| OpenMS 2.5.0

PeakPickerSH.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Florian Zeller $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/KERNEL/MSExperiment.h>
39 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
40 #include <OpenMS/CONCEPT/ProgressLogger.h>
41
42 // TODO: Check if I need this # PeakPickerSH.h
43 #define DEBUG_PEAK_PICKING
44 #undef DEBUG_PEAK_PICKING
45
46 namespace OpenMS
47 {
48 class OPENMS_DLLAPI PeakPickerSH :
49 public DefaultParamHandler,
50 public ProgressLogger
51 {
52 public:
53 PeakPickerSH();
54
55 ~PeakPickerSH() override;
56
60 void pick(const MSSpectrum & input, MSSpectrum & output, float fWindowWidth)
61 {
62 int i, hw, j;
63 double cm, toti, min_dh;
64
65 // Hack: Prepare data structures for Lukas' algorithm
66 std::vector<double> masses, intens;
67 // TODO: Probably we could save some time when we resize the vectors... # PeakPickerSH.cpp
68 //masses.resize(input.size());
69 //intens.resize(input.size());
70 for (Size k = 0; k < input.size() - 1; ++k)
71 {
72 // Lukas requires a minimum of intensity (=50). His vectors do not contain
73 // other data, so I strip the low ones out right here.
74 // TODO: Read 50.0 from parameters # PeakPickerSH.cpp
75 if (input[k].getIntensity() >= 50.0)
76 {
77 masses.push_back(input[k].getMZ());
78 intens.push_back(input[k].getIntensity());
79 }
80 }
81
82 min_dh = 50.0; // min height
83 hw = fWindowWidth / 2;
84
85 for (i = 2; i < (int)masses.size() - 2; i++)
86 {
87
88 // Peak must be concave in the interval [i-2 .. i+2]
89 if (intens[i] > min_dh && intens[i] > intens[i - 1] + min_dh && intens[i] >= intens[i + 1] && intens[i - 1] > intens[i - 2] + min_dh && intens[i + 1] >= intens[i + 2])
90 {
91
92 cm = 0.0; // centroid mass:
93 toti = 0.0; // total intensity:
94
95 for (j = -hw; j <= hw; j++)
96 {
97 double inte = intens[i - j];
98 double mz = masses[i - j];
99
100 cm += inte * mz;
101 toti += (double) intens[i - j];
102 }
103 cm = cm / toti; // Centre of gravity = centroid
104
105 Peak1D peak;
106 peak.setMZ(cm);
107 peak.setIntensity(intens[i]);
108 output.push_back(peak);
109 }
110 }
111 }
112
119 void pickExperiment(const PeakMap & input, PeakMap & output);
120 };
121 }
122
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::Constants::k
const double k
OpenMS::Peak1D::setIntensity
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:112
OpenMS::PeakPickerSH::pick
void pick(const MSSpectrum &input, MSSpectrum &output, float fWindowWidth)
Picks peaks in one spectrum.
Definition: PeakPickerSH.h:60
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::PeakPickerSH
Definition: PeakPickerSH.h:48
StandardTypes.h
OpenMS::Peak1D::setMZ
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:121
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
ProgressLogger.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
DefaultParamHandler.h
double
int
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127