Added script for musrfit chain fitting and mlog-to-db conversion
This commit is contained in:
Bastian M. Wojek
parent
3cda938f0c
commit
6492f5ee1b
307
src/external/scripts/mlog2db
vendored
Executable file
307
src/external/scripts/mlog2db
vendored
Executable file
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#!/bin/bash
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if [ ! -e /usr/bin/awk ]; then
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echo Please make sure you have installed awk!
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exit 1
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fi
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if [ $# -lt 3 ] ; then
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cat <<EOFHELP
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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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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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If you want to generate a file without the header information just run the script with the option "noheader".
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If you additionally want to fit some data using musrfit specify the option "fit-TEMPLATERUN#".
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In this case a mlog-outputfile has to be present for the specified template run. The subsequent inputfiles will be created.
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Example 2:
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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 is used as template for the first musrfit input file.
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The results of the fits will be written to ABC.db.
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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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Furthermore the histogram files that were fitted have to have the name "XXX_RUN#_YYY" or "ZZZ_his_RUN#", where XXX,YYY,ZZZ are strings
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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 local directory.
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EOFHELP
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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=${6:4}
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fi
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fi
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fi
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if [ "$TEMP" != "" ]; then
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if [ -e $TEMP$3.mlog ]; then
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TEMPLATE=$TEMP$3.mlog
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else if [ -e $TEMP$3.msr ]; then
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TEMPLATE=$TEMP$3.msr
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fi
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fi
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fi
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while [ $COUNT -le $2 ]
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do
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let NEXTCOUNT=COUNT+1
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NEXTINPUT=$NEXTCOUNT$3.msr
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FIRSTINPUT=$1$3.msr
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if [ "$TEMP" != "" ]; then
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if [ "$TEMPLATE" == "" ]; then
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echo The specified musrfit files $TEMP$3.mlog and $TEMP$3.msr do not exist!
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exit 1
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fi
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if [ "$COUNT" == "$1" ]; then
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awk -v count=$TEMP -v nextcount=$1 -v nextinput=$FIRSTINPUT '{
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if(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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sub(count, nextcount, $0);
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print $0 >> nextinput
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}
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else print $0 >> nextinput
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}' $TEMPLATE
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fi
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musrfit $COUNT$3.msr
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if [ $NEXTCOUNT -le $2 ]; then
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awk -v count=$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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if (substr(count,1,1) != "_"){ count = sprintf("_%04u", count); nextcount = sprintf("_%04u", nextcount);}
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sub(count, nextcount, $0);
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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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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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exit 1
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fi
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if [ -d $SUMMDIR ]; then
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RUNNUMBER=$( awk '{
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if(NR==1) X=0
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if($1 ~ /^RUN/ && X==0) {
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split($2, runNumber, "_")
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if(runNumber[1] ~ /lem/ && runNumber[2] != "his") {print runNumber[2] }
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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$3.mlog )
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RUNYEAR=$( awk '{
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if(NR==1) X=0
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if($1 ~ /^RUN/ && X==0) {
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split($2, runNumber, "_")
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if(runNumber[1] ~ /lem/) {print substr(runNumber[1],length(runNumber[1])-1)}
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else print "XX"
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X=1
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}
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}' $COUNT$3.mlog )
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if [ "$RUNYEAR" != "XX" ]; then
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SUMMFILE=$SUMMDIR/20$RUNYEAR/lem$RUNYEAR\_$RUNNUMBER.summ
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TITLE=$( awk '{ if(NR==4) print $0 }' $SUMMFILE )
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ENERGY=$( awk '{ if($0 ~ /implantation energy/) print $(NF-1)}' $SUMMFILE )
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TEMPERATURE=$( awk '{ if($1 == "Sample_CF1") print $(NF-1)}' $SUMMFILE )
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RALRAR=$( awk '{ if($5 == "RA-L") RAL=$7; if($1 == "RA-R") { RAR=$3; print RAL-RAR; nextfile } }' $SUMMFILE )
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RATRAB=$( awk '{ if($5 == "RA-T") RAT=$7; if($1 == "RA-B") { RAB=$3; print RAT-RAB; nextfile } }' $SUMMFILE )
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TRANSPORT=$( awk '{ if($1 == "Moderator") print $3}' $SUMMFILE )
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fi
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fi
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awk -v parFOUR=$4 -v parFIVE=$5 -v parSIX=$6 '{
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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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FS = " "
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OFS = " "
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if(NR==1){title=$0; X=0; Y=0; i=1}
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if(NR>4){
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if(X == 0){
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if($0 != ""){
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parArray[i] = $2
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dataArray[i] = $3
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if($4 ~ /^-/)
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negErrArray[i] = (-1.0)*$4
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else
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negErrArray[i] = $4
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if($5 ~ /none/)
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posErrArray[i] = $4
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else
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posErrArray[i] = $5
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i++
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}
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if($0 == "") X=1
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}
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}
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if($1 ~ /^RUN/ && X==1){ split($2, runNumber, "_"); X=2 }
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if($1 ~ /^chi/ && X==2){
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parArray[i] = "CHISQ"
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parArray[i+1] = "NDF"
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parArray[i+2] = "CHISQred"
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parArray[i+3] = "RUN"
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sub(/,/, "", $3); sub(/,/, "", $6);
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dataArray[i] = $3
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dataArray[i+1] = $6
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dataArray[i+2] = $9
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if(runNumber[2] != "his") {dataArray[i+3] = runNumber[2] }
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if(runNumber[2] == "his") {dataArray[i+3] = substr(runNumber[3],1,4) }
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negErrArray[i] = ""
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negErrArray[i+1] = ""
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negErrArray[i+2] = ""
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negErrArray[i+3] = ""
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posErrArray[i] = ""
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posErrArray[i+1] = ""
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posErrArray[i+2] = ""
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posErrArray[i+3] = ""
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# Output to file in the case, the LEM summary file is accessible
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if("'"$TEMPERATURE"'" != "") {
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if("'"$COUNT"'" == "'"$1"'" && parFOUR != "noheader" && parFIVE != "noheader" && parSIX != "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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print ">>>Put your abstract here<<<\n" >> outfile
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print "LABELS" >> outfile
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print "T" >> outfile
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print "Tr" >> outfile
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print "E" >> outfile
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print "RAL-RAR" >> outfile
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print "RAT-RAB" >> outfile
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for(k=1;k<i+4;k++){
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print parArray[k] >> outfile
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}
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$1 = "Data"
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$2 = "T"
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$3 = "Tr"
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$4 = "E"
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$5 = "RALRAR"
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$6 = "RATRAB"
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for(k=1;k<i+4;k++){
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$(k+6)=parArray[k]
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}
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print "\n" $0 >> outfile
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print "\\-e" >> outfile
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}
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print "T = " "'"$TEMPERATURE"'" ",,,\\" >> outfile
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print "Tr = " "'"$TRANSPORT"'" ",,,\\" >> outfile
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if ("'"$ENERGY"'" != "") print "E = " "'"$ENERGY"'" ",,,\\" >> outfile
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else print "E = -999,,,\\" >> outfile
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if ("'"$RALRAR"'" != "") print "RALRAR = " "'"$RALRAR"'" ",,,\\" >> outfile
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else print "RALRAR = -999,,,\\" >> outfile
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if ("'"$RATRAB"'" != "") print "RATRAB = " "'"$RATRAB"'" ",,,\\" >> outfile
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else print "RATRAB = -999,,,\\" >> outfile
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for(l=1;l<i+3;l++){
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print parArray[l] " = " dataArray[l] ", " posErrArray[l] ", " negErrArray[l] ",\\" >> outfile
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}
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print dataArray[i+3] ",,, " "'"$TITLE"'" >> outfile
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if("'"$COUNT"'" == "'"$2"'") print "\n" >> outfile
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}
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# If we do not have the information from the summary file
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else {
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if("'"$COUNT"'" == "'"$1"'" && parFOUR != "noheader" && parFIVE != "noheader" && parSIX != "noheader"){
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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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print ">>>Put your abstract here<<<\n" >> outfile
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print "LABELS" >> outfile
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for(k=1;k<i+4;k++){
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print parArray[k] >> outfile
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}
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$1 = "Data"
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for(k=1;k<i+4;k++){
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$(k+2)=parArray[k]
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}
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print "\n" $0 >> outfile
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print "\\-e" >> outfile
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}
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for(l=1;l<i+3;l++){
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print parArray[l] " = " dataArray[l] ", " posErrArray[l] ", " negErrArray[l] ",\\" >> outfile
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}
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print dataArray[i+3] ",,, " title >> outfile
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if("'"$COUNT"'" == "'"$2"'") 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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done
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fi
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