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