kome::objects::PeakElement Class Reference

peak element More...

#include <PeakElement.h>

Collaboration diagram for kome::objects::PeakElement:

Public Member Functions
	PeakElement ()
	constructor
	PeakElement (Peaks *peaks)
	constructor
	PeakElement (Peaks *peaks, const double x, const double y)
	constructor More...
virtual	~PeakElement ()
	destructor
void	setX (const double x)
	sets x element value More...
double	getX ()
	gets x element value More...
void	setY (const double y)
	sets y element value More...
double	getY ()
	gets y element value More...
void	setLeft (const double x, const double y)
	sets peak left More...
double	getLeftX ()
	gets x element of peak left More...
double	getLeftY ()
	gets y element of peak left More...
void	setRight (const double x, const double y)
	sets peak right More...
double	getRightX ()
	gets x element of peak right More...
double	getRightY ()
	gets y elemtn of peak right More...
void	setApex (const double x, const double y)
	sets peak apex More...
double	getApexX ()
	gets x element of peak apex More...
double	getApexY ()
	gets y element of peak apex More...
void	searchApex (kome::core::XYData &xyData)
	searches apex More...
bool	hasApex ()
	judges whether this peak has apex information or not. More...
void	setArea (const double area)
	sets area More...
double	getArea ()
	gets peak area More...
bool	hasArea ()
	judges whether this peak has area value or not More...
double	calcArea (kome::core::XYData &xyData)
	calculates area More...
void	setFwhm (const double fwhm)
	sets the FWHM More...
double	getFwhm ()
	gets the FWHM More...
bool	hasFwhm ()
	judges whether this peak has FWHM value of not More...
double	calcFwhm (kome::core::XYData &xyData)
	calculates FWHM More...
void	setId (int id)
	sets peak ID More...
int	getId ()
	gets peak ID
void	setCharge (const int charge)
	sets the charge state More...
int	getCharge ()
	gets the charge state More...

Protected Attributes
Peaks *	m_peaks
double	m_x
double	m_y
kome::core::Point< double >	m_left
kome::core::Point< double >	m_right
kome::core::Point< double >	m_apex
int	m_charge
double	m_area
double	m_fwhm
int	m_peakId

Detailed Description

peak element

Definition at line 28 of file PeakElement.h.

Constructor & Destructor Documentation

kome::objects::PeakElement::PeakElement	(	Peaks *	peaks,
		const double	x,
		const double	y
	)

constructor

Parameters

[in]	peaks	peaks object
[in]	x	x element value
[in]	y	y element value

Definition at line 67 of file PeakElement.cpp.

        : m_x( x ), m_y( y ), m_left( x, 0.0 ), m_right( x, 0.0 ), m_apex( x, y )
{
    m_peaks = peaks;

    m_area = - FLT_MAX;
    m_fwhm = - FLT_MAX;

    m_charge = -1;

    // issue peak id
    if( m_peaks != NULL ){
        m_peakId = m_peaks->issueId( this );
    }
}

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Member Function Documentation

double kome::objects::PeakElement::calcArea

(

kome::core::XYData &

xyData

)

calculates area

Parameters

[in]

xyData

data points

Returns

area

Definition at line 255 of file PeakElement.cpp.

                                                     {
    // calculate area
    double s = 0.0;

    // base line
    const double lx = getLeftX();
    const double ly = getLeftY();
    const double rx = getRightX();
    const double ry = getRightY();

    const double w = rx - lx;
    if( w < 0.0000001 ) {
        return s;
    }

    const double a = ( ry - ly ) / w;

    // index
    int idx0 = xyData.getNearestIndex( lx );
    int idx1 = xyData.getNearestIndex( rx );

    for( int i = idx0; i < idx1 - 1; i++ ) {
        // coordinates
        const double x0 = xyData.getX( i );
        const double x1 = xyData.getX( i + 1 );
        const double y0 = xyData.getY( i ) - ( a * ( x0 - lx ) + ly );
        const double y1 = xyData.getY( i + 1 ) - ( a * ( x1 - lx ) + ly );

        if( y0 >= 0.0 && y1 >= 0.0 ) {
            s += ( y0 + y1 ) * ( x1 - x0 ) / 2.0;   // @date 2011/02/23 <Comment> OKADA : ��`�̖ʐρF�i���(y0)�{����(y1)�j�~����(x1-x0)���Q
        }
        // baseline�̏㑤�̖ʐς̂݋��߂�
        else if( y0 > 0.0 ) {   // @date 2011/02/23 <Comment> OKADA : (y1<0.0)�̏ꍇ�A
            s += - y0 * y0 * ( x1 - x0 ) / ( y1 - y0 ) / 2.0;   // �O�p�`�̍����Fy0 * ( x1 - x0 ) / ( y1 - y0 )
        }
        else if( y1 > 0.0 ) {   // @date 2011/02/23 <Comment> OKADA : (y0<0.0)�̏ꍇ
            s += y1 * y1 * ( x1 - x0 ) / ( y1 - y0 ) / 2.0;
        }
    }

    // apex
    searchApex( xyData );

    return s;
}

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double kome::objects::PeakElement::calcFwhm

(

kome::core::XYData &

xyData

)

calculates FWHM

Parameters

[in]

xyData

data points

Returns

FWHM

Definition at line 321 of file PeakElement.cpp.

                                                     {
    // return value
    double fwhm = -1.0;

    // apex
    if( m_apex.px < 0.0 ) {
        searchApex( xyData );
    }

    const double ax = m_apex.px;
    const double ay = m_apex.py;
    if( ax < 0.0 ) {
        return fwhm;
    }
    const double height = ay / 2.0;

    int idx = xyData.getNearestIndex( ax );
    if( idx < 0 || ax >= (double)xyData.getLength() ) {
        return fwhm;
    }

    // left
    double lx = -1.0;
    double prevX = ax;
    double prevY = ay;
    for( int i = idx - 1; i >= 0 && lx < 0.0; i-- ) {
        const double x = xyData.getX( i );
        const double y = xyData.getY( i );

        if( prevY >= height && y <= height ) {
            if( fabs( y - prevY ) < 0.00001 ) {
                lx = prevX;
            }
            else {
                lx = ( prevX * ( y - height ) + x * ( height - prevY ) ) / ( y - prevY );
            }
        }
        else if( y > ay ) {
            i = -1;
        }

        prevX = x;
        prevY = y;
    }

    if( lx < 0.0 ) {
        return fwhm;
    }

    // right
    double rx = -1.0;
    prevX = ax;
    prevY = ay;
    for( int i = idx + 1; i < (int)xyData.getLength() && rx < 0.0; i++ ) {
        const double x = xyData.getX( i );
        const double y = xyData.getY( i );

        if( prevY >= height && y <= height ) {
            if( fabs( y - prevY ) < 0.00001 ) {
                rx = prevX;
            }
            else {
                rx = ( prevX * ( y - height ) + x * ( height - prevY ) ) / ( y - prevY );
            }
        }
        else if( y > ay ) {
            i = (int)xyData.getLength();
        }

        prevX = x;
        prevY = y;
    }

    if( rx < 0.0 ) {
        return fwhm;
    }

    fwhm = fabs( rx - lx );

    return fwhm;
}

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double kome::objects::PeakElement::getApexX

(

)

gets x element of peak apex

Returns

x element of peak apex

Definition at line 173 of file PeakElement.cpp.

                             {
    if( m_apex.px < 0.0 ) {
        m_peaks->calcArea();
    }
    return m_apex.px;
}

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double kome::objects::PeakElement::getApexY

(

)

gets y element of peak apex

Returns

y element of peak apex

Definition at line 181 of file PeakElement.cpp.

                             {
    if( m_apex.px < 0.0 ) {
        m_peaks->calcArea();
    }
    return m_apex.py;
}

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double kome::objects::PeakElement::getArea

(

)

gets peak area

Returns

peak area

Definition at line 241 of file PeakElement.cpp.

                            {
    if( !hasArea() && m_peaks != NULL ) {
        m_peaks->calcArea();
    }

    return m_area;
}

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int kome::objects::PeakElement::getCharge

(

)

gets the charge state

Returns

charge state

Definition at line 419 of file PeakElement.cpp.

                           {
    return m_charge;
}

double kome::objects::PeakElement::getFwhm

(

)

gets the FWHM

Returns

FWHM

Definition at line 307 of file PeakElement.cpp.

                            {
    if( !hasFwhm() && m_peaks != NULL ) {
        m_peaks->calcArea();
    }

    return m_fwhm;
}

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double kome::objects::PeakElement::getLeftX

(

)

gets x element of peak left

Returns

x element of peak left

Definition at line 134 of file PeakElement.cpp.

                             {
    return m_left.px;
}

double kome::objects::PeakElement::getLeftY

(

)

gets y element of peak left

Returns

y element of peak left

Definition at line 139 of file PeakElement.cpp.

                             {
    return m_left.py;
}

double kome::objects::PeakElement::getRightX

(

)

gets x element of peak right

Returns

x element of peak right

Definition at line 157 of file PeakElement.cpp.

                              {
    return m_right.px;
}

double kome::objects::PeakElement::getRightY

(

)

gets y elemtn of peak right

Returns

y elemtn of peak right

Definition at line 162 of file PeakElement.cpp.

                              {
    return m_right.py;
}

double kome::objects::PeakElement::getX

(

)

gets x element value

Returns

x element

Definition at line 100 of file PeakElement.cpp.

                         {
    return m_x;
}

double kome::objects::PeakElement::getY

(

)

gets y element value

Returns

y element

Definition at line 117 of file PeakElement.cpp.

                         {
    return m_y;
}

bool kome::objects::PeakElement::hasApex

(

)

judges whether this peak has apex information or not.

Returns

If true, this peak has apex information

Definition at line 231 of file PeakElement.cpp.

                          {
    return ( m_apex.px >= 0.0 );
}

bool kome::objects::PeakElement::hasArea

(

)

judges whether this peak has area value or not

Returns

If true, this peak has area value

Definition at line 250 of file PeakElement.cpp.

                          {
    return ( m_area > -1000.0 );
}

bool kome::objects::PeakElement::hasFwhm

(

)

judges whether this peak has FWHM value of not

Returns

If true, this peak has FWHM value

Definition at line 316 of file PeakElement.cpp.

                          {
    return ( m_fwhm > -1000.0 );
}

void kome::objects::PeakElement::searchApex

(

kome::core::XYData &

xyData

)

searches apex

Parameters

[in]

xyData

data points

Definition at line 189 of file PeakElement.cpp.

                                                     {
    // left X
    const double lx = getLeftX();
    const double rx = getRightX();

    // index
    int idx0 = xyData.searchIndex( lx );
    if( idx0 < 0 ) {
        idx0 = - idx0 - 2;
        if( idx0 < 0 ) {
            idx0 = 0;
        }
    }
    int idx1 = xyData.searchIndex( rx );
    if( idx1 < 0 ) {
        idx1 = - idx1 - 1;
        if( idx1 >= (int)xyData.getLength() ) {
            idx1 = (int)xyData.getLength() - 1;
        }
    }

    // apex
    double apexY = 0.0;
    double apexX = -1.0;
    for( int i = idx0; i <= idx1; i++ ) {
        const double x = xyData.getX( i );
        const double y = xyData.getY( i );

        if( y > apexY || apexX < 0.0 ) {
            apexX = x;
            apexY = y;
        }
    }

    // set
    if( apexX >= 0.0 ) {
        m_apex.px = apexX;
        m_apex.py = apexY;
    }
}

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void kome::objects::PeakElement::setApex	(	const double	x,
		const double	y
	)

sets peak apex

Parameters

[in]	x	x element of peak apex
[in]	y	y element of peak apex

Definition at line 167 of file PeakElement.cpp.

                                                          {
    m_apex.px = x;
    m_apex.py = y;
}

void kome::objects::PeakElement::setArea

(

const double

area

)

sets area

Parameters

[in]

area

area

Definition at line 236 of file PeakElement.cpp.

                                             {
    m_area = area;
}

void kome::objects::PeakElement::setCharge

(

const int

charge

)

sets the charge state

Parameters

[in]

charge

charge state

Definition at line 414 of file PeakElement.cpp.

                                              {
    m_charge = charge;
}

void kome::objects::PeakElement::setFwhm

(

const double

fwhm

)

sets the FWHM

Parameters

[in]

fwhm

FWHM

Definition at line 302 of file PeakElement.cpp.

                                             {
    m_fwhm = fwhm;
}

void kome::objects::PeakElement::setId

(

int

id

)

sets peak ID

Parameters

[in]

id

peak ID

Definition at line 404 of file PeakElement.cpp.

                               {
    m_peakId = id;
}

void kome::objects::PeakElement::setLeft	(	const double	x,
		const double	y
	)

sets peak left

Parameters

[in]	x	x element of peak left
[in]	y	y element of peak left

Definition at line 122 of file PeakElement.cpp.

                                                          {
    if( m_left.px != x || m_left.py != y ) {
        m_left.px = x;
        m_left.py = y;

        m_area = - FLT_MAX;
        m_apex.px = -1.0;
        m_apex.py = -1.0;
    }
}

void kome::objects::PeakElement::setRight	(	const double	x,
		const double	y
	)

sets peak right

Parameters

[in]	x	x element of peak right
[in]	y	y element of peak right

Definition at line 144 of file PeakElement.cpp.

                                                           {
    if( m_right.px != x || m_right.py != y ) {
        // set 
        m_right.px = x;
        m_right.py = y;

        m_area = - FLT_MAX;
        m_apex.px = -1.0;
        m_apex.py = -1.0;
    }
}

void kome::objects::PeakElement::setX

(

const double

x

)

sets x element value

Parameters

[in]

x

x element

Definition at line 88 of file PeakElement.cpp.

                                       {
    m_x = x;

    if( m_left.px < 0.0 ) {
        m_left.px = x;
    }
    if( m_right.px < 0.0 ) {
        m_right.px = x;
    }
}

void kome::objects::PeakElement::setY

(

const double

y

)

sets y element value

Parameters

[in]

y

y element

Definition at line 105 of file PeakElement.cpp.

                                       {
    m_y = y;

    if( m_left.py < 0.0 ) {
        m_left.py = 0.0;
    }
    if( m_right.py < 0.0 ) {
        m_right.py = 0.0;
    }
}

Member Data Documentation

kome::core::Point< double > kome::objects::PeakElement::m_apex

protected

apex

Definition at line 74 of file PeakElement.h.

double kome::objects::PeakElement::m_area

protected

peak area

Definition at line 81 of file PeakElement.h.

int kome::objects::PeakElement::m_charge

protected

charge

Definition at line 77 of file PeakElement.h.

double kome::objects::PeakElement::m_fwhm

protected

FWHM

Definition at line 84 of file PeakElement.h.

kome::core::Point< double > kome::objects::PeakElement::m_left

protected

peak left

Definition at line 68 of file PeakElement.h.

int kome::objects::PeakElement::m_peakId

protected

peak ID

Definition at line 87 of file PeakElement.h.

Peaks* kome::objects::PeakElement::m_peaks

protected

peaks

Definition at line 59 of file PeakElement.h.

kome::core::Point< double > kome::objects::PeakElement::m_right

protected

peak right

Definition at line 71 of file PeakElement.h.

double kome::objects::PeakElement::m_x

protected

x element value

Definition at line 62 of file PeakElement.h.

double kome::objects::PeakElement::m_y

protected

y element value

Definition at line 65 of file PeakElement.h.

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

• DataObjects/PeakElement.h
• DataObjects/PeakElement.cpp