DataFromSQL.h

Go to the documentation of this file.

#pragma once
/*
 * (C) Copyright 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.
 */
/** @file DataFromSQL.h
 * @brief implements ODC bindings
**/
 
#include <cctype>
#include <iomanip>
#include <map>
#include <string>
#include <vector>
 
#include "ioda/defs.h"
#include "ioda/ObsGroup.h"
#include "unsupported/Eigen/CXX11/Tensor"
 
namespace ioda {
namespace Engines {
namespace ODC {
 
  // TODO(DJDavies2): Take these obsgroup and varno
  // definitions and encapsulate these into the YAML
  // file structure.
  static constexpr int obsgroup_scatwind     = 2;
  static constexpr int obsgroup_aircraft     = 4;
  static constexpr int obsgroup_sonde        = 5;
  static constexpr int obsgroup_atovs        = 7;
  static constexpr int obsgroup_airs         = 16;
  static constexpr int obsgroup_gpsro        = 18;
  static constexpr int obsgroup_ssmis        = 19;
  static constexpr int obsgroup_iasi         = 26;
  static constexpr int obsgroup_seviriclr    = 27;
  static constexpr int obsgroup_geocloud     = 28;
  static constexpr int obsgroup_amsr         = 29;
  static constexpr int obsgroup_abiclr       = 37;
  static constexpr int obsgroup_atms         = 38;
  static constexpr int obsgroup_cris         = 39;
  static constexpr int obsgroup_surfacecloud = 42;
  static constexpr int obsgroup_mwsfy3       = 44;
  static constexpr int obsgroup_ahiclr       = 51;
  static constexpr int obsgroup_mwri         = 55;
  static constexpr int obsgroup_gmilow       = 56;
  static constexpr int obsgroup_gmihigh      = 57;
  static constexpr int obsgroup_hiras        = 60;
 
  static constexpr int varno_dd                     = 111;
  static constexpr int varno_rawbt                  = 119;
  static constexpr int varno_bending_angle          = 162;
  static constexpr int varno_rawsca                 = 233;
  static constexpr int varno_u_amb                  = 242;
  static constexpr int varno_rawbt_hirs             = 248;
  static constexpr int varno_rawbt_amsu             = 249;
  static constexpr int varno_cloud_fraction_covered = 266;
  static constexpr int varno_rawbt_amsr_89ghz       = 267;
  static constexpr int varno_rawbt_mwts             = 274;
  static constexpr int varno_rawbt_mwhs             = 275;
 
  static constexpr int odb_type_int      = 1;
  static constexpr int odb_type_real     = 2;
  static constexpr int odb_type_string   = 3;
  static constexpr int odb_type_bitfield = 4;
 
  static constexpr float odb_missing_float = -2147483648.0f;
  static constexpr int odb_missing_int = 2147483647;
 
class DataFromSQL {
private:
  std::vector<std::string> columns_;
  std::vector<int> column_types_;
  std::vector<int> varnos_;
  std::vector<double> data_;
  size_t number_of_rows_           = 0;
  size_t number_of_metadata_rows_  = 0;
  size_t number_of_varnos_         = 0;
  int obsgroup_                    = 0;
  std::map<int, size_t> varnos_and_levels_;
 
  /// \brief Returns a count of the rows extracted by an sql
  /// \param sql The SQL to check
  static size_t countRows(const std::string& sql);
 
  /// \brief Returns the value for a particular row/column
  /// \param row Get data for this row
  /// \param column Get data for this column
  double getData(size_t row, size_t column) const;
 
  /// \brief Returns the value for a particular row/column (as name)
  /// \param row Get data for this row
  /// \param column Get data for this column
  double getData(size_t row, const std::string& column) const;
 
  /// \brief Set a value for a row,column element
  /// \param row The row to set
  /// \param column The column to set
  /// \param val Set this value
  void setData(size_t row, size_t column, double val);
 
  /// \brief Populate structure with data from an sql
  /// \param sql The SQL string to generate the data for the structure
  void setData(const std::string& sql);
 
  /// \brief Returns the number of rows for a particular varno
  /// \param varno The varno to check
  size_t numberOfRowsForVarno(int varno) const;
 
  /// \brief Returns true if a particular varno is present
  /// \param varno The varno to check
  bool hasVarno(int varno) const;
 
  /// \brief Returns the index of a specified column
  /// \param column The column to check
  int getColumnIndex(const std::string& column) const;
 
  /// \brief Returns the number of levels for each varno
  size_t numberOfLevels(int varno) const;
 
  /// \brief Returns data for a (metadata) column
  /// \param column Get data for this column
  Eigen::ArrayXf getMetadataColumn(std::string const& column) const;
 
  /// \brief Returns data for a (metadata) column
  /// \param column Get data for this column
  Eigen::ArrayXi getMetadataColumnInt(std::string const& column) const;
 
  /// \brief Returns data for a (metadata) column
  /// \param column Get data for this column
  std::vector<std::string> getMetadataStringColumn(std::string const& column) const;
 
  /// \brief Returns data for a varno for a varno column
  /// \param varno Get data for this varno
  /// \param column Get data for this column
  /// \param nchans Number of channels to store
  /// \param nchans_actual Actual number of channels
  Eigen::ArrayXf getVarnoColumn(const std::vector<int>& varnos, std::string const& column,
                                           const int nchans, const int nchans_actual) const;
 
public:
  /// \brief Simple constructor
  DataFromSQL();
 
  /// \brief Returns the number of "metadata" rows, i.e. hdr-type rows
  size_t numberOfMetadataRows() const;
 
  /// \brief Returns the dimensions for the ODB
  NewDimensionScales_t getVertcos() const;
 
  /// \brief Populate structure with data from specified columns, file and varnos
  /// \param columns List of columns to extract
  /// \param filename Extract from this file
  /// \param varnos List of varnos to extract
  void select(const std::vector<std::string>& columns, const std::string& filename,
              const std::vector<int>& varnos, const std::string& query);
 
  /// \brief Returns a vector of date strings
  std::vector<std::string> getDates(std::string const& date_col, std::string const& time_col) const;
 
  /// \brief Returns a vector of columns
  const std::vector<std::string>& getColumns() const;
 
  /// \brief Returns an ioda variable for a specified column
  /// \param column Get data for this column
  ioda::Variable getIodaVariable(std::string const& column, ioda::ObsGroup og,
                                 ioda::VariableCreationParameters params) const;
 
  /// \brief Returns an ioda variable for a specified column
  ioda::Variable getIodaObsvalue(int varno, ioda::ObsGroup og,
                                 ioda::VariableCreationParameters params) const;
 
  /// \brief Returns the type of a specified column
  /// \param column The column to check
  int getColumnTypeByName(std::string const& column) const;
 
  /// \brief Returns the obsgroup number
  int getObsgroup() const;
};
 
}  // namespace ODC
}  // namespace Engines
}  // namespace ioda