2.2   2007-01-29/NJW   Copying .par files to local dir
#    Version  2.3   2007-11-27/NL    Using OSA7.0
#    Version  3.0   2009-01-09/NJW   No longer tied to ../analysis7
#    Version  8.5   2016-02-25/NJW   Using OSA10.3 (OSA10.2 with new j_ima_iros)
#    Version  8.6   2016-02-26/NL    Modified for NL environment
#
#  Syntax: dojsa_nl <parameter list>
#
#     This version takes parameters either from the command line or from "dojsa_nl.par"
#     in the IRAF and DAL fashion: dojsa_nl obsDir=work jemxNum=2
#     _but_ use the +exten convention in stead of the [exten] convention
#
#  Environment variables: JARCHIVE  can be:  NRTDATA
#
#  Required input:
#    1) The file 'swid.list' with a table of the 12 digit SWIDs to analyze
#    2) The file 'ebin.list' with energy limits given in keV
#                  Three lines e.g. identifier e.g. a2
#                                   Number_of_energy_bins e.g. 2
#                                   4.0 6.0 10.0 14.5
#                  These energies are interpreted by 'kev2pi -dn ...'
#
#  Files produced: jemx.lst for og_create is copied to ../analysis
#                  rev.list contains the 4 digit revolution numbers
#                  tmp is a temporary file used
#  The result is stored under ../analysis/obs/$OBSDIR
#
#     Required executables:     str_wrap
#                               falign
#                               mstrstr
#                               get_insta_swijd
#
if ( ! -e swid.list ) then
   echo No file: swid.list exists - terminate
   exit 0
endif
if ( ! -e ebin.list ) then
   echo No file: ebin.list exists - terminate
   exit 0
endif
if ( ! -e setup_env ) then
   echo No file: setup_env exists - terminate
   exit 0
endif
#
echo zzzz
echo This is dojsa_qqq_104
echo and JARCHIVE is $JARCHIVE
echo zzzz
#
#  Set flag for saving resulting files
#
set FLAG = 0
#set RESULTPATH = /nfs/jemx/nl_mosa
#
#  Set the call parameters
#
set ALLPARAMS = "$argv[*]"
set OBSDIR = `script_get_par dojsa_nl obsDir $ALLPARAMS`
set JEMXNUM = `script_get_par dojsa_nl jemxNum $ALLPARAMS`
set ENDLEVEL = `script_get_par dojsa_nl endLevel $ALLPARAMS`
set SKIPLEVELS = `script_get_par dojsa_nl skipLevels $ALLPARAMS`
set STARTLEVEL = `script_get_par dojsa_nl startLevel $ALLPARAMS`
set INSTMOD = `script_get_par dojsa_nl instMod $ALLPARAMS`
if ( $INSTMOD != "" ) set INSTMOD = `plus2brack $INSTMOD`
set RESPONSE = `script_get_par dojsa_nl response $ALLPARAMS`
if ( $RESPONSE != "" ) set RESPONSE = `plus2brack $RESPONSE`
set DOLBPL = `script_get_par dojsa_nl dolBPL $ALLPARAMS`
if ( $DOLBPL != "" ) set DOLBPL = `plus2brack $DOLBPL`
set USRCAT = `script_get_par dojsa_nl usrCat $ALLPARAMS`
if ( $USRCAT != "" ) set USRCAT = `plus2brack $USRCAT`
set GAINHIST = `script_get_par dojsa_nl gainHist $ALLPARAMS`
if ( $GAINHIST != "" ) set GAINHIST = `plus2brack $GAINHIST`
set GAINMODEL = `script_get_par dojsa_nl gainModel $ALLPARAMS`
set SKYIMAGESOUT = `script_get_par dojsa_nl skyImagesOut $ALLPARAMS`
set USEIROS = `script_get_par dojsa useIROS $ALLPARAMS`
set TIMESTEP = `script_get_par dojsa timeStep $ALLPARAMS`
#
#  Set the local path to templates
#
set LOCALTEMPLATES = /home/njw/jemx/issw/templates_osa103
#
#  Make *.par files for this particular run
#   and set PFILES accordingly
#
setenv STARTDIR $PWD
mkdir pfiles
cd pfiles
cp /home/njw/pfiles_osa104/j_export_par_osa104.tar .
tar xf j_export_par_osa104.tar
cd ..
set LOCALPFILES = "$STARTDIR/pfiles;"


set GNRLREFRCATPATH = /r6/jemx/catalogs
#
#   Display parameters
#
echo obsDir: $OBSDIR
echo jemxNum: $JEMXNUM
echo startLevel: $STARTLEVEL
echo endLevel: $ENDLEVEL
echo instMod: "$INSTMOD"
echo response: "$RESPONSE"
echo dolBPL: "$DOLBPL"
echo usrCat: "$USRCAT"
echo gainHist: "$GAINHIST"
echo gainModel: $GAINMODEL
echo skyImagesOut: $SKYIMAGESOUT
#
#   Log parameters in dojsa_nl.log
#
echo ------- `date` -------- >> dojsa_nl.log
echo obsDir: $OBSDIR >> dojsa_nl.log
echo jemxNum: $JEMXNUM >> dojsa_nl.log
echo startLevel: $STARTLEVEL >> dojsa_nl.log
echo endLevel: $ENDLEVEL >> dojsa_nl.log
echo instMod: "$INSTMOD" >> dojsa_nl.log
echo response: "$RESPONSE" >> dojsa_nl.log
echo dolBPL: "$DOLBPL" >> dojsa_nl.log
echo usrCat: "$USRCAT" >> dojsa_nl.log
echo gainHist: "$GAINHIST" >> dojsa_nl.log
echo gainModel: $GAINMODEL >> dojsa_nl.log
echo skyImagesOut: $SKYIMAGESOUT >> dojsa_nl.log
echo localpfiles: $LOCALPFILES >> dojsa_nl.log
echo swid.list first line: `head -1 swid.list` >> dojsa_nl.log
echo ebin.list first line: `head -1 ebin.list` >> dojsa_nl.log
#
if ( $JEMXNUM != 1 && $JEMXNUM != 2 ) then
   echo Illegal JEMX number - terminate
   exit 0
endif
##if ( $JEMXNUM == 1 ) set INSTRU = 4
##if ( $JEMXNUM == 2 ) set INSTRU = 5
#
#
# Identify number of energy bins
#
set BINID = `head -1 ebin.list`
set NEBINS = `head -2 ebin.list | tail -1`
kev2pi `tail -1 ebin.list` > tmp_kev2pi
set CHANLOW = `head -1 tmp_kev2pi`
set CHANHIGH = `tail -1 tmp_kev2pi`
#
#  Produce the revolution list
#
cut -c 1-4 swid.list > rev.list
echo the file rev.list has been produced
set REVOL = `head -1 rev.list`
set SWID = `head -1 swid.list`
set RMFINSTANCE = `get_insta_swijd -swid $SWID $JEMXNUM rmf 15`
if ( "$RESPONSE" == "" ) then
   set RESPONSE = "/r6/jemx/ic/rmf_grp/jmx${JEMXNUM}_rmf_grp_$RMFINSTANCE.fits[1]"
   echo "response set to default: $RESPONSE" >> dojsa_nl.log
endif
#
#  If there are several revolutions involved then
#  issue a warning if level SPE is requested
#
if ( $ENDLEVEL == "SPE" ) then
   sort -u rev.list > rev.ulist
   set NUMDIFFREV = `wclines rev.ulist`
   echo $NUMDIFFREV different revolutions are requested
   if ( $NUMDIFFREV > 1 ) then
      echo "*********************************************"
      echo "*"
      echo "*  NB - level SPE is requested and there are $NUMDIFFREV different revolutions"
      echo "*"
      echo "*********************************************"
   endif
endif
#
falign rev.list swid.list / > tmp
#
source setup_env
echo $PATH > current_path.txt
#
#  Analyze environment variable JARCHIVE
#
if ( $JARCHIVE == "NRTDATA" ) then
   str_wrap 00 "./scw/" ".000/swg.fits[1]" < tmp > jemx.lst 
   source setup_links_nrt
else
   source setup_links_jarc
   #  find out if rev.002 exists for each SWID
   if ( -e tmpq ) /bin/rm tmpq
   foreach qqq ( `cat tmp` )
      if ( -e ./scw/${qqq}.002/swg.fits ) then
         echo .002 >> tmpq
      else
         if ( -e ./scw/${qqq}.001/swg.fits ) then
            echo .001 >> tmpq
         else
            echo .000 >> tmpq
         endif
      endif
   end
   falign tmp tmpq "" > tmpr
   str_wrap 00 "./scw/" "/swg.fits[1]" < tmpr > jemx.lst 
   #source setup_links_arc_lin6
endif
#
#  Remove old directory if it exists
#
if ( -d obs/$OBSDIR ) rm -r obs/$OBSDIR
#
#  Create the observation group
#
setenv PFILES "${LOCALPFILES}"
og_create idxSwg=jemx.lst ogid=$OBSDIR baseDir="./" instrument=JEMX$JEMXNUM
#
# --- get rid of the SCP. (e-mail from Stephane Paltani 2009-11-27)
#
cd obs/$OBSDIR
dal_detach og_jmx${JEMXNUM}.fits pattern="JMX${JEMXNUM}-GAIN-SCP"
#
#       running jemx_science_analysis
#
setenv PFILES "${LOCALPFILES}"
#
#
jemx_science_analysis ogDOL="og_jmx$JEMXNUM.fits[1]" \
   jemxNum="$JEMXNUM" \
   startLevel="$STARTLEVEL" \
   endLevel="$ENDLEVEL" \
   skipLevels="" \
   COR_gainHist="$GAINHIST" \
   COR_gainModel="$GAINMODEL" \
   CAT_I_refCat="$GNRLREFRCATPATH/gnrl_refr_cat_0027.fits[1]" \
   CAT_I_usrCat="$USRCAT" \
   GTI_gtiJemxNames="" \
   skipLevels="BKG" \
   instMod="$INSTMOD" \
   nChanBins="$NEBINS" \
   chanLow="$CHANLOW" \
   chanHigh="$CHANHIGH" \
   radiusLimit=125. \
   timeStart=-1.0 \
   timeStop=-1.0 \
   BIN_I_shdType=2 \
   IMA_detAccLimit=65535 \
   IMA_detSigSingle=20.0 \
   IMA_makeNewBPL=no \
   IMA_newBackProjFile="" \
   IMA_loopLimitPeak=0.025 \
   IMA_skyImageDim=2 \
   IMA_bkgShdDOL="empty" \
#   IMA_bkgShdDOL="jmx2_src_lc.fits(JMX2-SRC.-LCR-IDX.tpl)" \
   IMA_dolBPL="$DOLBPL" \
   IMA_pixelFold=1 \
   IMA_skyImagesOut="$SKYIMAGESOUT" \
   IMA_useTrace=n \
   IMA_tracestring="FFFFFFFFFFFFFFFF" \
   IMA_detImagesOut=n \
   IMA_userImagesOut=n \
   response="$RESPONSE" \
   LCR_useIROS="$USEIROS" \
   LCR_doBurstSearch=y \
   LCR_burstThreshSrc=7. \
   LCR_burstThreshDet=6. \
   LCR_vignCorr="y" \
   LCR_timeStep="$TIMESTEP" \
   LCR_referenceTime=0. \
   LCR_vignCorr="y" \
   LCR_timeStep=4.0 \
   LCR_evtType=0 \
   LCR_useRaDec=y
#
ebm_set_par ${STARTDIR}/pfiles/j_ima_iros.par userImagesOut=1 \
#
#      Stop here if FLAG has not been set to 1
#
if( $FLAG != 1 ) exit
#
#  Make copies of the crucial files
#

#find scw -name jmx${JEMXNUM}_evts_shd.fits -print > tmpa
#if ( 0 != `wcchar tmpa` ) then
#   extr_swids < tmpa | str_wrap 00 "" .fits > tmpb
#   str_wrap mv "$RESULTPATH/evts_shd/jmx${JEMXNUM}_evts_shd${BINID}_" < tmpa > tmpc
#   falign tmpc tmpb "" > tmpa
#   source tmpa
#endif
#

find scw -name jmx${JEMXNUM}_sky_ima.fits -print > tmpa
if ( 0 != `wcchar tmpa` ) then
   extr_swids < tmpa | str_wrap 00 "" .fits > tmpb
   str_wrap cp "$RESULTPATH/sky_ima/jmx${JEMXNUM}_sky_ima${BINID}_" < tmpa > tmpc
   falign tmpc tmpb "" > tmpa
   source tmpa
endif
#
find scw -name jmx${JEMXNUM}_srcl_res.fits -print > tmpa
if ( 0 != `wcchar tmpa` ) then
   extr_swids < tmpa | str_wrap 00 "" .fits > tmpb
   str_wrap cp "$RESULTPATH/srcl_res/jmx${JEMXNUM}_srcl_res${BINID}_" < tmpa > tmpc
   falign tmpc tmpb "" > tmpa
   source tmpa
endif
#
find scw -name jmx${JEMXNUM}_srcl_spe.fits -print > tmpa
if ( 0 != `wcchar tmpa` ) then
   extr_swids < tmpa | str_wrap 00 "" .fits > tmpb
   str_wrap cp "$RESULTPATH/srcl_res/jmx${JEMXNUM}_srcl_spe${BINID}_" < tmpa > tmpc
   falign tmpc tmpb "" > tmpa
   source tmpa
endif
#
find scw -name jmx${JEMXNUM}_srcl_arf.fits -print > tmpa
if ( 0 != `wcchar tmpa` ) then
   extr_swids < tmpa | str_wrap 00 "" .fits > tmpb
   str_wrap cp "$RESULTPATH/srcl_res/jmx${JEMXNUM}_srcl_arf${BINID}_" < tmpa > tmpc
   falign tmpc tmpb "" > tmpa
   source tmpa
endif
find scw -name jmx${JEMXNUM}_full_dsp.fits -print > tmpa
if ( 0 != `wcchar tmpa` ) then
   extr_swids < tmpa | str_wrap 00 "" .fits > tmpb
   str_wrap cp "$RESULTPATH/srcl_res/jmx${JEMXNUM}_full_dsp${BINID}_" < tmpa > tmpc
   falign tmpc tmpb "" > tmpa
   source tmpa
endif
find scw -name jmx${JEMXNUM}_dete_lcr.fits -print > tmpa
if ( 0 != `wcchar tmpa` ) then
   extr_swids < tmpa | str_wrap 00 "" .fits > tmpb
   str_wrap cp "$RESULTPATH/srcl_res/jmx${JEMXNUM}_dete_lcr${BINID}_" < tmpa > tmpc
   falign tmpc tmpb "" > tmpa
   source tmpa
endif
find scw -name jmx${JEMXNUM}_src_iros_lc.fits -print > tmpa
if ( 0 != `wcchar tmpa` ) then
   extr_swids < tmpa | str_wrap 00 "" .fits > tmpb
   str_wrap cp "$RESULTPATH/srcl_res/jmx${JEMXNUM}_src_iros_lc${BINID}_" < tmpa > tmpc
   falign tmpc tmpb "" > tmpa
   source tmpa
endif

##chmod a-w $RESULTPATH/sky_ima/jmx${JEMXNUM}*.fits