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/***********************************************/
/**
* @file netCdf2GriddedData.cpp
*
* @brief Convert COARDS compliant grids to gridded data.
*
* @author Andreas Kvas
* @author Torsten Mayer-Guerr
* @date 2023-07-04
*/
/***********************************************/
// Latex documentation
#define DOCSTRING docstring
static const char *docstring = R"(
This program converts a COARDS compliant NetCDF file into an
\configFile{outputfileGriddedData}{griddedData}.
If no specific input \config{variableNameData} are selected all suitable data are used.
If the NETCDF file contains a time axis (\config{variableNameData}) an specific epoch
can be selected with \config{time}. The nearest epoch in file is used.
See also \program{NetCdfInfo}, \program{GriddedData2NetCdf}, \program{NetCdf2GriddedDataTimeSeries}.
)";
/***********************************************/
#include "programs/program.h"
#include "inputOutput/fileNetCdf.h"
#include "files/fileGriddedData.h"
#include "misc/miscGriddedData.h"
/***** CLASS ***********************************/
/** @brief Convert COARDS compliant grids to gridded data.
* @ingroup programsConversionGroup */
class NetCdf2GriddedData
{
public:
void run(Config &config, Parallel::CommunicatorPtr comm);
};
GROOPS_REGISTER_PROGRAM(NetCdf2GriddedData, SINGLEPROCESS, "Convert COARDS compliant grids to gridded data", Conversion, Grid)
/***********************************************/
void NetCdf2GriddedData::run(Config &config, Parallel::CommunicatorPtr /*comm*/)
{
try
{
FileName fileNameGriddedData, fileNameNetcdf;
std::string lonName, latName, timeName;
std::vector<std::string> dataNames;
Time time;
Double a, f;
readConfig(config, "outputfileGriddedData", fileNameGriddedData, Config::MUSTSET, "", "");
readConfig(config, "inputfileNetCdf", fileNameNetcdf, Config::MUSTSET, "", "");
readConfig(config, "variableNameLongitude", lonName, Config::MUSTSET, "lon", "name of NetCDF variable");
readConfig(config, "variableNameLatitude", latName, Config::MUSTSET, "lat", "name of NetCDF variable");
readConfig(config, "variableNameTime", timeName, Config::OPTIONAL, "time", "if with time axis: name of NetCDF variable");
readConfig(config, "variableNameData", dataNames, Config::OPTIONAL, "", "data variables, otherwise all suitable data are used");
readConfig(config, "time", time, Config::OPTIONAL, "", "if with time axis: nearest epoch is used");
readConfig(config, "R", a, Config::DEFAULT, STRING_DEFAULT_GRS80_a, "reference radius for ellipsoidal coordinates");
readConfig(config, "inverseFlattening", f, Config::DEFAULT, STRING_DEFAULT_GRS80_f, "reference flattening for ellipsoidal coordinates");
if(isCreateSchema(config)) return;
#ifdef GROOPS_DISABLE_NETCDF
throw(Exception("Compiled without NetCDF library"));
#else
// open netCDF file
// ----------------
logStatus<<"read NETCDF file <"<<fileNameNetcdf<<">"<<Log::endl;
NetCdf::InFile file(fileNameNetcdf);
NetCdf::Variable lon = file.variable(lonName);
NetCdf::Variable lat = file.variable(latName);
NetCdf::Dimension dimLon = lon.dimensions().at(0);
NetCdf::Dimension dimLat = lat.dimensions().at(0);
// set up grid
// -----------
GriddedDataRectangular grid;
grid.ellipsoid = Ellipsoid(a, f);
grid.longitudes = NetCdf::convertAngles(lon.values());
grid.latitudes = NetCdf::convertAngles(lat.values());
grid.heights.resize(grid.latitudes.size(), 0.0);
// set up time axis
// ----------------
UInt dimSize = 2; // lat, lon
UInt idEpoch = 0;
NetCdf::Dimension dimTime;
if(!timeName.empty() && file.hasVariable(timeName))
{
auto var = file.variable(timeName);
dimTime = var.dimensions().at(0);
std::vector<Time> epochs = NetCdf::convertTimes(var.values(), var.attribute("units").value());
idEpoch = std::distance(epochs.begin(), std::min_element(epochs.begin(), epochs.end(),
[&](Time &t1, Time &t2) {return std::fabs((t1-time).mjd()) < std::fabs((t2-time).mjd());}));
logInfo<<" epoch used: "<<epochs.at(idEpoch).dateTimeStr()<<Log::endl;
dimSize++; // time, lat, lon
}
else
timeName = std::string();
// set up data columns
// -------------------
if(!dataNames.size())
{
for(auto &var : file.variables())
{
auto dims = var.dimensions();
if((dims.size() != dimSize) ||
(std::find(dims.begin(), dims.end(), dimLat) == dims.end()) ||
(std::find(dims.begin(), dims.end(), dimLon) == dims.end()) ||
(!timeName.empty() && (std::find(dims.begin(), dims.end(), dimTime) == dims.end())))
continue;
dataNames.push_back(var.name());
}
if(!dataNames.size())
logWarning<<"No suitable variables found"<<Log::endl;
}
// read data variables
// -------------------
UInt idx = 0;
for(const std::string &name : dataNames)
{
auto var = file.variable(name);
auto dims = var.dimensions();
logInfo<<" data"<<idx++<<" = "<<var.name()<<Log::endl;
for(auto &attr : var.attributes())
logInfo<<" - "<<attr.name()<<" value = "<<attr.value()<<Log::endl;
std::vector<UInt> start(dims.size(), 0);
std::vector<UInt> count;
for(auto &dim : dims)
count.push_back(dim.length());
if(dims.size() != dimSize)
throw(Exception("variable <"+name+"> has wrong dimensions"));
if(!timeName.empty() && (dims.size() > 2))
{
if(dims.at(0) != dimTime)
throw(Exception("variable <"+name+"> must have time as first dimension"));
start.at(0) = idEpoch;
count.at(0) = 1;
}
Matrix values = reshape(var.values(start, count), count.at(dims.size()-1), count.at(dims.size()-2));
if((dims.at(dims.size()-1) == dimLat) && (dims.at(dims.size()-2) == dimLon))
grid.values.push_back(values);
else if((dims.at(dims.size()-1) == dimLon) && (dims.at(dims.size()-2) == dimLat))
grid.values.push_back(values.trans());
else
throw(Exception("variable <"+name+"> must have ("+latName+", "+lonName+") dimensions"));
}
// write grid
// ----------
logStatus<<"write gridded data to <"<<fileNameGriddedData<<">"<<Log::endl;
writeFileGriddedData(fileNameGriddedData, grid);
MiscGriddedData::printStatistics(grid);
#endif
}
catch(std::exception &e)
{
GROOPS_RETHROW(e)
}
}
/***********************************************/
|
