Merge pull request #5 from CommerceGov/usr/nnz/fix_analysis_template

- Corrects environment and imports needed for MIDAS.
- Fixes EKE script.
- Fixes #2.

ice_ocean_SIS/OM4_025/ocn_annual.frepp

@@ -70,34 +70,38 @@ set target
 if ($#argv) set argu = ($argv:q)
 
 
-set freanalysismodule = fre-analysis/test
+#set freanalysismodule = fre-analysis/test
 
 # make sure valid platform and required modules are loaded
 if (`gfdl_platform` == "hpcs-csc") then
    source $MODULESHOME/init/csh
    module use -a /home/fms/local/modulefiles #/usr/local/paida/Modules
    module purge
-   module load $fremodule
-   module load $freanalysismodule
-   module load gcc
+#   module load $fremodule
+#   module load $freanalysismodule
+#   module load gcc
    module load netcdf/4.2
    module load python/2.7.3
+   module load intel_compilers
 else
    echo "ERROR: invalid platform"
    exit 1
 endif
 
 # check again?
-if (! $?FRE_ANALYSIS_HOME) then
-   echo "ERROR: environment variable FRE_ANALYSIS_HOME not set."
-   exit 1
-endif
+#if (! $?FRE_ANALYSIS_HOME) then
+#   echo "ERROR: environment variable FRE_ANALYSIS_HOME not set."
+#   exit 1
+#endif
+
+# Build MIDAS libs and set PYTHONPATH
+(cd ${out_dir}/mom6/tools/python/025gridGeneration ; make frepp_local )
+setenv PYTHONPATH ${out_dir}/mom6/tools/python/025gridGeneration/local/lib/python
 
 # Run script
 set src_dir = ${out_dir}/mom6/tools/analysis
 set script_bash = ${src_dir}/MOM6_ts_annual.bash
 set script_dir = ${out_dir}/mom6/tools/analysis
-setenv PYTHONPATH ${out_dir}/mom6/tools/python/025gridGeneration/local/lib/python
 set woa05=/archive/gold/datasets/OM4_025/obs/WOA05_ptemp_salt_annual.v20141006.nc
 set mosaicDir=/archive/gold/datasets/OM4_025/mosaic.v20140610.unpacked
 

tools/analysis/EddyKineticEnergy.py

@@ -25,11 +25,12 @@
 y = netCDF4.Dataset(cmdLineArgs.gridspec+'/ocean_hgrid.nc').variables['y'][::2,::2]
 msk = netCDF4.Dataset(cmdLineArgs.gridspec+'/ocean_mask.nc').variables['mask'][:]
 area = msk*netCDF4.Dataset(cmdLineArgs.gridspec+'/ocean_hgrid.nc').variables['area'][:,:].reshape([msk.shape[0], 2, msk.shape[1], 2]).sum(axis=-3).sum(axis=-1)
-msk = numpy.ma.array(msk, mask=(msk==0))
+#msk = numpy.ma.array(msk, mask=(msk==0))
 
 #[t,z,y,x] corresponds to axis [0,1,2,3] which can be indexed by [-4,-3,-2,-1]
 
 ssu = rootGroup.variables['ssu']
+
 ssu_mean = ssu[:].mean(axis=0)
 eke_u = (0.5*(ssu-ssu_mean)**2).mean(axis=0)
 eke = (eke_u + numpy.roll(eke_u,1,axis=-1))/2 # U-point to T-point transform
@@ -39,10 +40,23 @@
 eke_v = (0.5*(ssv-ssv_mean)**2).mean(axis=0)
 eke = eke + (eke_v + numpy.roll(eke_v,1,axis=-2))/2 
 
-ci=m6plot.pmCI(0.0,0.5,0.1)
+#factor of 10000 to convert to (cm/s)^2
+eke = 10000*eke
+
+#clip the extreme small values that cause log to blow up
+eke = eke.clip(min=1.0e-8)
+
+#Plot with logscale=True
+#ci=m6plot.pmCI(0.0,10.0,0.1)
+#plot_title = 'Eddy Kinetic Energy annual mean [(cm/s)^2]'
+
+#The logscale=True of matplotlib.pyplot does not work!
+#So, pass the log to be plotted instead
+eke = numpy.log(eke)
+plot_title = 'Log of Eddy Kinetic Energy annual mean [(cm/s)^2]'
 
-m6plot.xyplot( 10000*eke, x, y, area=area,
-      suptitle=rootGroup.title+' '+cmdLineArgs.label, title='Eddy Kinetic Energy annual mean [(cm/s)^2]',
-      clim=ci, logscale=True,
+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')
 

tools/analysis/TS_depth_integrals.py

@@ -6,6 +6,9 @@
 
 from midas.rectgrid import *
 from midas.rectgrid_gen import *
+import matplotlib
+# Force matplotlib to not use any Xwindows backend.
+matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 import numpy as np
 import netCDF4 as nc