TissueSimulationArchiver.hpp

/*

Copyright (C) University of Oxford, 2005-2009

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_

#include <climits> // work around boost bug

// Must be included before any other serialisation headers
#include <boost/archive/text_oarchive.hpp>
#include <boost/archive/text_iarchive.hpp>

#include <string>
#include <iostream>

#include "OutputFileHandler.hpp"
#include "SimulationTime.hpp"
#include "WntConcentration.hpp"
#include "CellwiseData.hpp"
#include "MeshArchiveInfo.hpp"

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

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

    static void Save(SIM* pSim);

private:

    static std::string GetArchivePathname(const std::string& rArchiveDirectory, const double& rTimeStamp);
};


template<unsigned DIM, class SIM>
std::string TissueSimulationArchiver<DIM, SIM>::GetArchivePathname(const std::string& rArchiveDirectory, const double& rTimeStamp)
{
    // Find the right archive and mesh to load
    std::ostringstream time_stamp;
    time_stamp << rTimeStamp;

    std::string test_output_directory = OutputFileHandler::GetChasteTestOutputDirectory();

    std::string archive_filename = test_output_directory + rArchiveDirectory + "/archive/tissue_sim_at_time_"+time_stamp.str() +".arch";
    std::string mesh_filename = test_output_directory + rArchiveDirectory + "/archive/mesh_" + time_stamp.str();
    MeshArchiveInfo::meshPathname = mesh_filename;
    //MeshArchiver::SetMeshPath(mesh_filename);
    return archive_filename;
}

template<unsigned DIM, class SIM>
SIM* TissueSimulationArchiver<DIM, SIM>::Load(const std::string& rArchiveDirectory, const double& rTimeStamp)
{
    std::string archive_filename = TissueSimulationArchiver<DIM, SIM>::GetArchivePathname(rArchiveDirectory, rTimeStamp);

    // Create an input archive
    std::ifstream ifs(archive_filename.c_str(), std::ios::binary);
    boost::archive::text_iarchive input_arch(ifs);

    // Load any data that isn't the simulation itself, mainly singletons
    // - simulation time
    SimulationTime* p_simulation_time = SimulationTime::Instance();
    assert(p_simulation_time->IsStartTimeSetUp());
    input_arch & *p_simulation_time;
    // - Wnt concentration (if used)
    bool archive_wnt;
    input_arch & archive_wnt;
    if (archive_wnt)
    {
        WntConcentration* p_wnt = WntConcentration::Instance();
        input_arch & *p_wnt;
    }
    // - CellwiseData (if used)
    bool archive_cellwise_data;
    input_arch & archive_cellwise_data;
    if (archive_cellwise_data)
    {
        CellwiseData<DIM>* p_cellwise_data = CellwiseData<DIM>::Instance();
        input_arch & *p_cellwise_data;
    }

    // Load the simulation
    SIM* p_sim;
    input_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();

    // Create an output file handler in order to get the full path of the
    // archive directory.  Note the false is so the handler doesn't clean
    // the directory.
    std::string archive_directory = pSim->GetOutputDirectory() + "/archive/";
    OutputFileHandler handler(archive_directory, false);
    std::string archive_filename = handler.GetOutputDirectoryFullPath() + "tissue_sim_at_time_" + time_stamp.str() + ".arch";
    std::string mesh_filename = std::string("mesh_") + time_stamp.str();

    // Write the mesh to file. Call Update() first to
    // ensure that the tissue is in a good state.
    pSim->rGetTissue().Update();
    if (pSim->rGetTissue().HasMesh())
    {
        pSim->rGetTissue().WriteMeshToFile(archive_directory, mesh_filename);
    }

    // Create a new archive
    std::ofstream ofs(archive_filename.c_str());
    boost::archive::text_oarchive output_arch(ofs);

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

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

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

    // Archive the simulation itself
    output_arch & pSim; // const-ness would be a pain here
}

#endif /*TISSUESIMULATIONARCHIVER_HPP_*/

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