pappso::FilterPseudoCentroid Class Reference

#include <filterpseudocentroid.h>

Inheritance diagram for pappso::FilterPseudoCentroid:

Public Member Functions
	FilterPseudoCentroid (double resolution, double smoothwidth=2., double integrationWidth=4, double intensityThreshold=10., bool area=true, uint32_t maxnumberofpeaks=0)
	FilterPseudoCentroid (const FilterPseudoCentroid &other)
	~FilterPseudoCentroid ()
Trace &	filter (Trace &data_points) const override
Public Member Functions inherited from pappso::FilterInterface
virtual	~FilterInterface ()

Private Attributes
double	m_resolution
	instrument resolution More...
double	m_smoothwidth = 2.
	smoothwidth More...
double	m_integrationWidth = 4
double	m_intensityThreshold = 10.
	integration width More...
bool	m_area = true
	do you want to store are or intensity More...
uint32_t	m_maxnumberofpeaks = 0
	max number of peaks returned by picker More...

Detailed Description

Todo:

write docs

Definition at line 40 of file filterpseudocentroid.h.

Constructor & Destructor Documentation

FilterPseudoCentroid() [1/2]

FilterPseudoCentroid::FilterPseudoCentroid	(	double	resolution,
		double	smoothwidth = 2.,
		double	integrationWidth = 4,
		double	intensityThreshold = 10.,
		bool	area = true,
		uint32_t	maxnumberofpeaks = 0
	)

Default constructor

< instrument resolution

< smoothwidth

integration width

< do you want to store are or intensity

< max number of peaks returned by picker

Parameters

resolution	instrument resolution
smoothwidth	smoothwidth
intensityThreshold	integration width
area	do you want to store are or intensity
maxnumberofpeaks	max number of peaks returned by picker

Definition at line 34 of file filterpseudocentroid.cpp.

{
 
  m_resolution         = resolution;       //!< instrument resolution
  m_smoothwidth        = smoothwidth;      //!< smoothwidth
  m_integrationWidth   = integrationWidth; //! integration width
  m_intensityThreshold = intensityThreshold;
  m_area               = area; //!< do you want to store are or intensity
  m_maxnumberofpeaks =
    maxnumberofpeaks; //!< max number of peaks returned by picker
}

References m_area, m_integrationWidth, m_intensityThreshold, m_maxnumberofpeaks, m_resolution, and m_smoothwidth.

FilterPseudoCentroid() [2/2]

FilterPseudoCentroid::FilterPseudoCentroid

(

const FilterPseudoCentroid &

other

)

Copy constructor

Parameters

other

TODO

< instrument resolution

< smoothwidth

integration width

< do you want to store are or intensity

< max number of peaks returned by picker

Definition at line 51 of file filterpseudocentroid.cpp.

{
  m_resolution         = other.m_resolution;       //!< instrument resolution
  m_smoothwidth        = other.m_smoothwidth;      //!< smoothwidth
  m_integrationWidth   = other.m_integrationWidth; //! integration width
  m_intensityThreshold = other.m_intensityThreshold;
  m_area = other.m_area; //!< do you want to store are or intensity
  m_maxnumberofpeaks =
    other.m_maxnumberofpeaks; //!< max number of peaks returned by picker
}

References m_area, m_integrationWidth, m_intensityThreshold, m_maxnumberofpeaks, m_resolution, and m_smoothwidth.

~FilterPseudoCentroid()

FilterPseudoCentroid::~FilterPseudoCentroid

(

)

Destructor

Definition at line 62 of file filterpseudocentroid.cpp.

{
}

Member Function Documentation

filter()

Trace & FilterPseudoCentroid::filter ( Trace &  data_points ) const

overridevirtual

Implements pappso::FilterInterface.

Definition at line 67 of file filterpseudocentroid.cpp.

{
  /*
QTOFPeakPickerFilter(
      const pwiz::msdata::SpectrumListPtr & inner, //!< spectrum list
      double resolution, //!< instrument resolution
      double smoothwidth = 2., //!< smoothwidth
      double integrationWidth = 4, //! integration width
      double intensityThreshold = 10.,
      bool area = true, //!< do you want to store are or intensity
uint32_t maxnumberofpeaks = 0 //!< max number of peaks returned by picker
      )
      */
  qDebug();
 
  std::pair<double, double> range =
    std::make_pair(data_points.front().x, data_points.back().x);
  // construct peak picker
  qDebug() << "===========================================\n" << m_resolution << range << m_smoothwidth << m_integrationWidth << m_intensityThreshold << m_area << m_maxnumberofpeaks << "\n================================================";
  ralab::base::ms::PeakPicker<double, ralab::base::ms::SimplePeakArea> pp(
    m_resolution,
    range,
    m_smoothwidth,
    m_integrationWidth,
    m_intensityThreshold,
    m_area,
    m_maxnumberofpeaks);
 
  std::vector<double> mzs         = data_points.xValues();
  std::vector<double> intensities = data_points.yValues();
  qDebug() << data_points.xValues().size();
  qDebug() << data_points.yValues().size();
  qDebug() << data_points.xValues();
  qDebug() << data_points.yValues();
  pp(mzs.begin(), mzs.end(), intensities.begin());
  qDebug();
  data_points.clear();
  qDebug();
  auto itmz  = pp.getPeakMass().begin();
  auto itint = pp.getPeakArea().begin();
 
  qDebug() << pp.getPeakMass().size();
  while(itmz != pp.getPeakMass().end())
    {
      data_points.push_back({*itmz, *itint});
      itmz++;
      itint++;
    }
 
  qDebug();
  return data_points;
}

References ralab::base::ms::PeakPicker< TReal, TIntegrator >::getPeakArea(), ralab::base::ms::PeakPicker< TReal, TIntegrator >::getPeakMass(), m_area, m_integrationWidth, m_intensityThreshold, m_maxnumberofpeaks, m_resolution, m_smoothwidth, pappso::Trace::xValues(), and pappso::Trace::yValues().

Member Data Documentation

m_area

bool pappso::FilterPseudoCentroid::m_area = true

private

do you want to store are or intensity

Definition at line 75 of file filterpseudocentroid.h.

Referenced by FilterPseudoCentroid(), and filter().

m_integrationWidth

double pappso::FilterPseudoCentroid::m_integrationWidth = 4

private

Definition at line 73 of file filterpseudocentroid.h.

Referenced by FilterPseudoCentroid(), and filter().

m_intensityThreshold

double pappso::FilterPseudoCentroid::m_intensityThreshold = 10.

private

integration width

Definition at line 74 of file filterpseudocentroid.h.

Referenced by FilterPseudoCentroid(), and filter().

m_maxnumberofpeaks

uint32_t pappso::FilterPseudoCentroid::m_maxnumberofpeaks = 0

private

max number of peaks returned by picker

Definition at line 76 of file filterpseudocentroid.h.

Referenced by FilterPseudoCentroid(), and filter().

m_resolution

double pappso::FilterPseudoCentroid::m_resolution

private

instrument resolution

Definition at line 71 of file filterpseudocentroid.h.

Referenced by FilterPseudoCentroid(), and filter().

m_smoothwidth

double pappso::FilterPseudoCentroid::m_smoothwidth = 2.

private

smoothwidth

Definition at line 72 of file filterpseudocentroid.h.

Referenced by FilterPseudoCentroid(), and filter().

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

• pappsomspp/processing/filters/filterpseudocentroid.h
• pappsomspp/processing/filters/filterpseudocentroid.cpp