Index: trunk/DataCheck/Processing/FillAuxThresholds.sh
===================================================================
--- trunk/DataCheck/Processing/FillAuxThresholds.sh	(revision 15066)
+++ trunk/DataCheck/Processing/FillAuxThresholds.sh	(revision 15066)
@@ -0,0 +1,220 @@
+#!/bin/bash
+
+# option 
+doupdate="yes" # update all entries (needed when new fields have been added)
+doupdate="no" # fill only entries which are not yet existing (default)
+
+source `dirname $0`/../Sourcefile.sh
+printprocesslog "INFO starting $0 with option doupdate="$doupdate
+
+logfile=$runlogpath"/FillTemp-"$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 last 3, 6 or 9 nights
+dates=( `date +%Y/%m/%d --date="-12hour"` `date +%Y/%m/%d --date="-36hour"` `date +%Y/%m/%d --date="-60hour"` \
+#        `date +%Y/%m/%d --date="-84hour"` `date +%Y/%m/%d --date="-108hour"` `date +%Y/%m/%d --date="-132hour"` \
+#        `date +%Y/%m/%d --date="-156hour"` `date +%Y/%m/%d --date="-180hour"` `date +%Y/%m/%d --date="-204hour"` \
+        )
+#dates=( `find -L $ziprawdata -mindepth 3 -type d | sort -r | sed "s/\${ziprawdata_for_sed}//g" | sed -e 's/^\///'` ) #all available dates in /loc_data/zipraw
+#dates=( `find -L $rawdata -mindepth 3 -type d | sort -r | sed "s/\${rawdata_for_sed}//g" | sed -e 's/^\///'` ) #all available dates in /fact/raw
+
+#dates=( "2013/01/31" )
+
+printprocesslog "INFO processing the following night(s): "${dates[@]}
+echo  `date`": processing the following night(s): "${dates[@]} >> $logfile 2>&1
+
+echo ${dates[@]}
+
+cd $mars
+
+# do filling of aux data 
+for date in ${dates[@]}
+do 
+   auxdir=$auxdata/$date
+   runnumber=`echo $date | sed -e 's/\///g'`
+
+   echo $auxdir
+   
+   # 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 "$auxdir
+   fi
+   
+   thresholdfile=$auxdir/$runnumber.RATE_CONTROL_THRESHOLD.fits
+   ls $thresholdfile
+   if ! [ -e $thresholdfile ]
+   then 
+      printprocesslog "WARN "$thresholdfile" not found."
+      continue
+   else
+      threshnumerrors=`fverify $thresholdfile 2>/dev/null | grep -o '[0-9][ ]error(s)'  | grep -E -o '[0-9]'`
+      if [ $threshnumerrors -gt 0 ]
+      then 
+         printprocesslog "WARN for $thresholdfile fverify returned "$threshnumerrors" error(s)."
+      fi
+   fi
+
+   thresholdfile2=$auxdir/$runnumber.FTM_CONTROL_STATIC_DATA.fits
+   ls $thresholdfile2
+   if ! [ -e $thresholdfile2 ]
+   then 
+      printprocesslog "WARN "$thresholdfile2" not found."
+      continue
+   else
+      threshnumerrors2=`fverify $thresholdfile2 2>/dev/null | grep -o '[0-9][ ]error(s)'  | grep -E -o '[0-9]'`
+      if [ $threshnumerrors2 -gt 0 ]
+      then 
+         printprocesslog "WARN for $thresholdfile2 fverify returned "$threshnumerrors2" error(s)."
+      fi
+   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=$query" AND ISNULL(fThresholdMedMean) AND ISNULL(fThresholdMinSet) "
+   fi
+
+   printprocesslog "DEBUG get filenumbers from DB: QUERY: "$query
+   filenumbers=( `sendquery $query` )
+   if [ ${#filenumbers} -eq 0 ]
+   then
+      printprocesslog "INFO No files found in the DB for night "$date
+      continue
+   fi
+
+   # 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.gz
+      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
+
+      # build query to update runinfo in DB
+      query="UPDATE RunInfo SET "
+
+      # get information 
+      if [ -e $threshcurrentsfile ] && [ $threshnumerrors -eq 0 ]
+      then 
+         thresholds1=( `root -q -b -l fact/threshold.C\("\"$thresholdfile2\""\,$tstart\,$tstop\) | grep "result" | grep -E -o '[0-9]+[.]?[0-9]*'` )
+         #root -q -b -l fact/threshold.C\("\"$thresholdfile2\""\,$tstart\,$tstop\) | grep "result"
+         echo ${thresholds1[@]}
+         if [ "${thresholds1[0]}" == "" ]
+         then 
+            query=$query"fThresholdMedMean=NULL"
+         else
+            query=$query"fThresholdMedMean="${thresholds1[0]}
+         fi
+         if [ "${thresholds1[1]}" == "" ]
+         then 
+            query=$query", fThresholdMedRms=NULL"
+         else
+            query=$query", fThresholdMedRms="${thresholds1[1]}
+         fi
+         if [ "${thresholds1[2]}" == "" ]
+         then 
+            query=$query", fThresholdMax=NULL"
+         else
+            query=$query", fThresholdMax="${thresholds1[2]}
+         fi
+         if [ "${thresholds1[3]}" == "" ]
+         then 
+            query=$query", fThresholdAvgMean=NULL"
+         else
+            query=$query", fThresholdAvgMean="${thresholds1[3]}
+         fi
+      else
+         query=$query" fThresholdMedMean=NULL"
+         query=$query", fThresholdMedRms=NULL"
+         query=$query", fThresholdMax=NULL"
+         query=$query", fThresholdAvgMean=NULL"
+      fi
+      
+      # get information 
+      if [ -e $threshcurrentsfile2 ] && [ $threshnumerrors2 -eq 0 ]
+      then 
+         thresholds2=( `root -q -b -l fact/lastth.C\("\"$thresholdfile\""\,$tstart\) | grep "result" | grep -E -o '[0-9]+[.]?[0-9]*'` )
+         #root -q -b -l fact/lastth.C\("\"$thresholdfile\""\,$tstart\) | grep "result"
+         echo ${thresholds2[@]}
+         if [ "${thresholds2[0]}" == "" ]
+         then 
+            query=$query", fThresholdMinSet=NULL"
+         else
+            query=$query", fThresholdMinSet="${thresholds2[0]}
+         fi
+         if [ "${thresholds2[1]}" == "" ]
+         then 
+            query=$query", fThresholdMinTimeDiff=NULL"
+         else
+            query=$query", fThresholdMinTimeDiff="${thresholds2[1]}
+         fi
+      else
+         query=$query", fThresholdMinSet=NULL"
+         query=$query", fThresholdMinTimeDiff=NULL"
+      fi
+      
+      # add where condition
+      query=$query" WHERE fNight="$runnumber" AND fRunID="$filenum
+      
+      echo $query
+      # send query to DB
+      sendquery >/dev/null
+   done
+done
+
+finish
+
+