#include <map.h>

Inheritance diagram for FuzzyMap:

Collaboration diagram for FuzzyMap:

Public Member Functions
	FuzzyMap (const std::string &_layout, unsigned _width, const unsigned &_height, const unsigned &_size, const double &_lower, const double &_upper)

	FuzzyMap (const std::string &_layout, unsigned _width, const unsigned &_height, const ClassicTrainingVectors &_ts, const bool _use_rand_cvs=false)

	FuzzyMap (std::istream &_is, const unsigned _size=0, bool _cv=true)

	FuzzyMap (const FuzzyMap &other)

virtual	~FuzzyMap ()

virtual void	add (const FeatureVector &_v, const Label &_l=Label())

const std::string &	layout () const

std::vector< unsigned >	neighborhood (const SomPos &_center, double _radius) const

void	neighborhood (const SomPos &_center, double _radius, std::vector< unsigned > &_neig) const

void	localAve (const SomPos &_center, std::vector< double > &_aveVector) const

double	neighDist (const SomPos &_center, const SomPos &_v) const

unsigned	width () const

unsigned	height () const

SomIn &	itemAtPos (const SomPos &_pos)

const SomIn &	itemAtPos (const SomPos &_pos) const

Label &	targetAtPos (const SomPos &_pos)

const Label &	targetAtPos (const SomPos &_pos) const

void	clear ()

SomPos	indexToPos (const unsigned &_i) const

unsigned	PosToIndex (const SomPos &_pos) const

SomPos	codVecPos (SomIn &_v)

SomPos	applyPos (const unsigned &_in)

FuzzyMap &	operator= (const FuzzyMap &op1)

virtual void	printSelf (std::ostream &_os) const

virtual void	readSelf (std::istream &_is, const unsigned _size=0)

virtual void	saveObject (std::ostream &_os) const

virtual void	loadObject (std::istream &_is)

virtual const Layout &	getLayout () const

Public Member Functions inherited from FuzzyCodeBook
	FuzzyCodeBook (const bool &_calib=false)

	FuzzyCodeBook (unsigned _n, unsigned _size, unsigned _data, bool _cal=false)

	FuzzyCodeBook (unsigned _n, unsigned _size, unsigned _data, double _lower=0, double _upper=1, bool _cal=false)

	FuzzyCodeBook (unsigned _n, const ClassicTrainingVectors &_ts, const bool _use_rand_cvs=false)

	FuzzyCodeBook (std::istream &_is, const unsigned _size=0)

virtual	~FuzzyCodeBook ()

floatFeature &	membAt (unsigned _di, unsigned _ci)

unsigned	membClusters () const

unsigned	membVectors () const

virtual FeatureVector &	fuzzyTest (unsigned _in) const

virtual unsigned	fuzzyTestIndex (unsigned _in) const

virtual unsigned	fuzzyWinner (unsigned _in) const

virtual unsigned	fuzzyOutput (unsigned _in) const

virtual void	classify (const ClassicTrainingVectors *_ts)

virtual TS	alphaCore (TS _ts, double _alpha, unsigned _cluster) const

virtual void	writeMembership (std::ostream &_os) const

virtual void	readMembership (std::istream &_is)

Public Member Functions inherited from CodeBook
	CodeBook (const bool &_calib=false)

	CodeBook (unsigned _n, unsigned _size, bool _cal=false)

	CodeBook (unsigned _n, unsigned _size, floatFeature _lower=0, floatFeature _upper=1, bool _cal=false)

	CodeBook (unsigned _n, const ClassicTrainingVectors &_ts, const bool _use_rand_cvs)

	CodeBook (std::istream &_is)

virtual	~CodeBook ()

virtual FeatureVector &	test (const FeatureVector &_in) const

virtual unsigned	testIndex (const FeatureVector &_in) const

virtual const std::vector< unsigned > &	classifAt (const unsigned &_index) const

virtual unsigned	classifSizeAt (const unsigned &_index) const

virtual Label	apply (const FeatureVector &_in) const

virtual void	calibrate (ClassicTrainingVectors &_ts, Label _def="")

virtual unsigned	output (const FeatureVector &_in) const

virtual void	readSelf (std::istream &_is, long _dim=-1, long _size=-1)

virtual void	Normalize (const std::vector< ClassicTrainingVectors::statsStruct > &_varStats)

virtual void	unNormalize (const std::vector< ClassicTrainingVectors::statsStruct > &_varStats)

virtual void	printHistogram (std::ostream &_os) const

virtual void	printQuantError (std::ostream &_os) const

Public Member Functions inherited from ClassificationDataSet< FeatureVector, Label >
	ClassificationDataSet ()

virtual	~ClassificationDataSet ()

Public Member Functions inherited from ClassificationTrainingSet< FeatureVector, Label >
	ClassificationTrainingSet (const bool &_calib=true, unsigned _n=0)

	ClassificationTrainingSet (std::istream &_is)

virtual	~ClassificationTrainingSet ()

void	setSplit (float _tp, float _vp)

splitIt	beginSubset (unsigned _um)

splitIt	endSubset (unsigned _um)
	Returns an iterator to the end of the subset. More...

virtual void	add (const FeatureVector &_i)

virtual bool	remove (unsigned int _idx)

size_t	size () const

const Label &	targetAt (unsigned _i) const

Label &	targetAt (unsigned _i)

const FeatureVector &	itemAt (unsigned _i) const

FeatureVector &	itemAt (unsigned _i)

bool	calibrated () const

void	calibrated (const bool &_calib)

void	clear ()

virtual void	readSelf (std::istream &_is)

unsigned	numTargets () const

virtual bool	swapItems (unsigned _i, unsigned _j)

Protected Attributes
const Layout *	somLayout

unsigned	somWidth

unsigned	somHeight

Protected Attributes inherited from ClassificationTrainingSet< FeatureVector, Label >
bool	isCalibrated

splitTS	splitTrainingSet

unsigned	nTargets

Friends
std::ostream &	operator<< (std::ostream &_os, const FuzzyMap &_fsom)

std::istream &	operator>> (std::istream &_is, FuzzyMap &_fsom)

Additional Inherited Members
Public Types inherited from FuzzyCodeBook
typedef std::vector< std::vector< floatFeature > >	MM

typedef ClassicTrainingVectors	TS
	Alias for Membership Matrix. More...

typedef ClassificationTrainingSet< std::vector< floatFeature >, floatFeature >	FV
	Alias for a Training set. More...

Public Types inherited from ClassificationDataSet< FeatureVector, Label >
typedef FeatureVector	In
	Class of input vectors. Usually a FeatureVector (vector of Feature) More...

typedef Label	Out
	Class of the target. Can be a double, string, unsigned, even a vector ... More...

typedef ClassificationTrainingSet< In, Out >	TS
	Training set. Set of vectors (training vectors), probably classified. More...

Public Types inherited from ClassificationTrainingSet< FeatureVector, Label >
enum	splitMode
	Ways the training set can be used. More...

enum	useMode
	use of samples More...

typedef std::multimap< unsigned, unsigned, std::less< unsigned > >	splitTS
	Training sets mode. More...

typedef splitTS::iterator	splitIt
	iterator More...

Public Attributes inherited from FuzzyCodeBook
MM	memb
	Alias for Fuzzy vectors. More...

Public Attributes inherited from CodeBook
std::vector< std::vector< unsigned > >	classifVectors

std::vector< double >	aveDistances

Public Attributes inherited from ClassificationTrainingSet< FeatureVector, Label >
std::vector< FeatureVector >	theItems

std::vector< Label >	theTargets

Protected Member Functions inherited from CodeBook
void	readClassifVectors (std::istream &_is)

void	writeClassifVectors (std::ostream &_os) const

Protected Member Functions inherited from ClassificationTrainingSet< FeatureVector, Label >
void	computeNumTargets ()

void	checkCalibrated (std::istream &_is)

void	readItems (std::istream &_is)

void	writeCalibrated (std::ostream &_os) const

void	writeItems (std::ostream &_os, bool _delim=false) const

void	skipComments (std::istream &_is) const

std::vector< FeatureVector >::const_iterator	itemsBegin () const

std::vector< FeatureVector >::const_iterator	itemsEnd () const

std::vector< Label >::const_iterator	targetsBegin () const

std::vector< Label >::const_iterator	targetsEnd () const

Detailed Description

This class implements a Fuzzy Map of the type used by Fuzzy mapping Algorithms

Definition at line 308 of file map.h.

Constructor & Destructor Documentation

◆ FuzzyMap() [1/4]

FuzzyMap::FuzzyMap	(	const std::string &	_layout,
		unsigned	_width,
		const unsigned &	_height,
		const unsigned &	_size,
		const double &	_lower,
		const double &	_upper
	)

Constructs a Fuzzy SOM with random initial code vectors Parameter: _layout Type of layout Parameter: _width Width of the output plane Parameter: _height Height of the output plane Parameter: _size Size of code vectors Parameter: _lower Lower value for random elements Parameter: _upper Upper value for random elements

Definition at line 785 of file map.cpp.

         : FuzzyCodeBook(_width*_height, _size, 0, _lower, _upper, false), somWidth(_width), somHeight(_height)
 {
     if (_layout == "HEXA")
     {
         auto *tmpLayout = new HEXALayout();
         somLayout = tmpLayout;
     }
     else
     {
         auto *tmpLayout = new RECTLayout();
         somLayout = tmpLayout;
     }
 }

◆ FuzzyMap() [2/4]

FuzzyMap::FuzzyMap	(	const std::string &	_layout,
		unsigned	_width,
		const unsigned &	_height,
		const ClassicTrainingVectors &	_ts,
		const bool	_use_rand_cvs = `false`
	)

Constructs a Fuzzy SOM with initial code vectors taken randomly from the training file. Parameter: _layout Type of layout Parameter: _width Width of the output plane Parameter: _height Height of the output plane Parameter: _ts Training set; will be used to get initial values Parameter: _use_rand_cvs Use random code vector pixel values

Definition at line 815 of file map.cpp.

         : FuzzyCodeBook(_width*_height, _ts, _use_rand_cvs),
         somWidth(_width), somHeight(_height)
 {
     if (_layout == "HEXA")
     {
         auto *tmpLayout = new HEXALayout();
         somLayout = tmpLayout;
     }
     else
     {
         auto *tmpLayout = new RECTLayout();
         somLayout = tmpLayout;
     }
 }

◆ FuzzyMap() [3/4]

FuzzyMap::FuzzyMap	(	std::istream &	_is,
		const unsigned	_size = `0`,
		bool	_cv = `true`
	)

Construct a Fuzzy SOM from the code vectors in a stream Parameter: _is The stream Parameter: _size Size of code vectors (number of data points) Parameter: _cv If the stream holds a codevector file or a whole codebook file

Exceptions

runtime_error If there are problems with the stream

Construct a SOM from the code vectors in a stream Parameter: _is The stream Parameter: _size Size of code vectors (number of data points)

Exceptions

runtime_error If there are problems with the stream

Definition at line 839 of file map.cpp.

                                                                   : FuzzyCodeBook(false)
 {
     somLayout = NULL;
     if (_cv)
         readSelf(_is, _size);
     else
         loadObject(_is);
 }

◆ FuzzyMap() [4/4]

FuzzyMap::FuzzyMap ( const FuzzyMap & other )

explicit

Definition at line 848 of file map.cpp.

                                         : FuzzyCodeBook(false){
     *this=other;
 }

◆ ~FuzzyMap()

virtual FuzzyMap::~FuzzyMap ( )

inlinevirtual

Virtual destructor is needed

Definition at line 356 of file map.h.

357 {};

Member Function Documentation

◆ add()

void FuzzyMap::add	(	const FeatureVector &	_v,
		const Label &	_l = `Label()`
	)

virtual

This method throws an exception if called. There is no sense in adding vectors to a som

Exceptions

range_error If this method is called

Reimplemented from ClassificationTrainingSet< FeatureVector, Label >.

Definition at line 857 of file map.cpp.

 {
     throw std::runtime_error("You can't add vectors to a S.O.M.");
 }

◆ applyPos()

SomPos FuzzyMap::applyPos ( const unsigned & _in )

Returns the position of the code vector that represents the input in the som Parameter: _in Sample to classify (index to the sample)

Definition at line 1079 of file map.cpp.

 {
     return codVecPos(fuzzyTest(_in));
 }

◆ clear()

void FuzzyMap::clear ( )

Clears the Fuzzy Som

Clears the Som

Definition at line 1019 of file map.cpp.

 {
     FuzzyCodeBook::clear();
     if (somLayout)
         delete somLayout;
     somWidth = 0;
     somHeight = 0;
 }

◆ codVecPos()

SomPos FuzzyMap::codVecPos ( SomIn & _v )

Returns the position in the som of a code vector Parameter: _v Reference to the code vector

Definition at line 1069 of file map.cpp.

 {
     return indexToPos(&_v - &(itemAt(0)));
 }

◆ getLayout()

virtual const Layout& FuzzyMap::getLayout ( ) const

inlinevirtual

Const Reference to the Map Layout

Definition at line 539 of file map.h.

     {
         return (Layout&) *somLayout;
     };

◆ height()

unsigned FuzzyMap::height ( ) const

Returns the height of the SOM

Definition at line 924 of file map.cpp.

 {
     return somHeight;
 }

◆ indexToPos()

SomPos FuzzyMap::indexToPos ( const unsigned & _i ) const

Return the position associated to an index Parameter: _i Index of the code vector

Exceptions

out_of _range If _i is out of range

Definition at line 1033 of file map.cpp.

 {
     if (_i >= somWidth * somHeight)
     {
         std::ostringstream msg;
         msg << "Out of range. No item at position " << _i;
 
         throw std::out_of_range(msg.str());
     }
 
     return SomPos(_i % somWidth, _i / somWidth);
 }

◆ itemAtPos() [1/2]

SomIn & FuzzyMap::itemAtPos ( const SomPos & _pos )

Returns a code vector given its position Parameter: _pos The position of the code vector

Exceptions

out_of _range If _pos is out of range

Definition at line 934 of file map.cpp.

 {
     if (_pos.first >= (signed)somWidth || _pos.second >= (signed)somHeight)
     {
         std::ostringstream msg;
         msg << "Out of range. No item at position (" << _pos.first << ", " << _pos.second << ")";
         throw std::out_of_range(msg.str());
     }
 
     return itemAt((somWidth * _pos.second) + _pos.first);
 }

◆ itemAtPos() [2/2]

const SomIn & FuzzyMap::itemAtPos ( const SomPos & _pos ) const

Returns a const reference to a code vector given its position Parameter: _pos The position of the code vector

Exceptions

out_of _range If _pos is out of range

Definition at line 952 of file map.cpp.

 {
     if (_pos.first >= (signed)somWidth || _pos.second >= (signed)somHeight)
     {
         std::ostringstream msg;
         msg << "Out of range. No item at position (" << _pos.first << ", " << _pos.second << ")";
         throw std::out_of_range(msg.str());
     }
 
     return itemAt((somWidth * _pos.second) + _pos.first);
 }

◆ layout()

const std::string & FuzzyMap::layout ( ) const

Returns the id of layout that som has

Definition at line 865 of file map.cpp.

 {
     return somLayout->id();
 }

◆ loadObject()

void FuzzyMap::loadObject ( std::istream & _is )

virtual

Loads the FuzzyMap class from a stream. this method can be used to load the status of the class. Parameter: _is The output stream

Reimplemented from FuzzyCodeBook.

Definition at line 1164 of file map.cpp.

 {
     clear();
     std::string layout;
     _is >> layout;
     if (layout == "HEXA")
     {
         auto *tmpLayout = new HEXALayout();
         somLayout = tmpLayout;
     }
     else
     {
         auto *tmpLayout = new RECTLayout();
         somLayout = tmpLayout;
     }
     _is >> somWidth;
     _is >> somHeight;
     readClassifVectors(_is);
     readMembership(_is);
     ClassificationTrainingSet<FeatureVector, Label>::loadObject(_is);
 }

◆ localAve()

void FuzzyMap::localAve	(	const SomPos &	_center,
		std::vector< double > &	_aveVector
	)		const

Returns the local average of a neuron in a non-const reference. (average of the sourounding vectors) Parameter: _center Reference to the center of neighborhood Parameter: _aveVector: returns the average vector

Definition at line 896 of file map.cpp.

 {
     somLayout->localAve(this, _center, _aveVector);
 }

◆ neighborhood() [1/2]

std::vector< unsigned > FuzzyMap::neighborhood	(	const SomPos &	_center,
		double	_radius
	)		const

Returns the neighborhood of a neuron Parameter: _center Reference to the center of neighborhood Parameter: _radius Radius of neighbohood

Definition at line 875 of file map.cpp.

 {
     return somLayout->neighborhood(this, _center, _radius);
 }

◆ neighborhood() [2/2]

void FuzzyMap::neighborhood	(	const SomPos &	_center,
		double	_radius,
		std::vector< unsigned > &	_neig
	)		const

Returns the neighborhood of a neuron in a non-const reference. Parameter: _center Reference to the center of neighborhood Parameter: _radius Radius of neighbohood

Definition at line 885 of file map.cpp.

 {
     _neig = somLayout->neighborhood(this, _center, _radius);
 }

◆ neighDist()

double FuzzyMap::neighDist	(	const SomPos &	_center,
		const SomPos &	_v
	)		const

Returns the distance between two neurons according to the Layout Parameter: _center Reference to the center of neighborhood Parameter: _v Position of the code vector

Definition at line 907 of file map.cpp.

 {
     return somLayout->dist(_center, _v);
 }

◆ operator=()

FuzzyMap & FuzzyMap::operator= ( const FuzzyMap & op1 )

Operator "=" Parameter: op1 FuzzyMap

Definition at line 1089 of file map.cpp.

 {
     std::stringstream _str;
     op1.printSelf(_str);
     readSelf(_str);
     return *this;
 }

◆ PosToIndex()

unsigned FuzzyMap::PosToIndex ( const SomPos & _pos ) const

Return the index associated to a position Parameter: _pos Position of the code vector

Exceptions

out_of _range If _i is out of range

Definition at line 1052 of file map.cpp.

 {
     if (_pos.first >= (signed)somWidth || _pos.second >= (signed)somHeight)
     {
         std::ostringstream msg;
         msg << "Out of range. No item at position (" << _pos.first << ", " << _pos.second << ")";
         throw std::out_of_range(msg.str());
     }
 
     return (unsigned)((somWidth * _pos.second) + _pos.first);
 }

◆ printSelf()

void FuzzyMap::printSelf ( std::ostream & _os ) const

virtual

Standard output for a fuzzy map Parameter: _os The output stream

Standard output for a Fuzzy SOM Parameter: _os The output stream

Reimplemented from CodeBook.

Definition at line 1101 of file map.cpp.

 {
     _os << itemAt(0).size() << " " <<
     somLayout->id() << " " << somWidth << " " << somHeight << " gaussian" << std::endl;
     writeItems(_os);
 }

◆ readSelf()

void FuzzyMap::readSelf	(	std::istream &	_is,
		const unsigned	_size = `0`
	)

virtual

Standard input for a fuzzy map Parameter: _size Size of code vectors (number of data points) Parameter: _is The input stream

Standard input for a Fuzzy SOM Parameter: _is The input stream

Reimplemented from FuzzyCodeBook.

Definition at line 1113 of file map.cpp.

 {
     clear();
     int dim;
     std::string layout;
     std::string str;
     _is >> dim;
     _is >> layout;
     if (layout == "HEXA")
     {
         auto *tmpLayout = new HEXALayout();
         somLayout = tmpLayout;
     }
     else
     {
         auto *tmpLayout = new RECTLayout();
         somLayout = tmpLayout;
     }
     _is >> somWidth;
     _is >> somHeight;
     str = integerToString(dim);
     str += " ";
     str += integerToString(somWidth * somHeight);
     str += " ";
     for (int i = str.size() - 1; i >= 0; i--)
         if (_is)
             _is.putback((char) str[i]);
     FuzzyCodeBook::readSelf(_is, _size);
 
 }

◆ saveObject()

void FuzzyMap::saveObject ( std::ostream & _os ) const

virtual

Saves the FuzzyMap class into a stream. this method can be used to save the status of the class. Parameter: _os The output stream

Reimplemented from FuzzyCodeBook.

Definition at line 1150 of file map.cpp.

 {
     _os << somLayout->id() << " " << somWidth << " " << somHeight << std::endl;
     writeClassifVectors(_os);
     writeMembership(_os);
     ClassificationTrainingSet<FeatureVector, Label>::saveObject(_os);
 }

◆ targetAtPos() [1/2]

Label & FuzzyMap::targetAtPos ( const SomPos & _pos )

Returns the target of a code vector given its position Parameter: _pos The position of the code vector

Definition at line 969 of file map.cpp.

 {
     if (!calibrated())
     {
         std::ostringstream msg;
         msg << "The S.O.M. is not calibrated. No target at position ("
         << _pos.first << ", " << _pos.second << ")";
         throw std::out_of_range(msg.str());
     }
     if (_pos.first >= (signed)somWidth || _pos.second >= (signed)somHeight)
     {
         std::ostringstream msg;
         msg << "Out of range. No target at position (" << _pos.first << ", "
         << _pos.second << ")";
         throw std::out_of_range(msg.str());
     }
 
     return targetAt((somWidth * _pos.second) + _pos.first);
 }

◆ targetAtPos() [2/2]

const Label & FuzzyMap::targetAtPos ( const SomPos & _pos ) const

Returns a const target of a code vector given its position Parameter: _pos The position of the code vector

Definition at line 994 of file map.cpp.

 {
     if (!calibrated())
     {
         std::ostringstream msg;
         msg << "The S.O.M. is not calibrated. No target at position ("
         << _pos.first << ", " << _pos.second << ")";
         throw std::out_of_range(msg.str());
     }
     if (_pos.first >= (signed)somWidth || _pos.second >= (signed)somHeight)
     {
         std::ostringstream msg;
         msg << "Out of range. No target at position (" << _pos.first << ", "
         << _pos.second << ")";
         throw std::out_of_range(msg.str());
     }
 
     return targetAt((somWidth * _pos.second) + _pos.first);
 }

◆ width()

unsigned FuzzyMap::width ( ) const

Returns the width of the SOM

Definition at line 916 of file map.cpp.

 {
     return somWidth;
 }

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	_os,
		const FuzzyMap &	_fsom
	)

friend

Definition at line 479 of file map.h.

     {
         _fsom.printSelf(_os);
         return _os;
     };

◆ operator>>

std::istream& operator>>	(	std::istream &	_is,
		FuzzyMap &	_fsom
	)

friend

Definition at line 491 of file map.h.

     {
         _fsom.readSelf(_is);
         return _is;
     };

Member Data Documentation

◆ somHeight

unsigned FuzzyMap::somHeight

protected

Definition at line 549 of file map.h.

◆ somLayout

const Layout* FuzzyMap::somLayout

protected

Definition at line 542 of file map.h.

◆ somWidth

unsigned FuzzyMap::somWidth

protected

Definition at line 548 of file map.h.

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

xmipp/libraries/classification/map.h
xmipp/libraries/classification/map.cpp

Public Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FuzzyMap() [1/4]

◆ FuzzyMap() [2/4]

◆ FuzzyMap() [3/4]

◆ FuzzyMap() [4/4]

◆ ~FuzzyMap()

Member Function Documentation

◆ add()

◆ applyPos()

◆ clear()

◆ codVecPos()

◆ getLayout()

◆ height()

◆ indexToPos()

◆ itemAtPos() [1/2]

◆ itemAtPos() [2/2]

◆ layout()

◆ loadObject()

◆ localAve()

◆ neighborhood() [1/2]

◆ neighborhood() [2/2]

◆ neighDist()

◆ operator=()

◆ PosToIndex()

◆ printSelf()

◆ readSelf()

◆ saveObject()

◆ targetAtPos() [1/2]

◆ targetAtPos() [2/2]

◆ width()

Friends And Related Function Documentation

◆ operator<<

◆ operator>>

Member Data Documentation

◆ somHeight

◆ somLayout

◆ somWidth