1 | #!/bin/sh -xvf
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2 | #Basic tuning of system fuction used.
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3 | AWK=/bin/awk
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4 | SED=/bin/sed
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5 | GREP=/bin/grep
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6 | WC=/usr/bin/wc
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7 | RM=/bin/rm
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8 | CAT=/bin/cat
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9 | TOUCH=/bin/touch
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10 | DATE=/bin/date
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11 | ECHO=/bin/echo
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12 | LS=/bin/ls
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13 | MKDIR=/bin/mkdir
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14 | TR=/usr/bin/tr
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15 | FIND=/usr/bin/find
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16 | PRINTF=/usr/bin/printf
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17 | XARGS=/usr/bin/xargs
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18 | SORT=/bin/sort
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19 | QSUB=qsub
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20 |
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21 | DefaultIFS=$' \t\n'
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22 | IFS=$DefaultIFS
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23 |
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24 |
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25 | scriptName="`basename $0`"
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26 | $ECHO "Processing script ${scriptName} at `date`"
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27 | ######
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28 | # Local functions
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29 | ######
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30 | usage() {
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31 | echo "usage: $scriptName <source> <YYYYMMDD-directory> <type of process>"
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32 | echo " -<source> as Abell85"
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33 | echo " -<YYYYMMDD-directory> as 20110428"
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34 | echo " -<type of process> as GAIN|CALIBON|CALIBOFF|ON|OFF"
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35 | }
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36 | ######
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37 | # argument test
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38 | ######
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39 |
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40 | #Process cmd line args: the -src option is mandatory (source name as Abell85)
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41 | sourceRadio=
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42 | dateSelected=
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43 | typeofproc=
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44 | #use -sim option to simulate processing (debug the script as if...)
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45 | simulationMode=Off
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46 | #
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47 | #first and last cycle to process
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48 | #
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49 | firstCycle=
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50 | lastCycle=
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51 | while [ $# -gt 0 ]
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52 | do
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53 | case "$1" in
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54 | -src) sourceRadio=$2; shift;;
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55 | -date) dateSelected=$2; shift;;
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56 | -type) typeofproc=$2; shift;;
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57 | -fcycle) firstCycle=$2; shift;;
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58 | -lcycle) lastCycle=$2; shift;;
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59 | -sim) simulationMode=On;;
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60 | -h)
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61 | echo >&2 \
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62 | "usage: $0 -src souce -date YYYYMMDD -type type [-fcycle firstCycle] [-lcycle lastCycle] [-sim to trig simulation mode]"
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63 | exit 1;;
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64 | *) break;; # terminate while loop
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65 | esac
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66 | shift
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67 | done
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68 |
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69 | #Check input
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70 |
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71 | if [ "<${sourceRadio}>" = "<>" ]; then
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72 | $ECHO "FATAL: You have forgotten to select the source option (-src)"
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73 | exit 1
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74 | fi
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75 |
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76 | if [ "<${dateSelected}>" = "<>" ]; then
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77 | $ECHO "FATAL: You have forgotten to select the date option (-date)"
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78 | exit 1
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79 | fi
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80 |
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81 | if [ "<${typeofproc}>" = "<>" ]; then
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82 | $ECHO "FATAL: You have forgotten to select the type option (-type)"
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83 | exit 1
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84 | fi
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85 |
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86 |
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87 |
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88 | srclower=`${ECHO} ${sourceRadio} | ${TR} "[:upper:]" "[:lower:]" `
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89 |
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90 |
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91 | #Path to public backupable path
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92 | publicpath="/afs/in2p3.fr/home/c/campagne/public"
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93 |
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94 | #temporary files to synchronize scripts
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95 | tmppublicpath=${TMPPUBLICPATH}
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96 | $LS -l ${tmppublicpath} > /dev/null
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97 |
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98 |
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99 | #Path where the job will do temporary IO
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100 | if [ ${ENVIRONMENT} = "INTERACTIVE" ]; then
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101 | iojobpath="/sps/baoradio/AmasNancay/JEC"
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102 | $MKDIR -p $iojobpath
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103 | elif [ ${ENVIRONMENT} = "BATCH" ] ; then
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104 | iojobpath=${TMPBATCH}
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105 | else
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106 | $ECHO "FATAL (${scriptName}): environment is ${ENVIRONMENT} not allowed"
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107 | touch ${tmppublicpath}/proc_script.finished
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108 | exit 1
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109 | fi
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110 | cd ${iojobpath}
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111 |
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112 | localpath="${sourceRadio}/${dateSelected}${srclower}"
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113 | $MKDIR -p ./${localpath}
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114 | cd ./${localpath}
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115 | mainDirectory=`pwd`
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116 |
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117 |
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118 | #Path of the utility scripts
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119 | scriptpath="/afs/in2p3.fr/home/c/campagne/private/work/AmasNancay"
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120 |
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121 |
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122 | #select file per cycle
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123 | #$ECHO "Select files process..."
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124 | #keep only lines with structure: cycle_number first,last,step
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125 | #Get sca files
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126 | $ECHO "DEBUG (${scriptName}): START call getscafiles.sh ${sourceRadio} ${dateSelected}"
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127 | OUT1=./getScaStatus.$$
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128 | $RM -f ${tmppublicpath}/getscafiles.finished
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129 | ${scriptpath}/getscafiles.sh ${sourceRadio} ${dateSelected} > ${OUT1} 2>&1
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130 | while [ ! -f "${tmppublicpath}/getscafiles.finished" ]; do
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131 | $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/getscafiles.finished"
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132 | date +%T
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133 | sleep 30
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134 | done
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135 | $RM -f ${tmppublicpath}/getscafiles.finished
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136 | $ECHO "DEBUG (${scriptName}): END"
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137 |
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138 |
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139 | getScaStatus=`$GREP "^\(FATAL\|ERROR\)" ${OUT1}`
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140 |
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141 | if [ "<${getScaStatus}>" != "<>" ]; then
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142 | $ECHO "FATAL (${scriptName}): error to get sca file for $sourceRadio $dateSelected"
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143 | $ECHO "DEBUG (${scriptName}): START with cat ${OUT1}"
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144 | $CAT ${OUT1}
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145 | $ECHO "DEBUG (${scriptName}): END"
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146 | touch ${tmppublicpath}/proc_script.finished
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147 | exit 1
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148 | fi
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149 |
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150 |
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151 | scaFileSummarized=`$FIND . -name "sca*.sum" -print`
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152 | if [ "<${scaFileSummarized}>" = "<>" ]; then
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153 | $ECHO "FATAL (${scriptName}): strange sca file summarized not available: $sourceRadio $dateSelected"
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154 | $ECHO "DEBUG (${scriptName}): START with cat ${OUT1}"
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155 | $CAT ${OUT1}
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156 | $ECHO "DEBUG (${scriptName}): END"
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157 | touch ${tmppublicpath}/proc_script.finished
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158 | exit 1
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159 | fi
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160 | $RM ${OUT1}
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161 |
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162 | scaFileSummarized=`basename $scaFileSummarized`
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163 |
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164 | #set Irods environment
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165 | . /usr/local/shared/bin/irods_env.sh -noverbose
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166 | #download header files to be used for signal files selction
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167 | $MKDIR -p ./Fiber1
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168 | dirFiberfile=`pwd`/Fiber1
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169 |
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170 | dirIrods="/baoradio/data/AmasNancay/${sourceRadio}/${dateSelected}${srclower}/Fiber1"
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171 |
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172 | listOfFiles=( `ils ${dirIrods} | $GREP -i "header" | $XARGS -i basename {} | $SORT -k1.7n` )
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173 | IFS='
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174 | '
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175 | listOfFiles=( $( $PRINTF "%s\n" "${listOfFiles[@]}" | $AWK 'x[$0]++ == 0' ) )
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176 | IFS=$DefaultIFS
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177 |
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178 | #
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179 | $ECHO "DEBUG (${scriptName}): Download if necessary the headers"
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180 | #
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181 | for ifile in ${listOfFiles[@]}
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182 | do
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183 | #test if the headers have not yet been downloaded
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184 | if [ ! -e ${dirFiberfile}/${ifile} ]; then
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185 | OUT2=./getheaders.$$
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186 | iget -f -K ${dirIrods}/${ifile} ${dirFiberfile} >${OUT2} 2>&1
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187 | igetStatus=`$GREP "^ERROR" ${OUT2}`
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188 | if [ "<$igetStatus>" != "<>" ]; then
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189 | $ECHO "FATAL (${scriptName}): error while iget:"
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190 | $ECHO $igetStatus
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191 | touch ${tmppublicpath}/proc_script.finished
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192 | exit 1
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193 | fi
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194 | $RM -f $OUT2
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195 | fi
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196 | done
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197 | #
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198 | $ECHO "DEBUG (${scriptName}): START call select.sh ${scaFileSummarized} ${dirFiberfile} ${typeofproc}"
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199 | #
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200 | #Get list of file to process
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201 | headerFileSelected=./selectSignal.$$
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202 | $RM -f ${tmppublicpath}/select.finished
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203 | ${scriptpath}/select.sh ${scaFileSummarized} ${dirFiberfile} ${typeofproc} | $GREP "^#[0-9]" | $SED "s/^#//" > $headerFileSelected
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204 | while [ ! -f "${tmppublicpath}/select.finished" ]; do
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205 | $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/select.finished"
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206 | date +%T
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207 | sleep 30
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208 | done
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209 | $RM ${tmppublicpath}/select.finished
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210 | #
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211 | $ECHO "DEBUG (${scriptName}): END"
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212 | #
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213 | $ECHO "DEBUG (${scriptName}): START filling cycleArray, filesArray"
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214 | #
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215 | declare -a cycleArray
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216 | declare -a filesArray
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217 | $ECHO "DEBUG (${scriptName}): IFS value between<>: <$IFS>"
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218 | IFS=$DefaultIFS
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219 | $ECHO "DEBUG (${scriptName}): START cat $headerFileSelected"
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220 | $CAT $headerFileSelected
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221 | $ECHO "DEBUG (${scriptName}): END cat $headerFileSelected"
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222 |
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223 | while read v1 v2
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224 | do
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225 | cycleArray[${#cycleArray[*]}]=$v1
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226 | filesArray[${#filesArray[*]}]=$v2
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227 | done < $headerFileSelected
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228 |
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229 | if [ ${#cycleArray[*]} -eq 0 -o ${#filesArray[*]} -eq 0 ]; then
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230 | $ECHO "FATAL (${scriptName}): no header file selected (${#cycleArray[*]}, ${#filesArray[*]})"
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231 | touch ${tmppublicpath}/proc_script.finished
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232 | exit 1
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233 | else
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234 | $ECHO "DEBUG (${scriptName}): non zero elements found for cycleArray and filesArray"
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235 | fi
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236 |
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237 | #
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238 | $ECHO "DEBUG (${scriptName}): number of elements <${#cycleArray[*]}> <${#filesArray[*]}>"
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239 | $ECHO "DEBUG (${scriptName}): END"
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240 | #
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241 | # (timeShift)
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242 | #Add 3sec to start ON / OFF
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243 | #Substract 4sec to start DAB ON / OFF
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244 | #
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245 | #Take care: Cycle numbering starts at 1 in SCAFiles while Arrays index start at 0
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246 | #
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247 | #for GAIN the reference cycle takes the middle of the run
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248 | #
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249 | #nwinmean donne le nombre de fenetre tspwin utilise pour faire calculer la moyenne des medianes de chaque fenetre
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250 | #This is the nimber of paquets of the time window which change according to processing type
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251 | $ECHO "DEBUG (${scriptName}): START switch on $typeofproc"
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252 | #
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253 | case "$typeofproc" in
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254 | GAIN)
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255 | $ECHO "process signal files for GAIN phase"
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256 | ingain=""
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257 | freqfilter="-freqfilter -"
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258 | nwinmean="1"
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259 | tspwin="5120"
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260 | dirName="Off"
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261 | cyclebasename="gaincycle"
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262 | indexStartHour="6"
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263 | timeShift="-4"
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264 | timeDuration="14"
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265 | firstCycleId=`expr ${#cycleArray[*]} / 2`
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266 | firstCycleId=`expr ${firstCycleId} - 1`
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267 | lastp1CycleId=`expr ${firstCycleId} + 1`
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268 | ;;
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269 | ON)
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270 | $ECHO "process signal files for ON phases"
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271 | ingain="-gain gain_${dateSelected}_${srclower}.fits"
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272 | freqfilter="-freqfilter 16"
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273 | nwinmean="5"
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274 | tspwin="5120"
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275 | dirName="On"
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276 | cyclebasename="datacycle"
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277 | indexStartHour="4"
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278 | timeShift="3"
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279 | timeDuration="30"
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280 | firstCycleId="0"
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281 | lastp1CycleId="${#cycleArray[@]}"
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282 | ;;
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283 | OFF)
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284 | $ECHO "process signal files for OFF phases"
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285 | ingain="-gain gain_${dateSelected}_${srclower}.fits"
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286 | freqfilter="-freqfilter 16"
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287 | nwinmean="5"
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288 | tspwin="5120"
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289 | dirName="Off"
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290 | cyclebasename="datacycle"
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291 | indexStartHour="8"
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292 | timeShift="3"
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293 | timeDuration="30"
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294 | firstCycleId="0"
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295 | lastp1CycleId="${#cycleArray[@]}"
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296 | ;;
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297 | CALIBON)
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298 | $ECHO "process signal files for CALIBRATION ON phases"
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299 | ingain="-gain gain_${dateSelected}_${srclower}.fits"
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300 | freqfilter="-freqfilter 16"
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301 | nwinmean="1"
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302 | tspwin="1024"
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303 | dirName="On"
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304 | cyclebasename="calibcycle"
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305 | indexStartHour="2"
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306 | timeShift="-4"
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307 | timeDuration="14"
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308 | firstCycleId="0"
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309 | lastp1CycleId="${#cycleArray[@]}"
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310 | ;;
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311 | CALIBOFF)
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312 | $ECHO "process signal files for CALIBRATION OFF phases"
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313 | ingain="-gain gain_${dateSelected}_${srclower}.fits"
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314 | freqfilter="-freqfilter 16"
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315 | nwinmean="1"
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316 | tspwin="1024"
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317 | dirName="Off"
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318 | cyclebasename="calibcycle"
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319 | indexStartHour="6"
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320 | timeShift="-4"
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321 | timeDuration="14"
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322 | firstCycleId="0"
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323 | lastp1CycleId="${#cycleArray[@]}"
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324 | ;;
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325 | *)
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326 | $ECHO "FATAL (${scriptName}): type of processing"
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327 | usage
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328 | touch ${tmppublicpath}/proc_script.finished
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329 | exit 1
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330 | ;;
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331 | esac
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332 | #
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333 | $ECHO "DEBUG (${scriptName}): END"
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334 | #
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335 | #
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336 | #Compute time windows (Warning usage of GMT date)
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337 | #
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338 | $ECHO "DEBUG (${scriptName}): START compute time windows"
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339 | OUT=./baotiming.$$
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340 | ${AWK} -v datesys=${DATE} -v type=${indexStartHour} -v shift=${timeShift} '
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341 | BEGIN {FS=","}
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342 | {
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343 | phaseStart=$type
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344 | cmd=sprintf("%s +%%s -d \"%s\" ",datesys,phaseStart);
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345 | (cmd | getline phstart);
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346 | close(cmd);
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347 | newstart = phstart+shift;
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348 | cmd=sprintf("%s +%%T -d \"1970-01-01 %s sec GMT\"",datesys,newstart);
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349 | (cmd | getline newStart);
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350 | close(cmd);
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351 | print $1,newStart,phaseStart;
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352 | }
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353 | ' ${scaFileSummarized} > ${OUT}
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354 | #
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355 | $ECHO "DEBUG (${scriptName}): END"
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356 | #
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357 | $ECHO "DEBUG (${scriptName}): START cat ${OUT}"
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358 | $CAT ${OUT}
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359 | $ECHO "DEBUG (${scriptName}): END cat ${OUT}"
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360 | #
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361 | $ECHO "DEBUG (${scriptName}): START filling cylceArrayBis timeArray"
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362 | #
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363 | declare -a cycleArrayBis
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364 | declare -a timeArray
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365 | $ECHO "DEBUG (${scriptName}): IFS value between<>: <$IFS>"
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366 | IFS=$DefaultIFS
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367 | #select the selected cycles
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368 | idtofind="0"
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369 | while read v1 v2 v3
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370 | do
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371 | if [ ${idtofind} -lt ${#cycleArray[*]} ]; then
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372 | if [ ${v1} = ${cycleArray[${idtofind}]} ]; then
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373 | cycleArrayBis[${#cycleArrayBis[*]}]=$v1
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374 | timeArray[${#timeArray[*]}]=$v2
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375 | idtofind=`expr ${idtofind} + 1`
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376 | fi
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377 | fi
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378 | done < ${OUT}
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379 | $ECHO "DEBUG (${scriptName}): number of elements ${#cycleArrayBis[*]} ${#timeArray[*]}"
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380 | $ECHO "DEBUG (${scriptName}): END"
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381 |
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382 |
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383 | #########################
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384 | # specmfib exe
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385 | #########################
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386 | prg="/afs/in2p3.fr/throng/baoradio/Library/Progs/TAcq/Objs/specmfib"
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387 | if [ ! -e $prg ]; then
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388 | $ECHO "FATAL (${scriptName}): $prg not found"
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389 | touch ${tmppublicpath}/proc_script.finished
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390 | exit 1
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391 | fi
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392 |
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393 |
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394 | dirFiberfile=${iojobpath}/${localpath}
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395 |
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396 | curDir=`pwd`
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397 | #
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398 | $ECHO "DEBUG (${scriptName}): in principle $dirFiberfile == $curDir "
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399 | #
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400 | #force single channel
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401 | forceSingle="-singlechan"
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402 | #debug
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403 | prtlevel="1"
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404 |
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405 |
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406 | #Loop on cycles
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407 | ##
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408 | $ECHO "DEBUG (${scriptName}): START loop on cycles Ids ${firstCycleId} to ${lastp1CycleId}"
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409 |
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410 | #write the script to be send to Batch
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411 | #get gain file if necessary
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412 | if [ ${typeofproc} != "GAIN" ]; then
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413 | OUT2=./igetStatus.$$
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414 | iget /baoradio/data/AmasNancay/${localpath}/gain_${dateSelected}_${srclower}.fits >${OUT2} 2>&1
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415 | igetStatus=`$GREP "^ERROR" ${OUT2}`
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416 | if [ "<${igetStatus}>" != "<>" ]; then
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417 | $ECHO "FATAL (${scriptName}): error while iget:"
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418 | $ECHO $igetStatus
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419 | touch ${tmppublicpath}/${jobBatchName}.finished
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420 | exit 1
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421 | fi
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422 | $RM ${OUT2}
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423 | fi
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424 |
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425 |
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426 | for ((i=${firstCycleId};i<${lastp1CycleId};i++)); do
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427 | #
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428 | #time window selection
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429 | tmproc="-tmproc ${timeArray[${i}]},${timeDuration}"
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430 | #cycle <number>
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431 | cycle="${cycleArray[${i}]}"
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432 | if [ "<${firstCycle}>" != "<>" -a "<${lastCycle}>" != "<>" ]; then
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433 | if [ ${cycle} -lt ${firstCycle} -o ${cycle} -gt ${lastCycle} ]; then
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434 | continue
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435 | fi
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436 | fi
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437 | $ECHO "DEBUG (${scriptName}): process cycle $cycle"
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438 |
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439 | #cycle <name><number>
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440 | cycle="${cyclebasename}${cycleArray[${i}]}"
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441 | #signal files selection
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442 | infiles="${filesArray[${i}]}"
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443 | #
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444 | #Prepare BQS parameters: MEMORY, CPU...#
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445 | infilesArray=( `$ECHO $infiles | $AWK 'BEGIN {FS=","} {for(i=1;i<NF;i++)print $i;}'` )
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446 | IFS='
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447 | '
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448 | infilesArray=( $( printf "%s\n" "${infilesArray[@]}" | awk 'x[$0]++ == 0' ) )
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449 | IFS=$DefaultIFS
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450 | firstFile=${infilesArray[0]}
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451 | lastFile=${infilesArray[1]}
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452 | #
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453 | #
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454 | #
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455 | #get signals files
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456 | OUT3=./getsignals.$$
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457 | $RM -f ${tmppublicpath}/getsignalfiles.finished
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458 | ${scriptpath}/getsignalfiles.sh ${sourceRadio} ${dateSelected} ${firstFile} ${lastFile} > ${OUT3} 2>&1
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459 | while [ ! -f "${tmppublicpath}/getsignalfiles.finished" ]; do
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460 | $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/getsignalfiles.finished"
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461 | date +%T
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462 | sleep 30
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463 | done
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464 | $RM ${tmppublicpath}/getsignalfiles.finished
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465 |
|
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466 | getSignals=`$GREP "^FATAL" ${OUT3}`
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467 | if [ "<$getSignals>" != "<>" ]; then
|
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468 | $ECHO "FATAL (${scriptName}): error while get signals"
|
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469 | $ECHO $getSignals
|
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470 | touch ${tmppublicpath}/${jobBatchName}.finished
|
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471 | exit 1
|
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472 | fi
|
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473 | $RM ${OUT3}
|
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474 |
|
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475 | #location of the signal file
|
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476 | fibfile="${curDir} 1,2"
|
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477 | #
|
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478 | outDir=${curDir}/${dirName}/${cycle}
|
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479 | $MKDIR -p ${outDir}
|
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480 |
|
---|
481 | #
|
---|
482 | # where ami...
|
---|
483 | #
|
---|
484 | $ECHO "We are here `pwd`"
|
---|
485 | $LS -lrth
|
---|
486 | $FIND . -name "igetStatus.*" | $XARGS -i $CAT {}
|
---|
487 | $LS ./Fiber1 | $WC -l
|
---|
488 | $LS ./Fiber2 | $WC -l
|
---|
489 | $LS -lR ${outDir}
|
---|
490 |
|
---|
491 | #Note: here act=gain means only that specmfib will use median-like algorithms (not only for gains...)
|
---|
492 | $prg -act gain $forceSingle $freqfilter -prt $prtlevel -out ${outDir} -nmean $nwinmean $ingain $tmproc -tspwin ${tspwin},0,0 -in $infiles ${fibfile}
|
---|
493 |
|
---|
494 | $ECHO ${outDir}
|
---|
495 | $LS -lrt ${outDir}
|
---|
496 |
|
---|
497 | #save results to Irods (use option -f ONLY to force override)
|
---|
498 | iput -v -K -r ${curDir}/${dirName} /baoradio/data/AmasNancay/${localpath}
|
---|
499 | #
|
---|
500 | #clean the signal files which can at the end of the day fill completly the scratch directory of the batch work/AmasNancayer
|
---|
501 | $RM -rf ${iojobpath}/${localpath}/Fiber1
|
---|
502 | $RM -rf ${iojobpath}/${localpath}/Fiber2
|
---|
503 | $RM -rf ${iojobpath}/${localpath}/${typeofproc}
|
---|
504 |
|
---|
505 | #
|
---|
506 | #
|
---|
507 |
|
---|
508 | #end loop on cycles
|
---|
509 | done
|
---|
510 | #
|
---|
511 | $ECHO "DEBUG (${scriptName}): END loop on cycles"
|
---|
512 | #
|
---|
513 | touch ${tmppublicpath}/proc_script.finished
|
---|
514 | exit 0
|
---|