OpenMS  3.0.0
OptimizePeakDeconvolution.h
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35 
36 #pragma once
37 
41 
42 //#define DEBUG_DECONV
43 #include <vector>
44 
45 namespace OpenMS
46 {
47 
48  namespace OptimizationFunctions
49  {
50 
57  struct OPENMS_DLLAPI PenaltyFactorsIntensity :
58  public PenaltyFactors
59  {
61  PenaltyFactors(), height(0){}
63  PenaltyFactors(p), height(p.height) {}
65  {
66  height = p.height;
67  pos = p.pos;
68  lWidth = p.lWidth;
69  rWidth = p.rWidth;
70 
71  return *this;
72  }
73 
75 
76  double height;
77 
78 
79  };
80 
81 
82 
83  } //namespace OptimizationFunctions
84 
96  class OPENMS_DLLAPI OptimizePeakDeconvolution :
97  public DefaultParamHandler
98  {
99 public:
103  typedef std::vector<Peak1D> RawDataVector;
104  typedef RawDataVector::iterator PeakIterator;
106 
110  struct Data
111  {
112  std::vector<PeakShape> peaks;
113  std::vector<double> positions;
114  std::vector<double> signal;
117  };
118 
119 
120 
126 
129  DefaultParamHandler(opt),
130  penalties_(opt.penalties_),
131  charge_(opt.charge_){}
132 
136 
141  {
143  penalties_ = opt.penalties_;
144  charge_ = opt.charge_;
145 
146  return *this;
147  }
148 
150 
151 
155  inline const OptimizationFunctions::PenaltyFactorsIntensity & getPenalties() const { return penalties_; }
159  {
160  penalties_ = penalties;
161  param_.setValue("penalties:left_width", penalties_.lWidth);
162  param_.setValue("penalties:right_width", penalties_.rWidth);
163  param_.setValue("penalties:height", penalties_.height);
164  param_.setValue("penalties:position", penalties_.pos);
165  }
166 
168  inline Int getCharge() const { return charge_; }
170  inline void setCharge(const Int charge) { charge_ = charge; }
172 
173 
175  bool optimize(std::vector<PeakShape> & peaks, Data & data);
176  Size getNumberOfPeaks_(Int charge, std::vector<PeakShape> & temp_shapes, Data & data);
177 
178 protected:
179  // Penalty factors for some parameter in the optimization
181 
184 
186  static const double dist_;
187 
189  void setNumberOfPeaks_(Data & data, const std::vector<PeakShape> & temp_shapes, Int charge);
190 
191  void updateMembers_() override;
192  }; // class
193 
194 } // namespace OpenMS
195 
196 
DefaultParamHandler.h
OpenMS::OptimizePeakDeconvolution::charge_
Int charge_
Charge state of the current isotope pattern.
Definition: OptimizePeakDeconvolution.h:183
OpenMS::OptimizePeakDeconvolution::Data::penalties
OptimizationFunctions::PenaltyFactorsIntensity penalties
Definition: OptimizePeakDeconvolution.h:115
OpenMS::DefaultParamHandler::operator=
virtual DefaultParamHandler & operator=(const DefaultParamHandler &rhs)
Assignment operator.
OpenMS::OptimizationFunctions::PenaltyFactorsIntensity::operator=
PenaltyFactorsIntensity & operator=(const PenaltyFactorsIntensity &p)
Definition: OptimizePeakDeconvolution.h:64
OpenMS::OptimizePeakDeconvolution::penalties_
OptimizationFunctions::PenaltyFactorsIntensity penalties_
Definition: OptimizePeakDeconvolution.h:180
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::OptimizationFunctions::PenaltyFactors
Class for the penalty factors used during the optimization.
Definition: OptimizePick.h:68
OpenMS::OptimizePeakDeconvolution::~OptimizePeakDeconvolution
~OptimizePeakDeconvolution() override
Destructor.
Definition: OptimizePeakDeconvolution.h:134
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
PeakShape.h
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::OptimizePeakDeconvolution::Data
Class containing the data needed for optimization.
Definition: OptimizePeakDeconvolution.h:110
OpenMS::OptimizePeakDeconvolution::Data::signal
std::vector< double > signal
Definition: OptimizePeakDeconvolution.h:114
OpenMS::OptimizePeakDeconvolution::Data::charge
Int charge
Definition: OptimizePeakDeconvolution.h:116
OpenMS::OptimizePeakDeconvolution::setPenalties
void setPenalties(const OptimizationFunctions::PenaltyFactorsIntensity &penalties)
Mutable access to the penalty parameter.
Definition: OptimizePeakDeconvolution.h:158
OpenMS::OptimizePeakDeconvolution::setCharge
void setCharge(const Int charge)
Mutable access to the charge.
Definition: OptimizePeakDeconvolution.h:170
OpenMS::OptimizePeakDeconvolution::RawDataVector
std::vector< Peak1D > RawDataVector
Definition: OptimizePeakDeconvolution.h:103
OpenMS::OptimizationFunctions::PenaltyFactors::pos
double pos
Penalty factor for the peak shape's position.
Definition: OptimizePick.h:86
OpenMS::OptimizePeakDeconvolution
This class provides the deconvolution of peak regions using non-linear optimization.
Definition: OptimizePeakDeconvolution.h:96
OpenMS::OptimizePeakDeconvolution::Data::positions
std::vector< double > positions
Definition: OptimizePeakDeconvolution.h:113
OpenMS::OptimizationFunctions::PenaltyFactorsIntensity::PenaltyFactorsIntensity
PenaltyFactorsIntensity()
Definition: OptimizePeakDeconvolution.h:60
OpenMS::OptimizePeakDeconvolution::OptimizePeakDeconvolution
OptimizePeakDeconvolution(const OptimizePeakDeconvolution &opt)
Copy-Constructor.
Definition: OptimizePeakDeconvolution.h:128
OpenMS::OptimizationFunctions::PenaltyFactorsIntensity::height
double height
Definition: OptimizePeakDeconvolution.h:76
OptimizePick.h
OpenMS::OptimizePeakDeconvolution::dist_
static const double dist_
distance between two isotopic peaks
Definition: OptimizePeakDeconvolution.h:186
OpenMS::OptimizationFunctions::PenaltyFactorsIntensity::PenaltyFactorsIntensity
PenaltyFactorsIntensity(const PenaltyFactorsIntensity &p)
Definition: OptimizePeakDeconvolution.h:62
OpenMS::OptimizationFunctions::PenaltyFactorsIntensity::~PenaltyFactorsIntensity
~PenaltyFactorsIntensity()
Definition: OptimizePeakDeconvolution.h:74
OpenMS::OptimizationFunctions::PenaltyFactorsIntensity
Class for the penalty factors used during the optimization.
Definition: OptimizePeakDeconvolution.h:57
OpenMS::OptimizePeakDeconvolution::operator=
OptimizePeakDeconvolution & operator=(const OptimizePeakDeconvolution &opt)
Definition: OptimizePeakDeconvolution.h:140
OpenMS::OptimizationFunctions::PenaltyFactors::lWidth
double lWidth
Penalty factor for the peak shape's left width parameter.
Definition: OptimizePick.h:88
OpenMS::OptimizePeakDeconvolution::Data::peaks
std::vector< PeakShape > peaks
Definition: OptimizePeakDeconvolution.h:112
OpenMS::OptimizationFunctions::PenaltyFactors::rWidth
double rWidth
Penalty factor for the peak shape's right width parameter.
Definition: OptimizePick.h:90
OpenMS::OptimizePeakDeconvolution::PeakIterator
RawDataVector::iterator PeakIterator
Definition: OptimizePeakDeconvolution.h:104
OpenMS::OptimizePeakDeconvolution::getCharge
Int getCharge() const
Non-mutable access to the charge.
Definition: OptimizePeakDeconvolution.h:168