#include <aquamaps.hh>

Inheritance diagram for AquaMaps:

Collaboration diagram for AquaMaps:

Public Member Functions
	AquaMaps ()

	~AquaMaps ()

int	initialize ()

int	iterate ()

int	getConvergence (Scalar *const val) const

float	getProgress () const

int	done () const

Scalar	getValue (const Sample &x) const

Public Member Functions inherited from AlgorithmImpl
	AlgorithmImpl (AlgMetadata const *metadata)

virtual	~AlgorithmImpl ()

void	setParameters (int nparam, AlgParameter const *param)

void	setParameters (const ParamSetType &)

std::string const	getID () const

AlgMetadata const *	getMetadata () const

AlgorithmPtr	getFreshCopy ()

virtual int	supportsModelProjection () const

Model	createModel (const SamplerPtr &samp, CallbackWrapper *func=0)

void	setSampler (const SamplerPtr &samp)

virtual int	finalize ()

virtual int	needNormalization ()

Normalizer *	getNormalizer () const

void	setNormalization (const SamplerPtr &samp) const

void	setNormalization (const EnvironmentPtr &env) const

virtual Model	getModel () const

ConfigurationPtr	getConfiguration () const

void	setConfiguration (const ConstConfigurationPtr &)

Public Member Functions inherited from Configurable
virtual	~Configurable ()

Protected Member Functions
virtual void	_getConfiguration (ConfigurationPtr &) const

virtual void	_setConfiguration (const ConstConfigurationPtr &)

Protected Member Functions inherited from AlgorithmImpl
int	dimDomain ()

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

int	getParameter (std::string const &name, double *value)

int	getParameter (std::string const &name, float *value)

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

Private Member Functions
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)

Private Attributes
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

Additional Inherited Members
Public Types inherited from AlgorithmImpl
typedef std::map< icstring, std::string >	ParamSetType

Protected Attributes inherited from AlgorithmImpl
SamplerPtr	_samp

Normalizer *	_normalizerPtr

ParamSetType	_param

Detailed Description

AquaMaps Algorithm

Definition at line 183 of file aquamaps.hh.

Constructor & Destructor Documentation

AquaMaps::AquaMaps ( )

Definition at line 235 of file aquamaps.cpp.

AquaMaps::~AquaMaps ( )

Definition at line 255 of file aquamaps.cpp.

References _has_expert_range, and _use_layer.

Member Function Documentation

void AquaMaps::_adjustInterquartile	(	int	layerIndex,
		Scalar	adjmin,
		Scalar	adjmax
	)

private

Make the interquartile adjusting

Definition at line 882 of file aquamaps.cpp.

References _getRelatedIndex(), _lower_limit, _maximum, _minimum, and _upper_limit.

Referenced by _calculateEnvelopes().

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void AquaMaps::_calculateEnvelopes ( const OccurrencesPtr & occs )

private

Calculate the envelopes

Definition at line 423 of file aquamaps.cpp.

References _adjustInterquartile(), _ensureEnvelopeSize(), _has_expert_range, _lower_limit, _maximum, _minimum, _percentile(), _pref_maximum, _pref_minimum, _progress, _readSpeciesData(), _upper_limit, _use_surface_layers, BOTTOM_LOWER_LIMIT, BOTTOM_UPPER_LIMIT, Log::debug(), DEPTH_LIMIT, Log::info(), Log::instance(), MAXDEPTH, MINDEPTH, SALINITY, Sample::size(), and TEMPERATURE.

Referenced by iterate().

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void AquaMaps::_ensureEnvelopeSize ( int layerIndex )

private

Ensure that the envelope has a minimum size

Definition at line 899 of file aquamaps.cpp.

References _getRelatedIndex(), _inner_size, _lower_limit, _maximum, _minimum, _pref_maximum, _pref_minimum, and _upper_limit.

Referenced by _calculateEnvelopes().

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

private

Get a Boolean parameter and check its value.

Parameters

name	Parameter name.
value	Parameter value.

Returns: Zero if the parameter does not exists or the parameters were not set yet.

Definition at line 401 of file aquamaps.cpp.

References Log::error(), AlgorithmImpl::getParameter(), and Log::instance().

Referenced by initialize().

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void AquaMaps::_getConfiguration ( ConfigurationPtr & config ) const

protectedvirtual

Reimplemented from AlgorithmImpl.

Definition at line 1111 of file aquamaps.cpp.

References _maximum, _minimum, _pelagic, _pref_maximum, _pref_minimum, _use_layer, _use_surface_layers, and done().

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int AquaMaps::_getRelatedIndex ( int index )

private

Return the 0-6 index from the constants defined in this header related to the 0-8 index from the complete set of layers.

Definition at line 1187 of file aquamaps.cpp.

Referenced by _adjustInterquartile(), and _ensureEnvelopeSize().

bool AquaMaps::_hasExpertRange	(	sqlite3_stmt *	stmt,
		int	varIndex
	)

private

Fetch expert range data for a specific variable

Definition at line 804 of file aquamaps.cpp.

References _maximum, _minimum, _pref_maximum, _pref_minimum, DISTANCE_TO_LAND, ICE_CONCENTRATION, PRIMARY_PRODUCTION, SALINITY, and TEMPERATURE.

Referenced by _readSpeciesData().

void AquaMaps::_logEnvelope ( )

private

Log the bioclimatic envelopes information.

Definition at line 1171 of file aquamaps.cpp.

References _maximum, _minimum, _pref_maximum, _pref_minimum, Log::info(), Log::instance(), and Sample::size().

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

private

Calculate a percentile

Definition at line 642 of file aquamaps.cpp.

Referenced by _calculateEnvelopes().

void AquaMaps::_readSpeciesData ( const char * species )

private

Read species data from expert database

Definition at line 671 of file aquamaps.cpp.

References _has_expert_range, _hasExpertRange(), _maximum, _minimum, _pelagic, _pref_maximum, _pref_minimum, Log::debug(), ICE_CONCENTRATION, Log::info(), Log::instance(), MAXDEPTH, MINDEPTH, NAME, omDataPath(), TEMPERATURE, and Log::warn().

Referenced by _calculateEnvelopes().

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void AquaMaps::_setConfiguration ( const ConstConfigurationPtr & config )

protectedvirtual

Reimplemented from AlgorithmImpl.

Definition at line 1132 of file aquamaps.cpp.

References _maximum, _minimum, _pelagic, _pref_maximum, _pref_minimum, _progress, _use_layer, _use_surface_layers, Log::error(), AttributeNotFound::getName(), and Log::instance().

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int AquaMaps::done ( ) const

virtual

Return != 0 if algorithm finished.

Reimplemented from AlgorithmImpl.

Definition at line 391 of file aquamaps.cpp.

References _progress.

Referenced by _getConfiguration().

int AquaMaps::getConvergence ( Scalar *const val ) const

virtual

Returns the algorithm's convergence value at the moment

Reimplemented from AlgorithmImpl.

Definition at line 372 of file aquamaps.cpp.

float AquaMaps::getProgress ( ) const

virtual

Returns progress so far (between 0.0 and 1.0)

Reimplemented from AlgorithmImpl.

Definition at line 382 of file aquamaps.cpp.

References _progress.

Scalar AquaMaps::getValue ( const Sample & x ) const

virtual

The algorithm must return the occurrence probability at the given environment conditions.

Parameters

x	Environmental conditions.

Returns: The occurrence probability in the range [0,1].

Implements AlgorithmImpl.

Definition at line 959 of file aquamaps.cpp.

References _maximum, _minimum, _pelagic, _pref_maximum, _pref_minimum, _use_layer, _use_surface_layers, MAXDEPTH, MINDEPTH, SALINITY, Sample::size(), and TEMPERATURE.

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int AquaMaps::initialize ( )

virtual

Initiate a new training.

Implements AlgorithmImpl.

Definition at line 271 of file aquamaps.cpp.

References _getAndCheckParameter(), _has_expert_range, AlgorithmImpl::_samp, _use_layer, _use_surface_layers, DISTANCE_TO_LAND, Log::error(), AlgorithmImpl::getParameter(), ICE_CONCENTRATION, Log::info(), Log::instance(), MAXDEPTH, MINDEPTH, PARAM_USE_DEPTH_RANGE, PARAM_USE_DISTANCE_TO_LAND, PARAM_USE_ICE_CONCENTRATION, PARAM_USE_PRIMARY_PRODUCTION, PARAM_USE_SALINITY, PARAM_USE_SURFACE_LAYERS, PARAM_USE_TEMPERATURE, PRIMARY_PRODUCTION, SALINITY, and TEMPERATURE.

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int AquaMaps::iterate ( )

virtual

One step further on the training. Return 0 if something wrong happened.

Reimplemented from AlgorithmImpl.

Definition at line 359 of file aquamaps.cpp.

References _calculateEnvelopes(), AlgorithmImpl::_samp, Log::info(), and Log::instance().

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Member Data Documentation

bool* AquaMaps::_has_expert_range

private

Indicates if the variable has an expert range in the local database.

Definition at line 277 of file aquamaps.hh.

Referenced by _calculateEnvelopes(), _readSpeciesData(), initialize(), and ~AquaMaps().

Sample AquaMaps::_inner_size

private

Recommended values for the inner envelope sizes

Definition at line 252 of file aquamaps.hh.

Referenced by _ensureEnvelopeSize().

Sample AquaMaps::_lower_limit

private

Lower limit for each variable

Definition at line 246 of file aquamaps.hh.

Referenced by _adjustInterquartile(), _calculateEnvelopes(), and _ensureEnvelopeSize().

Sample AquaMaps::_maximum

private

Maximum value for each variable.

Definition at line 258 of file aquamaps.hh.

Referenced by _adjustInterquartile(), _calculateEnvelopes(), _ensureEnvelopeSize(), _getConfiguration(), _hasExpertRange(), _logEnvelope(), _readSpeciesData(), _setConfiguration(), and getValue().

Sample AquaMaps::_minimum

private

Minimum value for each variable.

Definition at line 255 of file aquamaps.hh.

Referenced by _adjustInterquartile(), _calculateEnvelopes(), _ensureEnvelopeSize(), _getConfiguration(), _hasExpertRange(), _logEnvelope(), _readSpeciesData(), _setConfiguration(), and getValue().

int AquaMaps::_pelagic

private

Indicates if the species is pelagic or not (-1 indicates no data). Note: pelagic means "belonging to the upper layers of the open sea" (poetic, huh?).

Definition at line 269 of file aquamaps.hh.

Referenced by _getConfiguration(), _readSpeciesData(), _setConfiguration(), and getValue().

Sample AquaMaps::_pref_maximum

private

Prefered maximum for each variable.

Definition at line 264 of file aquamaps.hh.

Referenced by _calculateEnvelopes(), _ensureEnvelopeSize(), _getConfiguration(), _hasExpertRange(), _logEnvelope(), _readSpeciesData(), _setConfiguration(), and getValue().

Sample AquaMaps::_pref_minimum

private

Prefered minimum for each variable.

Definition at line 261 of file aquamaps.hh.

Referenced by _calculateEnvelopes(), _ensureEnvelopeSize(), _getConfiguration(), _hasExpertRange(), _logEnvelope(), _readSpeciesData(), _setConfiguration(), and getValue().

float AquaMaps::_progress

private

Indication of progress during model creation.

Definition at line 280 of file aquamaps.hh.

Referenced by _calculateEnvelopes(), _setConfiguration(), done(), and getProgress().

Sample AquaMaps::_upper_limit

private

Upper limit for each variable

Definition at line 249 of file aquamaps.hh.

Referenced by _adjustInterquartile(), _calculateEnvelopes(), and _ensureEnvelopeSize().

int* AquaMaps::_use_layer

private

Indicates if the respective layer should be used or not when calculating probabilities

Definition at line 243 of file aquamaps.hh.

Referenced by _getConfiguration(), _setConfiguration(), getValue(), initialize(), and ~AquaMaps().

int AquaMaps::_use_surface_layers

private

Indicates if surface layers should be used for temperature and salinity (-1 means that aquamaps should try to find out by using depth ranges specified in its internal database).

Definition at line 274 of file aquamaps.hh.

Referenced by _calculateEnvelopes(), _getConfiguration(), _setConfiguration(), getValue(), and initialize().

The documentation for this class was generated from the following files:

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation