PROGRAM COSMOS_to_obs

Overview

COSMOS “level 2” text file to DART converter

COSMOS is an NSF supported project to measure soil moisture on the horizontal scale of hectometers and depths of decimeters using cosmic-ray neutrons. The data for each station is available from the COSMOS data portal with several levels of processing. The metadata for each station (location, height, etc) is also available from the data portal. The Level 2 Data is most suited for use with DART.
Since each site has a separate input data file, and the metadata for each site must essentially be hand-input to the converter program, it is generally easiest to convert the observations for each site separately and then use the program obs_sequence_tool to combine the observations from multiple sites and restrict the DART observation sequence file to contain just the observations of the timeframe of interest.
FYI - in DART, the soil moisture profile is converted to expected neutron counts using the COsmic-ray Soil Moisture Interaction Code (COSMIC), developed at the University of Arizona by Rafael Rosolem and Jim Shuttleworth.
The workflow is usually:

  1. get the site metadata and enter it in the input.nml &COSMOS_to_obs_nml

  2. download the Level 2 Data and prefix the filename with the station name (or else they all get named corcounts.txt) and enter the filename into &COSMOS_to_obs_nml

  3. make sure the station soil parameters and COSMIC parameters are contained in the observations/COSMOS/data/COSMIC_parlist.nc (more on this in the section on COSMIC parameters)

  4. run COSMOS_to_obs to generate a DART observation sequence file for the station and rename the output file if necessary (you can explicity name the output file via the namelist).

  5. repeat steps 1-4 for this converter to generate a DART observation sequence file for each station.

  6. use the program obs_sequence_tool to combine the observations from multiple sites

Data sources

The COSMOS data portal can be found at: http://cosmos.hwr.arizona.edu/Probes/probemap.php The data for each station is available from the data portal with several levels of processing. The metadata for each station (location, height, etc) is also available from the data portal. The Level 2 Data is most suited for use with DART. An example of the Level 2 Data follows:

YYYY-MM-DD HH:MM  MOD PROBE PRESS  SCALE SANPE INTEN OTHER CORR ERR
2009-10-23 18:34 5996 0.800 1.087 06.901 2.486 1.062 1.000 1768 022
2009-10-23 19:34 5885 0.800 1.080 06.901 2.486 1.059 1.000 1729 022
2009-10-23 20:34 6085 0.800 1.072 06.901 2.486 1.059 1.000 1774 022
2009-10-23 21:34 6339 0.800 1.068 06.901 2.486 1.059 1.000 1843 023
...

Programs

The COSMOS_to_obs.f90 file is the source code for the main converter program. At present there is an uncomfortable assumption that the order of the columns in the Level 2 data is fixed. I hope to relax that requirement in the near future. COSMOS_to_obs reads each text line into a character buffer and then reads from that buffer to parse up the data items. The items are then combined with the COSMIC parameters for that site and written to a DART-format observation sequence file. The DART format allows for the additional COSMIC parameters to be contained as metadata for each observation.

To compile and test, go into the COSMOS/work subdirectory and run the quickbuild.sh script to build the converter and a couple of general purpose utilities. The program obs_sequence_tool manipulates (i.e. combines, subsets) DART observation files once they have been created. The default observations supported are those defined in DART/observations/forward_operators/obs_def_land_mod.f90 and DART/observations/forward_operators/obs_def_COSMOS_mod.f90. If you need additional observation types, you will have to add the appropriate obs_def_XXX_mod.f90 file to the input.nml &preprocess_nml:input_files variable and run quickbuild.sh again. It rebuilds the table of supported observation types before compiling the source code.

Guidance on COSMIC parameters

Additional information is needed by DART to convert soil moisture profiles to neutron counts. Each COSMOS instrument has site-specific parameters describing soil properties etc. Those parameters have been inserted into the observation file as metadata for each observation to simplify the DART observation operator. It is a bit redundant as currently implemented, but it is convenient.
COSMOS_to_obs reads the site name from the input namelist and the known station information from COSMIC_parlist.nc. The simplest way to add a new station to COSMIC_parlist.nc is probably to:

  1. manually enter the information into the “data” section of COSMIC_parlist_station.txt

  2. then use ncgen to convert COSMIC_parlist_station.txt to a netCDF file.

  3. That netCDF file can be concatenated onto COSMIC_parlist.nc with a simple ncrcat command.

Listing the sites already supported is easy:

observations/COSMOS/data % ncdump -v sitenames COSMIC_parlist.nc
netcdf COSMIC_parlist {
dimensions:
        nsites = UNLIMITED ; // (42 currently)
        strlength = 21 ;
variables:
        char sitenames(nsites, strlength) ;
                sitenames:long_name = "COSMOS Site Names" ;
        double longitude(nsites) ;
                longitude:long_name = "Longitude" ;
                longitude:units = "degrees" ;
        double latitude(nsites) ;
                latitude:long_name = "Latitude" ;
                latitude:units = "degrees" ;
        double elevation(nsites) ;
                elevation:long_name = "Elevation" ;
                elevation:units = "m" ;
        double bd(nsites) ;
                bd:long_name = "Dry Soil Bulk Density" ;
                bd:units = "g cm{-3}" ;
        double lattwat(nsites) ;
                lattwat:long_name = "Lattice Water Content" ;
                lattwat:units = "m{3} m{-3}" ;
        double N(nsites) ;
                N:long_name = "High Energy Neutron Intensity" ;
                N:units = "relative counts" ;
        double alpha(nsites) ;
                alpha:long_name = "Ratio of Fast Neutron Creation Factor (Soil to Water)" ;
                alpha:units = "-" ;
        double L1(nsites) ;
                L1:long_name = "High Energy Soil Attenuation Length" ;
                L1:units = "g cm{-2}" ;
        double L2(nsites) ;
                L2:long_name = "High Energy Water Attenuation Length" ;
                L2:units = "g cm{-2}" ;
        double L3(nsites) ;
                L3:long_name = "Fast Neutron Soil Attenuation Length" ;
                L3:units = "g cm{-2}" ;
        double L4(nsites) ;
                L4:long_name = "Fast Neutron Water Attenuation Length" ;
                L4:units = "g cm{-2}" ;

// global attributes:
                :website = "COsmic-ray Soil Moisture Observing System (COSMOS) -
                            http://cosmos.hwr.arizona.edu" ;
data:

 sitenames =
  "ARM-1                ",
  "Austin_Cary          ",
  "Bondville            ",
  "Brookings            ",
  "Chestnut_Ridge_NOAA  ",
  "Coastal_Sage_UCI     ",
  "Daniel_Forest        ",
  "Desert_Chaparral_UCI ",
  "Fort_Peck            ",
  "Harvard_Forest       ",
  "Hauser_Farm_North    ",
  "Hauser_Farm_South    ",
  "Howland              ",
  "Iowa_Validation_Site ",
  "Island_Dairy         ",
  "JERC                 ",
  "Kendall              ",
  "KLEE                 ",
  "Manitou_Forest_Ground",
  "Metolius             ",
  "Morgan_Monroe        ",
  "Mozark               ",
  "Mpala_North          ",
  "Neb_Field_3          ",
  "P301                 ",
  "Park_Falls           ",
  "Pe-de-Gigante        ",
  "Rancho_No_Tengo      ",
  "Reynolds_Creek       ",
  "Rietholzbach         ",
  "Rosemount            ",
  "San_Pedro_2          ",
  "Santa_Rita_Creosote  ",
  "Savannah_River       ",
  "Silver_Sword         ",
  "SMAP-OK              ",
  "Soaproot             ",
  "Sterling             ",
  "Tonzi_Ranch          ",
  "UMBS                 ",
  "UVA                  ",
  "Wind_River           " ;
}

The observation sequence files will look something like the following, the attributes on the “cosmic” record are the information from COSMIC_parlist.nc (in their closes 64-bit real representation):

 obs_sequence
obs_kind_definitions
           1
          20 COSMOS_NEUTRON_INTENSITY
  num_copies:            1  num_qc:            1
  num_obs:         3840  max_num_obs:         3840
observation
COSMOS QC
  first:            1  last:         3840
 OBS            1
   1048.0000000000000
   1.0000000000000000
          -1           2          -1
obdef
loc3d
     4.154723123116714        0.7997185899100618         0.000000000000000     -1
kind
          20

cosmic 0.88500000000000001    5.84099999999999966E-002    336.95696938999998    0.31918025877000000
        161.98621864285701     129.14558984999999         55.311849408000000     3.8086191933000002
              1

 77340     150034
   1225.0000000000000
   ...

Namelist

This namelist is read from the file input.nml. Namelists start with an ampersand ‘&’ and terminate with a slash ‘/’. Character strings that contain a ‘/’ must be enclosed in quotes to prevent them from prematurely terminating the namelist.

&COSMOS_to_obs_nml
   site_metadata_file = 'COSMIC_parlist.nc'
   text_input_file    = 'textdata.input',
   obs_out_file       = 'obs_seq.out',
   sitename           = 'missing',
   maxgoodqc          =  3,
   verbose            = .false.
   /

Contents

Type

Description

site_metadata_file

character(len=256)

The netCDF file containing the parameter values for each site.

text_input_file

character(len=128)

The text file containing the raw observations for each site.

obs_out_file

character(len=128)

The output observation sequence file for DART.

sitename

character(len=128)

The name of the site. Must match one of the site names in the site_metadata_file. Case-insensitive match, trailing blanks ignored. Use ncdump -v sitenames COSMIC_parlist.nc

maxgoodqc

integer

left for future implementation.

verbose

logical

A switch to specify the amount of run-time output. .true. the most amount of output. .false. the least amount of output.

Cosmos_to_obs namelist

&COSMOS_to_obs_nml
   site_metadata_file = 'COSMIC_parlist.nc',
   text_input_file    = 'SantaRita_corcounts.txt',
   obs_out_file       = 'SantaRita_obs_seq.out',
   sitename           = 'Santa_Rita_Creosote',

References

  • The COSMOS web page.

  • Franz, T.E, M. Zreda, T.P.A. Ferre, R. Rosolem, C. Zweck, S. Stillman, X. Zeng and W.J. Shuttleworth, 2012: Measurement depth of the cosmic-ray soil moisture probe affected by hydrogen from various sources. Water Resources Research 48, W08515, doi:10.1029/2012WR011871

  • Franz, T.E, M. Zreda, R. Rosolem, T.P.A. Ferre, 2012: Field validation of cosmic-ray soil moisture probe using a distributed sensor network. Vadose Zone Journal (in press), doi:10.2136/vzj2012.0046

Future Plans

  • Implement a routine to automatically determine the column indices of the columns of interest.

  • Implement a QC encoding that reflects the uncertainty of the measurement. Presently, all Level 2 data have an incoming QC of 1.