Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
CellMLLoader.cpp
1/*
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34*/
35
36#include "CellMLLoader.hpp"
37
38#include <algorithm>
39#include "EulerIvpOdeSolver.hpp"
40
41CellMLLoader::CellMLLoader(const FileFinder& rCellMLFile, const OutputFileHandler& rOutputFileHandler, const std::vector<std::string>& rOptions)
42 : mCellMLFile(rCellMLFile),
43 mOutputFileHandler(rOutputFileHandler),
44 mOptions(rOptions),
45 mpConverter(new CellMLToSharedLibraryConverter(true)), // Builds using just the 'heart' component
46 mUseCvode(boost::logic::indeterminate)
47{
48}
49
51{
52 std::string model_name = mCellMLFile.GetLeafNameNoExtension();
54
55 // If this is the first call, set up to do the conversion
56 if (boost::logic::indeterminate(mUseCvode))
57 {
58 mUseCvode = makeCvodeCell;
59
60 // Remove or add the "--cvode" option to get the desired cell type
61 std::vector<std::string>::iterator it = std::find(mOptions.begin(), mOptions.end(), "--cvode");
62 if (!makeCvodeCell && it != mOptions.end())
63 {
64 mOptions.erase(it);
65 }
66 if (makeCvodeCell && it == mOptions.end())
67 {
68 mOptions.push_back("--cvode");
69 }
70
71 // Chaste codegen doesn't use options files or outfiles, instead options are set directly here
72 mpConverter->SetOptions(mOptions);
74 }
75 // If however we've made a cell before, check that we're making the same type this time
76 else if (makeCvodeCell != mUseCvode)
77 {
78 EXCEPTION("You cannot call both LoadCvodeCell and LoadCardiacCell on the same CellMLLoader.");
79 }
80
81 // Convert the CellML to a shared library (no-op if shared library exists)
82 DynamicCellModelLoaderPtr p_loader = mpConverter->Convert(copied_model);
83
84 // Use the shared library to load a concrete cell
85 boost::shared_ptr<AbstractStimulusFunction> p_stimulus;
86 boost::shared_ptr<EulerIvpOdeSolver> p_solver;
87 if (!makeCvodeCell)
88 {
89 // Put in a Forward Euler solver as a default for normal cells
90 p_solver.reset(new EulerIvpOdeSolver);
91 }
92 AbstractCardiacCellInterface* p_loaded_cell = p_loader->CreateCell(p_solver, p_stimulus);
93
94 // If the CellML file has a default stimulus we may as well use it.
95 if (p_loaded_cell->HasCellMLDefaultStimulus())
96 {
97 p_loaded_cell->UseCellMLDefaultStimulus();
98 }
99 return p_loaded_cell;
100}
101
102boost::shared_ptr<AbstractCardiacCell> CellMLLoader::LoadCardiacCell(void)
103{
104 AbstractCardiacCellInterface* p_loaded_cell = LoadCellMLFile(false);
105 boost::shared_ptr<AbstractCardiacCell> p_model(dynamic_cast<AbstractCardiacCell*>(p_loaded_cell));
106 return p_model;
107}
108
109#ifdef CHASTE_CVODE
110boost::shared_ptr<AbstractCvodeCell> CellMLLoader::LoadCvodeCell(void)
111{
112 AbstractCardiacCellInterface* p_loaded_cell = LoadCellMLFile(true);
113 boost::shared_ptr<AbstractCvodeCell> p_model(dynamic_cast<AbstractCvodeCell*>(p_loaded_cell));
114 return p_model;
115}
116#endif
117
118
#define EXCEPTION(message)
virtual boost::shared_ptr< RegularStimulus > UseCellMLDefaultStimulus()
std::vector< std::string > mOptions
FileFinder mCellMLFile
boost::shared_ptr< AbstractCvodeCell > LoadCvodeCell(void)
boost::shared_ptr< AbstractCardiacCell > LoadCardiacCell(void)
boost::logic::tribool mUseCvode
AbstractCardiacCellInterface * LoadCellMLFile(bool makeCvodeCell)
CellMLLoader(const FileFinder &rCellMLFile, const OutputFileHandler &rOutputFileHandler, const std::vector< std::string > &rOptions)
boost::shared_ptr< CellMLToSharedLibraryConverter > mpConverter
OutputFileHandler mOutputFileHandler
std::string GetLeafNameNoExtension() const
std::string GetLeafName() const
FileFinder CopyFileTo(const FileFinder &rSourceFile) const
FileFinder FindFile(std::string leafName) const