post_procesing now works from any computer

post_processing.sh

@@ -1,10 +1,10 @@
-#! /usr/bin/env zsh
+#! /bin/zsh
 
 function post_process_eee() {
-    # Three parameters are experimentected:
-    # - The experiment name (case insensitive).
-    # - The reference station to use in standardplots.
-    # - The calibrators to use in standardplots.
+    # Three parameters are expected:
+    #	- The experiment name (case insensitive).
+    #	- The reference station to use in standardplots.
+    #	- The calibrators to use in standardplots.
     # This script should be run from the experiment folder.
     if [[ ! ( -n $1 && -n $2 && -n $3 ) ]];then
         echo "Three parameters are required:"
@@ -14,32 +14,34 @@ function post_process_eee() {
         exit
     fi
 
-    export PATH=$PATH:/home/jops/scripts/:/home/jops/bin/:/home/jops/.local/bin:$PATH:/data0/marcote/scripts/evn_support/
-    experiment=$(echo "${(L)1}")
-    Experiment=$(echo "${(U)1}")
+    exp=$1
+    exp=${(L)1}
+    EXP=${(U)1}
 
-    epoch=$(ssh jops@ccs grep $Experiment /ccs/var/log2vex/MASTER_PROJECTS.LIS | cut -d " " -f 3)
+    date=${ssh jops@ccs grep EC067A /ccs/var/log2vex/MASTER_PROJECTS.LIS | cut -d " " -f 3}
     # In the case of eEVN with an experiment name different this method may not work
-    if [[ ! -n $epoch ]];then
-        epoch=$(ssh jops@ccs grep $Experiment /ccs/var/log2vex/MASTER_PROJECTS.LIS | cut -d " " -f 4)
+    if [[ -n $date ]];then
+        date=${ssh jops@ccs grep EC067A /ccs/var/log2vex/MASTER_PROJECTS.LIS | cut -d " " -f 4}
     fi
 
     # Sometimes it has a \n or empty spaces.
-    epoch=${${${epoch}:s/"\\n"/""}:s/" "/""}
-    epoch=$(echo $epoch | cut -c3-)
+    date=${${${date}:s/"\\n"/""}:s/" "/""}
 
-    echo "Processing experiment ${Experiment}_${epoch}.\n"
+    echo 'Processing experiment ${EXP}_${date}.\n'
 
 
     # Create the lis file from ccs
-    ssh jops@ccs "cd /ccs/expr/${Experiment};/ccs/bin/make_lis -e ${Experiment} -p prod -s ${experiment}.lis"
-    scp jops@ccs:/ccs/expr/${Experiment}/${experiment}.vix ./${experiment}.vix
-    scp jops@ccs:/ccs/expr/${Experiment}/${experiment}.lis ./${experiment}.lis
-    scp jops@jop83:piletters/${experiment}.piletter .
-    scp jops@jop83:piletters/${experiment}.expsum .
-    ln -s ${experiment}.vix ${Experiment}.vix
+    ssh jops@ccs "cd /ccs/expr/${EXP};/ccs/bin/make_lis -e ${EXP} -p prod -s ${exp}.lis"
 
-    checklis ${experiment}.lis
+    scp jops@ccs:/ccs/expr/${EXP}/${exp}.vix ./${exp}.vix
+    scp jops@ccs:/ccs/expr/${EXP}/${exp}.lis ./${exp}.lis
+
+    scp jops@jop83:piletters/${exp}.piletter .
+    scp jops@jop83:piletters/${exp}.expsum .
+
+    ln -s ${exp}.vix ${EXP}.vix
+
+    checklis ${exp}.lis
 
     read -q "REPLY?Are you happy with this lis file? (y/n) "
     if [[ ! $REPLY == 'y' ]];then
@@ -47,24 +49,17 @@ function post_process_eee() {
     fi
     echo '\n'
 
-    getdata.pl -proj ${Experiment} -lis ${experiment}.lis
-
-    j2ms2 -v ${experiment}.lis
-
-    standardplots -weight ${experiment}.ms $2 $3
+    getdata.pl -proj ${EXP} -lis ${exp}.lis
 
-    gv ${experiment}-weight.ps
-    ls ${experiment}-auto*ps | parallel 'gv {}'
-    ls ${experiment}-cross*ps | parallel 'gv {}'
-    ls ${experiment}-ampphase*ps | parallel 'gv {}'
+    j2ms2 -v ${exp}.lis
 
+    standardplots -weight ${exp}.ms $2 $3
 
-    ysfocus.py ${experiment}.ms
+    gv ${exp}-weight.ps
+    ls ${exp}-auto*ps | parallel 'gv {}'
+    ls ${exp}-cross*ps | parallel 'gv {}'
+    ls ${exp}-ampphase*ps | parallel 'gv {}'
 
-    read "THRESHOLD?Which weight threshold should be applied to the data? "
-    # echo '\n'
-
-    flag_weights.py ${experiment}.ms $THRESHOLD
 
     read -q "REPLY?Please, update the PI letter. Do you want to continue? (y/n) "
     if [[ ! $REPLY == 'y' ]];then
@@ -72,10 +67,18 @@ function post_process_eee() {
     fi
     echo '\n'
 
-    tConvert ${experiment}.ms ${experiment}_1_1.IDI
 
-    pass=$(date | md5sum | cut -b 1-12)
-    touch ${experiment}_${pass}.auth
+    ysfocus.py ${exp}.ms
+
+    read -q "THRESHOLD?Which weight threshold should be applied to the data? "
+    echo '\n'
+
+    flag_weights.py ${exp}.ms $THRESHOLD
+
+    tConvert ${exp}.ms ${exp}_1_1.IDI
+
+    export pass=$(date | md5sum | cut -b 1-12)
+    touch ${exp}_${pass}.auth
 
 
     read -q "REPLY?If you need to PolConvert, DO IT NOW. Do you want to continue? (y/n) "
@@ -85,53 +88,55 @@ function post_process_eee() {
     echo '\n'
 
     gzip *ps
-    archive.pl -auth -e ${experiment}_${epoch} -n ${experiment} -p ${pass}
-    echo "Archiving..."
-    archive.pl -stnd -e ${experiment}_${epoch} ${experiment}.piletter *ps.gz
-    archive.pl -fits -e ${experiment}_${epoch}  *IDI*
+    archive -auth -e ${exp}_${date} -n ${exp} -p ${pass}
+    archive -stnd -e ${exp}_${date} ${exp}.piletter *ps.gz
+    archive -fits -e ${exp}_${date}  *IDI*
 
-    pipelet.py ${experiment} marcote
+    pipelet.py ${exp} marcote
 
     echo '\n\nWork at eee finished.\n'
 }
 
 
 function archive_pipeline() {
-    # First argument should be experiment name (lower cases) second one epoch (YYMMDD)
+    # First argument should be experiment name (lower cases) second one date (YYMMDD)
     cd $IN/$1
-    su jops -c "/export/jive/jops/bin/archive/user/archive.pl -pipe -e ${1}_${2}"
+    archive -pipe -e ${1}_${2}
     cd $OUT/$1
-    su jops -c "/export/jive/jops/bin/archive/user/archive.pl -pipe -e ${1}_${2}"
+    archive -pipe -e ${1}_${2}
 }
 
 function post_process_pipe() {
+    # Three parameters are expected:
+    #	- The experiment name (case insensitive).
+    #	- The reference station to use in standardplots.
+    #	- The calibrators to use in standardplots.
     # This script should be run from the experiment folder.
-    if [[ ! ( -n $1 && -n $2 ) ]];then
-        echo "Two parameters are required:"
+    if [[ ! ( -n $1 && -n $2 && -n $3 ) ]];then
+        echo "Three parameters are required:"
         echo " - experiment name (case insensitive)."
         echo " - session (in mmmYY format e.g. feb18)."
+        echo " - Calibrators to be used for the plots."
         exit
     fi
-    export PATH=$PATH:/home/jops/scripts/:/home/jops/bin/:/home/jops/.local/bin:$PATH:/data0/marcote/scripts/evn_support/
-    source /jop83_0/pipe/in/marcote/.zshrc
-    experiment=$(echo "${(L)1}")
-    Experiment=$(echo "${(U)1}")
 
-    epoch=$(ssh jops@ccs grep $Experiment /ccs/var/log2vex/MASTER_PROJECTS.LIS | cut -d " " -f 3)
+    exp=$1
+    exp=${(L)1}
+    EXP=${(U)1}
+
+    date=${ssh jops@ccs grep EC067A /ccs/var/log2vex/MASTER_PROJECTS.LIS | cut -d " " -f 3}
     # In the case of eEVN with an experiment name different this method may not work
-    if [[ ! -n $epoch ]];then
-        epoch=$(ssh jops@ccs grep $Experiment /ccs/var/log2vex/MASTER_PROJECTS.LIS | cut -d " " -f 4)
+    if [[ -n $date ]];then
+        date=${ssh jops@ccs grep EC067A /ccs/var/log2vex/MASTER_PROJECTS.LIS | cut -d " " -f 4}
     fi
 
     # Sometimes it has a \n or empty spaces.
-    epoch=${${${epoch}:s/"\\n"/""}:s/" "/""}
-    epoch=$(echo $epoch | cut -c3-)
+    date=${${${date}:s/"\\n"/""}:s/" "/""}
 
-    echo "Processing experiment ${Experiment}_${epoch}.\n"
 
-    # Create all the required directories and move to marcote/experiment one
-    em ${experiment}
-    # vlbeerexp $2 ${experiment}
+    # Create all the required directories and move to marcote/exp one
+    em ${exp}
+    vlbeerexp $2 ${exp}
 
     read -q "REPLY?Do you have all ANTAB files? Do you want to continue? (y/n) "
     if [[ ! $REPLY == 'y' ]];then
@@ -139,8 +144,8 @@ function post_process_pipe() {
     fi
     echo '\n'
 
-    # uvflgall.csh
-    # antab_check.py
+    uvflgall.csh
+    antab_check.py
 
     read -q "REPLY?Have you fixed all ANTAB files? Do you want to continue? (y/n) "
     if [[ ! $REPLY == 'y' ]];then
@@ -148,32 +153,27 @@ function post_process_pipe() {
     fi
     echo '\n'
 
-    # cat ${experiment}*.antabfs > "${experiment}.antab"
-    # cat ${experiment}*.uvflgfs > "${experiment}.uvflg"
-    # cp "${experiment}.antab" "$IN/${experiment}/"
-    # cp "${experiment}.uvflg" "$IN/${experiment}/"
-    cd "$IN/${experiment}"
+    cat ${exp}*.antabfs > ${exp}.antab
+    cat ${exp}*.uvflgfs > ${exp}.uvflg
+    cp ${exp}.antab $IN/${exp}/
+    cp ${exp}.uvflg $IN/${exp}/
+    cd $IN/${exp}
 
     # Input file and minimal modifications
-    cp ../template.inp ${experiment}.inp.txt
-    replace "userno = 3602" "userno = $(give_me_next_userno.sh)" -- "${experiment}.inp.txt"
-    replace "experiment = n05c3" "experiment = ${experiment}" -- "${experiment}.inp.txt"
+    cp ../template.inp ${exp}.inp.txt
+    replace "userno = 3602" "userno = ${give_me_next_userno.sh}" -- ${exp}.inp.txt
+    replace "experiment = n05c3" "experiment = ${exp}" -- ${exp}.inp.txt
 
-    read -q "REPLY?You should now edit the input file. Do you want to continue? (y/n) "
-    if [[ ! $REPLY == 'y' ]];then
-        exit
-    fi
-    echo '\n'
-    EVN.py ${experiment}.inp.txt
+    echo "You should now edit the input file and run the EVN pipeline by your own.\n"
     read -q "REPLY?Do you want to continue (pipeline properly finished)? (y/n) "
     if [[ ! $REPLY == 'y' ]];then
         exit
     fi
     echo '\n'
 
-    cd $OUT/${experiment}
-    comment_tasav_file.py ${experiment}
-    feedback.pl -exp "${experiment}" -jss 'marcote'
+    cd $OUT/${exp}
+    comment_tasav_file.py ${exp}
+    feedback.pl -exp '${exp}' -jss 'marcote'
     echo "You may need to modify the comment file and/or run again feedback.pl\n"
 
     read -q "REPLY?You may want to archive the pipeline results and protect them afterwards. (y/n) "
@@ -181,23 +181,16 @@ function post_process_pipe() {
         exit
     fi
     echo '\n'
-<<<<<<< HEAD
     # su jops -c "archive_pipeline ${exp} ${date}"
-=======
-    archive_pipeline ${experiment} ${epoch}
->>>>>>> 8197cb68235ad745473fbdb9c2cf412268d39158
     ampcal.sh
 
 }
 
 
-if [[ `hostname` == "eee2" ]];then
-    echo "Executing steps from eee..."
-    post_process_eee $1 $2 $3
-elif [[ `hostname` == "jop83" ]];then
-    echo "Executing steps from pipe..."
+if [[ hostname=="eee2" ]];then
+    post_process_eee $1 $2
+elif [[ hostname=="jop83" ]];then
     post_process_pipe $1 $2
-<<<<<<< HEAD
     echo '\n\nWork at pipe finished. You may want to distribute the experiment!\n'
 else
     # Executing everything from the beginning via ssh.
@@ -205,10 +198,6 @@ else
     ssh pipe@jop83 "post_process_pipe $1 $2"
     ssh jops@jop83 "archive_pipeline ${exp} ${date}"
     echo '\n\nWork finished. You may want to distribute the experiment!\n'
-=======
-else
-    echo "Computer not recognized."
->>>>>>> 8197cb68235ad745473fbdb9c2cf412268d39158
 fi