Index: trunk/DataCheck/Processing/FillAuxContTemp.sh
===================================================================
--- trunk/DataCheck/Processing/FillAuxContTemp.sh	(revision 17577)
+++ trunk/DataCheck/Processing/FillAuxContTemp.sh	(revision 17577)
@@ -0,0 +1,164 @@
+#!/bin/bash
+
+# option whether to fill all row or only those where information is missing
+# $doupdate might be given as environment variable
+if [ "$doupdate" = "" ]
+then
+   doupdate="yes" # update all entries (needed when new fields have been added)
+   doupdate="no" # fill only entries which are not yet existing (default)
+fi
+
+source `dirname $0`/../Sourcefile.sh
+printprocesslog "INFO starting $0 with option doupdate="$doupdate
+
+logfile=$runlogpath"/FillContTemp-"$datetime".log"
+date >> $logfile
+
+# setup to use ftools
+source $HEADAS/headas-init.sh
+
+# check if software is available
+if ! ls $factpath/fitsdump >/dev/null 2>&1
+then 
+   printprocesslog "ERROR "$factpath"/fitsdump is not available."
+   finish
+fi
+
+# get dates
+if [ "$certaindate" != "" ]
+then
+   getdates $certaindate
+else
+   # get all night
+   #getdates "all"
+   # get last 6 nights
+   getdates 6
+fi
+
+printprocesslog "INFO processing the following night(s): "${dates[@]}
+echo  `date`": processing the following night(s): "${dates[@]} >> $logfile 2>&1
+
+cd $mars
+
+# do filling of aux data 
+for date in ${dates[@]}
+do 
+   auxdir=$auxdata/$date
+   runnumber=`echo $date | sed -e 's/\///g'`
+   if [ $runnumber -lt 20130413 ]
+   then
+      continue
+   fi
+
+   # check if aux files are available from that night
+   if ! [ -d $auxdir ]
+   then
+      printprocesslog "INFO no data available in "$auxdir
+      continue
+   else
+      printprocesslog "INFO processing files in "$auxdir
+   fi
+
+   # get file numbers from DB
+   #   but only for not-corrupted files
+   query="SELECT fRunID from RunInfo WHERE fNight="$runnumber" AND fFitsFileErrors=0 "
+   if [ "$doupdate" = "no" ]
+   then
+      query=$query" AND ISNULL(fContainerTempMean) "
+   fi
+
+   printprocesslog "DEBUG get filenumbers from DB: QUERY: "$query
+   filenumbers=( `sendquery $query` )
+   if [ ${#filenumbers} -eq 0 ]
+   then
+      printprocesslog "INFO No files found in the DB for night "$date
+      continue
+   fi
+
+   # get daily fits files 
+   conttempfile=$auxdir/$runnumber.TEMPERATURE_DATA.fits
+   if ! [ -e $conttempfile ]
+   then 
+      printprocesslog "WARN "$conttempfile" not found."
+      echo "WARN "$conttempfile" not found."
+      continue
+   else
+      conttempnumerrors=`fverify $conttempfile 2>/dev/null | grep -o '[0-9][ ]error(s)'  | grep -E -o '[0-9]'`
+      if [ $conttempnumerrors -gt 0 ]
+      then 
+         printprocesslog "WARN for $conttempfile fverify returned "$conttempnumerrors" error(s)."
+      fi
+   fi
+   
+   # fill auxiliary information for files
+   for filenum in ${filenumbers[@]}
+   do
+      printprocesslog "INFO processing file number "$runnumber"_"`printf %03d $filenum`
+      echo  `date`": processing file number "$runnumber"_"`printf %03d $filenum` >> $logfile 2>&1
+      # get information from rawfile
+      rawfile=$ziprawdata/$date/$runnumber"_"`printf %03d $filenum`.fits.fz
+      if ! [ -e $rawfile ]
+      then 
+         printprocesslog "ERROR: "$rawfile" not found."
+         continue
+      fi
+      runtype=`$factpath/fitsdump -h $rawfile  2>/dev/null | grep RUNTYPE | grep -E -o "['][a-z-]+[']" | sed -e "s/'//g"`
+      mjdrefraw=`$factpath/fitsdump -h $rawfile  2>/dev/null | grep 'MJDREF' | grep -E -o '[0-9]{5}'`
+      tstarti=`$factpath/fitsdump -h $rawfile  2>/dev/null | grep 'TSTARTI' | grep -E -o '[0-9]{5}'`
+      tstartf=`$factpath/fitsdump -h $rawfile  2>/dev/null | grep 'TSTARTF' | grep -E -o '0[.][0-9]+'`
+      tstopi=`$factpath/fitsdump -h $rawfile  2>/dev/null | grep 'TSTOPI' | grep -E -o '[0-9]{5}'`
+      tstopf=`$factpath/fitsdump -h $rawfile  2>/dev/null | grep 'TSTOPF' | grep -E -o '0[.][0-9]+'`
+      if [ "$tstarti" == "" ] || [ "$tstopi" == "" ] || [ "$tstartf" == "" ] || [ "$tstopf" == "" ]
+      then 
+         printprocesslog "WARN: "$rawfile": one of the following keywords is empty or 0: TSTARTI TSTARTF TSTOPI TSTOPF "
+         continue
+      fi
+      # assuming that at least TSTARTI and TSTOPI are consistent
+      #echo $rawfile
+      #echo $tstarti
+      #echo $tstopi
+      #echo $tstartf
+      #echo $tstopf
+      if [ $tstarti -gt 30000 ]
+      then 
+         tstart=`echo " $tstarti + $tstartf - 40587 " | bc -l`
+         tstart2=`echo " $tstarti + $tstartf - 40587 - 0.00011574 " | bc -l`  # 10 sec
+         #tstart2=`echo " $tstarti + $tstartf - 40587 - 0.000023148 " | bc -l` # 2 sec
+         tstop=`echo " $tstopi + $tstopf - 40587 " | bc -l`
+      else
+         tstart=`echo " $tstarti + $tstartf " | bc -l`
+         tstart2=`echo " $tstarti + $tstartf - 0.00011574 " | bc -l`  # 10 sec
+         #tstart2=`echo " $tstarti + $tstartf - 0.000023148 " | bc -l` # 2 sec
+         tstop=`echo " $tstopi + $tstopf " | bc -l`
+      fi
+      #echo "run "$filenum" "$tstart" "$tstop
+
+      # build query to update runinfo in DB
+      query="UPDATE RunInfo SET "
+
+      # get ctrl dev
+      if [ -e $conttempfile ] && [ $conttempnumerrors -eq 0 ]
+      then 
+         conttemps=( `root -q -b -l fact/processing/contemp.C\("\"$conttempfile\""\,$tstart\,$tstop\) | grep "result" | grep -E -o '[0-9]+[.]?[0-9]*'` )
+         #echo " "${conttemps[@]}
+         if [ "${conttemps[0]}" == "" ]
+         then 
+            query=$query" fContainerTempMean=NULL "
+         else
+            query=$query" fContainerTempMean="${conttemps[0]}
+         fi
+      else
+         query=$query" fContainerTempMean=NULL"
+      fi
+      
+      # add where condition
+      query=$query" WHERE fNight="$runnumber" AND fRunID="$filenum
+      
+      # send query to DB
+      sendquery >/dev/null
+   done
+done
+
+finish
+
+