Chaste  Release::2018.1
PostProcessingWriter.hpp
1 /*
2 
3 Copyright (c) 2005-2018, University of Oxford.
4 All rights reserved.
5 
6 University of Oxford means the Chancellor, Masters and Scholars of the
7 University of Oxford, having an administrative office at Wellington
8 Square, Oxford OX1 2JD, UK.
9 
10 This file is part of Chaste.
11 
12 Redistribution and use in source and binary forms, with or without
13 modification, 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 
23 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
25 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
26 ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
27 LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
28 CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
29 GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
30 HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
31 LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
32 OF 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 
56 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
58 {
59  friend class TestPostProcessingWriter;
60 
61 private:
63  std::string mHdf5File;
64  std::string mVoltageName;
68  unsigned mLo;
69  unsigned mHi;
73 public:
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 
118 private:
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_*/
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > & mrMesh
void WriteVariablesOverTimeAtNodes(std::vector< unsigned > &rNodeIndices)
PostProcessingWriter(AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, const FileFinder &rDirectory, const std::string &rHdf5FileName, const std::string &rVoltageName="V", hsize_t hdf5DataWriterChunkSize=0)
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")
std::string ConvertToHdf5FriendlyString(double threshold)
void WriteMaxUpstrokeVelocityMap(double threshold)
void WriteConductionVelocityMap(unsigned originNode, std::vector< double > distancesFromOriginNode)
void WriteUpstrokeTimeMap(double threshold)
void WriteGenericFileToMeshalyzer(std::vector< std::vector< double > > &rDataPayload, const std::string &rFolder, const std::string &rFileName)
PropagationPropertiesCalculator * mpCalculator
void WriteApdMapFile(double repolarisationPercentage, double threshold)
Hdf5DataReader * mpDataReader
void WriteAboveThresholdDepolarisationFile(double threshold)