Visualizing data in Cubed-Sphere grid

IN PROGRESS

Cubed-Sphere grid background

Several GEOS-5 products are now produced on the native cubed-sphere computational grid. Although this format may be less familiar, this choice has several advantages for some user communities. In particular, the Chemical Transport Modeling (CTM) community can use native mass-flux products to significantly improve conservation properties when running with GEOS-5. To minimize transition difficulties for GEOS-5 data consumers, this page provides instructions for visualizing cubed-sphere data products using a variety of common packages: python, Matlab, IDL, and GRaDS, and Panoply. This page also provides instructions for downloading and building an executable that can regrid cubed-sphere products onto a traditional lat-lon grid.

Fortran

To map the cubed-sphere grid data to lat-lon gird data, the program c2l_CFIO_offline.x is built with AGCM at src/GEOSgcs_GridComp/GEOSgcm_GridComp/GEOSagcm_GridComp/GEOSsuperdyn_GridComp/FVdycoreCubed_GridComp. The example configure file c2l_CFIO_offline.rc is also generated. It should be run as mpirun –np 6 ./c2l_CFIO_offline.x. This will produce a lat-lon grid data file whose name is configured in c2l_CFIO_offline.rc. Users then can use their familiar tools to visualize the lat-lon grid data.

Matlab

Users can find a “GridUtils” package in MATLAB ( R2015b and R2016a or above) at http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_HP_Output_Data#MATLAB_.28Cubed-sphere_and_regular_data.29 . The instructions are straight forward. Although it is intended for GCHP, it can be used for all the other outputs that use the same formats as that of GCHP. For the new format of the output, users can use the matlab codes here to transform the data to lat-lon grid and visualize the products.

1. Download source codes and save them as driver.m, CSnative.m, extendFace1.m,extendFace3.m, extendFace4.m, extendFace6.m, and the example data file respectively to the same folder. The extendFace(1-6).m are used to fill the seam between cubed-sphere faces. Face2 and Face5 are not necessary to be extended because they are redundant.
2. Users should specify the time, level , variable’s name and file name in driver.m
3. Run with Matlab: % driver

extendFace6.m

close all;
clear all;

% users specify the file name, variables, the the lat-lon resolution, level and time. 
% level is optional 

fname='example_prog.20141118_2130z.nc4';
varname='T';
Nlat=100;
Nlon=600;
level=1;
time=1;

[grid_data,X,Y]=CS2latlon(fname,varname,Nlat,Nlon,time,level);
pcolor(Y',X',squeeze(grid_data)'),shading('flat'),colorbar

% save below as CS2latlon.m

function [grid_data,X,Y]=CS2latlon(fname,varname,Nlat,Nlon,time,level)
   ncid=netcdf.open(fname,'NOWRITE');
   vinfo=ncinfo(fname,'T')
   S=size(vinfo.Size);
   ydim=vinfo.Size(1);
   xdim=vinfo.Size(2);
   nf=vinfo.Size(3);
   netcdf.close(ncid);

   lats=ncread(fname,'lats');
   lons=ncread(fname,'lons');
   if( S(2)==5)
      T=ncread(fname,'T',[1 1 1 level time],[ydim xdim nf level time]);
   else
      % surface, no level
      T=ncread(fname,'T',[1 1 1 time],[ydim xdim nf time]);
   end

   length = xdim*ydim*nf;

   lats=reshape(lats,1,length);
   lons=reshape(lons,1,length);
   T=reshape(T,1,length);
   lats=lats(~isnan(T));
   lons=lons(~isnan(T));
   T=T(~isnan(T));

   latlim=linspace(min(lats),max(lats),Nlat);
   lonlim=linspace(min(lons),max(lons),Nlon);
   [X,Y]=meshgrid(latlim,lonlim);

   grid_data=griddata(lats,lons,T,X,Y,'v4');

Python

For the new format of the output, users can use the python code here to transform the data to lat-lon grid and visualize it.

import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
import CSgrid

def main() :

   Time=0
   Level=0
   Nlat=500
   Nlon=1000
   filename = 'example_prog.20141118_2130z.nc4'
   #filename = 'MAX_Discharge.geosgcm_surf.20141118_2130z.nc4'
   var='T'
   #var = 'PHIS'
   # convert data trough interpolation
   grid_T=CSgrid.Convert2LatLon(filename,var,Nlat,Nlon,Time,Level)
   #grid_T=CSgrid.Convert2LatLon(filename,var,Nlat,Nlon,Time)
   # color plot
   plt.figure()
   ax=plt.gca()
   plt.xlabel('lon')
   plt.ylabel('lat')
   im=plt.imshow(grid_T.T,extent=(0,360,-90,90),origin='lower')
   divider = make_axes_locatable(ax)
   cax = divider.append_axes("right", size="5%", pad=0.05)
   plt.colorbar(im, cax=cax)
   plt.title(var)
   plt.show()
if __name__ == '__main__' :
   main()

# save below as CSgrid.py

import sys
from netCDF4 import Dataset
import numpy as np
from scipy.interpolate import griddata

def Convert2LatLon(filename,var,Nlat,Nlon,Time,Level=None):
   fh=Dataset(filename,mode='r')

   Times=fh.dimensions['time'].size
   #Levs=fh.dimensions['lev'].size
   nf=fh.dimensions['nf'].size
   Ydim=fh.dimensions['y'].size
   Xdim=fh.dimensions['x'].size
   if Level is None:
      T=fh.variables[var][Time,:,:,:]
   else :
      T = fh.variables[var][Time,Level, :, :, :]
   lon3d=fh.variables['lons'][:,:,:]
   lat3d=fh.variables['lats'][:,:,:]
   fh.close()

   lat3d=np.reshape(lat3d,(nf*Ydim*Xdim,))
   lon3d=np.reshape(lon3d,(nf*Ydim*Xdim,))
   T=np.reshape(T,(nf*Ydim*Xdim,))
   Tm=T
   # get rid of non values
   if(hasattr(T,'mask')):
      Tm=T[~T.mask]
      lat3d=lat3d[~T.mask]
      lon3d=lon3d[~T.mask]

   lat=np.linspace(min(lat3d),max(lat3d),Nlat)
   lon=np.linspace(min(lon3d),max(lon3d),Nlon)

   grid_x,grid_y=np.meshgrid(lat,lon)
   points=(lat3d,lon3d)
   grid_T=griddata(points,Tm,(grid_x,grid_y),'linear')

   # filled in extrapolated value with nearest

   lat3d =np.reshape(grid_x,(Nlon*Nlat,))
   lon3d =np.reshape(grid_y,(Nlon*Nlat,))
   Tm=np.reshape(grid_T,(Nlon*Nlat,))
   lat3d=lat3d[~np.isnan(Tm)]
   lon3d=lon3d[~np.isnan(Tm)]
   Tm=Tm[~np.isnan(Tm)]
   points=(lat3d,lon3d)

   grid_T=griddata(points,Tm,(grid_x,grid_y),'nearest')

   return grid_T

IDL

The script read_and_interpolate_cube.pro can read data in the cubed-sphere grid in NetCDF files, interpolate the data , map the data in lat-lon format and plot. The script cube_to_latlon.pro uses read_and_interpolate_cube.pro to convert the variables in cubed-sphere grid to lat-lon grid and write the variables to NetCDF files. It should be noted that the tile files, input and output files are hard-wired in the code. The users will need to provide those files and change the code accordingly.

GrADS

To use GrADS to display cube-sphere grid data in a NetCDF file, the path should be in the PATH environment: /discover/nobackup/projects/gmao/share/dasilva/opengrads/Contents/grads

Then the users can follow the steps. First, we assume a version of GEOS-5 is available.

1. run $ESMADIR/src/GMAO_Shared/GEOS_Util/plots/configure. This will produce a .quickplotrc in that directory
2. source $ESMADIR/src/GMAO_Shared/GEOS_Util/plots/.quickplotrc
3. run grads
4. sdfopen file.nc4
5. run command dc to plot the cube-sphere grid NetCDF file. Users can get help by just run dc without any argument.