Chaste  Release::2018.1
CellMLLoader.cpp
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35 
36 #include "CellMLLoader.hpp"
37 
38 #include <algorithm>
39 #include "EulerIvpOdeSolver.hpp"
40 
41 CellMLLoader::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  // Create an options file and put it in the output directory with the CellML file
72  mpConverter->CreateOptionsFile(mOutputFileHandler, model_name, mOptions);
74  // Copy a .out file also if present
75  FileFinder out_file(model_name + ".out", mCellMLFile);
76  if (out_file.Exists())
77  {
79  }
80  }
81  // If however we've made a cell before, check that we're making the same type this time
82  else if (makeCvodeCell != mUseCvode)
83  {
84  EXCEPTION("You cannot call both LoadCvodeCell and LoadCardiacCell on the same CellMLLoader.");
85  }
86 
87  // Convert the CellML to a shared library (no-op if shared library exists)
88  DynamicCellModelLoaderPtr p_loader = mpConverter->Convert(copied_model);
89 
90  // Use the shared library to load a concrete cell
91  boost::shared_ptr<AbstractStimulusFunction> p_stimulus;
92  boost::shared_ptr<EulerIvpOdeSolver> p_solver;
93  if (!makeCvodeCell)
94  {
95  // Put in a Forward Euler solver as a default for normal cells
96  p_solver.reset(new EulerIvpOdeSolver);
97  }
98  AbstractCardiacCellInterface* p_loaded_cell = p_loader->CreateCell(p_solver, p_stimulus);
99 
100  // If the CellML file has a default stimulus we may as well use it.
101  if (p_loaded_cell->HasCellMLDefaultStimulus())
102  {
103  p_loaded_cell->UseCellMLDefaultStimulus();
104  }
105  return p_loaded_cell;
106 }
107 
108 boost::shared_ptr<AbstractCardiacCell> CellMLLoader::LoadCardiacCell(void)
109 {
110  AbstractCardiacCellInterface* p_loaded_cell = LoadCellMLFile(false);
111  boost::shared_ptr<AbstractCardiacCell> p_model(dynamic_cast<AbstractCardiacCell*>(p_loaded_cell));
112  return p_model;
113 }
114 
115 #ifdef CHASTE_CVODE
116 boost::shared_ptr<AbstractCvodeCell> CellMLLoader::LoadCvodeCell(void)
117 {
118  AbstractCardiacCellInterface* p_loaded_cell = LoadCellMLFile(true);
119  boost::shared_ptr<AbstractCvodeCell> p_model(dynamic_cast<AbstractCvodeCell*>(p_loaded_cell));
120  return p_model;
121 }
122 #endif
123 
124 
OutputFileHandler mOutputFileHandler
std::vector< std::string > mOptions
boost::shared_ptr< AbstractCvodeCell > LoadCvodeCell(void)
FileFinder CopyFileTo(const FileFinder &rSourceFile) const
#define EXCEPTION(message)
Definition: Exception.hpp:143
FileFinder FindFile(std::string leafName) const
CellMLLoader(const FileFinder &rCellMLFile, const OutputFileHandler &rOutputFileHandler, const std::vector< std::string > &rOptions)
virtual boost::shared_ptr< RegularStimulus > UseCellMLDefaultStimulus()
boost::shared_ptr< CellMLToSharedLibraryConverter > mpConverter
AbstractCardiacCellInterface * LoadCellMLFile(bool makeCvodeCell)
bool Exists() const
Definition: FileFinder.cpp:183
std::string GetLeafNameNoExtension() const
Definition: FileFinder.cpp:245
boost::shared_ptr< AbstractCardiacCell > LoadCardiacCell(void)
boost::logic::tribool mUseCvode
std::string GetLeafName() const
Definition: FileFinder.cpp:240
FileFinder mCellMLFile