--- MITgcm_contrib/jmc_script/extract_StD	2006/01/07 16:23:29	1.1
+++ MITgcm_contrib/jmc_script/extract_StD	2008/05/29 23:47:13	1.3
@@ -1,40 +1,78 @@
 #!/bin/sh
+
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm_contrib/jmc_script/extract_StD,v 1.3 2008/05/29 23:47:13 jmc Exp $
+# $Name:  $
+
+add=0 ; mut=0 ;
+if [ $# -ge 3 ] 
+then
+ if test $1 = '-a' ; then add=1; shift; fi
+ if test $1 = '-s' ; then mut=1; shift; fi
+ if test $add = 0  ; then if test $1 = '-a' ; then add=1; shift; fi ; fi
+fi
+
 case $# in
-  0|1) echo "Usage: `basename $0` input_fil outp_sufix [field_name_list]"
+0|1|2) echo "Usage: `basename $0` [-a][-s] input_fil out_pfix out_sfix [field_name_list]"
        echo "   from ASCII Diagnostics-Stats file (=input_fil) and for each field"
        echo "   (in field_name_list), extract the associated numerical values and"
-       echo "   put them in a separated file: stDiag_{VAR}.{outp_sufix}"
+       echo "   put them in a separated file: {out_pfix}_{VAR}.{out_sfix}"
+       echo "   -a : append to output_file ; -s : silent mode "
+       echo "   '=' as out_pfix -> take {input_fil} basename "
        exit 9 ;;
-    2) listV='T' ;;
     *) ;;
 esac
 
 inpFil=$1
-#outFil=$2
-sufx=$2
+if test $2 = '='
+then prfx=`basename $inpFil | sed 's/\..*\.txt//'`
+else prfx=$2 ; fi
+sufx=$3
 tmpFil='TTT.'$$
-if test $# = '2'
-then listV='T'
+tmpfil='ttt.'$$
+
+echo 'output pre,sufix:' $prfx','$sufx '; input file:' $inpFil
+if test $# = '3'
+then listV=`sed -n '/^# Fields /s/# Fields       ://p' $inpFil`
 else
- shift; shift; listV=$*
+ shift; shift; shift; listV=$*
+fi
+if test $mut = 0 ; then 
+ grep '^# Fields ' $inpFil
+ echo 'selected var:' $listV
+#echo 'sufx, tmpFil:' $sufx $tmpFil
 fi
-echo $inpFil $sufx $listV $tmpFil
-grep '^# Fields ' $inpFil
 
+flag=1;
 for vv in $listV
 do
- outFil='stDiag_'$vv.$sufx
  case $vv in
-   'Eta') var='ETAN';;
-   'Et2') var='ETANSQ';;
-     'T') var='THETA';;
-     'S') var='SALT' ;;
-     'U') var='UVEL' ;;
-     'V') var='VVEL' ;;
-     'W') var='WVEL' ;;
-    'U2') var='UVELSQ' ;;
-    'V2') var='VVELSQ' ;;
-       *)  var=$vv ;;
+   'Eta') var='ETAN'     ; vfl=$vv ;;
+              'ETAN'     ) var=$vv ; vfl='Eta';;
+     'T') var='THETA'    ; vfl=$vv ;;
+              'THETA'    ) var=$vv ; vfl='T' ;;
+     'S') var='SALT'     ; vfl=$vv  ;;
+              'SALT'     ) var=$vv ; vfl='S' ;;
+     'U') var='UVEL'     ; vfl=$vv  ;;
+              'UVEL'     ) var=$vv ; vfl='U' ;;
+     'V') var='VVEL'     ; vfl=$vv  ;;
+              'VVEL'     ) var=$vv ; vfl='V' ;;
+     'W') var='WVEL'     ; vfl=$vv  ;;
+              'WVEL'     ) var=$vv ; vfl='W' ;;
+   'Phi') var='PHIHYD'   ; vfl=$vv  ;;
+              'PHIHYD'   ) var=$vv ; vfl='Phi';;
+   'Et2') var='ETANSQ'   ; vfl=$vv ;;
+              'ETANSQ'   ) var=$vv ; vfl='Et2';;
+    'T2') var='THETASQ'  ; vfl=$vv ;;
+              'THETASQ'  ) var=$vv ; vfl='T2' ;;
+    'S2') var='SALTSQ'   ; vfl=$vv  ;;
+              'SALTSQ'   ) var=$vv ; vfl='S2' ;;
+    'U2') var='UVELSQ'   ; vfl=$vv  ;;
+              'UVELSQ'   ) var=$vv ; vfl='U2' ;;
+    'V2') var='VVELSQ'   ; vfl=$vv  ;;
+              'VVELSQ'   ) var=$vv ; vfl='V2' ;;
+    'W2') var='WVELSQ'   ; vfl=$vv  ;;
+              'WVELSQ'   ) var=$vv ; vfl='W2' ;;
+       *)  var=$vv ; vfl=$vv ;;
  esac
 #echo 'grep -m 1' "^ field : ${var} " $inpFil
 #grep -m 1 "^ field : ${var} " $inpFil
@@ -43,8 +81,40 @@
  then
   echo 'WARNING variable:' $var 'not found in file' $inpFil
  else
-  echo 'extract variable:' $var ', outFil=' $outFil
 #echo 'nLev=' $nLev
+#- first variable: extract Header, then Iter Numbers:
+  if test $flag = 1
+  then flag=0
+    outFil=${prfx}'_head'.$sufx
+    nLin=`sed -n "/^# end of header/=" $inpFil`
+    head -$nLin $inpFil > $tmpFil 
+    if test -f $outFil -a $add = 0 ; then rm -f $outFil ; fi
+    if test -f $outFil
+    then
+      diff $tmpFil $outFil > /dev/null
+      out=$?
+      if test $out != '0'
+      then
+        echo 'WARNNING : get Different header file:' $outFil
+        cat $tmpFil >> $outFil
+      fi
+      rm -f $tmpFil
+    else mv $tmpFil $outFil
+      if test $mut = 0 ; then echo 'extract Header (' $nLin 'lines )  ==> ' $outFil ; fi
+    fi
+#----
+    outFil=${prfx}'_Iter'.$sufx
+    if test $mut = 0 ; then echo 'extract Iteration Nb ==> outFil=' $outFil ; fi
+    if test -f $outFil -a $add = 0 ; then rm -f $outFil ; fi
+    touch $outFil
+    rList=`sed -n '/^# Regions /s/# Regions      ://p' $inpFil`
+    for j in $rList ; do jj=$j ; done
+    grep "^ field : ${var} " $inpFil | grep "$j ; nb.Lev =" | \
+                  sed 's/.*Iter =//' | sed 's/; region.*//g' >> $outFil
+  fi
+#----
+  outFil=${prfx}'_'$vfl.$sufx
+  if test $mut = 0 ; then echo 'extract variable:' $var ', outFil=' $outFil ; fi
 #- echo set of sed instruction to file sedFil :
   sedFil=$tmpFil.$vv
   rm -f $sedFil
@@ -59,8 +129,10 @@
   echo "}" >> $sedFil
 #- extract records of variable "var" using sed command & sedFil
   sed -n -f $sedFil $inpFil > $tmpFil
-  head -1 $tmpFil
-  sed '/^ k /d' $tmpFil | sed '/^ field /d' > $outFil 
+  if test $mut = 0 ; then head -1 $tmpFil ; fi
+  if test -f $outFil -a $add = 0 ; then rm -f $outFil ; fi
+  touch $outFil
+  sed '/^ k /d' $tmpFil | sed '/^ field /d' >> $outFil 
   rm -f $sedFil $tmpFil
  fi
 done