ConvertToHDF5 WOA2005

The World Ocean Atlas (WOA) 2005 climatology provides results for water temperature, salinity and several water quality and biology properties. The data is provided by NOAA NODC.

Introduction

The ConvertToHDF5 action converts the climatological data for the following properties:

- Dissolved Oxygen

- Phosphate

- Nitrate

- Silicate

For temperature and salinity fields, refer to ConverToHDF5 LEVITUS FORMAT because these fields have a lower resolution(1º) than Levitus(0.25º).

Spacial Coverage

The resulting HDF5 files have a spatial resolution of 1 degree latitute and longitude. The resulting grid spans from -180º to 180º rather than the original 0º to 360º format. Thus, the lower left corner of the hdf5 grid is -180º longitude, 90ºS longitude.

Units

The data in netcdf format provided by NOAA is in uM for the nutrients and ml/l for dissolved oxygen. There is an option to convert to MOHID units, namelly mg/L for nutrients and mg/l for oxygen.

Kepler data folder

For those users working in MARETEC/HIDROMOD network, the following data folder contains the converted files, sample ConvertToHDF5 files(with WOA geometry and grid) and WOA05 documentation:

\\kepler\DataCenter\DadosBase\Oceanografia\World Ocean Atlas 2005\

Input file (ConvertToHDF5Action.dat)

<begin_file>
  ACTION                      : char    -    'CONVERT WOA FORMAT' to use this module
  FILEPATH                    : char    -    Path to WOA05 original netcdf files(n0112an1.nc for e.g.)
                                                               with ending slash
  OUTPUTFILENAME              : char    -    Path to WOA05 file generated from NETCDF file
  MOHID_UNITS                  : 0/1    -    Convert uunits to mg/l
  <<begin_woafiles>>
  (netcdf file)                 char    -    WOA05 netcdf file in path defined in FILEPATH, one per line
  (netcdf file2)                char         e.g.: n0112an1.nc i0112an1.nc p0112an1.nc o0112an1.nc 
   ...        
  <<end_woafiles>>
  CONVERT_TO_ASCII            : 0       -    Flag to convert to ascii file: not implemented
  CONVERT_TO_HDF5             : 1       -    Flag to convert to hdf5 file
  XX_VARIABLE                 : char    -    'longitude'
  YY_VARIABLE                 : char    -    'latitude'
  ZZ_VARIABLE                 : char    -    'depth'
  TIME_VARIABLE               : char    -    'time'
<end_file>

Remarks:

- only CONVERT_TO_HDF5 : 1 is implemented
- files in block begin/end_woafiles are all concatenated into one hdf5 file
- FILEPATH must have an ending slash

Sample

All sample files are named ConvertToHDF5Action.dat.

Convert

<begin_file>
ACTION                    : CONVERT WOA FORMAT

!WOA05_o2sat.hdf5 WOA05_nut_uM.hdf5 WOA05_nut_mg_l.hdf5
OUTPUTFILENAME            : WOA05_nut_uM.hdf5
MOHID_UNITS               : 0

!filepath with ending slash!
FILEPATH                  : Z:\netcdf\monthly\

<<begin_woafiles>>
n0112an1.nc
i0112an1.nc
p0112an1.nc
<<end_woafiles>>

CONVERT_TO_ASCII          : 0
CONVERT_TO_HDF5           : 1

XX_VARIABLE               : lon
YY_VARIABLE               : lat
ZZ_VARIABLE               : depth
TIME_VARIABLE             : time
<end_file>

Remarks
The converted files(O2 Saturation and Nutrients in uM and mg/l) are in kepler folder:
\\kepler\DataCenter\DadosBase\Oceanografia\World Ocean Atlas 2005\Data\data\
Since the conversion only is done one time for the whole grid, there is no need to convert every time.

Extrapolate

Extrapolate data for all regions for the interpolation(triagulation) to work fine.

<begin_file>
ACTION                   : INTERPOLATE GRIDS 

TYPE_OF_INTERPOLATION    : 1

FATHER_FILENAME           : \\kepler\DataCenter\DadosBase\Oceanografia\World Ocean Atlas 2005\Data\data\WOA05_nut_mg_l.hdf5
FATHER_GRID_FILENAME      : ..\WOA05_Grid_3D.dat

OUTPUTFILENAME           : ..\WOA05_nut_mg_l_alldata.hdf5
NEW_GRID_FILENAME        : ..\WOA05_Grid_3D.dat

START                    : -9999 1  1 0 0 0
END                      : -9999 12 1 0 0 0

INTERPOLATION3D          : 1
FATHER_GEOMETRY          : ..\WOA05_Geometry_3D_nuts.dat
NEW_GEOMETRY             : ..\WOA05_Geometry_3D_nuts.dat
AUX_GRID_FILENAME        : ..\WOA05_Grid_3D.dat
AUX_OUTPUTFILENAME       : ..\AuxAllPointsWithData.hdf5

POLI_DEGREE              : 1
DO_NOT_BELIEVE_MAP       : 1
EXTRAPOLATE_2D           : 2
<end_file>

Interpolate

Finally, interpolate to the final grid and geometry (same as the Interpolate 3D sample):

<begin_file>
ACTION                   : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION    : 1
FATHER_FILENAME          :  ..\WOA05_nut_mg_l_alldata.hdf5
OUTPUTFILENAME           : ..\NS_Nuts_3D.hdf5
FATHER_GRID_FILENAME     : ..\WOA05_Grid_3D.dat
NEW_GRID_FILENAME        : ..\NorthSea_submodel__.new

START                    : -9999 1  1 0 0 0
END                      : -9999 12 1 0 0 0

INTERPOLATION3D          : 1
FATHER_GEOMETRY          : ..\WOA05_Geometry_3D_nuts.dat
NEW_GEOMETRY             : ..\GeometryModel3D.dat
AUX_OUTPUTFILENAME       : ..\AuxCadizMonthlyLevitus.hdf5
AUX_GRID_FILENAME        : ..\NorthSea_submodel__.new 

POLI_DEGREE              : 1
DO_NOT_BELIEVE_MAP       : 1
<end_file>