PropagationPropertiesCalculator.hpp

00001 /*
00002 
00003 Copyright (c) 2005-2015, University of Oxford.
00004 All rights reserved.
00005 
00006 University of Oxford means the Chancellor, Masters and Scholars of the
00007 University of Oxford, having an administrative office at Wellington
00008 Square, Oxford OX1 2JD, UK.
00009 
00010 This file is part of Chaste.
00011 
00012 Redistribution and use in source and binary forms, with or without
00013 modification, are permitted provided that the following conditions are met:
00014  * Redistributions of source code must retain the above copyright notice,
00015    this list of conditions and the following disclaimer.
00016  * Redistributions in binary form must reproduce the above copyright notice,
00017    this list of conditions and the following disclaimer in the documentation
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00019  * Neither the name of the University of Oxford nor the names of its
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00022 
00023 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
00024 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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00026 ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
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00034 */
00035 
00036 
00037 #ifndef _PROPAGATIONPROPERTIESCALCULATOR_HPP_
00038 #define _PROPAGATIONPROPERTIESCALCULATOR_HPP_
00039 
00040 #include "Hdf5DataReader.hpp"
00041 #include <string>
00042 
00043 
00053 class PropagationPropertiesCalculator
00054 {
00055 private:
00057     Hdf5DataReader* mpDataReader;
00059     const std::string mVoltageName;
00061     std::vector<double> mTimes;
00063     unsigned mCachedNodeGlobalIndex;
00065     std::vector<double> mCachedVoltages;
00066 
00067 protected:
00077     std::vector<double>& rGetCachedVoltages(unsigned globalNodeIndex);
00078 
00079 public:
00087     PropagationPropertiesCalculator(Hdf5DataReader* pDataReader,
00088                                     const std::string voltageName = "V");
00089 
00091     virtual ~PropagationPropertiesCalculator();
00092 
00099     double CalculateMaximumUpstrokeVelocity(unsigned globalNodeIndex);
00100 
00108     std::vector<double> CalculateAllMaximumUpstrokeVelocities(unsigned globalNodeIndex, double threshold);
00109 
00117     std::vector<double> CalculateUpstrokeTimes(unsigned globalNodeIndex, double threshold);
00118 
00130     double CalculateConductionVelocity(unsigned globalNearNodeIndex,
00131                                        unsigned globalFarNodeIndex,
00132                                        const double euclideanDistance);
00133 
00145      std::vector<double> CalculateAllConductionVelocities(unsigned globalNearNodeIndex,
00146                                                           unsigned globalFarNodeIndex,
00147                                                           const double euclideanDistance);
00155     double CalculateActionPotentialDuration(const double percentage,
00156                                             unsigned globalNodeIndex);
00164     double CalculatePeakMembranePotential(unsigned globalNodeIndex);
00165 
00173     std::vector<double> CalculateAllActionPotentialDurations(const double percentage,
00174                                                              unsigned globalNodeIndex,
00175                                                              double threshold);
00176 
00185     std::vector<std::vector<double> > CalculateAllActionPotentialDurationsForNodeRange(const double percentage,
00186                                                                                        unsigned lowerNodeIndex,
00187                                                                                        unsigned upperNodeIndex,
00188                                                                                        double threshold);
00189 
00197     std::vector<unsigned> CalculateAllAboveThresholdDepolarisations(unsigned globalNodeIndex,
00198                                                                     double threshold);
00199 
00207     unsigned CalculateAboveThresholdDepolarisationsForLastAp(unsigned globalNodeIndex,
00208                                                              double threshold);
00209 
00215     void SetHdf5DataReader(Hdf5DataReader* pDataReader);
00216 
00217 };
00218 
00219 #endif //_PROPAGATIONPROPERTIESCALCULATOR_HPP_