#include <Occurrences.hh>

Inheritance diagram for OccurrencesImpl:

Collaboration diagram for OccurrencesImpl:

Public Types
typedef std::vector < OccurrencePtr > ::const_iterator	const_iterator
typedef std::vector < OccurrencePtr >::iterator	iterator
Public Member Functions
	OccurrencesImpl (double default_abundance)
	OccurrencesImpl (const std::string &label, const std::string &coord_system=GeoTransform::getDefaultCS())
	~OccurrencesImpl ()
OccurrencesImpl *	clone () const
void	reserve (int estimate)
char const *	label () const
char const *	coordSystem () const
bool	hasEnvironment () const
int	dimension () const
void	setLabel (const std::string &label)
void	setCoordinateSystem (const std::string &cs)
void	createOccurrence (const std::string &id, Coord longitude, Coord latitude, Scalar error, Scalar abundance, int num_attributes=0, Scalar attributes=0, int num_env=0, Scalar env=0)
void	createOccurrence (const std::string &id, Coord longitude, Coord latitude, Scalar error, Scalar abundance, std::vector< double > attributes, std::vector< double > env)
void	insert (const OccurrencePtr &)
iterator	erase (const iterator &it)
int	numAttributes () const
int	numOccurrences () const
bool	isEmpty () const
ConstOccurrencePtr	operator[] (int i) const
const_iterator	begin () const
const_iterator	end () const
iterator	begin ()
iterator	end ()
ConstOccurrencePtr	getRandom () const
void	getMinMax (Sample min, Sample max) const
void	normalize (Normalizer *normalizerPtr, size_t categoricalThreshold=0)
void	resetNormalization ()
void	setEnvironment (const EnvironmentPtr &env, const char *type="Sample")
void	appendFrom (const OccurrencesPtr &source)
std::vector< ScalarVector >	getEnvironmentMatrix ()
void	dump (std::string msg="") const
virtual ConfigurationPtr	getConfiguration () const
virtual void	setConfiguration (const ConstConfigurationPtr &)
Private Member Functions
void	initGeoTransform ()
Private Attributes
double	default_abundance_
std::string	label_
std::string	cs_
GeoTransform *	gt_
std::vector< OccurrencePtr >	occur_
Friends
class	ReferenceCountedPointer< OccurrencesImpl >
class	ReferenceCountedPointer< const OccurrencesImpl >

Detailed Description

Representation of a set of occurrences.

Definition at line 78 of file Occurrences.hh.

Member Typedef Documentation

typedef std::vector<OccurrencePtr>::const_iterator OccurrencesImpl::const_iterator

Definition at line 85 of file Occurrences.hh.

typedef std::vector<OccurrencePtr>::iterator OccurrencesImpl::iterator

Definition at line 86 of file Occurrences.hh.

Constructor & Destructor Documentation

OccurrencesImpl::OccurrencesImpl ( double default_abundance ) [inline]

Creates a collection of occurrences points.

Definition at line 91 of file Occurrences.hh.

Referenced by clone().

OccurrencesImpl::OccurrencesImpl	(	const std::string &	label,
		const std::string &	coord_system = `GeoTransform::getDefaultCS()`
	)		`[inline]`

Creates a collection of occurrence points.

Parameters:

label	Label for the collection.
coord_system	Coordinate system of the occurrences points to be inserted in this collection (in WKT format).

Definition at line 106 of file Occurrences.hh.

OccurrencesImpl::~OccurrencesImpl ( )

Definition at line 55 of file Occurrences.cpp.

References gt_.

Member Function Documentation

void OccurrencesImpl::appendFrom ( const OccurrencesPtr & source )

Appends all occurrences from source

Parameters:

source Occurrences object where occurrence pointers will be appended from.

Definition at line 379 of file Occurrences.cpp.

References end(), and insert().

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const_iterator OccurrencesImpl::begin ( ) const [inline]

Linear access

Definition at line 204 of file Occurrences.hh.

Referenced by setConfiguration().

iterator OccurrencesImpl::begin ( ) [inline]

Definition at line 206 of file Occurrences.hh.

OccurrencesImpl * OccurrencesImpl::clone ( ) const

Deep copy of this.

Definition at line 312 of file Occurrences.cpp.

References cs_, end(), insert(), label_, occur_, and OccurrencesImpl().

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char const* OccurrencesImpl::coordSystem ( ) const [inline]

coordinate system name

Definition at line 129 of file Occurrences.hh.

Referenced by getConfiguration().

void OccurrencesImpl::createOccurrence	(	const std::string &	id,
		Coord	longitude,
		Coord	latitude,
		Scalar	error,
		Scalar	abundance,
		int	num_attributes = `0`,
		Scalar *	attributes = `0`,
		int	num_env = `0`,
		Scalar *	env = `0`
	)

Create an occurrence.

Parameters:

id	Unique id
longitude	Longitude in native coordinates
latitude	Latitude in native coordinates
error	(longitude, latitude) uncertanty in meters.
abundance	- the abundance of the species: 0 for absence points.
num_attributes	Number of possible modelling attributes.
attributes	Vector with possible modelling attributes.
num_env	Number of environment variables at sample
env	Vector with environment variables.

deprecated by STL vector version.

Definition at line 273 of file Occurrences.cpp.

References gt_, insert(), and GeoTransform::transfOut().

Referenced by OccurrencesReader::_addAbsence(), OccurrencesReader::_addPresence(), and setConfiguration().

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void OccurrencesImpl::createOccurrence	(	const std::string &	id,
		Coord	longitude,
		Coord	latitude,
		Scalar	error,
		Scalar	abundance,
		std::vector< double >	attributes,
		std::vector< double >	env
	)

Create an occurrence using STL vectors to input attributes and environment data

Definition at line 290 of file Occurrences.cpp.

References gt_, insert(), and GeoTransform::transfOut().

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int OccurrencesImpl::dimension ( ) const

Definition at line 344 of file Occurrences.cpp.

References hasEnvironment(), and occur_.

Referenced by getEnvironmentMatrix().

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void OccurrencesImpl::dump ( std::string msg = "" ) const

Print occurrence data and its points.

Definition at line 438 of file Occurrences.cpp.

References end(), Log::info(), Log::instance(), label_, numOccurrences(), and occur_.

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const_iterator OccurrencesImpl::end ( ) const [inline]

Definition at line 205 of file Occurrences.hh.

Referenced by appendFrom(), clone(), dump(), getConfiguration(), getEnvironmentMatrix(), getMinMax(), normalize(), resetNormalization(), and setConfiguration().

iterator OccurrencesImpl::end ( ) [inline]

Definition at line 207 of file Occurrences.hh.

OccurrencesImpl::iterator OccurrencesImpl::erase ( const iterator & it )

Remove a single entry

Definition at line 370 of file Occurrences.cpp.

References occur_, and swap().

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ConfigurationPtr OccurrencesImpl::getConfiguration ( ) const [virtual]

Implements Configurable.

Definition at line 88 of file Occurrences.cpp.

References coordSystem(), end(), gt_, label(), occur_, and GeoTransform::transfIn().

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std::vector< ScalarVector > OccurrencesImpl::getEnvironmentMatrix ( )

Return matrix as a vector of vectors (layers X respective values for each occurrence).

Definition at line 400 of file Occurrences.cpp.

References dimension(), end(), numOccurrences(), and occur_.

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void OccurrencesImpl::getMinMax	(	Sample *	min,
		Sample *	max
	)		const

normalizable interface

Definition at line 251 of file Occurrences.cpp.

References end(), and occur_.

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ConstOccurrencePtr OccurrencesImpl::getRandom ( ) const

Choose an occurrence at random.

Definition at line 361 of file Occurrences.cpp.

References numOccurrences(), and occur_.

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bool OccurrencesImpl::hasEnvironment ( ) const

Definition at line 331 of file Occurrences.cpp.

References numOccurrences(), and occur_.

Referenced by dimension().

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void OccurrencesImpl::initGeoTransform ( ) [private]

Definition at line 74 of file Occurrences.cpp.

References cs_, GeoTransform::getDefaultCS(), and gt_.

Referenced by setConfiguration(), and setCoordinateSystem().

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void OccurrencesImpl::insert ( const OccurrencePtr & oc )

Add an occurrence created outside.

Definition at line 306 of file Occurrences.cpp.

References occur_.

Referenced by appendFrom(), clone(), and createOccurrence().

bool OccurrencesImpl::isEmpty ( ) const [inline]

Test for empty.

Definition at line 198 of file Occurrences.hh.

Referenced by setEnvironment().

char const* OccurrencesImpl::label ( ) const [inline]

label of the occurrences

Definition at line 126 of file Occurrences.hh.

Referenced by getConfiguration(), and setLabel().

void OccurrencesImpl::normalize	(	Normalizer *	normalizerPtr,
		size_t	categoricalThreshold = `0`
	)

Normalize

Definition at line 215 of file Occurrences.cpp.

References end(), and occur_.

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int OccurrencesImpl::numAttributes ( ) const [inline]

Number of attributes of the thing occurred. This is the number of dependent variables, ie the variables to be modelled.

Fixme - this is currently hard-coded to 0.

Definition at line 192 of file Occurrences.hh.

int OccurrencesImpl::numOccurrences ( ) const [inline]

Number of occurrences.

Definition at line 195 of file Occurrences.hh.

Referenced by dump(), getEnvironmentMatrix(), getRandom(), and hasEnvironment().

ConstOccurrencePtr OccurrencesImpl::operator[] ( int i ) const [inline]

Vector/Random access

Definition at line 201 of file Occurrences.hh.

void OccurrencesImpl::reserve ( int estimate ) [inline]

change the reserve setting for the container

Definition at line 123 of file Occurrences.hh.

Referenced by Garp::cacheSamples().

void OccurrencesImpl::resetNormalization ( )

Reset normalization

Definition at line 236 of file Occurrences.cpp.

References end(), and occur_.

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void OccurrencesImpl::setConfiguration ( const ConstConfigurationPtr & config ) [virtual]

Implements Configurable.

Definition at line 128 of file Occurrences.cpp.

References begin(), createOccurrence(), cs_, default_abundance_, end(), GeoTransform::getDefaultCS(), initGeoTransform(), Log::instance(), label_, UNUSED, and Log::warn().

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void OccurrencesImpl::setCoordinateSystem ( const std::string & cs )

set the coordinate system

All occurrences inserted after this call are assumed to be in this coordinate system.

Definition at line 67 of file Occurrences.cpp.

References cs_, and initGeoTransform().

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void OccurrencesImpl::setEnvironment	(	const EnvironmentPtr &	env,
		const char *	type = `"Sample"`
	)

Sets environment object in each occurrence object

Definition at line 181 of file Occurrences.cpp.

References Log::instance(), isEmpty(), occur_, Sample::size(), and Log::warn().

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void OccurrencesImpl::setLabel ( const std::string & label )

set the label

Definition at line 61 of file Occurrences.cpp.

References label(), and label_.

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Friends And Related Function Documentation

friend class ReferenceCountedPointer< const OccurrencesImpl > [friend]

Definition at line 81 of file Occurrences.hh.

friend class ReferenceCountedPointer< OccurrencesImpl > [friend]

Definition at line 80 of file Occurrences.hh.

Member Data Documentation

std::string OccurrencesImpl::cs_ [private]

Definition at line 249 of file Occurrences.hh.

Referenced by clone(), initGeoTransform(), setConfiguration(), and setCoordinateSystem().

double OccurrencesImpl::default_abundance_ [private]

Definition at line 246 of file Occurrences.hh.

Referenced by setConfiguration().

GeoTransform* OccurrencesImpl::gt_ [private]

Definition at line 251 of file Occurrences.hh.

Referenced by createOccurrence(), getConfiguration(), initGeoTransform(), and ~OccurrencesImpl().

std::string OccurrencesImpl::label_ [private]

Definition at line 248 of file Occurrences.hh.

Referenced by clone(), dump(), setConfiguration(), and setLabel().

std::vector< OccurrencePtr > OccurrencesImpl::occur_ [private]

Definition at line 253 of file Occurrences.hh.

Referenced by clone(), dimension(), dump(), erase(), getConfiguration(), getEnvironmentMatrix(), getMinMax(), getRandom(), hasEnvironment(), insert(), normalize(), resetNormalization(), and setEnvironment().

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

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation