From 0c51a857734268608345a52eae92e72c7f2328d1 Mon Sep 17 00:00:00 2001
From: Niki Zadeh <Niki.Zadeh@noaa.gov>
Date: Wed, 20 Jan 2016 16:43:54 -0500
Subject: [PATCH 1/2] Fix the analysis script to use ocean_5daily.nc

-The variables ssu, ssv required for this script are moved from ocean_daily to ocean_5daily
-Put all the figures in 1 dir rather than 1 dir per year
---
 tools/analysis/EddyKineticEnergy.py | 4 ++--
 tools/analysis/MOM6_refineDiag.csh  | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/analysis/EddyKineticEnergy.py b/tools/analysis/EddyKineticEnergy.py
index d47d19f825..779373222d 100755
--- a/tools/analysis/EddyKineticEnergy.py
+++ b/tools/analysis/EddyKineticEnergy.py
@@ -11,7 +11,7 @@
 parser = argparse.ArgumentParser(description='''Script for plotting annual-average eddy kinetic energy.''')
 parser.add_argument('annual_file', type=str, help='''Daily file containing ssu,ssv.''')
 parser.add_argument('-l','--label', type=str, default='', help='''Label to add to the plot.''')
-parser.add_argument('-o','--outdir', type=str, default='.', help='''Directory in which to place plots.''')
+parser.add_argument('-o','--outfile', type=str, default='.', help='''Output file plot.''')
 parser.add_argument('-g','--gridspec', type=str,
   help='''File containing variables geolon,geolat,wet,areacello. Usually the ocean_static.nc from diag_table.''')
 cmdLineArgs = parser.parse_args()
@@ -56,5 +56,5 @@
 m6plot.xyplot( eke, x, y, area=area,
       suptitle=rootGroup.title+' '+cmdLineArgs.label, title=plot_title,
 #      clim=ci, logscale=True,
-      save=cmdLineArgs.outdir+'/EKE_mean.png')
+      save=cmdLineArgs.outfile )
 
diff --git a/tools/analysis/MOM6_refineDiag.csh b/tools/analysis/MOM6_refineDiag.csh
index 290123926e..1b59cda4fd 100755
--- a/tools/analysis/MOM6_refineDiag.csh
+++ b/tools/analysis/MOM6_refineDiag.csh
@@ -94,9 +94,9 @@ set script_dir=${out_dir}/mom6/tools/analysis
 echo '==Run some example annual scripts. These are not reviewed by scientists.' 
 
 echo '====annual mean Eddy Kinetic Energy======'
-mkdir -p $out_dir/refineDiag_ocean_annual/ocean_${yr1}/EddyKineticEnergy
+mkdir -p $out_dir/refineDiag_ocean_annual/EddyKineticEnergy
 
-$script_dir/EddyKineticEnergy.py  -g $yr1.ocean_static.nc -o $out_dir/refineDiag_ocean_annual/ocean_${yr1}/EddyKineticEnergy -l ${yr1} $yr1.ocean_daily.nc
+$script_dir/EddyKineticEnergy.py  -g $yr1.ocean_static.nc -o $out_dir/refineDiag_ocean_annual/EddyKineticEnergy/EKE_mean_${yr1}.png -l ${yr1} $yr1.ocean_5daily.nc
 $script_dir/calc_variance.py zos $yr1.ocean_5daily.nc $refineDiagDir/$yr1.ocean_month_refined.nc
 
 echo "  ---------- end yearly analysis ----------  "

From 6470d1b39dca3e857fb65ff007fa91f363771cca Mon Sep 17 00:00:00 2001
From: Niki Zadeh <Niki.Zadeh@noaa.gov>
Date: Fri, 29 Jan 2016 10:16:07 -0500
Subject: [PATCH 2/2] Use full grid ocean_static.nc

- Use the full grid ocean_static.nc (produced with no mask_table) if it is present in the history tar ball
---
 tools/analysis/MOM6_refineDiag.csh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tools/analysis/MOM6_refineDiag.csh b/tools/analysis/MOM6_refineDiag.csh
index 1b59cda4fd..41a1ab5feb 100755
--- a/tools/analysis/MOM6_refineDiag.csh
+++ b/tools/analysis/MOM6_refineDiag.csh
@@ -95,8 +95,9 @@ echo '==Run some example annual scripts. These are not reviewed by scientists.'
 
 echo '====annual mean Eddy Kinetic Energy======'
 mkdir -p $out_dir/refineDiag_ocean_annual/EddyKineticEnergy
-
-$script_dir/EddyKineticEnergy.py  -g $yr1.ocean_static.nc -o $out_dir/refineDiag_ocean_annual/EddyKineticEnergy/EKE_mean_${yr1}.png -l ${yr1} $yr1.ocean_5daily.nc
+set ocean_static_file = $yr1.ocean_static.nc
+if ( -e $yr1.ocean_static_no_mask_table.nc ) set ocean_static_file = $yr1.ocean_static_no_mask_table.nc
+$script_dir/EddyKineticEnergy.py  -g $ocean_static_file -o $out_dir/refineDiag_ocean_annual/EddyKineticEnergy/EKE_mean_${yr1}.png -l ${yr1} $yr1.ocean_5daily.nc
 $script_dir/calc_variance.py zos $yr1.ocean_5daily.nc $refineDiagDir/$yr1.ocean_month_refined.nc
 
 echo "  ---------- end yearly analysis ----------  "