aquamaps.hh

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#ifndef _AQUAMAPSHH_
#define _AQUAMAPSHH_

#include <openmodeller/om.hh>

#include <string.h>
#include <sqlite3.h>

/********************************************************/
/*********************** AquaMaps ***********************/

/****************************************/
/*********** Expert's values ************/

const Scalar DEPTH_LIMIT = 200.0; // used to choose between surface or bottom layers (temp/sal)

const Scalar MINIMUM_MAXDEPTH = 0.0;
const Scalar MAXIMUM_MAXDEPTH = 9999.0;
const Scalar MINIMUM_ENVELOPE_SIZE_FOR_MAXDEPTH = 0.0; // not used, just defined

const Scalar MINIMUM_MINDEPTH = 0.0;
const Scalar MAXIMUM_MINDEPTH = 9999.0;
const Scalar MINIMUM_ENVELOPE_SIZE_FOR_MINDEPTH = 0.0; // not used, just defined

const Scalar MINIMUM_ICE_CONCENTRATION = 0.0;
const Scalar MAXIMUM_ICE_CONCENTRATION = 1.5;
const Scalar MINIMUM_ENVELOPE_SIZE_FOR_ICE_CONCENTRATION = 0.0; // not used, just defined

const Scalar MINIMUM_DISTANCE_TO_LAND = 0.0;
const Scalar MAXIMUM_DISTANCE_TO_LAND = 4200.0;
const Scalar MINIMUM_ENVELOPE_SIZE_FOR_DISTANCE_TO_LAND = 2.0;

const Scalar MINIMUM_PRIMARY_PRODUCTION = 0.0;
const Scalar MAXIMUM_PRIMARY_PRODUCTION = 6000.0;
const Scalar MINIMUM_ENVELOPE_SIZE_FOR_PRIMARY_PRODUCTION = 2.0;

const Scalar MINIMUM_SURFACE_SALINITY = 3.56;
const Scalar MAXIMUM_SURFACE_SALINITY = 40.2;

const Scalar MINIMUM_BOTTOM_SALINITY = 3.5;
const Scalar MAXIMUM_BOTTOM_SALINITY = 40.9;

const Scalar MINIMUM_ENVELOPE_SIZE_FOR_SALINITY = 1.0;

const Scalar MINIMUM_SURFACE_TEMPERATURE = -2.0;
const Scalar MAXIMUM_SURFACE_TEMPERATURE = 30.0;

const Scalar MINIMUM_BOTTOM_TEMPERATURE = -2.0;
const Scalar MAXIMUM_BOTTOM_TEMPERATURE = 30.0;

const Scalar MINIMUM_ENVELOPE_SIZE_FOR_TEMPERATURE = 1.0;

const Scalar SURFACE_LOWER_LIMIT [7] = { MINIMUM_MAXDEPTH,
                                         MINIMUM_MINDEPTH,
                                         MINIMUM_ICE_CONCENTRATION,
                                         MINIMUM_DISTANCE_TO_LAND,
                                         MINIMUM_PRIMARY_PRODUCTION,
                                         MINIMUM_SURFACE_SALINITY,
                                         MINIMUM_SURFACE_TEMPERATURE };

const Scalar BOTTOM_LOWER_LIMIT [7] = { MINIMUM_MAXDEPTH,
                                        MINIMUM_MINDEPTH,
                                        MINIMUM_ICE_CONCENTRATION,
                                        MINIMUM_DISTANCE_TO_LAND,
                                        MINIMUM_PRIMARY_PRODUCTION,
                                        MINIMUM_BOTTOM_SALINITY,
                                        MINIMUM_BOTTOM_TEMPERATURE };

const Scalar SURFACE_UPPER_LIMIT [7] = { MAXIMUM_MAXDEPTH,
                                         MAXIMUM_MINDEPTH,
                                         MAXIMUM_ICE_CONCENTRATION,
                                         MAXIMUM_DISTANCE_TO_LAND,
                                         MAXIMUM_PRIMARY_PRODUCTION,
                                         MAXIMUM_SURFACE_SALINITY,
                                         MAXIMUM_SURFACE_TEMPERATURE };

const Scalar BOTTOM_UPPER_LIMIT [7] = { MAXIMUM_MAXDEPTH,
                                        MAXIMUM_MINDEPTH,
                                        MAXIMUM_ICE_CONCENTRATION,
                                        MAXIMUM_DISTANCE_TO_LAND,
                                        MAXIMUM_PRIMARY_PRODUCTION,
                                        MAXIMUM_BOTTOM_SALINITY,
                                        MAXIMUM_BOTTOM_TEMPERATURE };

const Scalar INNER_SIZE [7] = { MINIMUM_ENVELOPE_SIZE_FOR_MAXDEPTH,
                                MINIMUM_ENVELOPE_SIZE_FOR_MINDEPTH,
                                MINIMUM_ENVELOPE_SIZE_FOR_ICE_CONCENTRATION,
                                MINIMUM_ENVELOPE_SIZE_FOR_DISTANCE_TO_LAND,
                                MINIMUM_ENVELOPE_SIZE_FOR_PRIMARY_PRODUCTION,
                                MINIMUM_ENVELOPE_SIZE_FOR_SALINITY,
                                MINIMUM_ENVELOPE_SIZE_FOR_TEMPERATURE };

const std::string NAME [7] = { "maximum depth",
                               "minimum depth",
                               "ice concentration",
                               "distance to land",
                               "primary production",
                               "salinity",
                               "temperature" };

// Variable position in sample or arrays

const int MAXDEPTH = 0;
const int MINDEPTH = 1;
const int ICE_CONCENTRATION = 2;
const int DISTANCE_TO_LAND = 3;
const int PRIMARY_PRODUCTION = 4;
const int SALINITY = 5;
const int TEMPERATURE = 6;

class AquaMaps : public AlgorithmImpl
{
public:

  AquaMaps();
  ~AquaMaps();

  // Basic methods inherited from Algorithm class

  int initialize();
  int iterate();
  int getConvergence( Scalar * const val ) const;
  float getProgress() const;
  int done() const;
  Scalar getValue( const Sample& x ) const;

protected:

  // Model Serialization
  virtual void _getConfiguration( ConfigurationPtr& ) const;

  // Model Deserialization
  virtual void _setConfiguration( const ConstConfigurationPtr & );

private:

  int _getAndCheckParameter( std::string const &name, int * value );

  void _calculateEnvelopes( const OccurrencesPtr& );

  void _percentile( Scalar *result, int n, double percent, std::vector<ScalarVector> *matrix, int layerIndex );

  void _readSpeciesData( const char *species );

  bool _hasExpertRange( sqlite3_stmt * stmt, int varIndex );

  void _adjustInterquartile( int layerIndex, Scalar adjmin, Scalar adjmax );

  void _ensureEnvelopeSize( int layerIndex );

  void _logEnvelope();

  int _getRelatedIndex( int index );

  int * _use_layer;

  Sample _lower_limit;

  Sample _upper_limit;

  Sample _inner_size;

  Sample _minimum;

  Sample _maximum;

  Sample _pref_minimum;

  Sample _pref_maximum;

  int _pelagic;

  int _use_surface_layers;

  bool * _has_expert_range;

  float _progress;
};


#endif