lib/fpa/Base/Mori.h

   1 // =========================================================================
   2 // @author Leonardo Florez Valencia
   3 // @email florez-l@javeriana.edu.co
   4 // =========================================================================
   5
   6 // https://stackoverflow.com/questions/22583391/peak-signal-detection-in-realtime-timeseries-data
   7
   8
   9 #ifndef __fpa__Base__Mori__h__
  10 #define __fpa__Base__Mori__h__
  11
  12 #include <deque>
  13 #include <set>
  14 #include <vector>
  15 #include <itkConceptChecking.h>
  16 #include <itkFunctionBase.h>
  17
  18 #include <fpa/Generic/PeakDetector.h>
  19 #include <fpa/Base/Functors/RegionGrow/BinaryThreshold.h>
  20
  21 namespace fpa
  22 {
  23   namespace Base
  24   {
  25     /**
  26      */
  27     template< class _TAlgorithm >
  28     class Mori
  29       : public _TAlgorithm
  30     {
  31     public:
  32       typedef Mori                            Self;
  33       typedef _TAlgorithm                     Superclass;
  34       typedef itk::SmartPointer< Self >       Pointer;
  35       typedef itk::SmartPointer< const Self > ConstPointer;
  36
  37       typedef typename _TAlgorithm::TNode        TNode;
  38       typedef typename _TAlgorithm::TNodes       TNodes;
  39       typedef typename _TAlgorithm::TInputValue  TInputValue;
  40       typedef typename _TAlgorithm::TOutputValue TOutputValue;
  41       typedef typename _TAlgorithm::TFrontId     TFrontId;
  42       typedef typename _TAlgorithm::TVertex      TVertex;
  43
  44       typedef std::deque< TNode >     TQueue;
  45       typedef std::set< TInputValue > TThresholds;
  46       typedef std::pair< TInputValue, unsigned long > TSignalData;
  47       typedef std::vector< TSignalData >              TSignal;
  48
  49       typedef fpa::Generic::PeakDetector TPeakDetector;
  50       typedef fpa::Base::Functors::RegionGrow::BinaryThreshold< TInputValue > TPredicate;
  51
  52     public:
  53       itkConceptMacro(
  54         Check_TOutputValue,
  55         ( itk::Concept::IsUnsignedInteger< TOutputValue > )
  56         );
  57
  58       itkGetConstMacro( InsideValue, TOutputValue );
  59       itkGetConstMacro( MinimumThreshold, TInputValue );
  60
  61       itkSetMacro( InsideValue, TOutputValue );
  62       itkSetMacro( MinimumThreshold, TInputValue );
  63
  64       itkGetConstReferenceMacro( Signal, TSignal );
  65       itkGetConstMacro( SignalLag, unsigned long );
  66       itkGetConstMacro( SignalThreshold, double );
  67       itkGetConstMacro( SignalInfluence, double );
  68
  69       itkSetMacro( SignalLag, unsigned long );
  70       itkSetMacro( SignalThreshold, double );
  71       itkSetMacro( SignalInfluence, double );
  72
  73     public:
  74       virtual itk::ModifiedTimeType GetMTime( ) const override;
  75
  76       TOutputValue GetOutsideValue( ) const;
  77       void SetOutsideValue( const TOutputValue& v );
  78
  79       void ClearThresholds( );
  80       void AddThreshold( const TInputValue& thr );
  81       void SetThresholds(
  82         const TInputValue& init,
  83         const TInputValue& end,
  84         const TInputValue& delta
  85         );
  86       unsigned long GetNumberOfEvaluatedThresholds( ) const;
  87       TInputValue GetOptimumThreshold( ) const;
  88
  89     protected:
  90       Mori( );
  91       virtual ~Mori( );
  92
  93       virtual void _BeforeGenerateData( ) override;
  94       virtual void _FinishOneLoop( ) override;
  95       virtual void _ComputeOutputValue( TNode& n ) override;
  96       virtual void _UpdateOutputValue( TNode& n ) override;
  97       virtual void _QueueClear( ) override;
  98       virtual TNode _QueuePop( ) override;
  99       virtual void _QueuePush( const TNode& node ) override;
 100       virtual unsigned long _QueueSize( ) const override;
 101       virtual void _PrepareSeeds( TNodes& nodes ) override;
 102
 103     private:
 104       // Purposely not implemented.
 105       Mori( const Self& other );
 106       Self& operator=( const Self& other );
 107
 108     protected:
 109       typename TPredicate::Pointer m_Predicate;
 110       TThresholds m_Thresholds;
 111       typename TThresholds::const_iterator m_CurrentThreshold;
 112       TQueue m_Queues[ 2 ];
 113       unsigned int m_CurrentQueue;
 114       unsigned long m_Count;
 115
 116       TPeakDetector m_PeakDetector;
 117
 118       TSignal m_Signal;
 119       unsigned long m_SignalLag;
 120       double m_SignalThreshold;
 121       double m_SignalInfluence;
 122       std::vector< double > m_FilteredSignal;
 123       std::vector< double > m_SignalAverages;
 124       std::vector< double > m_SignalDeviations;
 125       std::vector< short >  m_SignalPeaks;
 126       double m_CurrentAverage;
 127       double m_CurrentVariance;
 128
 129       TInputValue  m_MinimumThreshold;
 130       TOutputValue m_InsideValue;
 131     };
 132
 133   } // ecapseman
 134
 135 } // ecapseman
 136
 137 #ifndef ITK_MANUAL_INSTANTIATION
 138 #  include <fpa/Base/Mori.hxx>
 139 #endif // ITK_MANUAL_INSTANTIATION
 140
 141 #endif // __fpa__Base__Mori__h__
 142
 143 // eof - $RCSfile$