G5NR Data Access Guide

For questions or comments please send an email to g5nr at lists dot nasa dot gov.

The following recipes are available for accessing G5NR data

G5NR background

TODO: Some text here

File format and organization

GEOS-5 files are generated with the Network Common Data Form (NetCDF-4) library, which uses Hierarchical Data Format Version 5 (HDF-5) as the underlying format. NetCDF-4 is an open-source product of UCAR/Unidata (https://www.unidata.ucar.edu/software/netcdf/) and HDF-5 is developed by the HDF Group (http://www.hdfgroup.org/). One convenient method of reading GEOS-5 files is to use the NetCDF-4 library, but the HDF-5 library can also be used directly. These files can be easily read by applications such as IDL, Matlab, GrADS, FERRET, NCL, Panoply as well in Python using the netCDF4, h5py or PyTables packages.

Recipes for OPeNDAP client access

OPeNDAP is a data server architecture that allows users to use data files that are stored on remote computers with their favorite analysis and visualization tools. Opening an OPeNDAP file is as easy replacing the file name in the client software by an OPeNDAP URL. All G5NR collections that are provided by ftp/download-tool are also available on the OPeNDAP server

http://opendap.nccs.nasa.gov/dods/OSSE/GEOS-5.12/BETA9.

Client access

In the following, we read the field 'T' (air temperature) from collection inst01hr_3d_T_Cv, compute its min/max and if applicable, plot it. We give an example for each of the two cases

1. a file has been downloaded either via ftp or using the download tool
2. using the OPenDAP server

For each case, we compute min/max for both

1. global temperature
2. temperature over North America

Programming

Fortran

For reading a downloaded file or accessing directly via OPeNDAP using Fortran, please see this page.

Free clients

In this section we read air temperature, compute it min/max (as with the 'programming' examples) and display the surface air temperature.

Python

netcdf4-python

If netcdf4-python module is available, the following script would read air temperature for the specified time, compute its min and max values and plot it.

#!/usr/bin/env python                                                                                 

import sys
import numpy as np
import netCDF4 as nc4
import matplotlib.pyplot as plt                                                                       
                                                                                                      
from mpl_toolkits.basemap import Basemap                                                              

rootgrp = nc4.Dataset('http://opendap.nccs.nasa.gov:9090/dods/OSSE/GEOS-5.12/BETA9/0.5000_deg/inst/inst01hr_3d_T_Cv', 'r')

# read air temperature                                                                                
print 'Reading T for time=37...',; sys.stdout.flush()
Ttime37 = rootgrp.variables['t'][36,:,:,:]
print 'done.'; sys.stdout.flush()

# min/max                                                                                             
print 'min(T):', np.min(Ttime37)
print 'max(T):', np.max(Ttime37)

# set up cylindrical map                                                                              
m = Basemap(                                                                                          
    projection='cyl',                                                                                 
    llcrnrlat=-90, urcrnrlat=90,                                                                      
    llcrnrlon=-180, urcrnrlon=180,                                                                    
    resolution='c'                                                                                    
    )                                                                                                 
m.drawcoastlines(linewidth=0.5)                                                                       
m.drawmapboundary()                                                                                   
                                                                                                      
# plot contour                                                                                        
level = 71                                                                                            
X = np.arange(-180.0, 180.0, .5)                                                                      
Y = np.arange(-90.0, 90.1, .5) # 90 is the last element                                               
cp = plt.contour(X, Y, T[0,level,:,:], 20, zorder=2)                                                  
plt.clabel(cp, inline=1, fontsize=9)                                                                  
plt.title('Air temperature at the surface')                                                           
plt.show()

R

This example requires the ncdf4 and rworldmap packages.

> library(ncdf4)
> library(rworldmap)
Loading required package: sp
### Welcome to rworldmap ###
For a short introduction type : 	 vignette('rworldmap')
> im <- 720
> jm <- 361
> lm <- 72
> nc <- nc_open("http://opendap.nccs.nasa.gov:9090/dods/OSSE/GEOS-5.12/BETA9/0.5000_deg/inst/inst01hr_3d_T_Cv")
< t <- ncvar_get(nc,"t",start=c(1,1,1,37),count=c(im,jm,lm,1))
> str(t)
 num [1:720, 1:361, 1:72] 218 218 218 218 218 ...
> summary(t)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  179.7   220.9   241.7   243.4   265.3   316.7 
> mapGriddedData(t[1:im,1:jm,71])

IDV

IDV is an OPeNDAP tool that can access and display the nature run data. In our OPenDAP server, all files are time aggregated, so they appear as a single dataset for each location.

This is an example to open and display the field 'T' (air temperature) from the collection 'inst01hr_3d_T_Cv'. The OPenDAP URL for this dataset is http://opendap.nccs.nasa.gov:80/dods/OSSE/GEOS-5.12/BETA9/0.5000_deg/inst/inst01hr_3d_T_Cv. The following steps are valid for IDV version 5.0u1 running on a Linux desktop.

From the 'Dashboard' panel

• Select Data Choosers -> URLS.In the URL field, enter the above OPenDAP URL and click on 'Add Source'

• Select Field Selector and choose the 3D field'air_temperature'. The 'Times' tab lists all the available levels and times for this data. At this point, one can select specific times, level and regions (subsetting) from the 'Times' and 'Level' and 'Region' tabs. Click on 'Create Display'.