Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
PostProcessingWriter.hpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
4All rights reserved.
5
6University of Oxford means the Chancellor, Masters and Scholars of the
7University of Oxford, having an administrative office at Wellington
8Square, Oxford OX1 2JD, UK.
9
10This file is part of Chaste.
11
12Redistribution and use in source and binary forms, with or without
13modification, are permitted provided that the following conditions are met:
14 * Redistributions of source code must retain the above copyright notice,
15 this list of conditions and the following disclaimer.
16 * Redistributions in binary form must reproduce the above copyright notice,
17 this list of conditions and the following disclaimer in the documentation
18 and/or other materials provided with the distribution.
19 * Neither the name of the University of Oxford nor the names of its
20 contributors may be used to endorse or promote products derived from this
21 software without specific prior written permission.
22
23THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
25IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
26ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
27LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
28CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
29GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
30HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
31LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
32OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
33
34*/
35
36#ifndef POSTPROCESSINGWRITER_HPP_
37#define POSTPROCESSINGWRITER_HPP_
38
39
40#include "Hdf5DataReader.hpp"
41#include "PropagationPropertiesCalculator.hpp"
42#include "AbstractTetrahedralMesh.hpp"
43#include <string>
44
56template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
58{
59 friend class TestPostProcessingWriter;
60
61private:
63 std::string mHdf5File;
64 std::string mVoltageName;
68 unsigned mLo;
69 unsigned mHi;
73public:
85 const FileFinder& rDirectory,
86 const std::string& rHdf5FileName,
87 const std::string& rVoltageName = "V",
88 hsize_t hdf5DataWriterChunkSize=0);
89
95
100
116 void WriteAboveThresholdDepolarisationFile(double threshold);
117
118private:
119
145 void WriteVariablesOverTimeAtNodes(std::vector<unsigned>& rNodeIndices);
146
159 void WriteApdMapFile(double repolarisationPercentage, double threshold);
160
161
173 void WriteUpstrokeTimeMap(double threshold);
174
186 void WriteMaxUpstrokeVelocityMap(double threshold);
187
200 void WriteConductionVelocityMap(unsigned originNode, std::vector<double> distancesFromOriginNode);
201
211 void WriteGenericFileToMeshalyzer(std::vector<std::vector<double> >& rDataPayload, const std::string& rFolder, const std::string& rFileName);
212
222 void WriteOutputDataToHdf5(const std::vector<std::vector<double> >& rDataPayload,
223 const std::string& rDatasetName,
224 const std::string& rDatasetUnit,
225 const std::string& rUnlimitedVariableName = "PaceNumber",
226 const std::string& rUnlimitedVariableUnit = "dimensionless");
227
240 std::string ConvertToHdf5FriendlyString(double threshold);
241};
242
243#endif /*POSTPROCESSINGWRITER_HPP_*/
void WriteMaxUpstrokeVelocityMap(double threshold)
void WriteConductionVelocityMap(unsigned originNode, std::vector< double > distancesFromOriginNode)
void WriteVariablesOverTimeAtNodes(std::vector< unsigned > &rNodeIndices)
void WriteUpstrokeTimeMap(double threshold)
void WriteGenericFileToMeshalyzer(std::vector< std::vector< double > > &rDataPayload, const std::string &rFolder, const std::string &rFileName)
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > & mrMesh
std::string ConvertToHdf5FriendlyString(double threshold)
void WriteApdMapFile(double repolarisationPercentage, double threshold)
void WriteOutputDataToHdf5(const std::vector< std::vector< double > > &rDataPayload, const std::string &rDatasetName, const std::string &rDatasetUnit, const std::string &rUnlimitedVariableName="PaceNumber", const std::string &rUnlimitedVariableUnit="dimensionless")
void WriteAboveThresholdDepolarisationFile(double threshold)
PropagationPropertiesCalculator * mpCalculator