libpappsomspp
Library for mass spectrometry
pappso::FilterPseudoCentroid Class Reference

#include <filterpseudocentroid.h>

Inheritance diagram for pappso::FilterPseudoCentroid:
pappso::FilterInterface

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 ()
 
Tracefilter (Trace &data_points) const override
 

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
resolutioninstrument resolution
smoothwidthsmoothwidth
intensityThresholdintegration width
areado you want to store are or intensity
maxnumberofpeaksmax number of peaks returned by picker

Definition at line 34 of file filterpseudocentroid.cpp.

40 {
41 
42  m_resolution = resolution; //!< instrument resolution
43  m_smoothwidth = smoothwidth; //!< smoothwidth
44  m_integrationWidth = integrationWidth; //! integration width
45  m_intensityThreshold = intensityThreshold;
46  m_area = area; //!< do you want to store are or intensity
48  maxnumberofpeaks; //!< max number of peaks returned by picker
49 }

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
otherTODO

< 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.

52 {
53  m_resolution = other.m_resolution; //!< instrument resolution
54  m_smoothwidth = other.m_smoothwidth; //!< smoothwidth
55  m_integrationWidth = other.m_integrationWidth; //! integration width
57  m_area = other.m_area; //!< do you want to store are or intensity
59  other.m_maxnumberofpeaks; //!< max number of peaks returned by picker
60 }

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.

63 {
64 }

Member Function Documentation

◆ filter()

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

Implements pappso::FilterInterface.

Definition at line 67 of file filterpseudocentroid.cpp.

68 {
69  /*
70 QTOFPeakPickerFilter(
71  const pwiz::msdata::SpectrumListPtr & inner, //!< spectrum list
72  double resolution, //!< instrument resolution
73  double smoothwidth = 2., //!< smoothwidth
74  double integrationWidth = 4, //! integration width
75  double intensityThreshold = 10.,
76  bool area = true, //!< do you want to store are or intensity
77 uint32_t maxnumberofpeaks = 0 //!< max number of peaks returned by picker
78  )
79  */
80  qDebug();
81 
82  std::pair<double, double> range =
83  std::make_pair(data_points.front().x, data_points.back().x);
84  // construct peak picker
85  qDebug() << "===========================================\n" << m_resolution << range << m_smoothwidth << m_integrationWidth << m_intensityThreshold << m_area << m_maxnumberofpeaks << "\n================================================";
88  range,
92  m_area,
94 
95  std::vector<double> mzs = data_points.xValues();
96  std::vector<double> intensities = data_points.yValues();
97  qDebug() << data_points.xValues().size();
98  qDebug() << data_points.yValues().size();
99  qDebug() << data_points.xValues();
100  qDebug() << data_points.yValues();
101  pp(mzs.begin(), mzs.end(), intensities.begin());
102  qDebug();
103  data_points.clear();
104  qDebug();
105  auto itmz = pp.getPeakMass().begin();
106  auto itint = pp.getPeakArea().begin();
107 
108  qDebug() << pp.getPeakMass().size();
109  while(itmz != pp.getPeakMass().end())
110  {
111  data_points.push_back({*itmz, *itint});
112  itmz++;
113  itint++;
114  }
115 
116  qDebug();
117  return data_points;
118 }

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().


The documentation for this class was generated from the following files:
pappso::FilterPseudoCentroid::m_intensityThreshold
double m_intensityThreshold
integration width
Definition: filterpseudocentroid.h:74
pappso::FilterPseudoCentroid::m_resolution
double m_resolution
instrument resolution
Definition: filterpseudocentroid.h:71
pappso::FilterPseudoCentroid::m_maxnumberofpeaks
uint32_t m_maxnumberofpeaks
max number of peaks returned by picker
Definition: filterpseudocentroid.h:76
ralab::base::ms::PeakPicker
Definition: peakpickerqtof.hpp:159
pappso::FilterPseudoCentroid::m_smoothwidth
double m_smoothwidth
smoothwidth
Definition: filterpseudocentroid.h:72
pappso::Trace::xValues
std::vector< pappso_double > xValues() const
Definition: trace.cpp:544
pappso::FilterPseudoCentroid::m_integrationWidth
double m_integrationWidth
Definition: filterpseudocentroid.h:73
pappso::Trace::yValues
std::vector< pappso_double > yValues() const
Definition: trace.cpp:558
pappso::FilterPseudoCentroid::m_area
bool m_area
do you want to store are or intensity
Definition: filterpseudocentroid.h:75