From 2241a65714f0e6ee853edf175e4aab3beea648e3 Mon Sep 17 00:00:00 2001
From: alinalerner <96520701+alinalerner@users.noreply.github.com>
Date: Thu, 14 Mar 2024 14:17:27 +0200
Subject: [PATCH] Domain properties authomatic retrieval + try/except plotting
 correction (#39)

Co-authored-by: Alina Lerner <eela@ac6-100.bullx>
---
 README.md             |  5 ++---
 scripts/plotdiacov.py | 12 +++++++++--
 scripts/rundiacov.sh  | 48 +++++--------------------------------------
 3 files changed, 17 insertions(+), 48 deletions(-)

diff --git a/README.md b/README.md
index fc0a0d0..b040de9 100644
--- a/README.md
+++ b/README.md
@@ -98,11 +98,10 @@ dfscomp -p CCMA_2022050112.dat -u CCMA_2022050112_unpert.dat -o dfs2022050112.da
 
 ### DIACOV
 First, you should have Festat output and the DIACOV binary compiled by Harmonie stored somewhere.
-Then, create the new directory, copy the DIACOV binary and Jb files there. Example:
+Then, create the new directory, Jb files there. Example:
 ```
 mkdir DiacovTest
 cd DiacovTest
-cp /path/to/DIACOV .
 mkdir dataTest
 cp /path/to/Jb/data dataTest/.
 ```
@@ -115,7 +114,7 @@ rundiacov -h
 
 Example:
 ```
-rundiacov -i dataTest -c METCOOP25D_65_2021100300-2021111006_412 -l 65 -g 2.5 -m 539 -n 1080 -d DIACOV
+rundiacov -i dataTest -c METCOOP25D_65_2021100300-2021111006_412 -g 2.5 -d /path/to/DIACOV
 ```
 
 #### Produce diagonal stats
diff --git a/scripts/plotdiacov.py b/scripts/plotdiacov.py
index 2a40c7f..dae2aec 100644
--- a/scripts/plotdiacov.py
+++ b/scripts/plotdiacov.py
@@ -63,13 +63,21 @@ def main(argv) :
   args = parser.parse_args()
 
   if args.idata != False and args.indir == False:
-    plotme(args.idata,args.oplot)
+      try:
+          plotme(args.idata,args.oplot)
+      except:
+          pass
+      
   elif args.indir != False and args.idata == False:
     datlist=glob.glob(args.indir+'/*.dat') 
     for infile in datlist:
       output=infile.replace('.dat','.png')
       print (' ... plotting '+output)
-      plotme(infile,output)
+      try:
+          plotme(infile,output)
+      except:
+          print('Cannot produce the plot '+output+'!')
+          pass
   else:
     print ('Cannot do both!')
     sys.exit(1)
diff --git a/scripts/rundiacov.sh b/scripts/rundiacov.sh
index 763d273..b51d06e 100755
--- a/scripts/rundiacov.sh
+++ b/scripts/rundiacov.sh
@@ -17,10 +17,7 @@ ${bold}NAME${normal}
 ${bold}USAGE${normal}
         ${PROGNAME} -i <data-dir>
 		    -c <jb-file-name>
-		    -l <level-nr>
 		    -g <grid-spacing>
-		    -m <nsmax>
-		    -n <ndgl>
 		    -d <diacov-binary>
                     [ -h ]
 
@@ -34,18 +31,9 @@ ${bold}OPTIONS${normal}
         -c ${unline}jb-file-name${normal}
 	   Name of *.cv and *.cvt files (without extension)
 		   
-	-l ${unline}level-nr${normal}
-           Number of domain's vertical levels
-		   
 	-g ${unline}grid-spacing${normal}
            Grid-spacing in kilometers
 		   
-	-m ${unline}nsmax${normal}
-           NSMAX parameter specified in domain properties
-		   
-	-n ${unline}ndgl${normal}
-           NDGL parameter specified in domain properties
-		   
 	-d ${unline}diacov-binary${normal}
            PATH to DIACOV binary.
 
@@ -56,10 +44,7 @@ USAGE
 
 DATADIR=DUMMY
 JBFILE=DUMMY
-LEVELNUM=DUMMY
 GRIDSIZE=DUMMY
-NSMAX=DUMMY
-NDGL=DUMMY
 BINPATH=DUMMY
 
 #wrkdir=/home/eela/EoinDiacovTest/ #need to be changed to be more flexible
@@ -74,7 +59,7 @@ if [ ${#} -eq 0 ]; then
   exit 1
 fi
 
-while getopts i:c:l:g:m:n:d:h option
+while getopts i:c:g:d:h option
 do
   case $option in
     i)
@@ -83,18 +68,9 @@ do
     c)
        JBFILE=$OPTARG
        ;;
-    l)
-       LEVELNUM=$OPTARG
-       ;;
     g)
        GRIDSIZE=$OPTARG
        ;;
-    m)
-       NSMAX=$OPTARG
-       ;;
-    n)
-       NDGL=$OPTARG
-       ;;
     d)
        BINPATH=$OPTARG
        ;;
@@ -121,30 +97,12 @@ if [ ${JBFILE} == "DUMMY" ]; then
   exit 1
 fi
 
-if [ ${LEVELNUM} == "DUMMY" ]; then
-  echo "Please define number of vertical levels using -l"
-  echo "Try '${PROGNAME} -h' for more information"
-  exit 1
-fi
-
 if [ ${GRIDSIZE} == "DUMMY" ]; then
   echo "Please define grid-size using -g"
   echo "Try '${PROGNAME} -h' for more information"
   exit 1
 fi
 
-if [ ${NSMAX} == "DUMMY" ]; then
-  echo "Please define NSMAX using -m"
-  echo "Try '${PROGNAME} -h' for more information"
-  exit 1
-fi
-
-if [ ${NDGL} == "DUMMY" ]; then
-  echo "Please define NDGL using -n"
-  echo "Try '${PROGNAME} -h' for more information"
-  exit 1
-fi
-
 if [ ${BINPATH} == "DUMMY" ]; then
   echo "Please define path to DIACOV using -d"
   echo "Try '${PROGNAME} -h' for more information"
@@ -153,6 +111,10 @@ fi
 
 cd $tmpdir
 
+LEVELNUM=$(cv_header_list -i ../${DATADIR}/${JBFILE}.cv | grep "NFLEVG" | awk '{print $3}')
+NSMAX=$(cv_header_list -i ../${DATADIR}/${JBFILE}.cv | grep "NSMAX" | awk '{print $3}')
+NDGL=$(cv_header_list -i ../${DATADIR}/${JBFILE}.cv | grep "NDGL" | awk '{print $3}')
+
 # prepare namelist for diacov - full variables
 cat > nam_diag1 <<EOF
 &NAMDIACOV