TissueSimulationArchiver.hpp

/*

Copyright (C) University of Oxford, 2005-2010

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/

#ifndef TISSUESIMULATIONARCHIVER_HPP_
#define TISSUESIMULATIONARCHIVER_HPP_

// Must be included before any other serialisation headers
#include "CheckpointArchiveTypes.hpp"

#include <string>
#include <iostream>

#include "OutputFileHandler.hpp"
#include "SimulationTime.hpp"
#include "WntConcentration.hpp"
#include "CellwiseData.hpp"
#include "ArchiveLocationInfo.hpp"
#include "ArchiveOpener.hpp"

template<unsigned DIM, class SIM>
class TissueSimulationArchiver
{
public:

    static SIM* Load(const std::string& rArchiveDirectory, const double& rTimeStamp);

    static void Save(SIM* pSim);
};


template<unsigned DIM, class SIM>
SIM* TissueSimulationArchiver<DIM, SIM>::Load(const std::string& rArchiveDirectory, const double& rTimeStamp)
{
    std::ostringstream time_stamp;
    time_stamp << rTimeStamp;
    std::string archive_filename = "tissue_sim_at_time_" + time_stamp.str() + ".arch";
    std::string mesh_filename = "mesh_" + time_stamp.str();
    ArchiveLocationInfo::SetMeshPathname(OutputFileHandler::GetChasteTestOutputDirectory()
                                         + rArchiveDirectory + "/archive/", mesh_filename);

    // Create an input archive
    ArchiveOpener<boost::archive::text_iarchive, std::ifstream> arch_opener(rArchiveDirectory + "/archive/", archive_filename);
    boost::archive::text_iarchive* p_arch = arch_opener.GetCommonArchive();

    // Load any data that isn't the simulation itself, mainly singletons
    // - simulation time
    SimulationTime* p_simulation_time = SimulationTime::Instance();
    assert(p_simulation_time->IsStartTimeSetUp());
    (*p_arch) & *p_simulation_time;

    // - Wnt concentration (if used)
    bool archive_wnt;
    (*p_arch) & archive_wnt;
    if (archive_wnt)
    {
        WntConcentration<DIM>* p_wnt = WntConcentration<DIM>::Instance();
        (*p_arch) & *p_wnt;
    }

    // - CellwiseData (if used)
    bool archive_cellwise_data;
    (*p_arch) & archive_cellwise_data;
    if (archive_cellwise_data)
    {
        CellwiseData<DIM>* p_cellwise_data = CellwiseData<DIM>::Instance();
        (*p_arch) & *p_cellwise_data;
    }

    // Load the simulation
    SIM* p_sim;
    (*p_arch) >> p_sim;
    return p_sim;
}

template<unsigned DIM, class SIM>
void TissueSimulationArchiver<DIM, SIM>::Save(SIM* pSim)
{
    // Get the simulation time as a string
    const SimulationTime* p_sim_time = SimulationTime::Instance();
    assert(p_sim_time->IsStartTimeSetUp());
    std::ostringstream time_stamp;
    time_stamp << p_sim_time->GetTime();

    // Set up folder and filename of archive
    std::string archive_directory = pSim->GetOutputDirectory() + "/archive/";
    std::string archive_filename = "tissue_sim_at_time_" + time_stamp.str() + ".arch";
    ArchiveLocationInfo::SetMeshFilename(std::string("mesh_") + time_stamp.str());

    // Create output archive
    ArchiveOpener<boost::archive::text_oarchive, std::ofstream> arch_opener(archive_directory, archive_filename);
    boost::archive::text_oarchive* p_arch = arch_opener.GetCommonArchive();

    // Save the simulation.  We save the time directly first to maintain its
    // singleton-ness on load.
    (*p_arch) << *p_sim_time;

    // Archive the Wnt concentration if it's used
    bool archive_wnt = WntConcentration<DIM>::Instance()->IsWntSetUp();
    (*p_arch) & archive_wnt;
    if (archive_wnt)
    {
        WntConcentration<DIM>* p_wnt = WntConcentration<DIM>::Instance();
        (*p_arch) & *p_wnt;
    }

    // Archive the CellwiseData if it's used
    bool archive_cellwise_data = CellwiseData<DIM>::Instance()->IsSetUp();
    (*p_arch) & archive_cellwise_data;
    if (archive_cellwise_data)
    {
        CellwiseData<DIM>* p_cellwise_data = CellwiseData<DIM>::Instance();
        (*p_arch) & *p_cellwise_data;
    }

    // Archive the simulation itself
    (*p_arch) & pSim; // const-ness would be a pain here
}

#endif /*TISSUESIMULATIONARCHIVER_HPP_*/