test/ioda/ObsSpace.h

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/*
 * (C) Copyright 2018-2021 UCAR
 *
 * This software is licensed under the terms of the Apache Licence Version 2.0
 * which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
 */
 
#ifndef TEST_IODA_OBSSPACE_H_
#define TEST_IODA_OBSSPACE_H_
 
#include <cmath>
#include <set>
#include <string>
#include <vector>
 
#define ECKIT_TESTING_SELF_REGISTER_CASES 0
 
#include <boost/noncopyable.hpp>
#include <boost/shared_ptr.hpp>
 
#include "eckit/config/LocalConfiguration.h"
#include "eckit/testing/Test.h"
 
#include "oops/mpi/mpi.h"
#include "oops/runs/Test.h"
#include "oops/test/TestEnvironment.h"
 
#include "ioda/distribution/Accumulator.h"
#include "ioda/distribution/DistributionUtils.h"
#include "ioda/IodaTrait.h"
#include "ioda/ObsSpace.h"
 
namespace ioda {
namespace test {
 
// -----------------------------------------------------------------------------
 
class ObsSpaceTestFixture : private boost::noncopyable {
 public:
  static ioda::ObsSpace & obspace(const std::size_t ii) {
    return *getInstance().ospaces_.at(ii);
  }
  static std::size_t size() {return getInstance().ospaces_.size();}
  static void cleanup() {
    auto &spaces = getInstance().ospaces_;
    for (auto &space : spaces) {
      space->save();
      space.reset();
    }
  }
 
 private:
  static ObsSpaceTestFixture & getInstance() {
    static ObsSpaceTestFixture theObsSpaceTestFixture;
    return theObsSpaceTestFixture;
  }
 
  ObsSpaceTestFixture(): ospaces_() {
    util::DateTime bgn(::test::TestEnvironment::config().getString("window begin"));
    util::DateTime end(::test::TestEnvironment::config().getString("window end"));
 
    std::vector<eckit::LocalConfiguration> conf;
    ::test::TestEnvironment::config().get("observations", conf);
 
    for (std::size_t jj = 0; jj < conf.size(); ++jj) {
      eckit::LocalConfiguration obsconf(conf[jj], "obs space");
      std::string distname = obsconf.getString("distribution", "RoundRobin");
      boost::shared_ptr<ioda::ObsSpace> tmp(new ioda::ObsSpace(obsconf, oops::mpi::world(),
                                                               bgn, end, oops::mpi::myself()));
      ospaces_.push_back(tmp);
    }
  }
 
  ~ObsSpaceTestFixture() {}
 
  std::vector<boost::shared_ptr<ioda::ObsSpace> > ospaces_;
};
 
// -----------------------------------------------------------------------------
 
void testConstructor() {
  typedef ObsSpaceTestFixture Test_;
 
  std::vector<eckit::LocalConfiguration> conf;
  ::test::TestEnvironment::config().get("observations", conf);
 
  for (std::size_t jj = 0; jj < Test_::size(); ++jj) {
    // Grab the obs space and test data configurations
    eckit::LocalConfiguration obsConfig;
    eckit::LocalConfiguration testConfig;
    conf[jj].get("obs space", obsConfig);
    conf[jj].get("test data", testConfig);
 
    std::string DistMethod = obsConfig.getString("distribution", "RoundRobin");
 
    const ObsSpace &odb = Test_::obspace(jj);
 
    // Get the numbers of locations (nlocs) from the ObsSpace object
    std::size_t GlobalNlocs = odb.globalNumLocs();
    std::size_t Nlocs = odb.nlocs();
    std::size_t Nvars = odb.nvars();
 
    // Get the purturbation seed from the ObsSpace object
    int obsPertSeed = odb.params().obsPertSeed();
 
    // Get the expected nlocs from the obspace object's configuration
    std::size_t ExpectedGlobalNlocs = testConfig.getUnsigned("nlocs");
    std::size_t ExpectedNvars = testConfig.getUnsigned("nvars");
 
    // Get the expected purturbation seed from the config object
    int ExpectedObsPertSeed = testConfig.getUnsigned("obs perturbations seed");
 
    // Get the obs grouping/sorting parameters from the ObsSpace object
    std::vector<std::string> ObsGroupVars = odb.obs_group_vars();
    std::string ObsSortVar = odb.obs_sort_var();
    std::string ObsSortOrder = odb.obs_sort_order();
 
    // Get the expected obs grouping/sorting parameters from the configuration
    std::vector<std::string> ExpectedObsGroupVars =
      testConfig.getStringVector("expected group variables");
    std::string ExpectedObsSortVar = testConfig.getString("expected sort variable");
    std::string ExpectedObsSortOrder = testConfig.getString("expected sort order");
 
    oops::Log::debug() << "GlobalNlocs, ExpectedGlobalNlocs: " << GlobalNlocs << ", "
                       << ExpectedGlobalNlocs << std::endl;
    oops::Log::debug() << "Nvars, ExpectedNvars: " << Nvars << ", "
                       << ExpectedNvars << std::endl;
    // records are ambigious for halo distribution
    // e.g. consider airplane (a single record in round robin) flying accros the globe
    // for Halo distr this record will be considered unique on each PE
    if (DistMethod != "Halo") {
      std::size_t NRecs = 0;
      std::set<std::size_t> recIndices;
      auto accumulator = odb.distribution()->createAccumulator<std::size_t>();
      for (std::size_t loc = 0; loc < Nlocs; ++loc) {
        if (bool isNewRecord = recIndices.insert(odb.recnum()[loc]).second) {
          accumulator->addTerm(loc, 1);
          ++NRecs;
        }
      }
      std::size_t ExpectedNRecs = odb.nrecs();
      EXPECT_EQUAL(NRecs, ExpectedNRecs);
 
      // Calculate the global number of unique records
      std::size_t GlobalNRecs = accumulator->computeResult();
      std::size_t ExpectedGlobalNrecs = testConfig.getUnsigned("nrecs");
      EXPECT_EQUAL(GlobalNRecs, ExpectedGlobalNrecs);
    }
 
    oops::Log::debug() << "ObsGroupVars, ExpectedObsGroupVars: " << ObsGroupVars << ", "
                       << ExpectedObsGroupVars << std::endl;
    oops::Log::debug() << "ObsSortVar, ExpectedObsSortVar: " << ObsSortVar << ", "
                       << ExpectedObsSortVar << std::endl;
    oops::Log::debug() << "ObsSortOrder, ExpectedObsSortOrder: " << ObsSortOrder << ", "
                       << ExpectedObsSortOrder << std::endl;
 
    // get the standard nlocs and nchans dimension names and compare with expected values
    std::string nlocsName = odb.get_dim_name(ioda::ObsDimensionId::Nlocs);
    std::string nchansName = odb.get_dim_name(ioda::ObsDimensionId::Nchans);
 
    EXPECT(GlobalNlocs == ExpectedGlobalNlocs);
    EXPECT(Nvars == ExpectedNvars);
 
    EXPECT(obsPertSeed == ExpectedObsPertSeed);
 
    EXPECT(ObsGroupVars == ExpectedObsGroupVars);
    EXPECT(ObsSortVar == ExpectedObsSortVar);
    EXPECT(ObsSortOrder == ExpectedObsSortOrder);
 
    EXPECT(nlocsName == "nlocs");
    EXPECT(nchansName == "nchans");
 
    EXPECT(odb.get_dim_id("nlocs") == ioda::ObsDimensionId::Nlocs);
    EXPECT(odb.get_dim_id("nchans") == ioda::ObsDimensionId::Nchans);
  }
}
 
// -----------------------------------------------------------------------------
 
void testGetDb() {
  typedef ObsSpaceTestFixture Test_;
 
  std::vector<eckit::LocalConfiguration> conf;
  ::test::TestEnvironment::config().get("observations", conf);
 
  for (std::size_t jj = 0; jj < Test_::size(); ++jj) {
    // Grab the obs space and test data configurations
    eckit::LocalConfiguration obsConfig;
    eckit::LocalConfiguration testConfig;
    conf[jj].get("obs space", obsConfig);
    conf[jj].get("test data", testConfig);
 
    std::string DistMethod = obsConfig.getString("distribution", "RoundRobin");
 
    // Set up a pointer to the ObsSpace object for convenience
    ioda::ObsSpace * Odb = &(Test_::obspace(jj));
    std::size_t Nlocs = Odb->nlocs();
 
    // Get the variables section from the test data and perform checks accordingly
    std::vector<eckit::LocalConfiguration> varconf =
                            testConfig.getSubConfigurations("variables");
    double Tol = testConfig.getDouble("tolerance");
    for (std::size_t i = 0; i < varconf.size(); ++i) {
      // Read in the variable group, name and expected norm values from the configuration
      std::string VarName = varconf[i].getString("name");
      std::string GroupName = varconf[i].getString("group");
      std::string VarType = varconf[i].getString("type");
 
      // Do different checks according to type
      if (VarType == "float") {
        // Check the type from ObsSpace
        ObsDtype VarDataType = Odb->dtype(GroupName, VarName);
        EXPECT(VarDataType == ObsDtype::Float);
 
        // Check auto-conversion to double from ObsSpace float
        // Check the norm
        std::vector<double> TestVec(Nlocs);
        Odb->get_db(GroupName, VarName, TestVec);
 
        // Calculate the norm of the vector
        double ExpectedVnorm = varconf[i].getDouble("norm");
        double Vnorm = dotProduct(*Odb->distribution(), 1, TestVec, TestVec);
        Vnorm = sqrt(Vnorm);
 
        EXPECT(oops::is_close(Vnorm, ExpectedVnorm, Tol));
      } else if (VarType == "integer") {
        // Check the type from ObsSpace
        ObsDtype VarDataType = Odb->dtype(GroupName, VarName);
        EXPECT(VarDataType == ObsDtype::Integer);
 
        // Check the norm
        std::vector<int> TestVec(Nlocs);
        Odb->get_db(GroupName, VarName, TestVec);
 
        // Calculate the norm of the vector
        double ExpectedVnorm = varconf[i].getDouble("norm");
        double Vnorm = dotProduct(*Odb->distribution(), 1, TestVec, TestVec);
        Vnorm = sqrt(Vnorm);
 
        EXPECT(oops::is_close(Vnorm, ExpectedVnorm, Tol));
      } else if (VarType == "string") {
        // Check the type from ObsSpace
        ObsDtype VarDataType = Odb->dtype(GroupName, VarName);
        EXPECT(VarDataType == ObsDtype::String);
 
        // Check the first and last values of the vector
        std::string ExpectedFirstValue = varconf[i].getString("first value");
        std::string ExpectedLastValue = varconf[i].getString("last value");
        std::vector<std::string> TestVec(Nlocs);
        Odb->get_db(GroupName, VarName, TestVec);
        EXPECT(TestVec[0] == ExpectedFirstValue);
        EXPECT(TestVec[Nlocs-1] == ExpectedLastValue);
      }
    }
  }
}
 
// -----------------------------------------------------------------------------
 
void testPutDb() {
  typedef ObsSpaceTestFixture Test_;
 
  std::string VarName("DummyVar");
 
  for (std::size_t jj = 0; jj < Test_::size(); ++jj) {
    // Set up a pointer to the ObsSpace object for convenience
    ioda::ObsSpace * Odb = &(Test_::obspace(jj));
 
    // Create a dummy vector to put into the database
    // Load up the vector with contrived data, put the vector then
    // get the vector and see if the contrived data made it through.
    std::size_t Nlocs = Odb->nlocs();
    std::vector<double> TestVec(Nlocs);
    std::vector<double> ExpectedVec(Nlocs);
 
    for (std::size_t i = 0; i < Nlocs; ++i) {
      ExpectedVec[i] = static_cast<double>(i);
    }
 
    // Put the vector into the database. Then read the vector back from the database
    // and compare to the original
    Odb->put_db("MetaData", VarName, ExpectedVec);
    Odb->get_db("MetaData", VarName, TestVec);
 
    bool VecMatch = true;
    for (std::size_t i = 0; i < Nlocs; ++i) {
      VecMatch = VecMatch && (static_cast<int>(ExpectedVec[i]) == static_cast<int>(TestVec[i]));
    }
 
    EXPECT(VecMatch);
  }
}
 
// -----------------------------------------------------------------------------
 
void testWriteableGroup() {
  typedef ObsSpaceTestFixture Test_;
 
  std::string VarName("DummyVar");
 
  for (std::size_t jj = 0; jj < Test_::size(); ++jj) {
    // Set up a pointer to the ObsSpace object for convenience
    ioda::ObsSpace * Odb = &(Test_::obspace(jj));
 
    // Create a dummy vector to put into the database
    // All rows read from the input file should be read only.
    // All rows added since the read of the input file should be writeable.
    std::size_t Nlocs = Odb->nlocs();
    std::vector<double> TestVec(Nlocs);
    std::vector<double> ExpectedVec(Nlocs);
 
    for (std::size_t i = 0; i < Nlocs; ++i) {
      ExpectedVec[i] = static_cast<double>(i);
    }
 
    // Put the vector into the database. Then read the vector back from the database
    // and compare to the original
    Odb->put_db("TestGroup", VarName, ExpectedVec);
    Odb->get_db("TestGroup", VarName, TestVec);
 
    bool VecMatch = true;
    for (std::size_t i = 0; i < Nlocs; ++i) {
      VecMatch = VecMatch && (static_cast<int>(ExpectedVec[i]) == static_cast<int>(TestVec[i]));
    }
    EXPECT(VecMatch);
 
    // Now update the vector with the original multiplied by 2.
    for (std::size_t i = 0; i < Nlocs; ++i) {
      ExpectedVec[i] = ExpectedVec[i] * 2;
    }
 
    Odb->put_db("TestGroup", VarName, ExpectedVec);
    Odb->get_db("TestGroup", VarName, TestVec);
 
    VecMatch = true;
    for (std::size_t i = 0; i < Nlocs; ++i) {
      VecMatch = VecMatch && (static_cast<int>(ExpectedVec[i]) == static_cast<int>(TestVec[i]));
    }
    EXPECT(VecMatch);
  }
}
 
// -----------------------------------------------------------------------------
 
void testMultiDimTransfer() {
  typedef ObsSpaceTestFixture Test_;
 
  for (std::size_t jj = 0; jj < Test_::size(); ++jj) {
    // Set up a pointer to the ObsSpace object for convenience
    ioda::ObsSpace * Odb = &(Test_::obspace(jj));
 
    // Create a dummy array to put into the database
    // Load up the array with contrived data, put the array then
    // get the array and see if the contrived data made it through.
    // If Nchans comes back equal to zero, it means that this obs space does not
    // have an nchans dimension. In this case, this test is reduced to testing
    // a 1D vector.
    std::size_t Nlocs = Odb->nlocs();
    std::size_t Nchans = Odb->nchans();
 
    std::vector<int> TestValues;
    std::vector<int> ExpectedValues;
    std::vector<std::string> dimList;
 
    int numElements = Nlocs;
    dimList.push_back(Odb->get_dim_name(ObsDimensionId::Nlocs));
    if (Nchans > 0) {
        numElements *= Nchans;
        dimList.push_back(Odb->get_dim_name(ObsDimensionId::Nchans));
    }
 
    // Load up the expected values with numbers 0..n-1.
    TestValues.resize(numElements);
    ExpectedValues.resize(numElements);
    int testValue = 0;
    for (std::size_t i = 0; i < numElements; ++i) {
      ExpectedValues[i] = testValue;
      testValue++;
    }
 
    // Put the data into the ObsSpace, then get the data back from the ObsSpace and
    // compare to the original.
    Odb->put_db("MultiDimData", "DummyVar", ExpectedValues, dimList);
    Odb->get_db("MultiDimData", "DummyVar", TestValues, {} /*select all channels*/);
    EXPECT(TestValues == ExpectedValues);
 
    const int numOddChannels = Nchans/2;
    if (numOddChannels > 0) {
      // Test retrieval of only the odd channels.
 
      const std::vector<int>& channels = Odb->obsvariables().channels();
      ASSERT(channels.size() == Nchans);
 
      std::vector<int> chanSelect;
      for (int i = 0; i < numOddChannels; ++i) {
        const std::size_t channelIndex = 1 + 2 * i;
        chanSelect.push_back(channels[channelIndex]);
      }
 
      ExpectedValues.clear();
      for (std::size_t loc = 0; loc < Nlocs; ++loc) {
        for (int i = 0; i < numOddChannels; ++i) {
          const std::size_t channelIndex = 1 + 2 * i;
          ExpectedValues.push_back(loc * Nchans + channelIndex);
        }
      }
 
      Odb->get_db("MultiDimData", "DummyVar", TestValues, chanSelect);
      EXPECT_EQUAL(TestValues, ExpectedValues);
    }
 
    if (numOddChannels > 0) {
      // Test retrieval of a single channel using the old syntax
      // (variable name with a channel suffix)
 
      const std::vector<int>& channels = Odb->obsvariables().channels();
      const int channelIndex = 1;
      const int channelNumber = channels[channelIndex];
 
      ExpectedValues.clear();
      for (std::size_t loc = 0; loc < Nlocs; ++loc)
        ExpectedValues.push_back(loc * Nchans + channelIndex);
 
      Odb->get_db("MultiDimData", "DummyVar_" + std::to_string(channelNumber), TestValues);
      EXPECT_EQUAL(TestValues, ExpectedValues);
    }
  }
}
 
// -----------------------------------------------------------------------------
 
void testCleanup() {
  // This test removes the obsspaces and ensures that they evict their contents
  // to disk successfully.
  typedef ObsSpaceTestFixture Test_;
 
  Test_::cleanup();
}
 
// -----------------------------------------------------------------------------
 
class ObsSpace : public oops::Test {
 public:
  ObsSpace() {}
  virtual ~ObsSpace() {}
 
 private:
  std::string testid() const override {return "test::ObsSpace<ioda::IodaTrait>";}
 
  void register_tests() const override {
    std::vector<eckit::testing::Test>& ts = eckit::testing::specification();
 
    ts.emplace_back(CASE("ioda/ObsSpace/testConstructor")
      { testConstructor(); });
    ts.emplace_back(CASE("ioda/ObsSpace/testGetDb")
      { testGetDb(); });
    ts.emplace_back(CASE("ioda/ObsSpace/testPutDb")
      { testPutDb(); });
    ts.emplace_back(CASE("ioda/ObsSpace/testWriteableGroup")
      { testWriteableGroup(); });
    ts.emplace_back(CASE("ioda/ObsSpace/testMultiDimTransfer")
      { testMultiDimTransfer(); });
    ts.emplace_back(CASE("ioda/ObsSpace/testCleanup")
      { testCleanup(); });
  }
 
  void clear() const override {}
};
 
// -----------------------------------------------------------------------------
 
}  // namespace test
}  // namespace ioda
 
#endif  // TEST_IODA_OBSSPACE_H_