source: branches/trigger_burst_research/Archive/repairAuxFile.sh

#!/bin/bash
#sourceFolder="./backup"
#destFolder="./fixed"

#entries=`find $sourceFolder -type f -name '*.fits' | sort`

#for entry in ${entries[@]}
#do
#       echo $entry" "$destFolder
#       cp $entry $destFolder
#done

#entries=`find $destFolder -type f -name '*.fits' | sort`

#for entry in ${entries[@]}
#do

if [ "$#" != "5" ]
then
        echo "Error: repairAuxFile.sh should be called with 4 arguments please"
        exit
fi
entry=$1
errorFile=$2
wrongMjdFile=$3
reportFile=$4
processErrorFile=$5
        #verify file with fverify
        result=`fverify $entry 2>/dev/null | grep '0 error(s)'`
        if [ "$result" != "" ]
        then
                mjdref=`/home/isdc/lyard/FACT++/fitsdump $entry -h 2>/dev/null | grep 'MJDREF' | grep -E -o '[0-9]+'`
                if [ "$mjdref" != 40587 ]
                then
                        echo "$entry" >> $wrongMjdFile
                        result=""
                fi
        else
                echo "$entry" >> $errorFile
        fi
        
        if [ "$result" == "" ]
        then
        #fix it !
#               echo $entry
                headerSize=`ENDfixer $entry 2>/dev/null`
                echo "Fixed END $entry" >> $reportFile
                if [ "$headerSize" == "Error: header length not acceptable" ] || [ "$headerSize" == "Error: too much header space after END keyword" ] 
                then 
                        echo "File "$entry" looks really messed up: "$headerSize >> $errorFile
                        exit
                else 
                        filesize=`stat -c%s $entry`
#                       echo $headerSize" "$filesize
                        numrows=`/home/isdc/lyard/FACT++/fitsdump $entry -h 2>/dev/null | grep 'NAXIS2' | awk '{ print $4 }' | grep -E -o '[0-9]+'`
                        if [ "$numrows" == "" ]
                        then
                                echo "Cannot fitsdump $entry" >> $processErrorFile
                                rm $entry
                                exit
                        fi
                        rowWidth=`/home/isdc/lyard/FACT++/fitsdump $entry -h 2>/dev/null | grep 'NAXIS1' | awk '{ print $4 }' | grep -E -o '[0-9]+'`
                        
                        #is there any extra row that we can keep ?
                        #let RowCheck examine the time markers
                        numrows2=`RowChecker $entry $headerSize $rowWidth 0 $numrows 2>/dev/null`
                        if [ $numrows2 -gt $numrows ]
                        then
                                numrows=$numrows2
                                totSize=`echo " $headerSize + $numrows * $rowWidth " | bc -l`
                                fitsSize=`echo " 2880 - ($totSize % 2880) " | bc`
                                fitsSize=`echo " $totSize + $fitsSize " | bc -l`
#                               echo $headerSize" "$numrows" "$rowWidth" "$totSize" "$fitsSize
#                               echo " FileSize: "$filesize" should be "$fitsSize
                                truncate -s $totSize $entry 2>/dev/null
                                truncate -s $fitsSize $entry 2>/dev/null
                                echo "Resized   $entry" >> $reportFile
                        fi
                fi
        fi
#done