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Refactored AtlasProcessor class to UtilsAtlas functions file #8

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merged 2 commits into from
Aug 11, 2023
Merged

Refactored AtlasProcessor class to UtilsAtlas functions file #8

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954e1b8
Turned AtlasProcessor class into utility function file as it only con…
phlndrwd Aug 11, 2023
c3d2df4
Removed erroneous testing log.
phlndrwd Aug 11, 2023
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4 changes: 2 additions & 2 deletions src/CMakeLists.txt
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Expand Up @@ -11,8 +11,6 @@ include_directories(${CMAKE_CURRENT_SOURCE_DIR})
ecbuild_generate_config_headers( DESTINATION ${INSTALL_INCLUDE_DIR}/monio )

list(APPEND monio_src_files
monio/AtlasProcessor.cc
monio/AtlasProcessor.h
monio/AtlasReader.cc
monio/AtlasReader.h
monio/AtlasWriter.cc
Expand Down Expand Up @@ -48,6 +46,8 @@ monio/Reader.cc
monio/Reader.h
monio/Utils.cc
monio/Utils.h
monio/UtilsAtlas.cc
monio/UtilsAtlas.h
monio/Variable.cc
monio/Variable.h
monio/Writer.cc
Expand Down
189 changes: 0 additions & 189 deletions src/monio/AtlasProcessor.cc
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6 changes: 3 additions & 3 deletions src/monio/AtlasReader.cc
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Expand Up @@ -11,12 +11,12 @@
#include "oops/util/Logger.h"

#include "Utils.h"
#include "UtilsAtlas.h"

monio::AtlasReader::AtlasReader(const eckit::mpi::Comm& mpiCommunicator,
const atlas::idx_t mpiRankOwner):
mpiCommunicator_(mpiCommunicator),
mpiRankOwner_(mpiRankOwner),
atlasProcessor_(mpiCommunicator, mpiRankOwner) {
mpiRankOwner_(mpiRankOwner) {
oops::Log::debug() << "AtlasReader::AtlasReader()" << std::endl;
}

Expand Down Expand Up @@ -152,7 +152,7 @@ void monio::AtlasReader::populateField(atlas::Field& field,

std::vector<atlas::idx_t> dimVec = field.shape();
if (field.metadata().get<bool>("global") == false) {
dimVec[consts::eHorizontal] = atlasProcessor_.getSizeOwned(field);
dimVec[consts::eHorizontal] = utilsatlas::getSizeOwned(field);
}
auto fieldView = atlas::array::make_view<T, 2>(field);
atlas::idx_t numLevels = field.levels();
Expand Down
3 changes: 0 additions & 3 deletions src/monio/AtlasReader.h
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Expand Up @@ -13,7 +13,6 @@
#include <string>
#include <vector>

#include "AtlasProcessor.h"
#include "Constants.h"
#include "Data.h"
#include "DataContainerDouble.h"
Expand Down Expand Up @@ -68,7 +67,5 @@ class AtlasReader {

const eckit::mpi::Comm& mpiCommunicator_;
const std::size_t mpiRankOwner_;

AtlasProcessor atlasProcessor_;
};
} // namespace monio
8 changes: 4 additions & 4 deletions src/monio/AtlasWriter.cc
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Expand Up @@ -14,6 +14,7 @@

#include "Metadata.h"
#include "Utils.h"
#include "UtilsAtlas.h"
#include "Writer.h"

namespace {
Expand All @@ -29,7 +30,6 @@ namespace {

monio::AtlasWriter::AtlasWriter(const eckit::mpi::Comm& mpiCommunicator,
const atlas::idx_t mpiRankOwner):
atlasProcessor_(mpiCommunicator, mpiRankOwner),
mpiCommunicator_(mpiCommunicator),
mpiRankOwner_(mpiRankOwner) {
oops::Log::debug() << "AtlasWriter::AtlasWriter()" << std::endl;
Expand Down Expand Up @@ -109,7 +109,7 @@ void monio::AtlasWriter::populateMetadataWithField(Metadata& metadata,

// Check if Field is not global
if (field.metadata().get<bool>("global") == false) {
dimVec[0] = atlasProcessor_.getSizeOwned(field); // If so, get the 'size owned' by the Fields
dimVec[0] = utilsatlas::getSizeOwned(field); // If so, get the 'size owned' by the Fields
}
if (reverseDims == true) {
std::reverse(dimVec.begin(), dimVec.end());
Expand Down Expand Up @@ -311,7 +311,7 @@ void monio::AtlasWriter::populateMetadataAndDataWithFieldSet(Metadata& metadata,
for (const auto& field : fieldSet) {
std::vector<int> dimVec = field.shape();
if (field.metadata().get<bool>("global") == false) {
dimVec[0] = atlasProcessor_.getSizeOwned(field);
dimVec[0] = utilsatlas::getSizeOwned(field);
}
for (auto& dimSize : dimVec) {
std::string dimName = metadata.getDimensionName(dimSize);
Expand All @@ -323,7 +323,7 @@ void monio::AtlasWriter::populateMetadataAndDataWithFieldSet(Metadata& metadata,
}
populateMetadataWithField(metadata, field);
if (createdLonLat == false) {
std::vector<atlas::PointLonLat> atlasLonLat = atlasProcessor_.getAtlasCoords(field);
std::vector<atlas::PointLonLat> atlasLonLat = utilsatlas::getAtlasCoords(field);
std::vector<std::shared_ptr<DataContainerBase>> coordContainers =
convertLatLonToContainers(atlasLonLat, consts::kCoordVarNames);
for (const auto& coordContainer : coordContainers) {
Expand Down
3 changes: 0 additions & 3 deletions src/monio/AtlasWriter.h
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Expand Up @@ -13,7 +13,6 @@
#include <string>
#include <vector>

#include "AtlasProcessor.h"
#include "Constants.h"
#include "Data.h"
#include "DataContainerDouble.h"
Expand Down Expand Up @@ -108,8 +107,6 @@ class AtlasWriter {

int atlasTypeToMonioEnum(atlas::array::DataType atlasType);

AtlasProcessor atlasProcessor_;

const eckit::mpi::Comm& mpiCommunicator_;
const std::size_t mpiRankOwner_;
};
Expand Down
16 changes: 8 additions & 8 deletions src/monio/Monio.cc
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Expand Up @@ -17,6 +17,7 @@

#include "Constants.h"
#include "Utils.h"
#include "UtilsAtlas.h"

namespace {
std::string convertToAtlasDateTimeStr(std::string lfricDateTimeStr) {
Expand All @@ -42,7 +43,7 @@ void monio::Monio::readBackground(atlas::FieldSet& localFieldSet,
}
for (const auto& fieldMetadata : fieldMetadataVec) {
auto& localField = localFieldSet[fieldMetadata.jediName];
atlas::Field globalField = atlasProcessor_.getGlobalField(localField);
atlas::Field globalField = utilsatlas::getGlobalField(localField);
if (mpiCommunicator_.rank() == mpiRankOwner_) {
oops::Log::debug() << "Monio::readBackground() processing data for> \"" <<
fieldMetadata.jediName << "\"..." << std::endl;
Expand Down Expand Up @@ -91,7 +92,7 @@ void monio::Monio::readIncrements(atlas::FieldSet& localFieldSet,
}
for (const auto& fieldMetadata : fieldMetadataVec) {
auto& localField = localFieldSet[fieldMetadata.jediName];
atlas::Field globalField = atlasProcessor_.getGlobalField(localField);
atlas::Field globalField = utilsatlas::getGlobalField(localField);
if (mpiCommunicator_.rank() == mpiRankOwner_) {
oops::Log::debug() << "Monio::readIncrements() processing data for> \"" <<
fieldMetadata.jediName << "\"..." << std::endl;
Expand Down Expand Up @@ -131,7 +132,7 @@ void monio::Monio::writeIncrements(const atlas::FieldSet& localFieldSet,
if (localFieldSet.size() == 0) {
utils::throwException("Monio::writeIncrements()> localFieldSet has zero fields...");
}
atlas::FieldSet globalFieldSet = atlasProcessor_.getGlobalFieldSet(localFieldSet);
atlas::FieldSet globalFieldSet = utilsatlas::getGlobalFieldSet(localFieldSet);
if (mpiCommunicator_.rank() == mpiRankOwner_) {
auto& functionSpace = globalFieldSet[0].functionspace();
auto& grid = atlas::functionspace::NodeColumns(functionSpace).mesh().grid();
Expand All @@ -144,7 +145,7 @@ void monio::Monio::writeIncrements(const atlas::FieldSet& localFieldSet,
void monio::Monio::writeFieldSet(const atlas::FieldSet& localFieldSet,
const std::string outputFilePath) {
oops::Log::debug() << "Monio::writeFieldSet()" << std::endl;
atlas::FieldSet globalFieldSet = atlasProcessor_.getGlobalFieldSet(localFieldSet);
atlas::FieldSet globalFieldSet = utilsatlas::getGlobalFieldSet(localFieldSet);
atlasWriter_.writeFieldSetToFile(globalFieldSet, outputFilePath);
}

Expand All @@ -165,9 +166,9 @@ void monio::Monio::createLfricAtlasMap(FileData& fileData, const atlas::CubedSph
reader_.readFullData(fileData, consts::kLfricCoordVarNames);
std::vector<std::shared_ptr<monio::DataContainerBase>> coordData =
reader_.getCoordData(fileData, consts::kLfricCoordVarNames);
std::vector<atlas::PointLonLat> lfricCoords = atlasProcessor_.getLfricCoords(coordData);
std::vector<atlas::PointLonLat> atlasCoords = atlasProcessor_.getAtlasCoords(grid);
fileData.setLfricAtlasMap(atlasProcessor_.createLfricAtlasMap(atlasCoords, lfricCoords));
std::vector<atlas::PointLonLat> lfricCoords = utilsatlas::getLfricCoords(coordData);
std::vector<atlas::PointLonLat> atlasCoords = utilsatlas::getAtlasCoords(grid);
fileData.setLfricAtlasMap(utilsatlas::createLfricAtlasMap(atlasCoords, lfricCoords));
}
}
}
Expand Down Expand Up @@ -258,7 +259,6 @@ monio::Monio::Monio(const eckit::mpi::Comm& mpiCommunicator,
mpiCommunicator_(mpiCommunicator),
mpiRankOwner_(mpiRankOwner),
reader_(mpiCommunicator, mpiRankOwner_),
atlasProcessor_(mpiCommunicator, mpiRankOwner_),
atlasReader_(mpiCommunicator, mpiRankOwner_),
atlasWriter_(mpiCommunicator, mpiRankOwner_) {
oops::Log::debug() << "Monio::Monio()" << std::endl;
Expand Down
2 changes: 0 additions & 2 deletions src/monio/Monio.h
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Expand Up @@ -14,7 +14,6 @@
#include <utility>
#include <vector>

#include "AtlasProcessor.h"
#include "AtlasReader.h"
#include "AtlasWriter.h"
#include "FileData.h"
Expand Down Expand Up @@ -78,7 +77,6 @@ class Monio {
const std::size_t mpiRankOwner_;

Reader reader_;
AtlasProcessor atlasProcessor_;
AtlasReader atlasReader_;
AtlasWriter atlasWriter_;

Expand Down
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