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Support for Creating and Setting NetCDF Variables #39

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merged 6 commits into from
Feb 11, 2025
Merged

Support for Creating and Setting NetCDF Variables #39

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2a17ca1
Added support for adding and setting netcdf variables.
amstokely Jan 31, 2025
9a9a840
Updated docs.
amstokely Jan 31, 2025
5cf4cd2
Removed template declarations in netcdf_variable.h, updated docs, and…
Feb 6, 2025
0aff7f8
Renamed netcdfPutVar data argument to values.
amstokely Feb 7, 2025
01ee459
Removed @tparam from netcdf variable docstrings and added a default c…
amstokely Feb 8, 2025
7158937
Removed unused c_f_pointer import
amstokely Feb 11, 2025
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1 change: 1 addition & 0 deletions obs2ioda-v2/src/cxx/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@ set(obs2ioda_cxx_SOURCES
netcdf_file.cc
netcdf_group.cc
netcdf_dimension.cc
netcdf_variable.cc
)
set(obs2ioda_cxx_LIBRARIES
NetCDF::NetCDF_CXX
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220 changes: 220 additions & 0 deletions obs2ioda-v2/src/cxx/netcdf_variable.cc
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Original file line number Diff line number Diff line change
@@ -0,0 +1,220 @@
#include "netcdf_variable.h"
#include "netcdf_file.h"
#include "netcdf_error.h"

namespace Obs2Ioda {
int netcdfAddVar(
int netcdfID,
const char *groupName,
const char *varName,
nc_type netcdfDataType,
int numDims,
const char **dimNames
) {
try {
auto file = FileMap::getInstance().getFile(netcdfID);
const auto group = !groupName
? file
: std::make_shared<
netCDF::NcGroup>(
file->getGroup(
groupName));
std::vector<netCDF::NcDim> dims;
dims.reserve(numDims);
for (int i = 0; i < numDims; i++) {
dims.push_back(file->getDim(dimNames[i]));;
}
auto var = group->addVar(
varName,
netCDF::NcType(netcdfDataType),
dims
);
return 0;
} catch (netCDF::exceptions::NcException &e) {
return netcdfErrorMessage(
e,
__LINE__,
__FILE__
);
}
}

template<typename T>
int netcdfPutVar(
int netcdfID,
const char *groupName,
const char *varName,
const T *values
) {
try {
auto file = FileMap::getInstance().getFile(netcdfID);
const auto group = !groupName
? file
: std::make_shared<
netCDF::NcGroup>(
file->getGroup(
groupName));
auto var = group->getVar(varName);
var.putVar(values);
return 0;
} catch (netCDF::exceptions::NcException &e) {
return netcdfErrorMessage(
e,
__LINE__,
__FILE__
);
}
}

int netcdfPutVarInt(
int netcdfID,
const char *groupName,
const char *varName,
const int *values
) {
return netcdfPutVar(
netcdfID,
groupName,
varName,
values
);
}

int netcdfPutVarInt64(
int netcdfID,
const char *groupName,
const char *varName,
const long long *values
) {
return netcdfPutVar(
netcdfID,
groupName,
varName,
values
);
}

int netcdfPutVarReal(
int netcdfID,
const char *groupName,
const char *varName,
const float *values
) {
return netcdfPutVar(
netcdfID,
groupName,
varName,
values
);
}

int netcdfPutVarString(
int netcdfID,
const char *groupName,
const char *varName,
const char **values
) {
return netcdfPutVar(
netcdfID,
groupName,
varName,
values
);
}

template<typename T>
int netcdfSetFill(
int netcdfID,
const char *groupName,
const char *varName,
int fillMode,
T fillValue
) {
try {
auto file = FileMap::getInstance().getFile(netcdfID);
const auto group = !groupName
? file
: std::make_shared<
netCDF::NcGroup>(
file->getGroup(
groupName));
auto var = group->getVar(varName);
var.setFill(
fillMode,
fillValue
);
return 0;
} catch (netCDF::exceptions::NcException &e) {
return netcdfErrorMessage(
e,
__LINE__,
__FILE__
);
}
}

int netcdfSetFillInt(
int netcdfID,
const char *groupName,
const char *varName,
int fillMode,
int fillValue
) {
return netcdfSetFill(
netcdfID,
groupName,
varName,
fillMode,
fillValue
);
}

int netcdfSetFillReal(
int netcdfID,
const char *groupName,
const char *varName,
int fillMode,
float fillValue
) {
return netcdfSetFill(
netcdfID,
groupName,
varName,
fillMode,
fillValue
);
}

int netcdfSetFillInt64(
int netcdfID,
const char *groupName,
const char *varName,
int fillMode,
long long fillValue
) {
return netcdfSetFill(
netcdfID,
groupName,
varName,
fillMode,
fillValue
);
}

int netcdfSetFillString(
int netcdfID,
const char *groupName,
const char *varName,
int fillMode,
const char *fillValue
) {
return netcdfSetFill(
netcdfID,
groupName,
varName,
fillMode,
fillValue

);
}
}
118 changes: 118 additions & 0 deletions obs2ioda-v2/src/cxx/netcdf_variable.h
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Original file line number Diff line number Diff line change
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#ifndef NETCDF_VARIABLE_H
#define NETCDF_VARIABLE_H
#include <netcdf>

namespace Obs2Ioda {

extern "C" {
/**
* @brief Adds a variable to a NetCDF file.
*
* @param netcdfID The identifier of the NetCDF file where the variable will be added.
* @param groupName The name of the group in which the variable should be created.
* If nullptr, the variable is added to the root group.
* @param varName The name of the variable to be created.
* @param netcdfDataType The NetCDF data type of the variable (e.g., NC_INT, NC_FLOAT).
* @param numDims The number of dimensions associated with the variable.
* @param dimNames An array of dimension names specifying the shape of the variable.
* @return int A status code indicating the outcome of the operation:
* - 0: Success.
* - Non-zero: Failure, with an error message logged.
*/
int netcdfAddVar(
int netcdfID,
const char *groupName,
const char *varName,
nc_type netcdfDataType,
int numDims,
const char **dimNames
);

/**
* @brief Writes data to a variable in a NetCDF file.
*
* @param netcdfID The identifier of the NetCDF file where the data will be written.
* @param groupName The name of the group containing the variable. If nullptr, the variable is assumed to be in the root group.
* @param varName The name of the variable to which data will be written.
* @param values A pointer to the data to be written to the variable.
* @return int A status code indicating the outcome of the operation:
* - 0: Success.
* - Non-zero: Failure, with an error message logged.
*/
int netcdfPutVarInt(
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int netcdfID,
const char *groupName,
const char *varName,
const int *values
);

int netcdfPutVarInt64(
int netcdfID,
const char *groupName,
const char *varName,
const long long *values
);

int netcdfPutVarReal(
int netcdfID,
const char *groupName,
const char *varName,
const float *values
);

int netcdfPutVarString(
int netcdfID,
const char *groupName,
const char *varName,
const char **values
);

/**
* @brief Sets the fill mode and fill value for a variable in a NetCDF file.
*
* @param netcdfID The identifier of the NetCDF file containing the variable.
* @param groupName The name of the group containing the variable. If nullptr, the variable is assumed to be in the root group.
* @param varName The name of the variable for which the fill mode is set.
* @param fillMode The fill mode to be applied:
* - 0: Disable fill mode (use uninitialized values).
* - 1: Enable fill mode (use the specified fill value).
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* @param fillValue The fill value to be applied when fill mode is enabled. Must match the data type of the variable.
* @return int A status code indicating the outcome of the operation:
* - 0: Success.
* - Non-zero: Failure, with an error message logged.
*/
int netcdfSetFillInt(
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int netcdfID,
const char *groupName,
const char *varName,
int fillMode,
int fillValue
);

int netcdfSetFillReal(
int netcdfID,
const char *groupName,
const char *varName,
int fillMode,
float fillValue
);

int netcdfSetFillInt64(
int netcdfID,
const char *groupName,
const char *varName,
int fillMode,
long long fillValue
);

int netcdfSetFillString(
int netcdfID,
const char *groupName,
const char *varName,
int fillMode,
const char *fillValue
);
}
}

#endif //NETCDF_VARIABLE_H
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