Expanded mlog2db for use with non-consecutive runs.
This commit is contained in:
Bastian M. Wojek
parent
bf9ca156b6
commit
eaa297ef6e
135
src/external/scripts/mlog2db
vendored
135
src/external/scripts/mlog2db
vendored
@ -12,13 +12,20 @@ if [ $# -lt 3 ] ; then
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"musrfit-mlog to db converter"
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USAGE: mlog2db FIRSTRUN# LASTRUN# BLABLA [noheader | fit-TEMPLATERUN# | -oDB_OUTPUT_FILE]
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OR
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mlog2db \[LIST OF RUNS\] BLABLA [noheader | fit-TEMPLATERUN# | -oDB_OUTPUT_FILE]
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This small script converts subsequent musrfit output files (mlog) into one db file using bash/awk.
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Example 1:
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mlog2db 1423 1424 _ZF-LF-TF-supermeasurement
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generates the db-file "out.db" (or whatever filename you specified with the -o option) from 1423_ZF-LF-TF-supermeasurement.mlog and 1424_ZF-LF-TF-supermeasurement.mlog .
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It also includes the db header.
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Example 2:
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mlog2db [1423 1425] _ZF-LF-TF-supermeasurement
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generates the db-file "out.db" (or whatever filename you specified with the -o option) from 1423_ZF-LF-TF-supermeasurement.mlog and 1425_ZF-LF-TF-supermeasurement.mlog .
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The output files in both examples above also include the db header.
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In the case you are dealing with LEM-data AND have locally mounted the /mnt/data/nemu directory some available parameters like the
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temperature or transport settings will be taken from the summary files and added to the db-file.
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@ -28,7 +35,7 @@ If you additionally want to fit some data using musrfit specify the option "fit-
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In this case either a mlog-outputfile or a msr-inputfile have to be present for the specified template run.
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The subsequent inputfiles will be created.
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Example 2:
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Example 3:
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mlog2db 200 220 _tf_h13 -oABC.db fit-199
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This will fit the runs 200 to 220 using musrfit. The file 199_tf_h13.mlog (or if that is not available: 199_tf_h13.msr) is used as
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@ -36,7 +43,7 @@ template for the first musrfit input file. The results of the fits will be writt
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CAUTION:
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The "indexing number" of the .mlog has to be at the beginning of the filename.
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The "indexing number" of the .mlog has to be at the begin of the filename.
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Furthermore the data files that were fitted have to have the name "XXX_RUN#[_YYY]", where XXX,YYY are strings without whitespaces ("/" is OK).
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If you want to use the fitting feature, musrfit has to be installed either on the PATH or in the working directory.
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@ -47,15 +54,67 @@ else
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export PATH=./:$PATH
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COUNT=$1
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SUMMDIR="/mnt/data/nemu/summ"
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if [ "${4:0:3}" == "fit" ]; then
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TEMP=${4:4}
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else if [ "${5:0:3}" == "fit" ]; then
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TEMP=${5:4}
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else if [ "${6:0:3}" == "fit" ]; then
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TEMP=${6:4}
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# In case a list of runs is given by [...]
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if [ "${1:0:1}" == "[" ]; then
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RUNARRAY=($@)
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if [ "$1" == "[" ]; then
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RUNARRAY[0]=""
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else
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RUNARRAY[0]=${RUNARRAY[0]#"["}
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fi
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tLen=${#RUNARRAY[@]}
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for (( i=0; i<${tLen}; i++ ));
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do
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if [ "$1" == "[" ]; then
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RUNARRAY[$i]=${RUNARRAY[ (( i + 1 )) ]}
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fi
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if [ "${RUNARRAY[$i]:(-1)}" == "]" ]; then
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if [ "${RUNARRAY[$i]}" == "]" ]; then
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RUNARRAY[$i]=""
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LASTRUN=$(( i - 1 ))
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EMPTYENTRY=1
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else
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RUNARRAY[$i]=${RUNARRAY[$i]%"]"}
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LASTRUN=$i
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fi
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fi
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# echo ${RUNARRAY[$i]}
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done
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if [ "$EMPTYENTRY" == "1" ]; then
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EXTENSION=${RUNARRAY[ (( LASTRUN + 2 )) ]}
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OPT_PAR_ONE=${RUNARRAY[ (( LASTRUN + 3 )) ]}
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OPT_PAR_TWO=${RUNARRAY[ (( LASTRUN + 4 )) ]}
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OPT_PAR_THREE=${RUNARRAY[ (( LASTRUN + 5 )) ]}
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else
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EXTENSION=${RUNARRAY[ (( LASTRUN + 1 )) ]}
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OPT_PAR_ONE=${RUNARRAY[ (( LASTRUN + 2 )) ]}
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OPT_PAR_TWO=${RUNARRAY[ (( LASTRUN + 3 )) ]}
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OPT_PAR_THREE=${RUNARRAY[ (( LASTRUN + 4 )) ]}
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fi
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else # start and end-runs are given
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for (( j=0; j<=$2-$1; j++ ));
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do
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RUNARRAY[$j]=$(( $1 + $j ))
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# echo ${RUNARRAY[$j]}
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done
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LASTRUN=$(( $2 - $1 ))
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EXTENSION=$3
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OPT_PAR_ONE=$4
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OPT_PAR_TWO=$5
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OPT_PAR_THREE=$6
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fi
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# Check if fitting should be done
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if [ "${OPT_PAR_ONE:0:3}" == "fit" ]; then
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TEMP=${OPT_PAR_ONE:4}
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else if [ "${OPT_PAR_TWO:0:3}" == "fit" ]; then
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TEMP=${OPT_PAR_TWO:4}
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else if [ "${OPT_PAR_THREE:0:3}" == "fit" ]; then
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TEMP=${OPT_PAR_THREE:4}
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fi
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fi
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fi
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@ -73,21 +132,21 @@ if [ "$TEMP" != "" ]; then
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exit 1
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else
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if [ -e $TEMP$3.mlog ]; then
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TEMPLATE=$TEMP$3.mlog
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if [ -e $TEMP$EXTENSION.mlog ]; then
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TEMPLATE=$TEMP$EXTENSION.mlog
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else if [ -e $TEMP$3.msr ]; then
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TEMPLATE=$TEMP$3.msr
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TEMPLATE=$TEMP$EXTENSION.msr
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fi
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fi
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fi
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fi
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while [ $COUNT -le $2 ]
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for (( q=0; q<=${LASTRUN}; q++ ));
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do
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let NEXTCOUNT=COUNT+1
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NEXTINPUT=$NEXTCOUNT$3.msr
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FIRSTINPUT=$1$3.msr
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COUNT=${RUNARRAY[$q]}
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NEXTCOUNT=${RUNARRAY[ (( q + 1 )) ]}
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NEXTINPUT=$NEXTCOUNT$EXTENSION.msr
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FIRSTINPUT=${RUNARRAY[0]}$EXTENSION.msr
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if [ "$TEMP" != "" ]; then
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@ -96,8 +155,8 @@ if [ "$TEMP" != "" ]; then
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exit 1
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fi
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if [ "$COUNT" == "$1" ]; then
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awk -v count=$TEMP -v nextcount=$1 -v nextinput=$FIRSTINPUT '{
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if [ "$COUNT" == "${RUNARRAY[0]}" ]; then
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awk -v count=$TEMP -v nextcount=${RUNARRAY[0]} -v nextinput=$FIRSTINPUT '{
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if(NR==1) print nextcount > nextinput
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else if($1 == "RUN") {
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if (substr(count,1,1) != "_"){ count = sprintf("_%04u", count); nextcount = sprintf("_%04u", nextcount);}
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@ -107,10 +166,10 @@ if [ "$TEMP" != "" ]; then
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else print $0 >> nextinput
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}' $TEMPLATE
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fi
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musrfit $COUNT$EXTENSION.msr -k
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musrfit $COUNT$3.msr
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if [ $NEXTCOUNT -le $2 ]; then
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if [ "$NEXTCOUNT" != "${RUNARRAY[$LASTRUN]}" ]; then
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awk -v count=$COUNT -v nextcount=$NEXTCOUNT -v nextinput=$NEXTINPUT '{
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if(NR==1) print nextcount > nextinput
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else if($1 == "RUN") {
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@ -119,12 +178,12 @@ if [ "$TEMP" != "" ]; then
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print $0 >> nextinput
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}
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else print $0 >> nextinput
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}' $COUNT$3.mlog
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}' $COUNT$EXTENSION.mlog
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fi
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fi
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if [ ! -e $COUNT$3.mlog ]; then
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echo The specified musrfit output file $COUNT$3.mlog does not exist!
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if [ ! -e $COUNT$EXTENSION.mlog ]; then
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echo The specified musrfit output file $COUNT$EXTENSION.mlog does not exist!
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exit 1
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fi
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@ -137,7 +196,7 @@ RUNNUMBER=$( awk '{
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if(runNumber[1] ~ /lem/ && runNumber[2] == "his") {print substr(runNumber[3],1,4) }
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X=1
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}
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}' $COUNT$3.mlog )
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}' $COUNT$EXTENSION.mlog )
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RUNYEAR=$( awk '{
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if(NR==1) X=0
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@ -147,7 +206,7 @@ RUNYEAR=$( awk '{
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else print "XX"
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X=1
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}
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}' $COUNT$3.mlog )
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}' $COUNT$EXTENSION.mlog )
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if [ "$RUNYEAR" != "XX" ]; then
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@ -169,12 +228,12 @@ fi
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fi
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awk -v parFOUR=$4 -v parFIVE=$5 -v parSIX=$6 '{
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awk -v optPARone=$OPT_PAR_ONE -v optPARtwo=$OPT_PAR_TWO -v optPARthree=$OPT_PAR_THREE '{
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outfile="out.db"
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if(parFOUR ~ /^-o/) outfile = substr(parFOUR,3)
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if(parFIVE ~ /^-o/) outfile = substr(parFIVE,3)
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if(parSIX ~ /^-o/) outfile = substr(parSIX,3)
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if(optPARone ~ /^-o/) outfile = substr(optPARone,3)
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if(optPARtwo ~ /^-o/) outfile = substr(optPARtwo,3)
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if(optPARthree ~ /^-o/) outfile = substr(optPARthree,3)
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FS = " "
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OFS = " "
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@ -241,7 +300,7 @@ awk -v parFOUR=$4 -v parFIVE=$5 -v parSIX=$6 '{
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if("'"$TEMPERATURE"'" != "") {
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if("'"$COUNT"'" == "'"$1"'" && parFOUR != "noheader" && parFIVE != "noheader" && parSIX != "noheader"){
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if("'"$COUNT"'" == "'"${RUNARRAY[0]}"'" && optPARone != "noheader" && optPARtwo != "noheader" && optPARthree != "noheader"){
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print "TITLE" >> outfile
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print ">>>Put your title here<<<\n" >> outfile
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print "Abstract" >> outfile
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@ -285,14 +344,14 @@ awk -v parFOUR=$4 -v parFIVE=$5 -v parSIX=$6 '{
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print dataArray[i+3] ",,, " "'"$TITLE"'" >> outfile
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if("'"$COUNT"'" == "'"$2"'") print "\n" >> outfile
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if("'"$COUNT"'" == "'"${RUNARRAY[$LASTRUN]}"'") print "\n" >> outfile
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}
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# If we do not have the information from the summary file
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else {
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if("'"$COUNT"'" == "'"$1"'" && parFOUR != "noheader" && parFIVE != "noheader" && parSIX != "noheader"){
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if("'"$COUNT"'" == "'"${RUNARRAY[0]}"'" && optPARone != "noheader" && optPARtwo != "noheader" && optPARthree != "noheader"){
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print "TITLE" >> outfile
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print ">>>Put your title here<<<\n" >> outfile
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print "Abstract" >> outfile
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@ -321,15 +380,13 @@ awk -v parFOUR=$4 -v parFIVE=$5 -v parSIX=$6 '{
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print dataArray[i+3] ",,, " title >> outfile
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if("'"$COUNT"'" == "'"$2"'") print "\n" >> outfile
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if("'"$COUNT"'" == "'"${RUNARRAY[LASTRUN]}"'") print "\n" >> outfile
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}
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}
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}' $COUNT$3.mlog
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((COUNT++))
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}' $COUNT$EXTENSION.mlog
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done
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