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/***********************************************/
/**
* @file griddedDataTimeSeries2NetCdf.cpp
*
* @brief Converts a griddedDataTimeSeries file to a netCDF file.
*
* @author Andreas Kvas
* @author Torsten Mayer-Guerr
* @date 2018-06-17
*/
/***********************************************/
// Latex documentation
#define DOCSTRING docstring
static const char *docstring = R"(
Read a \configFile{inputfileGriddedDataTimeSeries}{griddedDataTimeSeries}
and converts it to a COARDS compliant NetCDF file.
The output data can be defined with \config{dataVariable}.
You should add at least the attributes \verb|units|, \verb|long_name|, and maybe \verb|_FillValue|
to the variables. The \config{dataVariable:inputColumn} selects the data from the input file.
If \configClass{timeSeries}{timeSeriesType} is not set
the temporal nodal points from the inputfile are used.
See also \program{NetCdfInfo}, \program{GriddedData2NetCdf}, \program{NetCdf2GriddedDataTimeSeries}.
)";
/***********************************************/
#include "programs/program.h"
#include "inputOutput/fileNetCdf.h"
#include "files/fileGriddedDataTimeSeries.h"
#include "classes/timeSeries/timeSeries.h"
#include "misc/miscGriddedData.h"
/***** CLASS ***********************************/
/** @brief Converts a griddedDataTimeSeries file to a netCDF file.
* @ingroup programsConversionGroup */
class GriddedDataTimeSeries2NetCdf
{
public:
class Attribute
{
public:
std::string name;
std::string text;
std::vector<Double> values;
NetCdf::DataType dataType;
};
class DataVariable
{
public:
std::string name;
UInt dataField;
NetCdf::DataType dataType;
std::vector<Attribute> attributes;
NetCdf::Variable variable;
};
void run(Config &config, Parallel::CommunicatorPtr comm);
};
GROOPS_REGISTER_PROGRAM(GriddedDataTimeSeries2NetCdf, SINGLEPROCESS, "Converts a griddedDataTimeSeries file to a netCDF file", Conversion, Grid)
/***********************************************/
template<> Bool readConfig(Config &config, const std::string &name, GriddedDataTimeSeries2NetCdf::Attribute &var, Config::Appearance mustSet, const std::string &defaultValue, const std::string &annotation)
{
std::string choice;
if(!readConfigChoice(config, name, choice, mustSet, defaultValue, annotation))
return FALSE;
if(readConfigChoiceElement(config, "text", choice, ""))
{
readConfig(config, "name", var.name, Config::MUSTSET, "", "");
readConfig(config, "value", var.text, Config::MUSTSET, "", "");
}
if(readConfigChoiceElement(config, "value", choice, ""))
{
std::string choice;
readConfig(config, "name", var.name, Config::MUSTSET, "", "");
readConfig(config, "value", var.values, Config::MUSTSET, "", "");
if(readConfigChoice(config, "dataType", choice, Config::MUSTSET, "", ""))
{
if(readConfigChoiceElement(config, "double", choice, "")) var.dataType = NetCdf::DOUBLE;
if(readConfigChoiceElement(config, "float", choice, "")) var.dataType = NetCdf::FLOAT;
if(readConfigChoiceElement(config, "int", choice, "")) var.dataType = NetCdf::INT;
endChoice(config);
}
}
endChoice(config);
return TRUE;
}
/***********************************************/
template<> Bool readConfig(Config &config, const std::string &name, GriddedDataTimeSeries2NetCdf::DataVariable &var, Config::Appearance mustSet, const std::string &defaultValue, const std::string &annotation)
{
if(!readConfigSequence(config, name, mustSet, defaultValue, annotation))
return FALSE;
readConfig(config, "name", var.name, Config::MUSTSET, "data0", "netCDF variable name");
readConfig(config, "inputColumn", var.dataField, Config::DEFAULT, "0", "input data column");
std::string choice;
if(readConfigChoice(config, "dataType", choice, Config::MUSTSET, "", ""))
{
if(readConfigChoiceElement(config, "double", choice, "")) var.dataType = NetCdf::DOUBLE;
if(readConfigChoiceElement(config, "float", choice, "")) var.dataType = NetCdf::FLOAT;
if(readConfigChoiceElement(config, "int", choice, "")) var.dataType = NetCdf::INT;
endChoice(config);
}
readConfig(config, "attribute", var.attributes, Config::OPTIONAL, "", "netCDF attributes");
endSequence(config);
return TRUE;
}
/***********************************************/
void GriddedDataTimeSeries2NetCdf::run(Config &config, Parallel::CommunicatorPtr /*comm*/)
{
try
{
FileName fileNameOut, fileNameIn;
std::vector<DataVariable> dataVariables;
std::vector<Attribute> globalAttributes;
TimeSeriesPtr timeSeries;
readConfig(config, "outputfileNetCdf", fileNameOut, Config::MUSTSET, "", "file name of NetCDF output");
readConfig(config, "inputfileGriddedDataTimeSeries", fileNameIn, Config::MUSTSET, "", "");
readConfig(config, "timeSeries", timeSeries, Config::OPTIONAL, "", "otherwise times from inputfile are used");
readConfig(config, "dataVariable", dataVariables, Config::MUSTSET, "", "metadata for data variables");
readConfig(config, "globalAttribute", globalAttributes, Config::OPTIONAL, "", "additional meta data");
if(isCreateSchema(config)) return;
#ifdef GROOPS_DISABLE_NETCDF
throw(Exception("Compiled without NetCDF library"));
#else
logStatus<<"read gridded data time series <"<<fileNameIn<<">"<<Log::endl;
InFileGriddedDataTimeSeries fileGriddedDataTimeSeries(fileNameIn);
GriddedDataRectangular grid;
if(!grid.init(fileGriddedDataTimeSeries.grid()))
throw(Exception("GriddedData must be a rectangle grid"));
MiscGriddedData::printStatistics(grid);
std::vector<Time> times = fileGriddedDataTimeSeries.times();
if(timeSeries)
times = timeSeries->times();
// write attributes
// ----------------
logStatus<<"write NETCDF file <"<<fileNameOut<<">"<<Log::endl;
NetCdf::OutFile file(fileNameOut);
for(const auto &attr : globalAttributes)
{
if(attr.text.empty())
file.addAttribute(attr.name, attr.dataType, attr.values);
else
file.addAttribute(attr.name, attr.text);
}
{
NetCdf::Dimension dim = file.addDimension("time"); // NC_UNLIMITED
NetCdf::Variable var = file.addVariable("time", NetCdf::DOUBLE, {dim});
var.addAttribute("units", "days since 1858-11-17 00:00:00"); // MJD
}
{
NetCdf::Dimension dim = file.addDimension("lat", grid.latitudes.size());
NetCdf::Variable var = file.addVariable("lat", NetCdf::DOUBLE, {dim});
var.addAttribute("units", "degrees_north");
Vector lats(grid.latitudes.size());
for(UInt i=0; i<grid.latitudes.size(); i++)
lats(i) = RAD2DEG * grid.latitudes.at(i);
var.setValues(lats);
}
{
NetCdf::Dimension dim = file.addDimension("lon", grid.longitudes.size());
NetCdf::Variable var = file.addVariable("lon", NetCdf::DOUBLE, {dim});
var.addAttribute("units", "degrees_east");
Vector lons(grid.longitudes.size());
for(UInt i=0; i<grid.longitudes.size(); i++)
lons(i) = RAD2DEG * grid.longitudes.at(i);
var.setValues(lons);
}
for(auto &data : dataVariables)
{
data.variable = file.addVariable(data.name, data.dataType, file.dimensions());
for(auto &attr : data.attributes)
{
if(attr.text.empty())
data.variable.addAttribute(attr.name, attr.dataType, attr.values);
else
data.variable.addAttribute(attr.name, attr.text);
}
}
Single::forEach(times.size(), [&](UInt idEpoch)
{
Matrix values = fileGriddedDataTimeSeries.data(times.at(idEpoch));
for(auto &data : dataVariables)
data.variable.setValues({idEpoch, 0, 0}, {1, grid.latitudes.size(), grid.longitudes.size()}, Vector(values.column(data.dataField)));
});
Vector mjd(times.size());
for(UInt i=0; i<times.size(); i++)
mjd(i) = times.at(i).mjd();
file.variable("time").setValues(mjd);
#endif
}
catch(std::exception &e)
{
GROOPS_RETHROW(e)
}
}
/***********************************************/
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