Nektar++
FilterElectrogram.h
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2 //
3 // File FilterElectrogram.h
4 //
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7 // The MIT License
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9 // Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
10 // Department of Aeronautics, Imperial College London (UK), and Scientific
11 // Computing and Imaging Institute, University of Utah (USA).
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31 //
32 // Description: Outputs virtual electrograms at specific locations.
33 //
34 ///////////////////////////////////////////////////////////////////////////////
35 
36 #ifndef NEKTAR_SOLVERUTILS_FILTERS_FILTERELECTROGRAM_H
37 #define NEKTAR_SOLVERUTILS_FILTERS_FILTERELECTROGRAM_H
38 
41 
42 namespace Nektar
43 {
44 
46 {
47 public:
49 
50  /// Creates an instance of this class
53  const ParamMap &pParams) {
55  ::AllocateSharedPtr(pSession, pParams);
56  return p;
57  }
58 
59  /// Name of the class
60  static std::string className;
61 
62  /// Electrogram filter constructor
65  const ParamMap &pParams);
66 
67  /// Electrogram filter destructor
68  virtual ~FilterElectrogram();
69 
70 protected:
71  /// Initialises the electrogram filter and open output file.
72  virtual void v_Initialise(
74  const NekDouble &time);
75  /// Compute extracellular potential at egm points at current time.
76  virtual void v_Update(
78  const NekDouble &time);
79  /// Finalise the electrogram filter and close output file.
80  virtual void v_Finalise(
82  const NekDouble &time);
83  /// Filter is time-dependent and should be called at each time-step.
84  virtual bool v_IsTimeDependent();
85 
86 private:
87  /// Gradient of the radius from each electrogram point in x-direction
89  /// Gradient of the radius from each electrogram point in y-direction
91  /// Gradient of the radius from each electrogram point in z-direction
93  /// List of electrogram points
95  /// Counts number of calls to update (number of timesteps)
96  unsigned int m_index;
97  /// Number of timesteps between outputs
98  unsigned int m_outputFrequency;
99  /// Filename to output electrogram data to
100  std::string m_outputFile;
101  /// Output file stream for electrogram data
102  std::ofstream m_outputStream;
103  /// Point coordinate input string
104  std::stringstream m_electrogramStream;
105 };
106 }
107 
108 #endif
unsigned int m_index
Counts number of calls to update (number of timesteps)
std::string m_outputFile
Filename to output electrogram data to.
static boost::shared_ptr< DataType > AllocateSharedPtr()
Allocate a shared pointer from the memory pool.
std::vector< PointGeomSharedPtr > PointGeomVector
Definition: Geometry3D.h:61
Array< OneD, Array< OneD, NekDouble > > m_grad_R_y
Gradient of the radius from each electrogram point in y-direction.
std::stringstream m_electrogramStream
Point coordinate input string.
General purpose memory allocation routines with the ability to allocate from thread specific memory p...
virtual void v_Finalise(const Array< OneD, const MultiRegions::ExpListSharedPtr > &pFields, const NekDouble &time)
Finalise the electrogram filter and close output file.
std::ofstream m_outputStream
Output file stream for electrogram data.
virtual bool v_IsTimeDependent()
Filter is time-dependent and should be called at each time-step.
SpatialDomains::PointGeomVector m_electrogramPoints
List of electrogram points.
virtual void v_Update(const Array< OneD, const MultiRegions::ExpListSharedPtr > &pFields, const NekDouble &time)
Compute extracellular potential at egm points at current time.
static std::string className
Name of the class.
boost::shared_ptr< SessionReader > SessionReaderSharedPtr
Definition: MeshPartition.h:50
unsigned int m_outputFrequency
Number of timesteps between outputs.
static SolverUtils::FilterSharedPtr create(const LibUtilities::SessionReaderSharedPtr &pSession, const ParamMap &pParams)
Creates an instance of this class.
boost::shared_ptr< Filter > FilterSharedPtr
A shared pointer to a Driver object.
Definition: Filter.h:50
double NekDouble
std::map< std::string, std::string > ParamMap
Definition: Filter.h:67
FilterElectrogram(const LibUtilities::SessionReaderSharedPtr &pSession, const ParamMap &pParams)
Electrogram filter constructor.
Array< OneD, Array< OneD, NekDouble > > m_grad_R_z
Gradient of the radius from each electrogram point in z-direction.
virtual ~FilterElectrogram()
Electrogram filter destructor.
virtual void v_Initialise(const Array< OneD, const MultiRegions::ExpListSharedPtr > &pFields, const NekDouble &time)
Initialises the electrogram filter and open output file.
Array< OneD, Array< OneD, NekDouble > > m_grad_R_x
Gradient of the radius from each electrogram point in x-direction.