baseline subtract class More...

#include <BaselineSubtract.h>

Inheritance diagram for kome::operation::BaselineSubtract:

Collaboration diagram for kome::operation::BaselineSubtract:

Public Member Functions
	BaselineSubtract ()
	constructor

virtual	~BaselineSubtract ()
	destructor

void	setBaselineInfo (kome::plugin::PluginCall func, kome::objects::SettingParameterValues settings)
	sets baseline information More...

Public Member Functions inherited from kome::objects::XYDataOperation
	XYDataOperation ()
	constructor

virtual	~XYDataOperation ()
	destructor

void	setName (const char *name)
	sets name More...

const char *	getName ()
	gets name More...

void	setIndex (int index)
	set index More...

int	getIndex ()
	get index More...

void	update (kome::core::XYData &src, kome::core::XYData &dst, Chromatogram &chrom)
	updates xy data More...

void	update (kome::core::XYData &src, kome::core::XYData &dst, Spectrum &spec)
	updates xy data More...

void	update (kome::core::XYData &src, kome::core::XYData &dst, Sample &sample)
	updates xy data More...

Protected Member Functions
void	init ()
	initializes

void	subtractBaseline (kome::core::XYData &src, kome::core::XYData &dst, kome::core::XYData &baseline)
	subtracts baseline More...

virtual void	getUpdatedData (kome::core::XYData &src, kome::core::XYData &dst)
	gets updated data points More...

virtual void	onUpdate (kome::core::XYData &src, kome::core::XYData &dst, kome::objects::Chromatogram &chrom)
	This method is called by update method. (override method) More...

virtual void	onUpdate (kome::core::XYData &src, kome::core::XYData &dst, kome::objects::Spectrum &spec)
	This method is called by update method. (override method) More...

virtual void	onUpdate (kome::core::XYData &src, kome::core::XYData &dst, kome::objects::Sample &sample)
	This method is called by update method. (override method) More...

Protected Attributes
kome::plugin::PluginCall *	m_fun

kome::objects::SettingParameterValues	m_settings

Protected Attributes inherited from kome::objects::XYDataOperation
std::string	m_name

int	m_index

Detailed Description

baseline subtract class

Definition at line 32 of file BaselineSubtract.h.

Member Function Documentation

void kome::operation::BaselineSubtract::getUpdatedData	(	kome::core::XYData &	src,
		kome::core::XYData &	dst
	)

protectedvirtual

gets updated data points

Parameters

[in]	src	source xy data
[out]	dst	the object to store updated xy data

Definition at line 126 of file BaselineSubtract.cpp.

   {
     // check the member
     if( m_fun == NULL ) {
         LOG_WARN( FMT( "The baseline function is not assigned." ) );
         return;
     }
 
     // check the parameter
     if( src.getLength() == 0 ) {
         return;
     }
 
     // baseline points
     kome::core::DataPoints baseline;
 
     // parameters
     kome::objects::Parameters params;
 
     kome::plugin::PluginCallTool::setXYData( params, src );
     kome::plugin::PluginCallTool::setBaseline( params, baseline );
     kome::plugin::PluginCallTool::setSettingValues( params, m_settings );
 
     m_fun->invoke( &params );
 
     // subtract baseline
     subtractBaseline( src, dst, baseline );
 
 }

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void kome::operation::BaselineSubtract::onUpdate	(	kome::core::XYData &	src,
		kome::core::XYData &	dst,
		kome::objects::Chromatogram &	chrom
	)

protectedvirtual

This method is called by update method. (override method)

Parameters

[in]	src	source xy data
[out]	dst	the object to store updated xy data
[in]	chrom	chromatogram

Implements kome::objects::XYDataOperation.

Definition at line 159 of file BaselineSubtract.cpp.

   {
     getUpdatedData( src, dst );
 }

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void kome::operation::BaselineSubtract::onUpdate	(	kome::core::XYData &	src,
		kome::core::XYData &	dst,
		kome::objects::Spectrum &	spec
	)

protectedvirtual

This method is called by update method. (override method)

Parameters

[in]	src	source xy data
[out]	dst	the object to store updated xy data
[in]	spec	spectrum

Implements kome::objects::XYDataOperation.

Definition at line 168 of file BaselineSubtract.cpp.

   {
     getUpdatedData( src, dst );
 }

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void kome::operation::BaselineSubtract::onUpdate	(	kome::core::XYData &	src,
		kome::core::XYData &	dst,
		kome::objects::Sample &	sample
	)

protectedvirtual

This method is called by update method. (override method)

Parameters

[in]	src	source xy data
[out]	dst	the object to store updated xy data
[in]	sample	sample

Implements kome::objects::XYDataOperation.

Definition at line 177 of file BaselineSubtract.cpp.

   {
     getUpdatedData( src, dst );
 }

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void kome::operation::BaselineSubtract::setBaselineInfo	(	kome::plugin::PluginCall *	func,
		kome::objects::SettingParameterValues *	settings
	)

sets baseline information

Parameters

[in]	func	baseline function
[in]	settings	baseline setting parameter values

Definition at line 49 of file BaselineSubtract.cpp.

                                                                                                                 {
     // initialize
     init();
     if( func == NULL ) {
         return;
     }
 
     // set information
     m_fun = func;
     if( settings != NULL ) {
         m_settings = *settings;
     }
 
     // function item
     kome::plugin::PluginFunctionItem item;
     item.setInfo( m_fun );
 
     // set name
     std::string name = FMT( "Baseline Subtract[%s", item.getLongName() );
     std::string paramStr;
     for( unsigned int i = 0; i < m_settings.getNumberOfParameters(); i++ ) {
         // add parameter name
         if( !paramStr.empty() ) {
             paramStr.append( ", " );
         }
 
         std::string name = m_settings.getParameterName( i );
         std::string value = m_settings.getParameterValue( i );
 
         paramStr.append( FMT( "%s=%s", name.c_str(), value.c_str() ) );
     }
 
     if( paramStr.empty() ) {
         name.append( "]" );
     }
     else {
         name.append( FMT( "(%s)]", paramStr.c_str() ) );
     }
 
     setName( name.c_str() );
 }

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void kome::operation::BaselineSubtract::subtractBaseline	(	kome::core::XYData &	src,
		kome::core::XYData &	dst,
		kome::core::XYData &	baseline
	)

protected

subtracts baseline

Parameters

[in]	src	source xy data
[out]	dst	the object to store subtracted xy data
[in]	baseline	baseline data

Definition at line 92 of file BaselineSubtract.cpp.

   {
 
     // linear interporeration
     unsigned int len = src.getLength();
     double* xArray = ( len == 0 ? NULL : new double[ len ] );
     for( unsigned int i = 0; i < src.getLength(); i++ ) {
         xArray[ i ] = src.getX( i );
     }
 
     kome::core::DataPoints baseline2;
     kome::numeric::Interpolation::linear( baseline, baseline2, xArray, src.getLength() );
 
     // delete array
     if( xArray != NULL ) {
         delete[] xArray;
         xArray = NULL;
     }
 
     // subtract
     dst.reserve( len );
     for( unsigned int i = 0; i < len; i++ ) {
         double x = src.getX( i );
         double y = src.getY( i ) - baseline2.getY( i );
         y = MAX( y, 0.0 );
 
         dst.addPoint( x, y );
     }
 }