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fix: update output format again after discussion
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@program--
program-- committed Aug 28, 2023
1 parent 3cbdf52 commit 40a02a7
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Showing 3 changed files with 33 additions and 45 deletions.
33 changes: 18 additions & 15 deletions include/utilities/nexus_writer.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@

// Changing these will affect both NetCDF and CSV outputs
#define NGEN_VARIABLE_NEXUS_ID "feature_id"
#define NGEN_VARIABLE_SEGMENT_ID "segment_id"
#define NGEN_VARIABLE_TIME "time"
#define NGEN_VARIABLE_Q_LATERAL "q_lateral"

namespace ngen {
Expand Down Expand Up @@ -44,17 +44,17 @@ struct nexus_writer
*
* @param file_name File path to create
* @param num_nexuses Number of nexuses contained in this output
* @param timestamp String timestamp for the timestep these values occur at
*/
virtual void next(const std::string& file_name, size_type num_nexuses) = 0;
virtual void next(const std::string& file_name, size_type num_nexuses, const std::string& timestamp) = 0;

/**
* @brief Write a line to the current file.
*
* @param segment_id Flowpath/segment ID
* @param nexus_id Nexus ID
* @param qlat Lateral streamflow
*/
virtual void write(const std::string& segment_id, const std::string& nexus_id, double qlat) = 0;
virtual void write(const std::string& nexus_id, double qlat) = 0;

/**
* @brief Flush current output
Expand Down Expand Up @@ -82,16 +82,16 @@ struct nexus_csv_writer : public nexus_writer
it_--;
}

void next(const std::string& file_name, size_type num_nexuses) override
void next(const std::string& file_name, size_type num_nexuses, const std::string& timestamp) override
{
it_++;
it_->open(file_name + ".csv");
(*it_) << NGEN_VARIABLE_NEXUS_ID "," NGEN_VARIABLE_SEGMENT_ID "," NGEN_VARIABLE_Q_LATERAL "\n";
(*it_) << NGEN_VARIABLE_NEXUS_ID "," << timestamp << "\n";
}

void write(const std::string& segment_id, const std::string& nexus_id, double contribution) override
void write(const std::string& nexus_id, double contribution) override
{
(*it_) << nexus_id << ',' << segment_id << ',' << std::setprecision(14) << contribution << '\n';
(*it_) << nexus_id << ',' << std::setprecision(14) << contribution << '\n';
}

void flush() override
Expand Down Expand Up @@ -127,7 +127,7 @@ struct nexus_netcdf_writer : public nexus_writer
#endif
}

void next(const std::string& file_name, size_type num_nexuses) override
void next(const std::string& file_name, size_type num_nexuses, const std::string& timestamp) override
{
#ifndef NETCDF_ACTIVE
NGEN_NETCDF_ERROR;
Expand All @@ -140,25 +140,28 @@ struct nexus_netcdf_writer : public nexus_writer

const auto& var_nexus_id = out->addVar(NGEN_VARIABLE_NEXUS_ID, netCDF::ncString, dim_fid);
var_nexus_id.putAtt("description", "Contributing Nexus ID");

const auto& var_segment_id = out->addVar(NGEN_VARIABLE_SEGMENT_ID, netCDF::ncString, dim_fid);
var_segment_id.putAtt("description", "Flowpath ID downstream from the corresponding nexus");

const auto& var_qlat = out->addVar(NGEN_VARIABLE_Q_LATERAL, netCDF::ncDouble, dim_fid);
var_qlat.putAtt("description", "Runoff into channel reach");
var_qlat.putAtt("units", "m3 s-1");

// TODO: Should be minutes since epoch? (aka netCDF::ncInt)
const auto& var_time = out->addVar(NGEN_VARIABLE_TIME, netCDF::ncString);
var_time.putAtt("description", "Output timestamp for this contribution");
var_time.putAtt("standard_name", "time");
var_time.putAtt("format", "%Y%m%s%H%M");
var_time.putVar({0}, timestamp);

index_ = 0;
#endif
}

void write(const std::string& segment_id, const std::string& nexus_id, double contribution) override
void write(const std::string& nexus_id, double contribution) override
{
#ifndef NETCDF_ACTIVE
NGEN_NETCDF_ERROR;
#else
it_->get()->getVar(NGEN_VARIABLE_NEXUS_ID).putVar({ index_ }, nexus_id);
it_->get()->getVar(NGEN_VARIABLE_SEGMENT_ID).putVar({ index_ }, segment_id);
it_->get()->getVar(NGEN_VARIABLE_Q_LATERAL).putVar({ index_ }, contribution);
index_++;
#endif
Expand Down Expand Up @@ -188,5 +191,5 @@ struct nexus_netcdf_writer : public nexus_writer

#undef NGEN_NETCDF_ERROR
#undef NGEN_VARIABLE_NEXUS_ID
#undef NGEN_VARIABLE_SEGMENT_ID
#undef NGEN_VARIABLE_TIME
#undef NGEN_VARIABLE_Q_LATERAL
8 changes: 2 additions & 6 deletions src/NGen.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -398,7 +398,7 @@ int main(int argc, char *argv[]) {
boost::algorithm::erase_all(output_timestamp, ":");
// Remove Seconds
output_timestamp = output_timestamp.substr(0, output_timestamp.size() - 2);
nexus_output->next(manager->get_output_root() + output_timestamp + "NEXOUT", num_nexuses);
nexus_output->next(manager->get_output_root() + output_timestamp + "NEXOUT", num_nexuses, output_timestamp);

for(const auto& id : features.nexuses()) {
#ifdef NGEN_MPI_ACTIVE
Expand All @@ -420,11 +420,7 @@ int main(int argc, char *argv[]) {

double contribution_at_t = features.nexus_at(id)->get_downstream_flow(cat_id, output_time_index, 100.0);

nexus_output->write(
nexus_collection->get_feature(id)->get_property("toid").as_string(),
id,
contribution_at_t
);
nexus_output->write(id, contribution_at_t);

#ifdef NGEN_MPI_ACTIVE
}
Expand Down
37 changes: 13 additions & 24 deletions test/utils/nexus_writer_Test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -21,11 +21,11 @@ class nexus_writer_Test : public ::testing::Test
std::string write_to_file()
{
std::unique_ptr<ngen::utils::nexus_writer> writer = std::make_unique<WriterType>();

writer->init(1);
writer->next(tempfile, 2);
writer->write("wb-1", "nex-1", 5);
writer->write("wb-2", "nex-2", 10);
writer->next(tempfile, 2, timestamp_);
writer->write("nex-1", 5);
writer->write("nex-2", 10);
writer->flush();

return tempfile + (
Expand All @@ -35,6 +35,8 @@ class nexus_writer_Test : public ::testing::Test
);
}

const std::string timestamp_ = "202308250000";

private:
std::string tempfile = testing::TempDir() + "/ngen_nexus_writer__test";
};
Expand All @@ -49,11 +51,11 @@ TEST_F(nexus_writer_Test, csv_writer)

std::string line;
stream >> line;
ASSERT_EQ(line, "feature_id,segment_id,q_lateral");
ASSERT_EQ(line, "feature_id," + timestamp_);
stream >> line;
ASSERT_EQ(line, "nex-1,wb-1,5");
ASSERT_EQ(line, "nex-1,5");
stream >> line;
ASSERT_EQ(line, "nex-2,wb-2,10");
ASSERT_EQ(line, "nex-2,10");
stream.close();
}

Expand All @@ -75,25 +77,12 @@ TEST_F(nexus_writer_Test, netcdf_writer)

const auto& var_nexus_id = stream.getVar("feature_id");
ASSERT_FALSE(var_nexus_id.isNull());
char* nex_id_1 = nullptr;
std::string nex_id_1(5, ' ');
var_nexus_id.getVar({ 0 }, &nex_id_1);
char* nex_id_2 = nullptr;
std::string nex_id_2(5, ' ');
var_nexus_id.getVar({ 1 }, &nex_id_2);
ASSERT_STREQ(nex_id_1, "nex-1");
ASSERT_STREQ(nex_id_2, "nex-2");
delete nex_id_1;
delete nex_id_2;

const auto& var_segment_id = stream.getVar("segment_id");
ASSERT_FALSE(var_segment_id.isNull());
char* seg_id_1 = nullptr;
var_segment_id.getVar({ 0 }, &seg_id_1);
char* seg_id_2 = nullptr;
var_segment_id.getVar({ 1 }, &seg_id_2);
ASSERT_STREQ(seg_id_1, "wb-1");
ASSERT_STREQ(seg_id_2, "wb-2");
delete seg_id_1;
delete seg_id_2;
ASSERT_EQ(nex_id_1, "nex-1");
ASSERT_EQ(nex_id_2, "nex-2");

const auto& var_qlat = stream.getVar("q_lateral");
ASSERT_FALSE(var_qlat.isNull());
Expand Down

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