1 | #!/bin/sh -xvf |
---|
2 | #do calibration |
---|
3 | DATE=/bin/date |
---|
4 | GREP=/bin/grep |
---|
5 | AWK=/bin/awk |
---|
6 | ECHO=/bin/echo |
---|
7 | WC=/usr/bin/wc |
---|
8 | CAT=/bin/cat |
---|
9 | PRINTF=/usr/bin/printf |
---|
10 | FIND=/usr/bin/find |
---|
11 | MKDIR=/bin/mkdir |
---|
12 | XARGS=/usr/bin/xargs |
---|
13 | SORT=/bin/sort |
---|
14 | RM=/bin/rm |
---|
15 | TR=/usr/bin/tr |
---|
16 | CP=/bin/cp |
---|
17 | LS=/bin/ls |
---|
18 | CHMOD=/bin/chmod |
---|
19 | |
---|
20 | DefaultIFS=$' \t\n' |
---|
21 | IFS=$DefaultIFS |
---|
22 | |
---|
23 | #set Irods environment |
---|
24 | . /usr/local/shared/bin/irods_env.sh -noverbose |
---|
25 | |
---|
26 | scriptName="`basename $0`" |
---|
27 | $ECHO "Processing script ${scriptName} at `date`" |
---|
28 | #which source to analyse |
---|
29 | |
---|
30 | #Process cmd line args: the -src option is mandatory (source name as Abell85) |
---|
31 | sourceRadio= |
---|
32 | dateSelected= |
---|
33 | #use -sim option to simulate processing (debug the script as if...) |
---|
34 | simulationMode=Off |
---|
35 | while [ $# -gt 0 ] |
---|
36 | do |
---|
37 | case "$1" in |
---|
38 | -src) sourceRadio=$2; shift;; |
---|
39 | -date) dateSelected=$2; shift;; |
---|
40 | -sim) simulationMode=On;; |
---|
41 | -h) |
---|
42 | echo >&2 \ |
---|
43 | "usage: $0 -src souce -date YYYYMMDD [-freq freq in MHz (default ${freqBAOCalib})] [-bwd bandwidth in MHz (default ${bwBAOCalib})]" |
---|
44 | exit 1;; |
---|
45 | *) break;; # terminate while loop |
---|
46 | esac |
---|
47 | shift |
---|
48 | done |
---|
49 | |
---|
50 | if [ ${simulationMode} = "On" ]; then |
---|
51 | $ECHO "INFO ${scriptName} running in SIMUL mode" |
---|
52 | fi |
---|
53 | |
---|
54 | if [ "<${sourceRadio}>" = "<>" ]; then |
---|
55 | $ECHO "FATAL: You have forgotten to select the source option (-src)" |
---|
56 | exit 1 |
---|
57 | fi |
---|
58 | |
---|
59 | #TODO in principe the naming convention is <SOURCE>DR but NGC4383 is an exception |
---|
60 | case ${sourceRadio} in |
---|
61 | NGC4383DR) $ECHO "INFO (${scriptName}): process ${sourceRadio}";; |
---|
62 | 3C273DR) $ECHO "INFO (${scriptName}): process ${sourceRadio}";; |
---|
63 | 3C161DR) $ECHO "INFO (${scriptName}): process ${sourceRadio}";; |
---|
64 | 3C161BDR) $ECHO "INFO (${scriptName}): process ${sourceRadio}";; |
---|
65 | *) ECHO "FATAL (${scriptName}): process ${sourceRadio} not yet foreseen" |
---|
66 | exit 1;; |
---|
67 | esac |
---|
68 | |
---|
69 | srclower=`${ECHO} ${sourceRadio} | ${TR} "[:upper:]" "[:lower:]" ` |
---|
70 | |
---|
71 | #Path to public backupable path |
---|
72 | publicpath="/afs/in2p3.fr/home/c/campagne/public" |
---|
73 | |
---|
74 | |
---|
75 | #temporary files to synchronize scripts |
---|
76 | tmppublicpath=${TMPPUBLICPATH} |
---|
77 | #wakeup the NFS disk |
---|
78 | $LS -l ${tmppublicpath} > /dev/null |
---|
79 | #clean previous spurious files |
---|
80 | $RM -f ${tmppublicpath}/*.finished |
---|
81 | |
---|
82 | #Path where the job will do temporary IO |
---|
83 | . ${SCRIPTPATH}/isInteractive.sh |
---|
84 | isInteractive=$(isInteractive) |
---|
85 | if [ ${isInteractive} == "1" ]; then |
---|
86 | $ECHO "Usage in INTERACTIVE may be destructive... To be used with great care !!!!" |
---|
87 | exit 0; |
---|
88 | fi |
---|
89 | |
---|
90 | . ${SCRIPTPATH}/set_iojobpath.sh |
---|
91 | iojobpath=$(set_iojobpath) |
---|
92 | cd ${iojobpath} |
---|
93 | |
---|
94 | localpath="${sourceRadio}" |
---|
95 | $MKDIR -p ./${localpath} |
---|
96 | cd ./${localpath} |
---|
97 | |
---|
98 | #save the top directory |
---|
99 | topDir=`pwd` |
---|
100 | |
---|
101 | #Path of the utility scripts |
---|
102 | scriptpath=${SCRIPTPATH} |
---|
103 | |
---|
104 | #Use generic baodaqstatus name |
---|
105 | OUT1=${publicpath}/baodaqstatus-current.txt |
---|
106 | if [ ! -e ${OUT1} -o ! -r ${OUT1} ]; then |
---|
107 | $ECHO "FATAL (${scriptName}): ${OUT1} has a problem" |
---|
108 | exit 1 |
---|
109 | fi |
---|
110 | |
---|
111 | |
---|
112 | #Nb: if we want to implement a loop on sources we have to take care of srclower... |
---|
113 | |
---|
114 | $ECHO "You have selected sourceRadio = $sourceRadio[date = ${dateSelected}]" |
---|
115 | #JEC 14/12/11 One should take care of DR extension for Drift Scan |
---|
116 | #tableau=( `$GREP -i "${dateSelected}${srclower}" ${OUT1} | $AWK '( NF==4 ) { print $2 }' ` ) |
---|
117 | tableau=( `$GREP -i "${sourceRadio}/${dateSelected}${srclower}" ${OUT1} | $AWK '( NF==4 ) { print $2 }' ` ) |
---|
118 | IFS=' |
---|
119 | ' |
---|
120 | tableau=( $( $PRINTF "%s\n" "${tableau[@]}" | $AWK 'x[$0]++ == 0' ) ) |
---|
121 | IFS=$DefaultIFS |
---|
122 | |
---|
123 | |
---|
124 | for i in ${tableau[@]} |
---|
125 | do |
---|
126 | # |
---|
127 | # start a "fresh" session |
---|
128 | cd ${topDir} |
---|
129 | $LS | $XARGS -i $RM -rf {} |
---|
130 | |
---|
131 | |
---|
132 | $ECHO "DEBUG: (${scriptName}) irods root dir $i" |
---|
133 | dateDAQ=`$ECHO ${i} | $AWK '{split($0,a,"/"); print a[6];}' | $AWK "{sub(/${srclower}/,\"\"); print}"` |
---|
134 | |
---|
135 | $ECHO "DEBUG: (${scriptName}): we are in directory `pwd` the topDir=${topDir}" |
---|
136 | $LS -lrt |
---|
137 | |
---|
138 | |
---|
139 | ###### |
---|
140 | $ECHO ">>>>>>>>>>>>> ANALYSIS Part of ${sourceRadio} ${dateDAQ}" |
---|
141 | #go to the .../source/date-sourcelowercase directory |
---|
142 | #download Off/calibcycle<> and On/calibcycle<> directories |
---|
143 | $MKDIR -p ${topDir}/${dateDAQ}${srclower} |
---|
144 | cd ${topDir}/${dateDAQ}${srclower} |
---|
145 | aboveOnOffDir=`pwd` |
---|
146 | $ECHO "DEBUG (${scriptName}): we are in directory: <`pwd`>" |
---|
147 | # |
---|
148 | mode="On" |
---|
149 | $ECHO "DEBUG (${scriptName}): START download the ${mode} fits files" |
---|
150 | inFileDirectory="./${mode}" |
---|
151 | $MKDIR -p ${inFileDirectory} |
---|
152 | |
---|
153 | listOfDataCycle=( `ils ${i}/${mode} 2>&1 | $GREP -i "datacycle" |$AWK 'BEGIN{FS="C- "}{print $2}' | $XARGS -i basename {} | $SORT -k1.10n` ) |
---|
154 | IFS=' |
---|
155 | ' |
---|
156 | listOfDataCycle=( $( $PRINTF "%s\n" "${listOfDataCycle[@]}" | $AWK 'x[$0]++ == 0' ) ) |
---|
157 | IFS=$DefaultIFS |
---|
158 | |
---|
159 | firstCycle=`$ECHO ${listOfDataCycle[0]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'` |
---|
160 | nCycles=`expr ${#listOfDataCycle[*]} - 1` |
---|
161 | |
---|
162 | lastCycle=`$ECHO ${listOfDataCycle[${nCycles}]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'` |
---|
163 | |
---|
164 | listOfDataCycle=( "${listOfDataCycle[@]/#/${i}/${mode}/}" ) |
---|
165 | |
---|
166 | $ECHO "INFO (${scriptName}): use cycles [${firstCycle}, ${lastCycle}]" |
---|
167 | |
---|
168 | |
---|
169 | for j in ${listOfDataCycle[@]} |
---|
170 | do |
---|
171 | irodsDownDir="${j}" |
---|
172 | OUT=./getInFits.$$ |
---|
173 | iget -r -f -K ${irodsDownDir} ${inFileDirectory} > ${OUT} 2>&1 |
---|
174 | igetStatus=`$GREP "^ERROR" ${OUT}` |
---|
175 | if [ "<$igetStatus>" != "<>" ]; then |
---|
176 | $ECHO "FATAL (${scriptName}): error while iget fits files:" |
---|
177 | $ECHO $igetStatus |
---|
178 | $ECHO " ==> skip this run $sourceRadio $dateDAQ" |
---|
179 | continue |
---|
180 | fi |
---|
181 | $RM -f ${OUT} |
---|
182 | done |
---|
183 | $ECHO "DEBUG (${scriptName}): END download the ${mode} fits files" |
---|
184 | #Get sca file |
---|
185 | $ECHO "DEBUG (${scriptName}): START call getscafiles.sh ${sourceRadio} ${dateDAQ}" |
---|
186 | OUT1=./getScaStatus.$$ |
---|
187 | # $RM -f ${tmppublicpath}/getscafiles.finished |
---|
188 | ${scriptpath}/getscafiles.sh ${sourceRadio} ${dateDAQ} > ${OUT1} 2>&1 |
---|
189 | # $RM ${tmppublicpath}/getscafiles.finished |
---|
190 | $ECHO "DEBUG (${scriptName}): END" |
---|
191 | # |
---|
192 | getScaStatus=`$GREP "^\(FATAL\|ERROR\)" ${OUT1}` |
---|
193 | # |
---|
194 | if [ "<${getScaStatus}>" != "<>" ]; then |
---|
195 | $ECHO "FATAL (${scriptName}): error to get sca file for $sourceRadio $dateDAQ" |
---|
196 | $ECHO "DEBUG (${scriptName}): START with cat ${OUT1}" |
---|
197 | $CAT ${OUT1} |
---|
198 | $ECHO "DEBUG (${scriptName}): END" |
---|
199 | continue |
---|
200 | fi |
---|
201 | $RM -f ${OUT1} |
---|
202 | |
---|
203 | scaFile=`$FIND . -name "sca*.sum.trans" | $XARGS -i basename {}` |
---|
204 | |
---|
205 | #prepare job submission |
---|
206 | cd ${aboveOnOffDir} |
---|
207 | #the default spectra name is medfiltmtx, otherwise use -specname <a_string> |
---|
208 | |
---|
209 | logFile="analyse_DRIFT_${sourceRadio}_${dateDAQ}.log" |
---|
210 | $ECHO "DEBUG (${scriptName}): execute the analysis... should not take long. `date`" |
---|
211 | if [ ${simulationMode} = "On" ]; then |
---|
212 | $ECHO "SIMUL: ${scriptpath}/Objs/analyse -act driftScanImg -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir datacycle -numcycle ${firstCycle},${lastCycle} -debug 1 >& ${logFile}" |
---|
213 | cat > ${logFile} <<EOF |
---|
214 | Ok calibration finished |
---|
215 | EOF |
---|
216 | #WARNING: the EOF must start at 1st column overwise the rest of the script is part of the file cat... |
---|
217 | else |
---|
218 | ${scriptpath}/Objs/analyse -act driftScanImg -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir datacycle -numcycle ${firstCycle},${lastCycle} -debug 1 >& ${logFile} |
---|
219 | fi |
---|
220 | # |
---|
221 | $ECHO "DEBUG (${scriptName}): analysis finished `date`. Look for errors before saving to Irods" |
---|
222 | rcstatus=`$GREP -i "Ok drift finished" ${logFile} | $WC -l` |
---|
223 | if [ ${rcstatus} -eq 0 ]; then |
---|
224 | $ECHO "INFO (${scriptName}): analysis problem for ${sourceRadio} ${dateDAQ}" |
---|
225 | $ECHO " START logfile" |
---|
226 | $CAT ${logFile} |
---|
227 | $ECHO " END logFile" |
---|
228 | #clean and leave |
---|
229 | cd ${aboveOnOffDir} |
---|
230 | $LS | $XARGS -i $RM -rf {} |
---|
231 | continue |
---|
232 | fi |
---|
233 | #Save into Irods |
---|
234 | $ECHO "DEBUG (${scriptName}): START save output files" |
---|
235 | $LS ${aboveOnOffDir} |
---|
236 | #use -f option for iput ONLY to force override |
---|
237 | if [ ${simulationMode} = "On" ]; then |
---|
238 | $ECHO "SIMUL: here we look for calib file and put them in Irods" |
---|
239 | else |
---|
240 | $LS -lrth |
---|
241 | $FIND . -name "img_*" -print | $XARGS -i iput -f -v -K {} ${i} |
---|
242 | fi |
---|
243 | #save analysis logfile |
---|
244 | $LS -l ${tmppublicpath} > /dev/null |
---|
245 | $CP ${logFile} ${tmppublicpath} |
---|
246 | $ECHO "DEBUG (${scriptName}): END save output files" |
---|
247 | #clean up to avoid scratch SIZE EXCEED LIMIT |
---|
248 | cd ${aboveOnOffDir} |
---|
249 | $LS | $XARGS -i $RM -rf {} |
---|
250 | |
---|
251 | done |
---|
252 | |
---|
253 | exit 0 |
---|