Expanded mlog2db for use with non-consecutive runs.

src/external/scripts/mlog2db

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