CellMLLoader.cpp

/*

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*/

#include "CellMLLoader.hpp"

#include <algorithm>
#include "EulerIvpOdeSolver.hpp"

CellMLLoader::CellMLLoader(const FileFinder& rCellMLFile, const OutputFileHandler& rOutputFileHandler, const std::vector<std::string>& rOptions)
    : mCellMLFile(rCellMLFile),
      mOutputFileHandler(rOutputFileHandler),
      mOptions(rOptions),
      mpConverter(new CellMLToSharedLibraryConverter(true)), // Builds using just the 'heart' component
      mUseCvode(boost::logic::indeterminate)
{
}

AbstractCardiacCellInterface* CellMLLoader::LoadCellMLFile(bool makeCvodeCell)
{
    std::string model_name = mCellMLFile.GetLeafNameNoExtension();
    FileFinder copied_model = mOutputFileHandler.FindFile(mCellMLFile.GetLeafName());

    // If this is the first call, set up to do the conversion
    if (boost::logic::indeterminate(mUseCvode))
    {
        mUseCvode = makeCvodeCell;

        // Remove or add the "--cvode" option to get the desired cell type
        std::vector<std::string>::iterator it = std::find(mOptions.begin(), mOptions.end(), "--cvode");
        if (!makeCvodeCell && it != mOptions.end())
        {
            mOptions.erase(it);
        }
        if (makeCvodeCell && it == mOptions.end())
        {
            mOptions.push_back("--cvode");
        }

        // Create an options file and put it in the output directory with the CellML file
        mpConverter->CreateOptionsFile(mOutputFileHandler, model_name, mOptions);
        mOutputFileHandler.CopyFileTo(mCellMLFile);
        // Copy a .out file also if present
        FileFinder out_file(model_name + ".out", mCellMLFile);
        if (out_file.Exists())
        {
            mOutputFileHandler.CopyFileTo(out_file);
        }
    }
    // If however we've made a cell before, check that we're making the same type this time
    else if (makeCvodeCell != mUseCvode)
    {
        EXCEPTION("You cannot call both LoadCvodeCell and LoadCardiacCell on the same CellMLLoader.");
    }

    // Convert the CellML to a shared library (no-op if shared library exists)
    DynamicCellModelLoaderPtr p_loader = mpConverter->Convert(copied_model);

    // Use the shared library to load a concrete cell
    boost::shared_ptr<AbstractStimulusFunction> p_stimulus;
    boost::shared_ptr<EulerIvpOdeSolver> p_solver;
    if (!makeCvodeCell)
    {
        // Put in a Forward Euler solver as a default for normal cells
        p_solver.reset(new EulerIvpOdeSolver);
    }
    AbstractCardiacCellInterface* p_loaded_cell = p_loader->CreateCell(p_solver, p_stimulus);

    // If the CellML file has a default stimulus we may as well use it.
    if (p_loaded_cell->HasCellMLDefaultStimulus())
    {
        p_loaded_cell->UseCellMLDefaultStimulus();
    }
    return p_loaded_cell;
}

boost::shared_ptr<AbstractCardiacCell> CellMLLoader::LoadCardiacCell(void)
{
    AbstractCardiacCellInterface* p_loaded_cell = LoadCellMLFile(false);
    boost::shared_ptr<AbstractCardiacCell> p_model(dynamic_cast<AbstractCardiacCell*>(p_loaded_cell));
    return p_model;
}

#ifdef CHASTE_CVODE
boost::shared_ptr<AbstractCvodeCell> CellMLLoader::LoadCvodeCell(void)
{
    AbstractCardiacCellInterface* p_loaded_cell = LoadCellMLFile(true);
    boost::shared_ptr<AbstractCvodeCell> p_model(dynamic_cast<AbstractCvodeCell*>(p_loaded_cell));
    return p_model;
}
#endif