HeartConfig.cpp

/*

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/>.

*/

// Work-around for newer Boost versions
#include "CheckpointArchiveTypesIfNeeded.hpp"

#include "UblasCustomFunctions.hpp"

#include "HeartConfig.hpp"
#include "OutputFileHandler.hpp"
#include "Exception.hpp"
#include "ChastePoint.hpp"
#include "Version.hpp"
#include "AbstractChasteRegion.hpp"
#include "HeartFileFinder.hpp"
#include "Warnings.hpp"

#include "SimpleStimulus.hpp"
#include "RegularStimulus.hpp"

#include <string>
#include <istream>
#include <fstream>
#include <cassert>

#include <xercesc/util/PlatformUtils.hpp>
#include <xercesc/util/QName.hpp>
#include <xercesc/util/XMLUniDefs.hpp> // chLatin_*
#include <xercesc/framework/Wrapper4InputSource.hpp>
#include <xercesc/validators/common/Grammar.hpp>
#include <xercesc/dom/DOMNamedNodeMap.hpp>
#include <xercesc/dom/DOMXPathEvaluator.hpp>
#include <xercesc/dom/DOMXPathResult.hpp>

#include <xsd/cxx/xml/string.hxx>
#include <xsd/cxx/xml/dom/auto-ptr.hxx>
#include <xsd/cxx/xml/sax/std-input-source.hxx>
#include <xsd/cxx/xml/dom/bits/error-handler-proxy.hxx>
#include <xsd/cxx/tree/exceptions.hxx>
#include <xsd/cxx/tree/error-handler.hxx>


using namespace xsd::cxx::tree;


// Coping with changes to XSD interface
#if (XSD_INT_VERSION >= 3000000L)
#define XSD_SEQUENCE_TYPE(base) base##_sequence
#define XSD_ITERATOR_TYPE(base) base##_iterator
#define XSD_NESTED_TYPE(t) t##_type
#define XSD_ANON_TYPE(t1, t2) \
    t1::t2##_type
#else
#define XSD_SEQUENCE_TYPE(base) base::container
#define XSD_ITERATOR_TYPE(base) base::iterator
#define XSD_NESTED_TYPE(t) t::type
#define XSD_ANON_TYPE(t1, t2) \
    t1::t2::_xsd_##t2##_::t2
#endif

// These are for convenience
#define XSD_ANON_SEQUENCE_TYPE(t1, t2, t3) \
    XSD_SEQUENCE_TYPE(XSD_ANON_TYPE(t1, t2)::t3)
#define XSD_ANON_ITERATOR_TYPE(t1, t2, t3) \
    XSD_ITERATOR_TYPE(XSD_ANON_TYPE(t1, t2)::t3)

// Newer versions don't allow you to set fixed attributes
#if (XSD_INT_VERSION >= 3020000L)
#define XSD_CREATE_WITH_FIXED_ATTR(type, name, attr) \
    type name
#define XSD_CREATE_WITH_FIXED_ATTR1(type, name, arg1, attr) \
    type name(arg1)
#define XSD_CREATE_WITH_FIXED_ATTR2(type, name, arg1, arg2, attr) \
    type name(arg1, arg2)
#define XSD_CREATE_WITH_FIXED_ATTR3(type, name, arg1, arg2, arg3, attr) \
    type name(arg1, arg2, arg3)
#else
#define XSD_CREATE_WITH_FIXED_ATTR(type, name, attr) \
    type name(attr)
#define XSD_CREATE_WITH_FIXED_ATTR1(type, name, arg1, attr) \
    type name(arg1, attr)
#define XSD_CREATE_WITH_FIXED_ATTR2(type, name, arg1, arg2, attr) \
    type name(arg1, arg2, attr)
#define XSD_CREATE_WITH_FIXED_ATTR3(type, name, arg1, arg2, arg3, attr) \
    type name(arg1, arg2, arg3, attr)
#endif

#define X(str) xsd::cxx::xml::string(str).c_str()

#define ENSURE_SECTION_PRESENT(location, type) \
    if (!location.present())                   \
    {                                          \
        type empty_item;                       \
        location.set(empty_item);              \
    }


class XmlTools
{
public:
    static xsd::cxx::xml::dom::auto_ptr<xercesc::DOMDocument> ReadFileToDomDocument(
        const std::string& rFileName,
        ::xml_schema::error_handler& rErrorHandler,
        const ::xml_schema::properties& rProps);
    
    static void PrintNode(const std::string& rMsg, xercesc::DOMNode* pNode, bool showChildren=false);
    
    static xercesc::DOMElement* SetNamespace(xercesc::DOMDocument* pDocument,
                                             xercesc::DOMElement* pElement,
                                             const std::string& rNamespace);

    static xercesc::DOMElement* SetNamespace(xercesc::DOMDocument* pDocument,
                                             xercesc::DOMElement* pElement,
                                             const XMLCh* pNamespace);

    static void WrapContentInElement(xercesc::DOMDocument* pDocument,
                                     xercesc::DOMElement* pElement,
                                     const XMLCh* pNewElementLocalName);

    static std::vector<xercesc::DOMElement*> FindElements(xercesc::DOMElement* pContextElement,
                                                          const std::string& rPath);

    static void FindElements(xercesc::DOMElement* pContextElement,
                             const std::vector<std::string>& rNames,
                             std::vector<xercesc::DOMElement*>& rResults,
                             unsigned depth=0);
};

class XmlTransforms
{
public:
    static void TransformIonicModelDefinitions(xercesc::DOMDocument* pDocument,
                                               xercesc::DOMElement* pRootElement);

    static void TransformArchiveDirectory(xercesc::DOMDocument* pDocument,
                                          xercesc::DOMElement* pRootElement);

    static void CheckForIluPreconditioner(xercesc::DOMDocument* pDocument,
                                          xercesc::DOMElement* pRootElement);
};

//
// Default settings
//
#include "HeartConfigDefaults.hpp"

//
// Definition of static member variables
//
std::auto_ptr<HeartConfig> HeartConfig::mpInstance;

//
// Methods
//

HeartConfig* HeartConfig::Instance()
{
    if (mpInstance.get() == NULL)
    {
        mpInstance.reset(new HeartConfig);
    }
    return mpInstance.get();
}

HeartConfig::HeartConfig()
{
    assert(mpInstance.get() == NULL);
    mUseFixedSchemaLocation = true;
    SetDefaultSchemaLocations();

    mpDefaultParameters = CreateDefaultParameters();
    mpUserParameters = mpDefaultParameters;
    //CheckTimeSteps(); // necessity of this line of code is not tested -- remove with caution!

    //initialise the member variable of the layers
    mEpiFraction = -1.0;
    mEndoFraction =  -1.0;
    mMidFraction = -1.0;
    mUserAskedForCellularTransmuralHeterogeneities=false;
    mUserAskedForCuboidsForCellularHeterogeneities=false;
    // initialise to senseless values (these should be only 0, 1 and 2)
    // note: the 'minus 3' is for checking purposes as we need to add 0, 1 or 2 to this initial value
    // and UINT_MAX+1 seems to be 0
    mIndexMid = UINT_MAX-3u;
    mIndexEpi = UINT_MAX-3u;
    mIndexEndo = UINT_MAX-3u;
}

HeartConfig::~HeartConfig()
{
}

void HeartConfig::SetDefaultsFile(const std::string& rFileName)
{
    bool same_target = (mpUserParameters == mpDefaultParameters);

    mpDefaultParameters = ReadFile(rFileName);

    if (same_target)
    {
        mpUserParameters = mpDefaultParameters;
    }
    CheckTimeSteps();
}

void HeartConfig::Write(bool useArchiveLocationInfo, std::string subfolderName)
{
    //Output file
    std::string output_dirname;
    if (useArchiveLocationInfo)
    {
        output_dirname = ArchiveLocationInfo::GetArchiveDirectory();
    }
    else
    {
        OutputFileHandler handler(GetOutputDirectory() + "/" + subfolderName, false);
        output_dirname = handler.GetOutputDirectoryFullPath();
    }
    if (!PetscTools::AmMaster())
    {
        //Only the master process is writing the configuration files
        return;
    }
    out_stream p_defaults_file( new std::ofstream( (output_dirname+"ChasteDefaults.xml").c_str() ) );
    out_stream p_parameters_file( new std::ofstream( (output_dirname+"ChasteParameters.xml").c_str() ) );

    if (!p_defaults_file->is_open() || !p_parameters_file->is_open())
    {
        EXCEPTION("Could not open XML file in HeartConfig");
    }

    //Schema map
    //Note - this location is relative to where we are storing the xml
    ::xml_schema::namespace_infomap map;
    // Release 1.1 (and earlier) didn't use a namespace
    map[""].schema = "ChasteParameters_1_1.xsd";
    // Later releases use namespaces of the form https://chaste.comlab.ox.ac.uk/nss/parameters/N_M
    map["cp20"].name = "https://chaste.comlab.ox.ac.uk/nss/parameters/2_0";
    map["cp20"].schema = "ChasteParameters_2_0.xsd";
    // We use 'cp' as prefix for the latest version to avoid having to change saved
    // versions for comparison at every release.
    map["cp"].name = "https://chaste.comlab.ox.ac.uk/nss/parameters/2_1";
    map["cp"].schema = "ChasteParameters_2_1.xsd";

    cp::ChasteParameters(*p_parameters_file, *mpUserParameters, map);
    cp::ChasteParameters(*p_defaults_file, *mpDefaultParameters, map);
    
    // If we're archiving, try to save a copy of the latest schema too
    if (useArchiveLocationInfo)
    {
        CopySchema(output_dirname); 
    }
}

void HeartConfig::CopySchema(const std::string& rToDirectory)
{
    std::string schema_name("ChasteParameters_2_1.xsd");
    FileFinder schema_location("heart/src/io/" + schema_name, RelativeTo::ChasteSourceRoot);
    if (!schema_location.Exists())
    {
        // Try a relative path instead
        schema_location.SetPath(schema_name, RelativeTo::CWD);
        if (!schema_location.Exists())
        {
            // Warn the user
            std::string message("Unable to locate schema file " + schema_name +
                                ". You will need to ensure it is available when resuming from the checkpoint.");
            WARN_ONCE_ONLY(message);
        }
    }
    if (schema_location.Exists())
    {
        system(("cp " + schema_location.GetAbsolutePath() + " " + rToDirectory).c_str());
    }
}

void HeartConfig::SetDefaultSchemaLocations()
{
    mSchemaLocations.clear();
    // Location of schemas in the source tree
    std::string root_dir = std::string(ChasteBuildInfo::GetRootDir()) + "/heart/src/io/";
    // Release 1.1 (and earlier) didn't use a namespace
    mSchemaLocations[""] = root_dir + "ChasteParameters_1_1.xsd";
    // Later releases use namespaces of the form https://chaste.comlab.ox.ac.uk/nss/parameters/N_M
    mSchemaLocations["https://chaste.comlab.ox.ac.uk/nss/parameters/2_0"] = root_dir + "ChasteParameters_2_0.xsd";
    mSchemaLocations["https://chaste.comlab.ox.ac.uk/nss/parameters/2_1"] = root_dir + "ChasteParameters_2_1.xsd";
}

unsigned HeartConfig::GetVersionFromNamespace(const std::string& rNamespaceUri)
{
    unsigned version_major = 0;
    unsigned version_minor = 0;
    if (rNamespaceUri == "")
    {
        version_major = 1;
        version_minor = 1;
    }
    else
    {
        std::string uri_base("https://chaste.comlab.ox.ac.uk/nss/parameters/");
        if (rNamespaceUri.substr(0, uri_base.length()) == uri_base)
        {
            std::istringstream version_string(rNamespaceUri.substr(uri_base.length()));
            version_string >> version_major;
            version_string.ignore(1);
            version_string >> version_minor;
            if (version_string.fail())
            {
                version_major = 0;
                version_minor = 0;
            }
        }
    }
    
    unsigned version = version_major * 1000 + version_minor;
    if (version == 0)
    {
        EXCEPTION(rNamespaceUri + " is not a recognised Chaste parameters namespace.");
    }
    return version;
}

void HeartConfig::SetFixedSchemaLocations(const SchemaLocationsMap& rSchemaLocations)
{
    mSchemaLocations = rSchemaLocations;
    SetUseFixedSchemaLocation(true);
}

void HeartConfig::SetUseFixedSchemaLocation(bool useFixedSchemaLocation)
{
    mUseFixedSchemaLocation = useFixedSchemaLocation;
}

std::string HeartConfig::EscapeSpaces(const std::string& rPath)
{
    std::string escaped_path;
    for (std::string::const_iterator it = rPath.begin(); it != rPath.end(); ++it)
    {
        if (*it == ' ')
        {
            escaped_path += "%20";
        }
        else
        {
            escaped_path += *it;
        }
    }
    return escaped_path;
}

boost::shared_ptr<cp::chaste_parameters_type> HeartConfig::ReadFile(const std::string& rFileName)
{
    // Determine whether to use the schema path given in the input XML, or our own schema
    ::xml_schema::properties props;
    if (mUseFixedSchemaLocation)
    {
        for (SchemaLocationsMap::iterator it = mSchemaLocations.begin();
             it != mSchemaLocations.end();
             ++it)
        {
            if (it->first == "")
            {
                props.no_namespace_schema_location(EscapeSpaces(it->second));
            }
            else
            {
                props.schema_location(it->first, EscapeSpaces(it->second));
            }
        }
    }

    // Get the parameters using the method 'ChasteParameters(rFileName)',
    // which returns a std::auto_ptr. We convert to a shared_ptr for easier semantics.
    try
    {
        // Make sure Xerces initialization & finalization happens
        ::xsd::cxx::xml::auto_initializer init_fini(true, true);
        // Set up an error handler
        ::xsd::cxx::tree::error_handler<char> error_handler;
        // Parse XML to DOM
        xsd::cxx::xml::dom::auto_ptr<xercesc::DOMDocument> p_doc = XmlTools::ReadFileToDomDocument(rFileName, error_handler, props);
        // Any errors?
        error_handler.throw_if_failed< ::xsd::cxx::tree::parsing< char > >();
        // Test the namespace on the root element
        xercesc::DOMElement* p_root_elt = p_doc->getDocumentElement();
        std::string namespace_uri(xsd::cxx::xml::transcode<char>(p_root_elt->getNamespaceURI()));
        switch (GetVersionFromNamespace(namespace_uri))
        {
            case 1001: // Release 1.1 and earlier
                XmlTransforms::TransformIonicModelDefinitions(p_doc.get(), p_root_elt);
            case 2000: // Release 2.0
                XmlTransforms::TransformArchiveDirectory(p_doc.get(), p_root_elt);
                XmlTransforms::CheckForIluPreconditioner(p_doc.get(), p_root_elt);
                XmlTools::SetNamespace(p_doc.get(), p_root_elt, "https://chaste.comlab.ox.ac.uk/nss/parameters/2_1");
            default: // Current release - nothing to do
                break;
        }
        // Parse DOM to object model
        std::auto_ptr<cp::chaste_parameters_type> p_params(cp::ChasteParameters(*p_doc, ::xml_schema::flags::dont_initialize, props));
        // Get rid of the DOM stuff
        p_doc.reset();

        return boost::shared_ptr<cp::chaste_parameters_type>(p_params);
    }
    catch (const xml_schema::parsing& e)
    {
        // Make sure we don't store invalid parameters
        mpUserParameters.reset();
        mpDefaultParameters.reset();
        // Test for missing schema/xml file
#if (XSD_INT_VERSION >= 3000000L)
        const xml_schema::diagnostics& diags = e.diagnostics();
        const xml_schema::error& first_error = diags[0];
#else
        const xml_schema::errors& errors = e.errors();
        const xml_schema::error& first_error = errors[0];
#endif
        if (first_error.line() == 0u)
        {
            std::cerr << first_error << std::endl;
            EXCEPTION("Missing file parsing configuration file: " + rFileName);
        }
        else
        {
            std::cerr << e << std::endl;
            EXCEPTION("XML parsing error in configuration file: " + rFileName);
        }
    }
    catch (const xml_schema::exception& e)
    {
        std::cerr << e << std::endl;
        // Make sure we don't store invalid parameters
        mpUserParameters.reset();
        mpDefaultParameters.reset();
        EXCEPTION("XML parsing error in configuration file: " + rFileName);
    }
}

void HeartConfig::SetParametersFile(const std::string& rFileName)
{
    mpUserParameters = ReadFile(rFileName);

    CheckTimeSteps(); // For consistency with SetDefaultsFile
}


void HeartConfig::UpdateParametersFromResumeSimulation(boost::shared_ptr<cp::chaste_parameters_type> pResumeParameters)
{
    // Check for user foolishness
    if ( (pResumeParameters->ResumeSimulation()->SpaceDimension() != HeartConfig::Instance()->GetSpaceDimension())
         ||(pResumeParameters->ResumeSimulation()->Domain() != HeartConfig::Instance()->GetDomain()))
    {
        EXCEPTION("Problem type and space dimension should match when restarting a simulation.");
    }

    // New simulation duration
    HeartConfig::Instance()->SetSimulationDuration(pResumeParameters->ResumeSimulation()->SimulationDuration());
    
    // Stimulus definition.  For these we always replace any previous definitions (at least for now...)
    if (pResumeParameters->ResumeSimulation()->Stimuli().present())
    {
        mpUserParameters->Simulation()->Stimuli().set(pResumeParameters->ResumeSimulation()->Stimuli().get());
    }

    // Cell heterogeneities.  Note that while we copy the elements here, other code in CardiacSimulation actually updates
    // the loaded simulation to take account of the new settings.
    if (pResumeParameters->ResumeSimulation()->CellHeterogeneities().present())
    {
        if (!mpUserParameters->Simulation()->CellHeterogeneities().present())
        {
            // Original parameters had no heterogeneities, so just copy the whole element
            mpUserParameters->Simulation()->CellHeterogeneities().set(pResumeParameters->ResumeSimulation()->CellHeterogeneities().get());
        }
        else
        {
            // Need to append the new heterogeneity defitions to the original sequence
            XSD_SEQUENCE_TYPE(cp::cell_heterogeneities_type::CellHeterogeneity)&
                new_seq = pResumeParameters->ResumeSimulation()->CellHeterogeneities()->CellHeterogeneity();
            XSD_SEQUENCE_TYPE(cp::cell_heterogeneities_type::CellHeterogeneity)&
                orig_seq = mpUserParameters->Simulation()->CellHeterogeneities()->CellHeterogeneity();
            for (XSD_ITERATOR_TYPE(cp::cell_heterogeneities_type::CellHeterogeneity) i = new_seq.begin();
                 i != new_seq.end();
                 ++i)
            {
                orig_seq.push_back(*i);
            }
        }
    }
    
    // Whether to checkpoint the resumed simulation
    if (pResumeParameters->ResumeSimulation()->CheckpointSimulation().present())
    {
        HeartConfig::Instance()->SetCheckpointSimulation(true,
                                                         pResumeParameters->ResumeSimulation()->CheckpointSimulation()->timestep(),
                                                         pResumeParameters->ResumeSimulation()->CheckpointSimulation()->max_checkpoints_on_disk());
    }

    //Visualization parameters are compulsory
    HeartConfig::Instance()->SetVisualizeWithVtk(pResumeParameters->ResumeSimulation()->OutputVisualizer().vtk() == cp::yesno_type::yes);
    HeartConfig::Instance()->SetVisualizeWithCmgui(pResumeParameters->ResumeSimulation()->OutputVisualizer().cmgui() == cp::yesno_type::yes);
    HeartConfig::Instance()->SetVisualizeWithMeshalyzer(pResumeParameters->ResumeSimulation()->OutputVisualizer().meshalyzer() == cp::yesno_type::yes);

    // Numerical parameters may be overridden
    {
        cp::numerical_type& r_resume = pResumeParameters->Numerical();
        cp::numerical_type& r_user = mpUserParameters->Numerical();
        if (r_resume.TimeSteps().present())
        {
            r_user.TimeSteps().set(r_resume.TimeSteps().get());
        }
        if (r_resume.KSPTolerances().present())
        {
            r_user.KSPTolerances().set(r_resume.KSPTolerances().get());
        }
        if (r_resume.KSPSolver().present())
        {
            r_user.KSPSolver().set(r_resume.KSPSolver().get());
        }
        if (r_resume.KSPPreconditioner().present())
        {
            r_user.KSPPreconditioner().set(r_resume.KSPPreconditioner().get());
        }
        if (r_resume.AdaptivityParameters().present())
        {
            r_user.AdaptivityParameters().set(r_resume.AdaptivityParameters().get());
        }
    }

    // Post-processing parameters may be overridden
    if (pResumeParameters->PostProcessing().present())
    {
        EnsurePostProcessingSectionPresent();
        cp::postprocessing_type& r_resume = pResumeParameters->PostProcessing().get();
        cp::postprocessing_type& r_user = mpUserParameters->PostProcessing().get();
        if (!r_resume.ActionPotentialDurationMap().empty())
        {
            r_user.ActionPotentialDurationMap() = r_resume.ActionPotentialDurationMap();
        }
        if (!r_resume.UpstrokeTimeMap().empty())
        {
            r_user.UpstrokeTimeMap() = r_resume.UpstrokeTimeMap();
        }
        if (!r_resume.MaxUpstrokeVelocityMap().empty())
        {
            r_user.MaxUpstrokeVelocityMap() = r_resume.MaxUpstrokeVelocityMap();
        }
        if (!r_resume.ConductionVelocityMap().empty())
        {
            r_user.ConductionVelocityMap() = r_resume.ConductionVelocityMap();
        }
    }
}


void HeartConfig::Reset()
{
    // Throw it away first, so that mpInstance is NULL when we...
    mpInstance.reset();
    // ...make a new one
    mpInstance.reset(new HeartConfig);
}

bool HeartConfig::IsSimulationDefined() const
{
    return mpUserParameters->Simulation().present();
}

bool HeartConfig::IsSimulationResumed() const
{
    return mpUserParameters->ResumeSimulation().present();
}


template<class TYPE>
TYPE* HeartConfig::DecideLocation(TYPE* ptr1, TYPE* ptr2, const std::string& nameParameter) const
{
    if (ptr1->present())
    {
        return ptr1;
    }
    if (ptr2->present())
    {
        return ptr2;
    }
    EXCEPTION("No " + nameParameter + " provided (neither default nor user defined)");
}

void HeartConfig::CheckSimulationIsDefined(std::string callingMethod) const
{
    if (IsSimulationResumed())
    {
        EXCEPTION(callingMethod + " information is not available in a resumed simulation.");
    }
}

void HeartConfig::CheckResumeSimulationIsDefined(std::string callingMethod) const
{
    if (IsSimulationDefined())
    {
        EXCEPTION(callingMethod + " information is not available in a standard (non-resumed) simulation.");
    }
}

unsigned HeartConfig::GetSpaceDimension() const
{
    if (IsSimulationDefined())
    {
        return DecideLocation( & mpUserParameters->Simulation().get().SpaceDimension(),
                               & mpDefaultParameters->Simulation().get().SpaceDimension(),
                               "SpaceDimension")->get();
    }
    else
    {
        return mpUserParameters->ResumeSimulation().get().SpaceDimension();
    }
}

double HeartConfig::GetSimulationDuration() const
{
    if (IsSimulationDefined())
    {
        return DecideLocation( & mpUserParameters->Simulation().get().SimulationDuration(),
                               & mpDefaultParameters->Simulation().get().SimulationDuration(),
                               "Simulation/SimulationDuration")->get();
    }
    else // IsSimulationResumed
    {
        return mpUserParameters->ResumeSimulation().get().SimulationDuration();
    }
}

cp::domain_type HeartConfig::GetDomain() const
{
    if (IsSimulationDefined())
    {
        return DecideLocation( & mpUserParameters->Simulation().get().Domain(),
                               & mpDefaultParameters->Simulation().get().Domain(),
                               "Domain")->get();
    }
    else
    {
        return mpUserParameters->ResumeSimulation().get().Domain();
    }
}

cp::ionic_model_selection_type HeartConfig::GetDefaultIonicModel() const
{
    CheckSimulationIsDefined("DefaultIonicModel");

    return DecideLocation( & mpUserParameters->Simulation().get().IonicModels(),
                           & mpDefaultParameters->Simulation().get().IonicModels(),
                           "IonicModel")->get().Default();
}

template<unsigned DIM>
void HeartConfig::GetIonicModelRegions(std::vector<ChasteCuboid<DIM> >& definedRegions,
                                       std::vector<cp::ionic_model_selection_type>& ionicModels) const
{
    CheckSimulationIsDefined("IonicModelRegions");
    definedRegions.clear();
    ionicModels.clear();

    XSD_SEQUENCE_TYPE(cp::ionic_models_type::Region)&
         regions = DecideLocation( & mpUserParameters->Simulation().get().IonicModels(),
                                   & mpDefaultParameters->Simulation().get().IonicModels(),
                                   "IonicModel")->get().Region();

    for (XSD_ITERATOR_TYPE(cp::ionic_models_type::Region) i = regions.begin();
         i != regions.end();
         ++i)
    {
        cp::ionic_model_region_type ionic_model_region(*i);
        if (ionic_model_region.Location().Cuboid().present())
        {
            cp::point_type point_a = ionic_model_region.Location().Cuboid()->LowerCoordinates();
            cp::point_type point_b = ionic_model_region.Location().Cuboid()->UpperCoordinates();

            switch (DIM)
            {
                case 1:
                {
                    ChastePoint<DIM> chaste_point_a ( point_a.x() );
                    ChastePoint<DIM> chaste_point_b ( point_b.x() );
                    definedRegions.push_back(ChasteCuboid<DIM>( chaste_point_a, chaste_point_b ));
                    break;
                }
                case 2:
                {
                    ChastePoint<DIM> chaste_point_a ( point_a.x(), point_a.y() );
                    ChastePoint<DIM> chaste_point_b ( point_b.x(), point_b.y() );
                    definedRegions.push_back(ChasteCuboid<DIM>( chaste_point_a, chaste_point_b ));
                    break;
                }
                case 3:
                {
                    ChastePoint<DIM> chaste_point_a ( point_a.x(), point_a.y(), point_a.z() );
                    ChastePoint<DIM> chaste_point_b ( point_b.x(), point_b.y(), point_b.z() );
                    definedRegions.push_back(ChasteCuboid<DIM>( chaste_point_a, chaste_point_b ));
                    break;
                }
                default:
                    NEVER_REACHED;
                    break;
            }

            ionicModels.push_back(ionic_model_region.IonicModel());
        }
        else
        {
            if(ionic_model_region.Location().EpiLayer().present() || ionic_model_region.Location().MidLayer().present() || ionic_model_region.Location().EndoLayer().present() )
            {
                EXCEPTION("Definition of transmural layers is not yet supported for defining different ionic models, please use cuboids instead");
            }
        }
    }
}


bool HeartConfig::IsMeshProvided() const
{
    CheckSimulationIsDefined("Mesh");

    try
    {
        DecideLocation( & mpUserParameters->Simulation().get().Mesh(),
                        & mpDefaultParameters->Simulation().get().Mesh(),
                        "Mesh");
        return true;
    }
    catch (Exception& e)
    {
        return false;
    }
}

bool HeartConfig::GetCreateMesh() const
{
    CheckSimulationIsDefined("Mesh");

    cp::mesh_type mesh = DecideLocation( & mpUserParameters->Simulation().get().Mesh(),
                                         & mpDefaultParameters->Simulation().get().Mesh(),
                                         "Mesh")->get();

    return (mesh.Slab().present() || mesh.Sheet().present() || mesh.Fibre().present());
}

bool HeartConfig::GetCreateSlab() const
{
    CheckSimulationIsDefined("Mesh");

    cp::mesh_type mesh = DecideLocation( & mpUserParameters->Simulation().get().Mesh(),
                                         & mpDefaultParameters->Simulation().get().Mesh(),
                                         "Mesh")->get();

    return (mesh.Slab().present());
}

bool HeartConfig::GetCreateSheet() const
{
    CheckSimulationIsDefined("Mesh");

    cp::mesh_type mesh = DecideLocation( & mpUserParameters->Simulation().get().Mesh(),
                                         & mpDefaultParameters->Simulation().get().Mesh(),
                                         "Mesh")->get();

    return (mesh.Sheet().present());
}

bool HeartConfig::GetCreateFibre() const
{
    CheckSimulationIsDefined("Mesh");

    cp::mesh_type mesh = DecideLocation( & mpUserParameters->Simulation().get().Mesh(),
                                         & mpDefaultParameters->Simulation().get().Mesh(),
                                         "Mesh")->get();

    return (mesh.Fibre().present());
}


bool HeartConfig::GetLoadMesh() const
{
    CheckSimulationIsDefined("Mesh");

    return (DecideLocation( & mpUserParameters->Simulation().get().Mesh(),
                            & mpDefaultParameters->Simulation().get().Mesh(),
                            "Mesh")->get().LoadMesh().present());
}

void HeartConfig::GetSlabDimensions(c_vector<double, 3>& slabDimensions) const
{
    CheckSimulationIsDefined("Slab");

    if (GetSpaceDimension()!=3 || !GetCreateSlab())
    {
        EXCEPTION("Tissue slabs can only be defined in 3D");
    }

    optional<cp::slab_type, false> slab_dimensions = DecideLocation( & mpUserParameters->Simulation().get().Mesh(),
                                                                     & mpDefaultParameters->Simulation().get().Mesh(),
                                                                     "Slab")->get().Slab();

    slabDimensions[0] = slab_dimensions->x();
    slabDimensions[1] = slab_dimensions->y();
    slabDimensions[2] = slab_dimensions->z();
}

void HeartConfig::GetSheetDimensions(c_vector<double, 2>& sheetDimensions) const
{
    CheckSimulationIsDefined("Sheet");

    if (GetSpaceDimension()!=2 || !GetCreateSheet())
    {
        EXCEPTION("Tissue sheets can only be defined in 2D");
    }

    optional<cp::sheet_type, false> sheet_dimensions = DecideLocation( & mpUserParameters->Simulation().get().Mesh(),
                                                                       & mpDefaultParameters->Simulation().get().Mesh(),
                                                                       "Sheet")->get().Sheet();

    sheetDimensions[0] = sheet_dimensions->x();
    sheetDimensions[1] = sheet_dimensions->y();
}

void HeartConfig::GetFibreLength(c_vector<double, 1>& fibreLength) const
{
    CheckSimulationIsDefined("Fibre");

    if (GetSpaceDimension()!=1 || !GetCreateFibre())
    {
        EXCEPTION("Tissue fibres can only be defined in 1D");
    }

    optional<cp::fibre_type, false> fibre_length = DecideLocation( & mpUserParameters->Simulation().get().Mesh(),
                                                                   & mpDefaultParameters->Simulation().get().Mesh(),
                                                                   "Fibre")->get().Fibre();

    fibreLength[0] = fibre_length->x();
}


double HeartConfig::GetInterNodeSpace() const
{
    CheckSimulationIsDefined("InterNodeSpace");
    assert(GetCreateMesh());

    switch(GetSpaceDimension())
    {
        case 3:
            return DecideLocation( & mpUserParameters->Simulation().get().Mesh(),
                                   & mpDefaultParameters->Simulation().get().Mesh(),
                                   "Slab")->get().Slab()->inter_node_space();
            break;
        case 2:
            return DecideLocation( & mpUserParameters->Simulation().get().Mesh(),
                                   & mpDefaultParameters->Simulation().get().Mesh(),
                                   "Sheet")->get().Sheet()->inter_node_space();
            break;
        case 1:
            return DecideLocation( & mpUserParameters->Simulation().get().Mesh(),
                                   & mpDefaultParameters->Simulation().get().Mesh(),
                                   "Fibre")->get().Fibre()->inter_node_space();
            break;
        default:
            NEVER_REACHED;
#define COVERAGE_IGNORE
            return 0.0; //To fool the compiler
#undef COVERAGE_IGNORE
    }
}

std::string HeartConfig::GetMeshName() const
{
    CheckSimulationIsDefined("LoadMesh");
    assert(GetLoadMesh());

    return DecideLocation( & mpUserParameters->Simulation().get().Mesh(),
                           & mpDefaultParameters->Simulation().get().Mesh(),
                           "LoadMesh")->get().LoadMesh()->name();
}

cp::media_type HeartConfig::GetConductivityMedia() const
{
    CheckSimulationIsDefined("LoadMesh");
    assert(GetLoadMesh());

    return DecideLocation( & mpUserParameters->Simulation().get().Mesh(),
                           & mpDefaultParameters->Simulation().get().Mesh(),
                           "LoadMesh")->get().LoadMesh()->conductivity_media();
}

template <unsigned DIM>
void HeartConfig::GetStimuli(std::vector<boost::shared_ptr<AbstractStimulusFunction> >& rStimuliApplied,
                             std::vector<ChasteCuboid<DIM> >& rStimulatedAreas) const
{
    CheckSimulationIsDefined("Stimuli");
    XSD_SEQUENCE_TYPE(cp::stimuli_type::Stimulus)&
         stimuli = DecideLocation( & mpUserParameters->Simulation().get().Stimuli(),
                                   & mpDefaultParameters->Simulation().get().Stimuli(),
                                   "Stimuli")->get().Stimulus();
    for (XSD_ITERATOR_TYPE(cp::stimuli_type::Stimulus) i = stimuli.begin();
         i != stimuli.end();
         ++i)
    {
        cp::stimulus_type stimulus(*i);
        if (stimulus.Location().Cuboid().present())
        {
            cp::point_type point_a = stimulus.Location().Cuboid()->LowerCoordinates();
            cp::point_type point_b = stimulus.Location().Cuboid()->UpperCoordinates();
            switch (DIM)
            {
                case 1:
                {
                    ChastePoint<DIM> chaste_point_a ( point_a.x() );
                    ChastePoint<DIM> chaste_point_b ( point_b.x() );
                    rStimulatedAreas.push_back( ChasteCuboid<DIM>( chaste_point_a, chaste_point_b ) );
                    break;
                }
                case 2:
                {
                    ChastePoint<DIM> chaste_point_a ( point_a.x(), point_a.y() );
                    ChastePoint<DIM> chaste_point_b ( point_b.x(), point_b.y() );
                    rStimulatedAreas.push_back( ChasteCuboid<DIM>( chaste_point_a, chaste_point_b ) );
                    break;
                }
                case 3:
                {
                    ChastePoint<DIM> chaste_point_a ( point_a.x(), point_a.y(), point_a.z() );
                    ChastePoint<DIM> chaste_point_b ( point_b.x(), point_b.y(), point_b.z() );
                    rStimulatedAreas.push_back( ChasteCuboid<DIM>( chaste_point_a, chaste_point_b ) );
                    break;
                }
                default:
                    NEVER_REACHED;
                    break;
            }
            
            boost::shared_ptr<AbstractStimulusFunction> stim;           
            
            if (stimulus.Period().present())
            {
                if (stimulus.StopTime().present())
                {
                    stim.reset(new RegularStimulus(stimulus.Strength(),
                                                   stimulus.Duration(),
                                                   stimulus.Period().get(),
                                                   stimulus.Delay(),
                                                   stimulus.StopTime().get()));                
                }
                else
                {
                    stim.reset(new RegularStimulus(stimulus.Strength(),
                                                   stimulus.Duration(),
                                                   stimulus.Period().get(),
                                                   stimulus.Delay()));
                }
                                
            }
            else
            {
                if (stimulus.StopTime().present())
                {
                    EXCEPTION("Stop time can not be defined for SimpleStimulus. Use Duration instead.");
                }                
                
                stim.reset(new SimpleStimulus(stimulus.Strength(),
                                              stimulus.Duration(),
                                              stimulus.Delay()));
            }
            rStimuliApplied.push_back( stim );
        }
        else
        {
            if(stimulus.Location().EpiLayer().present() || stimulus.Location().MidLayer().present() || stimulus.Location().EndoLayer().present() )
            {
                EXCEPTION("Definition of transmural layers is not yet supported for specifying stimulated areas, please use cuboids instead");
            }
        }
    }
}


template<unsigned DIM>
void HeartConfig::GetCellHeterogeneities(std::vector<AbstractChasteRegion<DIM>* >& rCellHeterogeneityRegions,
                                         std::vector<double>& rScaleFactorGks,
                                         std::vector<double>& rScaleFactorIto,
                                         std::vector<double>& rScaleFactorGkr,
                                         std::vector<std::map<std::string, double> >* pParameterSettings)
{
    CheckSimulationIsDefined("CellHeterogeneities");
    XSD_SEQUENCE_TYPE(cp::cell_heterogeneities_type::CellHeterogeneity)&
         cell_heterogeneity = DecideLocation( & mpUserParameters->Simulation().get().CellHeterogeneities(),
                                              & mpDefaultParameters->Simulation().get().CellHeterogeneities(),
                                              "CellHeterogeneities")->get().CellHeterogeneity();

    bool user_supplied_negative_value = false;
    bool user_asking_for_transmural_layers = false;
    unsigned counter_of_heterogeneities = 0;

    for (XSD_ITERATOR_TYPE(cp::cell_heterogeneities_type::CellHeterogeneity) i = cell_heterogeneity.begin();
         i != cell_heterogeneity.end();
         ++i)
    {
        cp::cell_heterogeneity_type ht(*i);

        if (ht.Location().Cuboid().present())
        {
            mUserAskedForCuboidsForCellularHeterogeneities = true;
            cp::point_type point_a = ht.Location().Cuboid()->LowerCoordinates();
            cp::point_type point_b = ht.Location().Cuboid()->UpperCoordinates();
            
            ChastePoint<DIM> chaste_point_a ( point_a.x(), point_a.y(), point_a.z() );
            ChastePoint<DIM> chaste_point_b ( point_b.x(), point_b.y(), point_b.z() );
            rCellHeterogeneityRegions.push_back(new ChasteCuboid<DIM> ( chaste_point_a, chaste_point_b ) );
        }
        else
        {

            if (ht.Location().EpiLayer().present())
            {
                mEpiFraction  =  ht.Location().EpiLayer().get();

                user_asking_for_transmural_layers = true;
                if (mEpiFraction <0)
                {
                    user_supplied_negative_value=true;
                }
                mIndexEpi = counter_of_heterogeneities;
            }
            if (ht.Location().EndoLayer().present())
            {
                mEndoFraction  =  ht.Location().EndoLayer().get();

                user_asking_for_transmural_layers = true;
                if (mEndoFraction <0)
                {
                    user_supplied_negative_value=true;
                }
                mIndexEndo = counter_of_heterogeneities;
            }
            if (ht.Location().MidLayer().present())
            {
                mMidFraction  =  ht.Location().MidLayer().get();

                user_asking_for_transmural_layers = true;
                if (mMidFraction <0)
                {
                    user_supplied_negative_value=true;
                }
                mIndexMid =  counter_of_heterogeneities;
            }
        }
        // Old scale factors
        rScaleFactorGks.push_back(ht.ScaleFactorGks().present() ? (double)ht.ScaleFactorGks().get() : 1.0);
        rScaleFactorIto.push_back(ht.ScaleFactorIto().present() ? (double)ht.ScaleFactorIto().get() : 1.0);
        rScaleFactorGkr.push_back(ht.ScaleFactorGkr().present() ? (double)ht.ScaleFactorGkr().get() : 1.0);
        
        // Named parameters
        if (pParameterSettings)
        {
            std::map<std::string, double> param_settings;
            XSD_SEQUENCE_TYPE(cp::cell_heterogeneity_type::SetParameter)& params = ht.SetParameter();
            for (XSD_ITERATOR_TYPE(cp::cell_heterogeneity_type::SetParameter) param_it = params.begin();
                 param_it != params.end();
                 ++param_it)
            {
                cp::set_parameter_type param(*param_it);
                param_settings[param.name()] = param.value();
            }
            pParameterSettings->push_back(param_settings);
        }
        
        counter_of_heterogeneities++;
    }

    //set the flag for request of transmural layers
    mUserAskedForCellularTransmuralHeterogeneities = user_asking_for_transmural_layers;

    // cuboids and layers at the same time are not yet supported
    if (mUserAskedForCuboidsForCellularHeterogeneities && mUserAskedForCellularTransmuralHeterogeneities)
    {
        // free the pointers before throwing the exception
        for (unsigned index=0;index < rCellHeterogeneityRegions.size(); index++)
        {
            delete rCellHeterogeneityRegions[index];
        }
        EXCEPTION ("Specification of cellular heterogeneities by cuboids and layers at the same time is not yet supported");
    }
    //check the user input if the transmural heterogeneities have been requested
    if (mUserAskedForCellularTransmuralHeterogeneities)
    {
        //check that the user supplied all three layers, the indexes should be 0, 1 and 2.
        // As they are initialised to a higher value, if their summation is higher than 3,
        // one (or more) is missing
        if ((mIndexMid+mIndexEndo+mIndexEpi) > 3)
        {
            EXCEPTION ("Three specifications of layers must be supplied");
        }
        if (fabs((mEndoFraction+mMidFraction+mEpiFraction)-1)>1e-2)
        {
            EXCEPTION ("Summation of epicardial, midmyocardial and endocardial fractions should be 1");
        }
        if (user_supplied_negative_value)
        {
           EXCEPTION ("Fractions must be positive");
        }
    }
}

bool HeartConfig::AreCellularTransmuralHeterogeneitiesRequested()
{
    return mUserAskedForCellularTransmuralHeterogeneities;
}

bool HeartConfig::AreCellularHeterogeneitiesSpecifiedByCuboids()
{
    return mUserAskedForCuboidsForCellularHeterogeneities;
}

double HeartConfig::GetEpiLayerFraction()
{
    return mEpiFraction;
}

double HeartConfig::GetEndoLayerFraction()
{
    return mEndoFraction;
}

double HeartConfig::GetMidLayerFraction()
{
    return mMidFraction;
}

unsigned HeartConfig::GetEpiLayerIndex()
{
    return mIndexEpi;
}

unsigned HeartConfig::GetEndoLayerIndex()
{
    return mIndexEndo;
}

unsigned HeartConfig::GetMidLayerIndex()
{
    return mIndexMid;
}

bool HeartConfig::GetConductivityHeterogeneitiesProvided() const
{
    CheckSimulationIsDefined("ConductivityHeterogeneities");
    try
    {
        DecideLocation( & mpUserParameters->Simulation().get().ConductivityHeterogeneities(),
                        & mpDefaultParameters->Simulation().get().ConductivityHeterogeneities(),
                        "ConductivityHeterogeneities");
        return true;
    }
    catch (Exception& e)
    {
        return false;
    }
}

template<unsigned DIM>
void HeartConfig::GetConductivityHeterogeneities(
        std::vector<AbstractChasteRegion<DIM>* >& conductivitiesHeterogeneityAreas,
        std::vector< c_vector<double,3> >& intraConductivities,
        std::vector< c_vector<double,3> >& extraConductivities) const
{
    CheckSimulationIsDefined("ConductivityHeterogeneities");
    XSD_ANON_SEQUENCE_TYPE(cp::simulation_type, ConductivityHeterogeneities, ConductivityHeterogeneity)&
         conductivity_heterogeneity = DecideLocation( & mpUserParameters->Simulation().get().ConductivityHeterogeneities(),
                                                      & mpDefaultParameters->Simulation().get().ConductivityHeterogeneities(),
                                                      "ConductivityHeterogeneities")->get().ConductivityHeterogeneity();

    for (XSD_ANON_ITERATOR_TYPE(cp::simulation_type, ConductivityHeterogeneities, ConductivityHeterogeneity) i = conductivity_heterogeneity.begin();
         i != conductivity_heterogeneity.end();
         ++i)
    {
        cp::conductivity_heterogeneity_type ht(*i);
        if (ht.Location().Cuboid().present())
        {
            cp::point_type point_a = ht.Location().Cuboid()->LowerCoordinates();
            cp::point_type point_b = ht.Location().Cuboid()->UpperCoordinates();
            ChastePoint<DIM> chaste_point_a ( point_a.x(), point_a.y(), point_a.z() );
            ChastePoint<DIM> chaste_point_b ( point_b.x(), point_b.y(), point_b.z() );
            conductivitiesHeterogeneityAreas.push_back( new ChasteCuboid<DIM> ( chaste_point_a, chaste_point_b ) );
        }
        else if (ht.Location().Ellipsoid().present())
        {
            cp::point_type centre = ht.Location().Ellipsoid()->Centre();
            cp::point_type radii  = ht.Location().Ellipsoid()->Radii();
            ChastePoint<DIM> chaste_point_a ( centre.x(), centre.y(), centre.z() );
            ChastePoint<DIM> chaste_point_b ( radii.x(), radii.y(), radii.z() );
            conductivitiesHeterogeneityAreas.push_back( new ChasteEllipsoid<DIM> ( chaste_point_a, chaste_point_b ) );
        }
        else
        {
            if(ht.Location().EpiLayer().present() || ht.Location().MidLayer().present() || ht.Location().EndoLayer().present() )
            {
                EXCEPTION("Definition of transmural layers is not allowed for conductivities heterogeneities, you may use fibre orientation support instead");
            }
        }

        if (ht.IntracellularConductivities().present())
        {
            double intra_x = ht.IntracellularConductivities().get().longi();
            double intra_y = ht.IntracellularConductivities().get().trans();
            double intra_z = ht.IntracellularConductivities().get().normal();

            intraConductivities.push_back( Create_c_vector(intra_x, intra_y, intra_z) );
        }
        else
        {
            c_vector<double, 3> intra_conductivities;
            GetIntracellularConductivities(intra_conductivities);
            intraConductivities.push_back(intra_conductivities);
        }

        if (ht.ExtracellularConductivities().present())
        {
            double extra_x = ht.ExtracellularConductivities().get().longi();
            double extra_y = ht.ExtracellularConductivities().get().trans();
            double extra_z = ht.ExtracellularConductivities().get().normal();

            extraConductivities.push_back( Create_c_vector(extra_x, extra_y, extra_z) );
        }
        else
        {
            c_vector<double, 3> extra_conductivities;
            GetExtracellularConductivities(extra_conductivities);
            extraConductivities.push_back(extra_conductivities);
        }

    }
}

std::string HeartConfig::GetOutputDirectory() const
{
    CheckSimulationIsDefined("Simulation/OutputDirectory");
    return DecideLocation( & mpUserParameters->Simulation().get().OutputDirectory(),
                           & mpDefaultParameters->Simulation().get().OutputDirectory(),
                           "Simulation/OutputDirectory")->get();
}

std::string HeartConfig::GetOutputFilenamePrefix() const
{
    CheckSimulationIsDefined("Simulation/OutputFilenamePrefix");
    return DecideLocation( & mpUserParameters->Simulation().get().OutputFilenamePrefix(),
                           & mpDefaultParameters->Simulation().get().OutputFilenamePrefix(),
                           "Simulation/OutputFilenamePrefix")->get();
}

bool HeartConfig::GetOutputVariablesProvided() const
{
    CheckSimulationIsDefined("OutputVariables");

    try
    {
        DecideLocation( & mpUserParameters->Simulation().get().OutputVariables(),
                        & mpDefaultParameters->Simulation().get().OutputVariables(),
                        "OutputVariables");
        return true;
    }
    catch (Exception& e)
    {
        return false;
    }
}

void HeartConfig::GetOutputVariables(std::vector<std::string>& rOutputVariables) const
{
    CheckSimulationIsDefined("OutputVariables");
    XSD_SEQUENCE_TYPE(cp::output_variables_type::Var)&
         output_variables = DecideLocation( & mpUserParameters->Simulation().get().OutputVariables(),
                                            & mpDefaultParameters->Simulation().get().OutputVariables(),
                                            "OutputVariables")->get().Var();
    rOutputVariables.clear();

    for (XSD_ITERATOR_TYPE(cp::output_variables_type::Var) i = output_variables.begin();
         i != output_variables.end();
         ++i)
    {
        cp::var_type& r_var(*i);

        // Add to outputVariables the string returned by var.name()
        rOutputVariables.push_back(r_var.name());
    }
}
bool HeartConfig::GetOutputUsingOriginalNodeOrdering()
{
    try 
    {
        return (DecideLocation(& mpUserParameters->Simulation().get().OutputUsingOriginalNodeOrdering(),
                               & mpDefaultParameters->Simulation().get().OutputUsingOriginalNodeOrdering(),
                              "OutputUsingOriginalNodeOrdering")->get()  == cp::yesno_type::yes);
    }
    catch (Exception &e)
    {
        //If it didn't exist, then we default to false
        return false;
    }
}

bool HeartConfig::GetCheckpointSimulation() const
{
    try
    {
        if (IsSimulationDefined())
        {
            CheckSimulationIsDefined("GetSaveSimulation");
            DecideLocation( & mpUserParameters->Simulation().get().CheckpointSimulation(),
                            & mpDefaultParameters->Simulation().get().CheckpointSimulation(),
                            "Simulation/SaveSimulation");
        }
        else 
        {
            CheckResumeSimulationIsDefined("GetSaveSimulation");
            DecideLocation( & mpUserParameters->ResumeSimulation().get().CheckpointSimulation(),
                            & mpDefaultParameters->Simulation().get().CheckpointSimulation(),
                            "ResumeSimulation/SaveSimulation");
        }
        return true;
    }
    catch (Exception& e)
    {
        return false;
    }
}

double HeartConfig::GetCheckpointTimestep() const
{
    if (IsSimulationDefined())
    {
        CheckSimulationIsDefined("GetSaveSimulation");
        return DecideLocation( & mpUserParameters->Simulation().get().CheckpointSimulation(),
                        & mpDefaultParameters->Simulation().get().CheckpointSimulation(),
                        "Simulation/SaveSimulation")->get().timestep();
    }
    else 
    {
        CheckResumeSimulationIsDefined("GetSaveSimulation");
        return DecideLocation( & mpUserParameters->ResumeSimulation().get().CheckpointSimulation(),
                        & mpDefaultParameters->Simulation().get().CheckpointSimulation(),
                        "ResumeSimulation/SaveSimulation")->get().timestep();
    }
}

unsigned HeartConfig::GetMaxCheckpointsOnDisk() const
{
    if (IsSimulationDefined())
    {
        CheckSimulationIsDefined("GetSaveSimulation");
        return DecideLocation( & mpUserParameters->Simulation().get().CheckpointSimulation(),
                        & mpDefaultParameters->Simulation().get().CheckpointSimulation(),
                        "Simulation/SaveSimulation")->get().max_checkpoints_on_disk();
    }
    else 
    {
        CheckResumeSimulationIsDefined("GetSaveSimulation");
        return DecideLocation( & mpUserParameters->ResumeSimulation().get().CheckpointSimulation(),
                        & mpDefaultParameters->Simulation().get().CheckpointSimulation(),
                        "ResumeSimulation/SaveSimulation")->get().max_checkpoints_on_disk();
    }
}


HeartFileFinder HeartConfig::GetArchivedSimulationDir() const
{
    CheckResumeSimulationIsDefined("GetArchivedSimulationDir");

    return HeartFileFinder(mpUserParameters->ResumeSimulation().get().ArchiveDirectory());
}


void HeartConfig::GetIntracellularConductivities(c_vector<double, 3>& intraConductivities) const
{
    optional<cp::conductivities_type, false>* intra_conductivities
        = DecideLocation( & mpUserParameters->Physiological().IntracellularConductivities(),
                          & mpDefaultParameters->Physiological().IntracellularConductivities(),
                          "IntracellularConductivities");
    double intra_x_cond = intra_conductivities->get().longi();
    double intra_y_cond = intra_conductivities->get().trans();
    double intra_z_cond = intra_conductivities->get().normal();;

    assert(intra_y_cond != DBL_MAX);
    assert(intra_z_cond != DBL_MAX);

    intraConductivities[0] = intra_x_cond;
    intraConductivities[1] = intra_y_cond;
    intraConductivities[2] = intra_z_cond;
}

void HeartConfig::GetIntracellularConductivities(c_vector<double, 2>& intraConductivities) const
{
    optional<cp::conductivities_type, false>* intra_conductivities
        = DecideLocation( & mpUserParameters->Physiological().IntracellularConductivities(),
                          & mpDefaultParameters->Physiological().IntracellularConductivities(),
                          "IntracellularConductivities");
    double intra_x_cond = intra_conductivities->get().longi();
    double intra_y_cond = intra_conductivities->get().trans();

    assert(intra_y_cond != DBL_MAX);

    intraConductivities[0] = intra_x_cond;
    intraConductivities[1] = intra_y_cond;
}

void HeartConfig::GetIntracellularConductivities(c_vector<double, 1>& intraConductivities) const
{
    optional<cp::conductivities_type, false>* intra_conductivities
        = DecideLocation( & mpUserParameters->Physiological().IntracellularConductivities(),
                          & mpDefaultParameters->Physiological().IntracellularConductivities(),
                          "IntracellularConductivities");
    double intra_x_cond = intra_conductivities->get().longi();

    intraConductivities[0] = intra_x_cond;
}

void HeartConfig::GetExtracellularConductivities(c_vector<double, 3>& extraConductivities) const
{
    optional<cp::conductivities_type, false>* extra_conductivities
        = DecideLocation( & mpUserParameters->Physiological().ExtracellularConductivities(),
                          & mpDefaultParameters->Physiological().ExtracellularConductivities(),
                          "ExtracellularConductivities");
    double extra_x_cond = extra_conductivities->get().longi();
    double extra_y_cond = extra_conductivities->get().trans();
    double extra_z_cond = extra_conductivities->get().normal();;

    assert(extra_y_cond != DBL_MAX);
    assert(extra_z_cond != DBL_MAX);

    extraConductivities[0] = extra_x_cond;
    extraConductivities[1] = extra_y_cond;
    extraConductivities[2] = extra_z_cond;
}

void HeartConfig::GetExtracellularConductivities(c_vector<double, 2>& extraConductivities) const
{
    optional<cp::conductivities_type, false>* extra_conductivities
        = DecideLocation( & mpUserParameters->Physiological().ExtracellularConductivities(),
                          & mpDefaultParameters->Physiological().ExtracellularConductivities(),
                          "ExtracellularConductivities");
    double extra_x_cond = extra_conductivities->get().longi();
    double extra_y_cond = extra_conductivities->get().trans();

    assert(extra_y_cond != DBL_MAX);

    extraConductivities[0] = extra_x_cond;
    extraConductivities[1] = extra_y_cond;
}

void HeartConfig::GetExtracellularConductivities(c_vector<double, 1>& extraConductivities) const
{
    optional<cp::conductivities_type, false>* extra_conductivities
        = DecideLocation( & mpUserParameters->Physiological().ExtracellularConductivities(),
                          & mpDefaultParameters->Physiological().ExtracellularConductivities(),
                          "ExtracellularConductivities");
    double extra_x_cond = extra_conductivities->get().longi();

    extraConductivities[0] = extra_x_cond;
}

double HeartConfig::GetBathConductivity() const
{
    /*bath conductivity mS/cm*/
    return DecideLocation( & mpUserParameters->Physiological().BathConductivity(),
                           & mpDefaultParameters->Physiological().BathConductivity(),
                           "BathConductivity")->get();
}

double HeartConfig::GetSurfaceAreaToVolumeRatio() const
{
    /*surface area to volume ratio: 1/cm*/
    return DecideLocation( & mpUserParameters->Physiological().SurfaceAreaToVolumeRatio(),
                           & mpDefaultParameters->Physiological().SurfaceAreaToVolumeRatio(),
                           "SurfaceAreaToVolumeRatio")->get();
}

double HeartConfig::GetCapacitance() const
{
    //         capacitance                 : uF/cm^2
    return DecideLocation( & mpUserParameters->Physiological().Capacitance(),
                           & mpDefaultParameters->Physiological().Capacitance(),
                           "Capacitance")->get();
}

double HeartConfig::GetOdeTimeStep() const
{
    return DecideLocation( & mpUserParameters->Numerical().TimeSteps(),
                           & mpDefaultParameters->Numerical().TimeSteps(),
                           "ode TimeStep")->get().ode();
}

double HeartConfig::GetPdeTimeStep() const
{
    return DecideLocation( & mpUserParameters->Numerical().TimeSteps(),
                           & mpDefaultParameters->Numerical().TimeSteps(),
                           "pde TimeStep")->get().pde();
}

double HeartConfig::GetPrintingTimeStep() const
{
    return DecideLocation( & mpUserParameters->Numerical().TimeSteps(),
                           & mpDefaultParameters->Numerical().TimeSteps(),
                           "printing TimeStep")->get().printing();
}

bool HeartConfig::GetUseAbsoluteTolerance() const
{
    return DecideLocation( & mpUserParameters->Numerical().KSPTolerances(),
                            & mpDefaultParameters->Numerical().KSPTolerances(),
                            "KSPTolerances")->get().KSPAbsolute().present();
}

double HeartConfig::GetAbsoluteTolerance() const
{
    if (!GetUseAbsoluteTolerance())
    {
        EXCEPTION("Absolute tolerance is not set in Chaste parameters");
    }
    return DecideLocation( & mpUserParameters->Numerical().KSPTolerances(),
                           & mpDefaultParameters->Numerical().KSPTolerances(),
                           "KSPTolerances")->get().KSPAbsolute().get();
}

bool HeartConfig::GetUseRelativeTolerance() const
{
     return DecideLocation( & mpUserParameters->Numerical().KSPTolerances(),
                            & mpDefaultParameters->Numerical().KSPTolerances(),
                            "KSPTolerances")->get().KSPRelative().present();
}

double HeartConfig::GetRelativeTolerance() const
{
    if (!GetUseRelativeTolerance())
    {
        EXCEPTION("Relative tolerance is not set in Chaste parameters");
    }
    return DecideLocation( & mpUserParameters->Numerical().KSPTolerances(),
                           & mpDefaultParameters->Numerical().KSPTolerances(),
                           "KSPTolerances")->get().KSPRelative().get();
}

const char* HeartConfig::GetKSPSolver() const
{
    switch ( DecideLocation( & mpUserParameters->Numerical().KSPSolver(),
                             & mpDefaultParameters->Numerical().KSPSolver(),
                            "KSPSolver")->get() )
    {
        case cp::ksp_solver_type::gmres :
            return "gmres";
        case cp::ksp_solver_type::cg :
            return "cg";
        case cp::ksp_solver_type::symmlq :
            return "symmlq";
    }
#define COVERAGE_IGNORE
    EXCEPTION("Unknown ksp solver");
#undef COVERAGE_IGNORE
}

const char* HeartConfig::GetKSPPreconditioner() const
{
    switch ( DecideLocation( & mpUserParameters->Numerical().KSPPreconditioner(),
                             & mpDefaultParameters->Numerical().KSPPreconditioner(),
                             "KSPPreconditioner")->get() )
    {
        case cp::ksp_preconditioner_type::jacobi :
            return "jacobi";
        case cp::ksp_preconditioner_type::bjacobi :
            return "bjacobi";
        case cp::ksp_preconditioner_type::hypre :
            return "hypre";
        case cp::ksp_preconditioner_type::ml :
            return "ml";
        case cp::ksp_preconditioner_type::spai :
            return "spai";
        case cp::ksp_preconditioner_type::blockdiagonal :
            return "blockdiagonal";
        case cp::ksp_preconditioner_type::ldufactorisation :
            return "ldufactorisation";
        case cp::ksp_preconditioner_type::twolevelsblockdiagonal :
            return "twolevelsblockdiagonal";
        case cp::ksp_preconditioner_type::none :
            return "none";

    }
#define COVERAGE_IGNORE
    EXCEPTION("Unknown ksp preconditioner");
#undef COVERAGE_IGNORE
}

bool HeartConfig::IsAdaptivityParametersPresent() const
{
    try
    {
        DecideLocation( & mpUserParameters->Numerical().AdaptivityParameters(),
                        & mpDefaultParameters->Numerical().AdaptivityParameters(),
                        "AdaptivityParameters")->present();
        //If there's a section
        return true;
    }
    catch (Exception &e)
    {
        //No section
        return false;
    }
}

double HeartConfig::GetTargetErrorForAdaptivity() const
{
    if ( IsAdaptivityParametersPresent() )
    {
        return DecideLocation( & mpUserParameters->Numerical().AdaptivityParameters(),
                               & mpDefaultParameters->Numerical().AdaptivityParameters(),
                               "TargetError")->get().target_error();
    }
    else
    {
        EXCEPTION("Adaptivity parameters have not been set");
    }
}

double HeartConfig::GetSigmaForAdaptivity() const
{
    if ( IsAdaptivityParametersPresent() )
    {
        return DecideLocation( & mpUserParameters->Numerical().AdaptivityParameters(),
                               & mpDefaultParameters->Numerical().AdaptivityParameters(),
                               "TargetError")->get().sigma();
    }
    else
    {
        EXCEPTION("Adaptivity parameters have not been set");
    }
}

double HeartConfig::GetMaxEdgeLengthForAdaptivity() const
{
    if ( IsAdaptivityParametersPresent() )
    {
    return DecideLocation( & mpUserParameters->Numerical().AdaptivityParameters(),
                           & mpDefaultParameters->Numerical().AdaptivityParameters(),
                           "TargetError")->get().max_edge_length();
    }
    else
    {
        EXCEPTION("Adaptivity parameters have not been set");
    }
}

double HeartConfig::GetMinEdgeLengthForAdaptivity() const
{
    if ( IsAdaptivityParametersPresent() )
    {
        return DecideLocation( & mpUserParameters->Numerical().AdaptivityParameters(),
                               & mpDefaultParameters->Numerical().AdaptivityParameters(),
                               "TargetError")->get().min_edge_length();
    }
    else
    {
        EXCEPTION("Adaptivity parameters have not been set");
    }
}

double HeartConfig::GetGradationForAdaptivity() const
{
    if ( IsAdaptivityParametersPresent() )
    {
        return DecideLocation( & mpUserParameters->Numerical().AdaptivityParameters(),
                               & mpDefaultParameters->Numerical().AdaptivityParameters(),
                               "TargetError")->get().gradation();
    }
    else
    {
        EXCEPTION("Adaptivity parameters have not been set");
    }
}

unsigned HeartConfig::GetMaxNodesForAdaptivity() const
{
    if ( IsAdaptivityParametersPresent() )
    {
        return DecideLocation( & mpUserParameters->Numerical().AdaptivityParameters(),
                               & mpDefaultParameters->Numerical().AdaptivityParameters(),
                               "TargetError")->get().max_nodes();
    }
    else
    {
        EXCEPTION("Adaptivity parameters have not been set");
    }
}

unsigned HeartConfig::GetNumberOfAdaptiveSweeps() const
{
    if ( IsAdaptivityParametersPresent() )
    {
        return DecideLocation( & mpUserParameters->Numerical().AdaptivityParameters(),
                               & mpDefaultParameters->Numerical().AdaptivityParameters(),
                               "TargetError")->get().num_sweeps();
    }
    else
    {
        EXCEPTION("Adaptivity parameters have not been set");
    }
}

/*
 * PostProcessing
 */

bool HeartConfig::IsPostProcessingSectionPresent() const
{
    try
    {
        DecideLocation( & mpUserParameters->PostProcessing(),
                        & mpDefaultParameters->PostProcessing(),
                        "PostProcessing")->present();
        //If there's a section
        return true;
    }
    catch (Exception &e)
    {
        //No section
        return false;
    }
}

void HeartConfig::EnsurePostProcessingSectionPresent()
{
    ENSURE_SECTION_PRESENT(mpUserParameters->PostProcessing(), cp::postprocessing_type);
}

bool HeartConfig::IsPostProcessingRequested() const
{
    if (IsPostProcessingSectionPresent() == false)
    {
        return false;
    }
    else
    {
        return(IsApdMapsRequested() ||
               IsUpstrokeTimeMapsRequested() ||
               IsMaxUpstrokeVelocityMapRequested() ||
               IsConductionVelocityMapsRequested());
    }
}
bool HeartConfig::IsApdMapsRequested() const
{
    assert(IsPostProcessingSectionPresent());

    XSD_SEQUENCE_TYPE(cp::postprocessing_type::ActionPotentialDurationMap)&
        apd_maps = DecideLocation( & mpUserParameters->PostProcessing(),
                                   & mpDefaultParameters->PostProcessing(),
                                   "ActionPotentialDurationMap")->get().ActionPotentialDurationMap();
    return (apd_maps.begin() != apd_maps.end());
}

void HeartConfig::GetApdMaps(std::vector<std::pair<double,double> >& apd_maps) const
{
    assert(IsApdMapsRequested());
    apd_maps.clear();

    XSD_SEQUENCE_TYPE(cp::postprocessing_type::ActionPotentialDurationMap)&
        apd_maps_sequence = DecideLocation( & mpUserParameters->PostProcessing(),
                                            & mpDefaultParameters->PostProcessing(),
                                            "ActionPotentialDurationMap")->get().ActionPotentialDurationMap();

    for (XSD_ITERATOR_TYPE(cp::postprocessing_type::ActionPotentialDurationMap) i = apd_maps_sequence.begin();
         i != apd_maps_sequence.end();
         ++i)
    {
        std::pair<double,double> map(i->repolarisation_percentage(),i->threshold());

        apd_maps.push_back(map);
    }
}

bool HeartConfig::IsUpstrokeTimeMapsRequested() const
{
    assert(IsPostProcessingSectionPresent());

    XSD_SEQUENCE_TYPE(cp::postprocessing_type::UpstrokeTimeMap)&
        upstroke_map = DecideLocation( & mpUserParameters->PostProcessing(),
                                       & mpDefaultParameters->PostProcessing(),
                                       "UpstrokeTimeMap")->get().UpstrokeTimeMap();
    return (upstroke_map.begin() != upstroke_map.end());
}
void HeartConfig::GetUpstrokeTimeMaps (std::vector<double>& upstroke_time_maps) const
{
    assert(IsUpstrokeTimeMapsRequested());
    assert(upstroke_time_maps.size() == 0);

    XSD_SEQUENCE_TYPE(cp::postprocessing_type::UpstrokeTimeMap)&
        upstroke_maps_sequence = DecideLocation( & mpUserParameters->PostProcessing(),
                                                 & mpDefaultParameters->PostProcessing(),
                                                 "UpstrokeTimeMap")->get().UpstrokeTimeMap();

    for (XSD_ITERATOR_TYPE(cp::postprocessing_type::UpstrokeTimeMap) i = upstroke_maps_sequence.begin();
         i != upstroke_maps_sequence.end();
         ++i)
    {
        upstroke_time_maps.push_back(i->threshold());
    }
}

bool HeartConfig::IsMaxUpstrokeVelocityMapRequested() const
{
    assert(IsPostProcessingSectionPresent());

    XSD_SEQUENCE_TYPE(cp::postprocessing_type::MaxUpstrokeVelocityMap)&
        max_upstroke_velocity_map = DecideLocation( & mpUserParameters->PostProcessing(),
                                                    & mpDefaultParameters->PostProcessing(),
                                                    "MaxUpstrokeVelocityMap")->get().MaxUpstrokeVelocityMap();

    return (max_upstroke_velocity_map.begin() != max_upstroke_velocity_map.end());
}

void HeartConfig::GetMaxUpstrokeVelocityMaps(std::vector<double>& upstroke_velocity_maps) const
{
    assert(IsMaxUpstrokeVelocityMapRequested());
    assert(upstroke_velocity_maps.size() == 0);

    XSD_SEQUENCE_TYPE(cp::postprocessing_type::MaxUpstrokeVelocityMap)&
        max_upstroke_velocity_maps_sequence = DecideLocation( & mpUserParameters->PostProcessing(),
                                                              & mpDefaultParameters->PostProcessing(),
                                                              "MaxUpstrokeVelocityMap")->get().MaxUpstrokeVelocityMap();

    for (XSD_ITERATOR_TYPE(cp::postprocessing_type::MaxUpstrokeVelocityMap) i = max_upstroke_velocity_maps_sequence.begin();
         i != max_upstroke_velocity_maps_sequence.end();
         ++i)
    {
        upstroke_velocity_maps.push_back(i->threshold());
    }
}

bool HeartConfig::IsConductionVelocityMapsRequested() const
{
    assert(IsPostProcessingSectionPresent());

    XSD_SEQUENCE_TYPE(cp::postprocessing_type::ConductionVelocityMap)&
        cond_vel_maps = DecideLocation( & mpUserParameters->PostProcessing(),
                                        & mpDefaultParameters->PostProcessing(),
                                        "ConductionVelocityMap")->get().ConductionVelocityMap();
    return (cond_vel_maps.begin() != cond_vel_maps.end());
}

void HeartConfig::GetConductionVelocityMaps(std::vector<unsigned>& conduction_velocity_maps) const
{
    assert(IsConductionVelocityMapsRequested());
    assert(conduction_velocity_maps.size() == 0);

    XSD_SEQUENCE_TYPE(cp::postprocessing_type::ConductionVelocityMap)&
        cond_vel_maps_sequence = DecideLocation( & mpUserParameters->PostProcessing(),
                                                 & mpDefaultParameters->PostProcessing(),
                                                 "ConductionVelocityMap")->get().ConductionVelocityMap();

    for (XSD_ITERATOR_TYPE(cp::postprocessing_type::ConductionVelocityMap) i = cond_vel_maps_sequence.begin();
         i != cond_vel_maps_sequence.end();
         ++i)
    {
        conduction_velocity_maps.push_back(i->origin_node());
    }
}

/*
 * Output visualization
 */

bool HeartConfig::IsOutputVisualizerPresent() const
{
    CheckSimulationIsDefined("OutputVisualizer");

    try
    {
        DecideLocation( & mpUserParameters->Simulation().get().OutputVisualizer(),
                        & mpDefaultParameters->Simulation().get().OutputVisualizer(),
                        "OutputVisualizer")->present();
        // If there's an element
        return true;
    }
    catch (Exception &e)
    {
        // No element
        return false;
    }
}

bool HeartConfig::GetVisualizeWithMeshalyzer() const
{
    if (!IsOutputVisualizerPresent())
    {
        return true;
    }
    else
    {
        return DecideLocation( & mpUserParameters->Simulation().get().OutputVisualizer(),
                               & mpDefaultParameters->Simulation().get().OutputVisualizer(),
                               "OutputVisualizer")->get().meshalyzer() == cp::yesno_type::yes;
    }
}

bool HeartConfig::GetVisualizeWithCmgui() const
{
    if (!IsOutputVisualizerPresent())
    {
        return false;
    }
    else
    {
        return DecideLocation( & mpUserParameters->Simulation().get().OutputVisualizer(),
                               & mpDefaultParameters->Simulation().get().OutputVisualizer(),
                               "OutputVisualizer")->get().cmgui() == cp::yesno_type::yes;
    }
}

bool HeartConfig::GetVisualizeWithVtk() const
{
    if (!IsOutputVisualizerPresent())
    {
        return false;
    }
    else
    {
        return DecideLocation( & mpUserParameters->Simulation().get().OutputVisualizer(),
                               & mpDefaultParameters->Simulation().get().OutputVisualizer(),
                               "OutputVisualizer")->get().vtk() == cp::yesno_type::yes;
    }
}


bool HeartConfig::IsElectrodesPresent() const
{
    try
    {
        DecideLocation( & mpUserParameters->Simulation().get().Electrodes(),
                        & mpDefaultParameters->Simulation().get().Electrodes(),
                        "Electrodes")->present();
        //If there's a section
        return true;
    }
    catch (Exception &e)
    {
        //No section
        return false;
    }
}

/*
 *  Set methods
 */
void HeartConfig::SetSpaceDimension(unsigned spaceDimension)
{
    mpUserParameters->Simulation().get().SpaceDimension().set(spaceDimension);
}

void HeartConfig::SetSimulationDuration(double simulationDuration)
{
    XSD_CREATE_WITH_FIXED_ATTR1(cp::time_type, time, simulationDuration, "ms");
    mpUserParameters->Simulation().get().SimulationDuration().set(time);
}

void HeartConfig::SetDomain(const cp::domain_type& rDomain)
{
    mpUserParameters->Simulation().get().Domain().set(rDomain);
}

void HeartConfig::SetDefaultIonicModel(const cp::ionic_models_available_type& rIonicModel)
{
    cp::ionic_model_selection_type ionic_model;
    ionic_model.Hardcoded(rIonicModel);
    cp::ionic_models_type container(ionic_model);
    mpUserParameters->Simulation().get().IonicModels().set(container);
}

void HeartConfig::SetSlabDimensions(double x, double y, double z, double inter_node_space)
{
    if ( ! mpUserParameters->Simulation().get().Mesh().present())
    {
        XSD_CREATE_WITH_FIXED_ATTR(cp::mesh_type, mesh_to_load, "cm");
        mpUserParameters->Simulation().get().Mesh().set(mesh_to_load);
    }

    cp::slab_type slab_definition(x, y, z, inter_node_space);
    mpUserParameters->Simulation().get().Mesh().get().Slab().set(slab_definition);
}

void HeartConfig::SetSheetDimensions(double x, double y, double inter_node_space)
{
    if ( ! mpUserParameters->Simulation().get().Mesh().present())
    {
        XSD_CREATE_WITH_FIXED_ATTR(cp::mesh_type, mesh_to_load, "cm");
        mpUserParameters->Simulation().get().Mesh().set(mesh_to_load);
    }

    cp::sheet_type sheet_definition(x, y, inter_node_space);
    mpUserParameters->Simulation().get().Mesh().get().Sheet().set(sheet_definition);
}

void HeartConfig::SetFibreLength(double x, double inter_node_space)
{
    if ( ! mpUserParameters->Simulation().get().Mesh().present())
    {
        XSD_CREATE_WITH_FIXED_ATTR(cp::mesh_type, mesh_to_load, "cm");
        mpUserParameters->Simulation().get().Mesh().set(mesh_to_load);
    }

    cp::fibre_type fibre_definition(x, inter_node_space);
    mpUserParameters->Simulation().get().Mesh().get().Fibre().set(fibre_definition);
}

void HeartConfig::SetMeshFileName(std::string meshPrefix, cp::media_type fibreDefinition)
{
    if ( ! mpUserParameters->Simulation().get().Mesh().present())
    {
        XSD_CREATE_WITH_FIXED_ATTR(cp::mesh_type, mesh_to_load, "cm");
        mpUserParameters->Simulation().get().Mesh().set(mesh_to_load);
    }

    XSD_NESTED_TYPE(cp::mesh_type::LoadMesh) mesh_prefix(meshPrefix, fibreDefinition);
    mpUserParameters->Simulation().get().Mesh().get().LoadMesh().set(mesh_prefix);
}

void HeartConfig::SetIonicModelRegions(std::vector<ChasteCuboid<3> >& rDefinedRegions,
                                       std::vector<cp::ionic_model_selection_type>& rIonicModels) const
{
    assert(rDefinedRegions.size() == rIonicModels.size());
    XSD_SEQUENCE_TYPE(cp::ionic_models_type::Region)&
        regions = mpUserParameters->Simulation().get().IonicModels().get().Region();
    regions.clear();
    for (unsigned region_index=0; region_index<rDefinedRegions.size(); region_index++)
    {
        cp::point_type point_a(rDefinedRegions[region_index].rGetLowerCorner()[0],
                               rDefinedRegions[region_index].rGetLowerCorner()[1],
                               rDefinedRegions[region_index].rGetLowerCorner()[2]);

        cp::point_type point_b(rDefinedRegions[region_index].rGetUpperCorner()[0],
                               rDefinedRegions[region_index].rGetUpperCorner()[1],
                               rDefinedRegions[region_index].rGetUpperCorner()[2]);

        XSD_CREATE_WITH_FIXED_ATTR(cp::location_type, locn, "cm");
        locn.Cuboid().set(cp::box_type(point_a, point_b));

        cp::ionic_model_region_type region(rIonicModels[region_index], locn);
        regions.push_back(region);
    }
}

void HeartConfig::SetConductivityHeterogeneities(std::vector<ChasteCuboid<3> >& conductivityAreas,
        std::vector< c_vector<double,3> >& intraConductivities,
        std::vector< c_vector<double,3> >& extraConductivities)
{
    assert ( conductivityAreas.size() == intraConductivities.size() );
    assert ( intraConductivities.size() == extraConductivities.size());

    XSD_ANON_SEQUENCE_TYPE(cp::simulation_type, ConductivityHeterogeneities, ConductivityHeterogeneity) heterogeneities_container;

    for (unsigned region_index=0; region_index<conductivityAreas.size(); region_index++)
    {
        cp::point_type point_a(conductivityAreas[region_index].rGetLowerCorner()[0],
                           conductivityAreas[region_index].rGetLowerCorner()[1],
                           conductivityAreas[region_index].rGetLowerCorner()[2]);

        cp::point_type point_b(conductivityAreas[region_index].rGetUpperCorner()[0],
                           conductivityAreas[region_index].rGetUpperCorner()[1],
                           conductivityAreas[region_index].rGetUpperCorner()[2]);

        XSD_CREATE_WITH_FIXED_ATTR(cp::location_type, locn, "cm");
        locn.Cuboid().set(cp::box_type(point_a, point_b));
        cp::conductivity_heterogeneity_type ht(locn);

        XSD_CREATE_WITH_FIXED_ATTR3(cp::conductivities_type, intra,
                                    intraConductivities[region_index][0],
                                    intraConductivities[region_index][1],
                                    intraConductivities[region_index][2],
                                    "mS/cm");

        ht.IntracellularConductivities(intra);

        XSD_CREATE_WITH_FIXED_ATTR3(cp::conductivities_type, extra,
                                    extraConductivities[region_index][0],
                                    extraConductivities[region_index][1],
                                    extraConductivities[region_index][2],
                                    "mS/cm");

        ht.ExtracellularConductivities(extra);

        heterogeneities_container.push_back(ht);
    }

    XSD_ANON_TYPE(cp::simulation_type, ConductivityHeterogeneities) heterogeneities_object;
    heterogeneities_object.ConductivityHeterogeneity(heterogeneities_container);

    mpUserParameters->Simulation().get().ConductivityHeterogeneities().set(heterogeneities_object);
}

void HeartConfig::SetConductivityHeterogeneitiesEllipsoid(std::vector<ChasteEllipsoid<3> >& conductivityAreas,
        std::vector< c_vector<double,3> >& intraConductivities,
        std::vector< c_vector<double,3> >& extraConductivities)
{
    assert ( conductivityAreas.size() == intraConductivities.size() );
    assert ( intraConductivities.size() == extraConductivities.size());

    XSD_ANON_SEQUENCE_TYPE(cp::simulation_type, ConductivityHeterogeneities, ConductivityHeterogeneity) heterogeneities_container;

    for (unsigned region_index=0; region_index<conductivityAreas.size(); region_index++)
    {
        cp::point_type centre(conductivityAreas[region_index].rGetCentre()[0],
                              conductivityAreas[region_index].rGetCentre()[1],
                              conductivityAreas[region_index].rGetCentre()[2]);

        cp::point_type radii(conductivityAreas[region_index].rGetRadii()[0],
                             conductivityAreas[region_index].rGetRadii()[1],
                             conductivityAreas[region_index].rGetRadii()[2]);

        XSD_CREATE_WITH_FIXED_ATTR(cp::location_type, locn, "cm");
        locn.Ellipsoid().set(cp::ellipsoid_type(centre, radii));
        cp::conductivity_heterogeneity_type ht(locn);

        XSD_CREATE_WITH_FIXED_ATTR3(cp::conductivities_type, intra,
                                    intraConductivities[region_index][0],
                                    intraConductivities[region_index][1],
                                    intraConductivities[region_index][2],
                                    "mS/cm");

        ht.IntracellularConductivities(intra);

        XSD_CREATE_WITH_FIXED_ATTR3(cp::conductivities_type, extra,
                                    extraConductivities[region_index][0],
                                    extraConductivities[region_index][1],
                                    extraConductivities[region_index][2],
                                    "mS/cm");

        ht.ExtracellularConductivities(extra);

        heterogeneities_container.push_back(ht);
    }

    XSD_ANON_TYPE(cp::simulation_type, ConductivityHeterogeneities) heterogeneities_object;
    heterogeneities_object.ConductivityHeterogeneity(heterogeneities_container);

    mpUserParameters->Simulation().get().ConductivityHeterogeneities().set(heterogeneities_object);
}

void HeartConfig::SetOutputDirectory(const std::string& rOutputDirectory)
{
    mpUserParameters->Simulation().get().OutputDirectory().set(rOutputDirectory);
}

void HeartConfig::SetOutputFilenamePrefix(const std::string& rOutputFilenamePrefix)
{
    mpUserParameters->Simulation().get().OutputFilenamePrefix().set(rOutputFilenamePrefix);
}

void HeartConfig::SetOutputVariables(const std::vector<std::string>& rOutputVariables)
{
    if ( ! mpUserParameters->Simulation()->OutputVariables().present())
    {
        cp::output_variables_type variables_requested;
        mpUserParameters->Simulation()->OutputVariables().set(variables_requested);
    }

    XSD_SEQUENCE_TYPE(cp::output_variables_type::Var)&
        var_type_sequence = mpUserParameters->Simulation()->OutputVariables()->Var();
    //Erase or create a sequence
    var_type_sequence.clear();

    for (unsigned i=0; i<rOutputVariables.size(); i++)
    {
        cp::var_type temp(rOutputVariables[i]);
        var_type_sequence.push_back(temp);
    }

    if (rOutputVariables.size() > 0)
    {
        // Turn off Meshalyzer etc. output, to avoid errors
        SetVisualizeWithMeshalyzer(false);
        SetVisualizeWithCmgui(false);
        SetVisualizeWithVtk(false);
    }
}

void  HeartConfig::SetOutputUsingOriginalNodeOrdering(bool useOriginal)
{
    //What if it doesn't exist?
    mpUserParameters->Simulation().get().OutputUsingOriginalNodeOrdering().set(useOriginal? cp::yesno_type::yes : cp::yesno_type::no);
}  

void HeartConfig::SetCheckpointSimulation(bool saveSimulation, double checkpointTimestep, unsigned maxCheckpointsOnDisk)
{
    if (saveSimulation)
    {
        // Make sure values for the optional parameters have been provided
        assert(checkpointTimestep!=-1.0 && maxCheckpointsOnDisk!=UINT_MAX);

        XSD_CREATE_WITH_FIXED_ATTR2(cp::simulation_type::XSD_NESTED_TYPE(CheckpointSimulation),
                                    cs,
                                    checkpointTimestep,
                                    maxCheckpointsOnDisk,
                                    "ms");
        mpUserParameters->Simulation().get().CheckpointSimulation().set(cs);
    }
    else
    {
        mpUserParameters->Simulation().get().CheckpointSimulation().reset();
    }

    CheckTimeSteps();
}

// Physiological
void HeartConfig::SetIntracellularConductivities(const c_vector<double, 3>& intraConductivities)
{
    XSD_CREATE_WITH_FIXED_ATTR3(cp::conductivities_type, intra,
                                intraConductivities[0],
                                intraConductivities[1],
                                intraConductivities[2],
                                "mS/cm");

    mpUserParameters->Physiological().IntracellularConductivities().set(intra);
}

void HeartConfig::SetIntracellularConductivities(const c_vector<double, 2>& intraConductivities)
{
    XSD_CREATE_WITH_FIXED_ATTR3(cp::conductivities_type, intra,
                                intraConductivities[0],
                                intraConductivities[1],
                                0.0, "mS/cm");

    mpUserParameters->Physiological().IntracellularConductivities().set(intra);
}

void HeartConfig::SetIntracellularConductivities(const c_vector<double, 1>& intraConductivities)
{
    XSD_CREATE_WITH_FIXED_ATTR3(cp::conductivities_type, intra,
                                intraConductivities[0],
                                0.0, 0.0, "mS/cm");

    mpUserParameters->Physiological().IntracellularConductivities().set(intra);
}

void HeartConfig::SetExtracellularConductivities(const c_vector<double, 3>& extraConductivities)
{
    XSD_CREATE_WITH_FIXED_ATTR3(cp::conductivities_type, extra,
                                extraConductivities[0],
                                extraConductivities[1],
                                extraConductivities[2],
                                "mS/cm");

    mpUserParameters->Physiological().ExtracellularConductivities().set(extra);
}

void HeartConfig::SetExtracellularConductivities(const c_vector<double, 2>& extraConductivities)
{
    XSD_CREATE_WITH_FIXED_ATTR3(cp::conductivities_type, extra,
                                extraConductivities[0],
                                extraConductivities[1],
                                0.0, "mS/cm");

    mpUserParameters->Physiological().ExtracellularConductivities().set(extra);
}

void HeartConfig::SetExtracellularConductivities(const c_vector<double, 1>& extraConductivities)
{
    XSD_CREATE_WITH_FIXED_ATTR3(cp::conductivities_type, extra,
                                extraConductivities[0],
                                0.0, 0.0, "mS/cm");

    mpUserParameters->Physiological().ExtracellularConductivities().set(extra);
}

void HeartConfig::SetBathConductivity(double bathConductivity)
{
    XSD_CREATE_WITH_FIXED_ATTR1(cp::conductivity_type, cond, bathConductivity, "mS/cm");
    mpUserParameters->Physiological().BathConductivity().set(cond);
}

void HeartConfig::SetSurfaceAreaToVolumeRatio(double ratio)
{
    XSD_CREATE_WITH_FIXED_ATTR1(cp::inverse_length_type, ratio_object, ratio, "1/cm");
    mpUserParameters->Physiological().SurfaceAreaToVolumeRatio().set(ratio_object);
}

void HeartConfig::SetCapacitance(double capacitance)
{
    XSD_CREATE_WITH_FIXED_ATTR1(cp::capacitance_type, capacitance_object, capacitance, "uF/cm^2");
    mpUserParameters->Physiological().Capacitance().set(capacitance_object);
}


// Numerical
void HeartConfig::SetOdePdeAndPrintingTimeSteps(double odeTimeStep, double pdeTimeStep, double printingTimeStep)
{
    XSD_CREATE_WITH_FIXED_ATTR3(cp::time_steps_type, time_steps,
                                odeTimeStep, pdeTimeStep, printingTimeStep, "ms");
    mpUserParameters->Numerical().TimeSteps().set(time_steps);
    CheckTimeSteps();
}

void HeartConfig::SetOdeTimeStep(double odeTimeStep)
{
    SetOdePdeAndPrintingTimeSteps(odeTimeStep, GetPdeTimeStep(), GetPrintingTimeStep());
}

void HeartConfig::SetPdeTimeStep(double pdeTimeStep)
{
    SetOdePdeAndPrintingTimeSteps(GetOdeTimeStep(), pdeTimeStep, GetPrintingTimeStep());
}

void HeartConfig::SetPrintingTimeStep(double printingTimeStep)
{
    SetOdePdeAndPrintingTimeSteps(GetOdeTimeStep(), GetPdeTimeStep(), printingTimeStep);
}

void HeartConfig::CheckTimeSteps() const
{
    if (GetOdeTimeStep() <= 0)
    {
        EXCEPTION("Ode time-step should be positive");
    }
    if (GetPdeTimeStep() <= 0)
    {
        EXCEPTION("Pde time-step should be positive");
    }
    if (GetPrintingTimeStep() <= 0.0)
    {
        EXCEPTION("Printing time-step should be positive");
    }

    if (GetPdeTimeStep()>GetPrintingTimeStep())
    {
        EXCEPTION("Printing time-step should not be smaller than PDE time-step");
    }

    if ( !Divides(GetPdeTimeStep(), GetPrintingTimeStep()) )
    {
        EXCEPTION("Printing time-step should be a multiple of PDE time step");
    }

    if ( GetOdeTimeStep() > GetPdeTimeStep() )
    {
        EXCEPTION("Ode time-step should not be greater than PDE time-step");
    }

    if (GetCheckpointSimulation())
    {
        if (GetCheckpointTimestep() <= 0.0)
        {
            EXCEPTION("Checkpoint time-step should be positive");
        }

        if ( !Divides(GetPrintingTimeStep(), GetCheckpointTimestep()) )
        {
            EXCEPTION("Checkpoint time-step should be a multiple of printing time-step");
        }
    }
}


void HeartConfig::SetUseRelativeTolerance(double relativeTolerance)
{
    ENSURE_SECTION_PRESENT(mpUserParameters->Numerical().KSPTolerances(), cp::ksp_tolerances_type);
    //Remove any reference to tolerances is user parameters
    mpUserParameters->Numerical().KSPTolerances()->KSPAbsolute().reset();
    mpUserParameters->Numerical().KSPTolerances()->KSPRelative().set(relativeTolerance);
}

void HeartConfig::SetUseAbsoluteTolerance(double absoluteTolerance)
{
    ENSURE_SECTION_PRESENT(mpUserParameters->Numerical().KSPTolerances(), cp::ksp_tolerances_type);
    //Remove any reference to tolerances is user parameters
    mpUserParameters->Numerical().KSPTolerances()->KSPRelative().reset();
    mpUserParameters->Numerical().KSPTolerances()->KSPAbsolute().set(absoluteTolerance);
}

void HeartConfig::SetKSPSolver(const char* kspSolver)
{
    /* Note that changes in these conditions need to be reflected in the Doxygen*/
    if ( strcmp(kspSolver, "gmres") == 0)
    {
        mpUserParameters->Numerical().KSPSolver().set(cp::ksp_solver_type::gmres);
        return;
    }
    if ( strcmp(kspSolver, "cg") == 0)
    {
        mpUserParameters->Numerical().KSPSolver().set(cp::ksp_solver_type::cg);
        return;
    }
    if ( strcmp(kspSolver, "symmlq") == 0)
    {
        mpUserParameters->Numerical().KSPSolver().set(cp::ksp_solver_type::symmlq);
        return;
    }

    EXCEPTION("Unknown solver type provided");
}

void HeartConfig::SetKSPPreconditioner(const char* kspPreconditioner)
{
    /* Note that changes in these conditions need to be reflected in the Doxygen*/
    if ( strcmp(kspPreconditioner, "jacobi") == 0)
    {
        mpUserParameters->Numerical().KSPPreconditioner().set(cp::ksp_preconditioner_type::jacobi);
        return;
    }
    if ( strcmp(kspPreconditioner, "bjacobi") == 0)
    {
        mpUserParameters->Numerical().KSPPreconditioner().set(cp::ksp_preconditioner_type::bjacobi);
        return;
    }
    if ( strcmp(kspPreconditioner, "hypre") == 0)
    {
        mpUserParameters->Numerical().KSPPreconditioner().set(cp::ksp_preconditioner_type::hypre);
        return;
    }
    if ( strcmp(kspPreconditioner, "ml") == 0)
    {
        mpUserParameters->Numerical().KSPPreconditioner().set(cp::ksp_preconditioner_type::ml);
        return;
    }
    if ( strcmp(kspPreconditioner, "spai") == 0)
    {
        mpUserParameters->Numerical().KSPPreconditioner().set(cp::ksp_preconditioner_type::spai);
        return;
    }
    if ( strcmp(kspPreconditioner, "twolevelsblockdiagonal") == 0)
    {
        mpUserParameters->Numerical().KSPPreconditioner().set(cp::ksp_preconditioner_type::twolevelsblockdiagonal);
        return;
    }
    if ( strcmp(kspPreconditioner, "blockdiagonal") == 0)
    {
        mpUserParameters->Numerical().KSPPreconditioner().set(cp::ksp_preconditioner_type::blockdiagonal);
        return;
    }
    if ( strcmp(kspPreconditioner, "ldufactorisation") == 0)
    {
        mpUserParameters->Numerical().KSPPreconditioner().set(cp::ksp_preconditioner_type::ldufactorisation);
        return;
    }
    if ( strcmp(kspPreconditioner, "none") == 0)
    {
        mpUserParameters->Numerical().KSPPreconditioner().set(cp::ksp_preconditioner_type::none);
        return;
    }

    EXCEPTION("Unknown preconditioner type provided");
}

void HeartConfig::SetAdaptivityParameters(double targetError,
                                          double sigma,
                                          double maxEdgeLength,
                                          double minEdgeLength,
                                          double gradation,
                                          unsigned maxNodes,
                                          unsigned numSweeps )
{
    if ( maxEdgeLength < minEdgeLength )
    {
        EXCEPTION("AdaptivityParameters: maxEdgeLength must be greater than minEdgeLength.");
    }
    if (!IsAdaptivityParametersPresent())
    {
        cp::adaptivity_parameters_type element(targetError,
                                               sigma,
                                               maxEdgeLength,
                                               minEdgeLength,
                                               gradation,
                                               maxNodes,
                                               numSweeps );
        mpUserParameters->Numerical().AdaptivityParameters().set(element);
    }
    else
    {
        mpUserParameters->Numerical().AdaptivityParameters().get().target_error(targetError);
        mpUserParameters->Numerical().AdaptivityParameters().get().sigma(sigma);
        mpUserParameters->Numerical().AdaptivityParameters().get().max_edge_length(maxEdgeLength);
        mpUserParameters->Numerical().AdaptivityParameters().get().min_edge_length(minEdgeLength);
        mpUserParameters->Numerical().AdaptivityParameters().get().gradation(gradation);
        mpUserParameters->Numerical().AdaptivityParameters().get().max_nodes(maxNodes);
        mpUserParameters->Numerical().AdaptivityParameters().get().num_sweeps(numSweeps);
    }
}

void HeartConfig::SetTargetErrorForAdaptivity(double targetError)
{
    SetAdaptivityParameters( targetError,
                             GetSigmaForAdaptivity(),
                             GetMaxEdgeLengthForAdaptivity(),
                             GetMinEdgeLengthForAdaptivity(),
                             GetGradationForAdaptivity(),
                             GetMaxNodesForAdaptivity(),
                             GetNumberOfAdaptiveSweeps() );
}

void HeartConfig::SetSigmaForAdaptivity(double sigma)
{
    SetAdaptivityParameters( GetTargetErrorForAdaptivity(),
                             sigma,
                             GetMaxEdgeLengthForAdaptivity(),
                             GetMinEdgeLengthForAdaptivity(),
                             GetGradationForAdaptivity(),
                             GetMaxNodesForAdaptivity(),
                             GetNumberOfAdaptiveSweeps() );
}

void HeartConfig::SetMaxEdgeLengthForAdaptivity(double maxEdgeLength)
{
    SetAdaptivityParameters( GetTargetErrorForAdaptivity(),
                             GetSigmaForAdaptivity(),
                             maxEdgeLength,
                             GetMinEdgeLengthForAdaptivity(),
                             GetGradationForAdaptivity(),
                             GetMaxNodesForAdaptivity(),
                             GetNumberOfAdaptiveSweeps() );
}

void HeartConfig::SetMinEdgeLengthForAdaptivity(double minEdgeLength)
{
    SetAdaptivityParameters( GetTargetErrorForAdaptivity(),
                             GetSigmaForAdaptivity(),
                             GetMaxEdgeLengthForAdaptivity(),
                             minEdgeLength,
                             GetGradationForAdaptivity(),
                             GetMaxNodesForAdaptivity(),
                             GetNumberOfAdaptiveSweeps() );
}

void HeartConfig::SetGradationForAdaptivity(double gradation)
{
    SetAdaptivityParameters( GetTargetErrorForAdaptivity(),
                             GetSigmaForAdaptivity(),
                             GetMaxEdgeLengthForAdaptivity(),
                             GetMinEdgeLengthForAdaptivity(),
                             gradation,
                             GetMaxNodesForAdaptivity(),
                             GetNumberOfAdaptiveSweeps() );
}

void HeartConfig::SetMaxNodesForAdaptivity(unsigned maxNodes)
{
    SetAdaptivityParameters( GetTargetErrorForAdaptivity(),
                             GetSigmaForAdaptivity(),
                             GetMaxEdgeLengthForAdaptivity(),
                             GetMinEdgeLengthForAdaptivity(),
                             GetGradationForAdaptivity(),
                             maxNodes,
                             GetNumberOfAdaptiveSweeps() );
}

void HeartConfig::SetNumberOfAdaptiveSweeps(unsigned numSweeps)
{
    SetAdaptivityParameters( GetTargetErrorForAdaptivity(),
                             GetSigmaForAdaptivity(),
                             GetMaxEdgeLengthForAdaptivity(),
                             GetMinEdgeLengthForAdaptivity(),
                             GetGradationForAdaptivity(),
                             GetMaxNodesForAdaptivity(),
                             numSweeps );
}

void HeartConfig::SetApdMaps(const std::vector<std::pair<double,double> >& apdMaps)
{
    EnsurePostProcessingSectionPresent();
    XSD_SEQUENCE_TYPE(cp::postprocessing_type::ActionPotentialDurationMap)& apd_maps_sequence
        = mpUserParameters->PostProcessing()->ActionPotentialDurationMap();
    //Erase or create a sequence
    apd_maps_sequence.clear();

    for (unsigned i=0; i<apdMaps.size(); i++)
    {
        XSD_CREATE_WITH_FIXED_ATTR2(cp::apd_map_type, temp,
                                    apdMaps[i].first, apdMaps[i].second,
                                    "mV");
        apd_maps_sequence.push_back( temp);
    }
}


void HeartConfig::SetUpstrokeTimeMaps (std::vector<double>& upstrokeTimeMaps)
{
    EnsurePostProcessingSectionPresent();
    XSD_SEQUENCE_TYPE(cp::postprocessing_type::UpstrokeTimeMap)& var_type_sequence
        = mpUserParameters->PostProcessing()->UpstrokeTimeMap();

    //Erase or create a sequence
    var_type_sequence.clear();

    for (unsigned i=0; i<upstrokeTimeMaps.size(); i++)
    {
        XSD_CREATE_WITH_FIXED_ATTR1(cp::upstrokes_map_type, temp,
                                    upstrokeTimeMaps[i],
                                    "mV");
        var_type_sequence.push_back(temp);
    }
}

void HeartConfig::SetMaxUpstrokeVelocityMaps (std::vector<double>& maxUpstrokeVelocityMaps)
{
    EnsurePostProcessingSectionPresent();
    XSD_SEQUENCE_TYPE(cp::postprocessing_type::MaxUpstrokeVelocityMap)& max_upstroke_velocity_maps_sequence
        = mpUserParameters->PostProcessing()->MaxUpstrokeVelocityMap();

    //Erase or create a sequence
    max_upstroke_velocity_maps_sequence.clear();

    for (unsigned i=0; i<maxUpstrokeVelocityMaps.size(); i++)
    {
        XSD_CREATE_WITH_FIXED_ATTR1(cp::max_upstrokes_velocity_map_type, temp,
                                    maxUpstrokeVelocityMaps[i],
                                    "mV");


        max_upstroke_velocity_maps_sequence.push_back(temp);
    }

}

void HeartConfig::SetConductionVelocityMaps (std::vector<unsigned>& conductionVelocityMaps)
{
    EnsurePostProcessingSectionPresent();
    XSD_SEQUENCE_TYPE(cp::postprocessing_type::ConductionVelocityMap)& conduction_velocity_maps_sequence
        = mpUserParameters->PostProcessing()->ConductionVelocityMap();

    //Erase or create a sequence
    conduction_velocity_maps_sequence.clear();

    for (unsigned i=0; i<conductionVelocityMaps.size(); i++)
    {
        cp::conduction_velocity_map_type temp(conductionVelocityMaps[i]);
        conduction_velocity_maps_sequence.push_back(temp);
    }
}

/*
 * Output visualizer
 */

void HeartConfig::EnsureOutputVisualizerExists()
{
    ENSURE_SECTION_PRESENT(mpUserParameters->Simulation()->OutputVisualizer(), cp::output_visualizer_type);
}

void HeartConfig::SetVisualizeWithMeshalyzer(bool useMeshalyzer)
{
    EnsureOutputVisualizerExists();

    mpUserParameters->Simulation().get().OutputVisualizer().get().meshalyzer(
        useMeshalyzer ? cp::yesno_type::yes : cp::yesno_type::no);
}

void HeartConfig::SetVisualizeWithCmgui(bool useCmgui)
{
    EnsureOutputVisualizerExists();

    mpUserParameters->Simulation().get().OutputVisualizer().get().cmgui(
        useCmgui ? cp::yesno_type::yes : cp::yesno_type::no);
}

void HeartConfig::SetVisualizeWithVtk(bool useVtk)
{
    EnsureOutputVisualizerExists();

    mpUserParameters->Simulation().get().OutputVisualizer().get().vtk(
        useVtk ? cp::yesno_type::yes : cp::yesno_type::no);
}

void HeartConfig::SetElectrodeParameters(bool groundSecondElectrode,
                                         unsigned index, double magnitude, 
                                         double startTime, double duration )
{
    assert(index < 3);
    
    cp::axis_type axis = cp::axis_type::x;
    if (index==1)
    {
        axis = cp::axis_type::y;
    }
    else if (index==2)
    {
        axis = cp::axis_type::z;
    }
        
    XSD_CREATE_WITH_FIXED_ATTR1(cp::surface_stimulus_strength_type, strength, magnitude, "uA/cm^2");
    XSD_CREATE_WITH_FIXED_ATTR1(cp::time_type, start_time, startTime, "ms");
    XSD_CREATE_WITH_FIXED_ATTR1(cp::time_type, duration_time, duration, "ms");
     
    if (!IsElectrodesPresent())
    {
        cp::electrodes_type element( groundSecondElectrode ? cp::yesno_type::yes : cp::yesno_type::no,
                                     axis,
                                     strength,
                                     start_time,
                                     duration_time );
        mpUserParameters->Simulation().get().Electrodes().set(element);
    }
    else
    {
        mpUserParameters->Simulation().get().Electrodes().get().GroundSecondElectrode(groundSecondElectrode ? cp::yesno_type::yes : cp::yesno_type::no);
        mpUserParameters->Simulation().get().Electrodes().get().PerpendicularToAxis(axis);
        mpUserParameters->Simulation().get().Electrodes().get().Strength(strength);
        mpUserParameters->Simulation().get().Electrodes().get().StartTime(start_time);
        mpUserParameters->Simulation().get().Electrodes().get().Duration(duration_time);
    }
}

void HeartConfig::GetElectrodeParameters(bool& rGroundSecondElectrode,
                                         unsigned& rIndex, double& rMagnitude, 
                                         double& rStartTime, double& rDuration )
{
    if (!IsElectrodesPresent())
    {
        EXCEPTION("Attempted to get electrodes that have not been defined.");
    }
    else
    {
        rGroundSecondElectrode = (mpUserParameters->Simulation().get().Electrodes().get().GroundSecondElectrode()==cp::yesno_type::yes);
        
        cp::axis_type axis = mpUserParameters->Simulation().get().Electrodes().get().PerpendicularToAxis();
        if (axis==cp::axis_type::x)
        {
            rIndex = 0;
        }
        else if (axis==cp::axis_type::y)
        {
            rIndex = 1;
        }
        else
        {
            rIndex = 2;
        }
        
        rMagnitude = mpUserParameters->Simulation().get().Electrodes().get().Strength();
        rStartTime = mpUserParameters->Simulation().get().Electrodes().get().StartTime();
        rDuration = mpUserParameters->Simulation().get().Electrodes().get().Duration();
    }
    
}

/**********************************************************************
 *                                                                    *
 *                                                                    *
 *            Utility methods for reading/transforming XML            *
 *                                                                    *
 *                                                                    *
 **********************************************************************/

xsd::cxx::xml::dom::auto_ptr<xercesc::DOMDocument> XmlTools::ReadFileToDomDocument(
        const std::string& rFileName,
        ::xml_schema::error_handler& rErrorHandler,
        const ::xml_schema::properties& rProps)
{
    using namespace xercesc;
    namespace xml = xsd::cxx::xml;
    namespace tree = xsd::cxx::tree;

    // Get an implementation of the Load-Store (LS) interface.
    const XMLCh ls_id [] = {chLatin_L, chLatin_S, chNull};
    DOMImplementation* p_impl(DOMImplementationRegistry::getDOMImplementation(ls_id));

#if _XERCES_VERSION >= 30000
    // Xerces-C++ 3.0.0 and later.
    xml::dom::auto_ptr<DOMLSParser> p_parser(p_impl->createLSParser(DOMImplementationLS::MODE_SYNCHRONOUS, 0));
    DOMConfiguration* p_conf(p_parser->getDomConfig());

    // Discard comment nodes in the document.
    p_conf->setParameter(XMLUni::fgDOMComments, false);

    // Enable datatype normalization.
    p_conf->setParameter(XMLUni::fgDOMDatatypeNormalization, true);

    // Do not create EntityReference nodes in the DOM tree.  No
    // EntityReference nodes will be created, only the nodes
    // corresponding to their fully expanded substitution text
    // will be created.
    p_conf->setParameter(XMLUni::fgDOMEntities, false);

    // Perform namespace processing.
    p_conf->setParameter(XMLUni::fgDOMNamespaces, true);

    // Do not include ignorable whitespace in the DOM tree.
    p_conf->setParameter(XMLUni::fgDOMElementContentWhitespace, false);

    // Enable validation.
    p_conf->setParameter(XMLUni::fgDOMValidate, true);
    p_conf->setParameter(XMLUni::fgXercesSchema, true);
    p_conf->setParameter(XMLUni::fgXercesSchemaFullChecking, false);
    // Code taken from xsd/cxx/xml/dom/parsing-source.txx
    if (!rProps.schema_location().empty())
    {
        xml::string locn(rProps.schema_location());
        const void* p_locn(locn.c_str());
        p_conf->setParameter(XMLUni::fgXercesSchemaExternalSchemaLocation,
                             const_cast<void*>(p_locn));
    }
    if (!rProps.no_namespace_schema_location().empty())
    {
        xml::string locn(rProps.no_namespace_schema_location());
        const void* p_locn(locn.c_str());

        p_conf->setParameter(XMLUni::fgXercesSchemaExternalNoNameSpaceSchemaLocation,
                             const_cast<void*>(p_locn));
    }

    // We will release the DOM document ourselves.
    p_conf->setParameter(XMLUni::fgXercesUserAdoptsDOMDocument, true);

    // Set error handler.
    xml::dom::bits::error_handler_proxy<char> ehp(rErrorHandler);
    p_conf->setParameter(XMLUni::fgDOMErrorHandler, &ehp);

#else // _XERCES_VERSION >= 30000
    // Same as above but for Xerces-C++ 2 series.
    xml::dom::auto_ptr<DOMBuilder> p_parser(p_impl->createDOMBuilder(DOMImplementationLS::MODE_SYNCHRONOUS, 0));

    p_parser->setFeature(XMLUni::fgDOMComments, false);
    p_parser->setFeature(XMLUni::fgDOMDatatypeNormalization, true);
    p_parser->setFeature(XMLUni::fgDOMEntities, false);
    p_parser->setFeature(XMLUni::fgDOMNamespaces, true);
    p_parser->setFeature(XMLUni::fgDOMWhitespaceInElementContent, false);
    p_parser->setFeature(XMLUni::fgDOMValidation, true);
    p_parser->setFeature(XMLUni::fgXercesSchema, true);
    p_parser->setFeature(XMLUni::fgXercesSchemaFullChecking, false);
    p_parser->setFeature(XMLUni::fgXercesUserAdoptsDOMDocument, true);

    // Code taken from xsd/cxx/xml/dom/parsing-source.txx
    if (!rProps.schema_location().empty())
    {
        xml::string locn(rProps.schema_location());
        const void* p_locn(locn.c_str());
        p_parser->setProperty(XMLUni::fgXercesSchemaExternalSchemaLocation,
                              const_cast<void*>(p_locn));
    }

    if (!rProps.no_namespace_schema_location().empty())
    {
        xml::string locn(rProps.no_namespace_schema_location());
        const void* p_locn(locn.c_str());

        p_parser->setProperty(XMLUni::fgXercesSchemaExternalNoNameSpaceSchemaLocation,
                              const_cast<void*>(p_locn));
    }

    xml::dom::bits::error_handler_proxy<char> ehp(rErrorHandler);
    p_parser->setErrorHandler(&ehp);

#endif // _XERCES_VERSION >= 30000

    // Do the parse
    xml::dom::auto_ptr<DOMDocument> p_doc(p_parser->parseURI(rFileName.c_str()));

    if (ehp.failed())
    {
        p_doc.reset();
    }

    return p_doc;
}

#define COVERAGE_IGNORE
void XmlTools::PrintNode(const std::string& rMsg, xercesc::DOMNode* pNode, bool showChildren)
{
    std::string prefix = xsd::cxx::xml::transcode<char>(pNode->getPrefix());
    std::string name = xsd::cxx::xml::transcode<char>(pNode->getLocalName());
    std::string nsuri = xsd::cxx::xml::transcode<char>(pNode->getNamespaceURI());
    std::cout << rMsg << " " << pNode << " " << prefix << ":" << name << " in " << nsuri << std::endl;
    if (showChildren)
    {
        for (xercesc::DOMNode* p_node = pNode->getFirstChild();
             p_node != NULL;
             p_node = p_node->getNextSibling())
        {
            std::cout << "     child type " << p_node->getNodeType();
            PrintNode("", p_node, false);
        }
        xercesc::DOMNamedNodeMap* p_attrs = pNode->getAttributes();
        if (p_attrs)
        {
            for (XMLSize_t i=0; i<p_attrs->getLength(); i++)
            {
                 xercesc::DOMNode* p_attr = p_attrs->item(i);
                 std::string value = xsd::cxx::xml::transcode<char>(p_attr->getNodeValue());
                 PrintNode("     attr (" + value + ")", p_attr, false);
            }
        }
    }
}
#undef COVERAGE_IGNORE

xercesc::DOMElement* XmlTools::SetNamespace(xercesc::DOMDocument* pDocument,
                                            xercesc::DOMElement* pElement,
                                            const XMLCh* pNamespace)
{
    using namespace xercesc;

    //PrintNode("Renaming", pElement, true);
    DOMNamedNodeMap* p_orig_attrs = pElement->getAttributes();
    std::vector<std::string> attr_values;
    if (p_orig_attrs)
    {
        for (XMLSize_t i=0; i<p_orig_attrs->getLength(); i++)
        {
            DOMNode* p_attr = p_orig_attrs->item(i);
            attr_values.push_back(xsd::cxx::xml::transcode<char>(p_attr->getNodeValue()));
        }
    }
    DOMElement* p_new_elt = static_cast<DOMElement*>(
        pDocument->renameNode(pElement, pNamespace, pElement->getLocalName()));
    //PrintNode("   to", p_new_elt, true);
    // Fix attributes - some get broken by the rename!
    if (p_orig_attrs)
    {
        DOMNamedNodeMap* p_new_attrs = p_new_elt->getAttributes();
        assert(p_new_attrs);
        assert(p_new_attrs == p_orig_attrs);
        assert(p_new_attrs->getLength() == attr_values.size());
        for (XMLSize_t i=0; i<p_new_attrs->getLength(); i++)
        {
            DOMNode* p_attr = p_new_attrs->item(i);
            p_attr->setNodeValue(X(attr_values[i]));
        }
    }
    //PrintNode("   after attr fix", p_new_elt, true);        

    for (DOMNode* p_node = p_new_elt->getFirstChild();
         p_node != NULL;
         p_node = p_node->getNextSibling())
    {
        if (p_node->getNodeType() == DOMNode::ELEMENT_NODE)
        {
            p_node = SetNamespace(pDocument, static_cast<DOMElement*>(p_node), pNamespace);
        }
    }

    return p_new_elt;
}

xercesc::DOMElement* XmlTools::SetNamespace(xercesc::DOMDocument* pDocument,
                                            xercesc::DOMElement* pElement,
                                            const std::string& rNamespace)
{
    return SetNamespace(pDocument, pElement, X(rNamespace));
}

void XmlTools::FindElements(xercesc::DOMElement* pContextElement,
                            const std::vector<std::string>& rNames,
                            std::vector<xercesc::DOMElement*>& rResults,
                            unsigned depth)
{
    xercesc::DOMNodeList* p_child_elts = pContextElement->getElementsByTagName(X(rNames[depth]));
    unsigned num_children = p_child_elts->getLength();
    for (unsigned i=0; i<num_children; i++)
    {
        xercesc::DOMElement* p_child_elt = static_cast<xercesc::DOMElement*>(p_child_elts->item(i));
        if (depth == rNames.size() - 1)
        {
            rResults.push_back(p_child_elt);
        }
        else
        {
            FindElements(p_child_elt, rNames, rResults, depth+1);
        }
    }
}

std::vector<xercesc::DOMElement*> XmlTools::FindElements(xercesc::DOMElement* pContextElement,
                                                         const std::string& rPath)
{
    std::vector<xercesc::DOMElement*> results;
    std::vector<std::string> path;
    size_t start_pos = 0;
    size_t slash_pos = 0;
    while (slash_pos != std::string::npos)
    {
        slash_pos = rPath.find('/', start_pos);
        if (slash_pos == std::string::npos)
        {
            path.push_back(rPath.substr(start_pos));
        }
        else
        {
            path.push_back(rPath.substr(start_pos, slash_pos-start_pos));
        }
        start_pos = slash_pos + 1;
    }
    FindElements(pContextElement, path, results);
    return results;
}

void XmlTools::WrapContentInElement(xercesc::DOMDocument* pDocument,
                                    xercesc::DOMElement* pElement,
                                    const XMLCh* pNewElementLocalName)
{
    const XMLCh* p_namespace_uri = pElement->getNamespaceURI();
    const XMLCh* p_prefix = pElement->getPrefix();
    const XMLCh* p_qualified_name;
    if (p_prefix)
    {
#define COVERAGE_IGNORE
        // We can't actually cover this code, since versions of the parameters file which need this
        // transform didn't use a namespace, so can't have a namespace prefix! 
        xercesc::QName qname(p_prefix, pNewElementLocalName, 0);
        p_qualified_name = qname.getRawName();
#undef COVERAGE_IGNORE
    }
    else
    {
        p_qualified_name = pNewElementLocalName;
    }
    xercesc::DOMElement* p_wrapper_elt = pDocument->createElementNS(p_namespace_uri, p_qualified_name);
    // Move all child nodes of pElement to be children of p_wrapper_elt
    xercesc::DOMNodeList* p_children = pElement->getChildNodes();
    for (unsigned i=0; i<p_children->getLength(); i++)
    {
        xercesc::DOMNode* p_child = pElement->removeChild(p_children->item(i));
        p_wrapper_elt->appendChild(p_child);
    }
    // Add the wrapper as the sole child of pElement
    pElement->appendChild(p_wrapper_elt);
}


void XmlTransforms::TransformArchiveDirectory(xercesc::DOMDocument* pDocument,
                                              xercesc::DOMElement* pRootElement)
{
    using namespace xercesc;
    std::vector<xercesc::DOMElement*> elts = XmlTools::FindElements(
        pRootElement,
        "ResumeSimulation/ArchiveDirectory");
    if (elts.size() > 0)
    {
        // We have an ArchiveDirectory element, so add the relative_to='chaste_test_output' attribute
        DOMElement* p_dir_elt = elts[0];
        //PrintNode(" before", p_dir_elt, true);
        p_dir_elt->setAttribute(X("relative_to"), X("chaste_test_output"));
        //PrintNode(" after", p_dir_elt, true);
    }
}

void XmlTransforms::TransformIonicModelDefinitions(xercesc::DOMDocument* pDocument,
                                                   xercesc::DOMElement* pRootElement)
{
    // Default ionic model
    std::vector<xercesc::DOMElement*> p_elt_list = XmlTools::FindElements(
        pRootElement,
        "Simulation/IonicModels/Default");
    if (p_elt_list.size() > 0)
    {
        assert(p_elt_list.size() == 1); // Asserted by schema
        XmlTools::WrapContentInElement(pDocument, p_elt_list[0], X("Hardcoded"));
        // Now do any region-specific definitions
        p_elt_list = XmlTools::FindElements(pRootElement, "Simulation/IonicModels/Region/IonicModel");
        for (unsigned i=0; i<p_elt_list.size(); i++)
        {
            XmlTools::WrapContentInElement(pDocument, p_elt_list[i], X("Hardcoded"));
        }
    }
}

void XmlTransforms::CheckForIluPreconditioner(xercesc::DOMDocument* pDocument,
                                              xercesc::DOMElement* pRootElement)
{
    std::vector<xercesc::DOMElement*> p_elt_list = XmlTools::FindElements(
        pRootElement,
        "Numerical/KSPPreconditioner");
    if (p_elt_list.size() > 0)
    {
        assert(p_elt_list.size() == 1); // Asserted by schema
        std::string text_value = xsd::cxx::xml::transcode<char>(p_elt_list[0]->getTextContent());
        if (text_value == "ilu")
        {
            EXCEPTION("PETSc does not have a parallel implementation of ilu, so we no longer allow it as an option.  Use bjacobi instead.");
        }
    }
}

// Explicit instantiation of the templated functions
#define COVERAGE_IGNORE //These methods are covered above with DIM=1,2,3 but the instantiations may fail spuriously

template void HeartConfig::GetIonicModelRegions<3u>(std::vector<ChasteCuboid<3u> >& , std::vector<cp::ionic_model_selection_type>&) const;
template void HeartConfig::GetStimuli<3u>(std::vector<boost::shared_ptr<AbstractStimulusFunction> >& , std::vector<ChasteCuboid<3u> >& ) const;
template void HeartConfig::GetCellHeterogeneities<3u>(std::vector<AbstractChasteRegion<3u>* >& ,std::vector<double>& ,std::vector<double>& ,std::vector<double>& ,std::vector<std::map<std::string, double> >*) ;
template void HeartConfig::GetConductivityHeterogeneities<3u>(std::vector<AbstractChasteRegion<3u>* >& ,std::vector< c_vector<double,3> >& ,std::vector< c_vector<double,3> >& ) const;

template void HeartConfig::GetIonicModelRegions<2u>(std::vector<ChasteCuboid<2u> >& , std::vector<cp::ionic_model_selection_type>&) const;
template void HeartConfig::GetStimuli<2u>(std::vector<boost::shared_ptr<AbstractStimulusFunction> >& , std::vector<ChasteCuboid<2u> >& ) const;
template void HeartConfig::GetCellHeterogeneities<2u>(std::vector<AbstractChasteRegion<2u>* >& ,std::vector<double>& ,std::vector<double>& ,std::vector<double>& ,std::vector<std::map<std::string, double> >*) ;
template void HeartConfig::GetConductivityHeterogeneities<2u>(std::vector<AbstractChasteRegion<2u>* >& ,std::vector< c_vector<double,3> >& ,std::vector< c_vector<double,3> >& ) const;

template void HeartConfig::GetIonicModelRegions<1u>(std::vector<ChasteCuboid<1u> >& , std::vector<cp::ionic_model_selection_type>&) const;
template void HeartConfig::GetStimuli<1u>(std::vector<boost::shared_ptr<AbstractStimulusFunction> >& , std::vector<ChasteCuboid<1u> >& ) const;
template void HeartConfig::GetCellHeterogeneities<1u>(std::vector<AbstractChasteRegion<1u>* >& ,std::vector<double>& ,std::vector<double>& ,std::vector<double>& ,std::vector<std::map<std::string, double> >*);
template void HeartConfig::GetConductivityHeterogeneities<1u>(std::vector<AbstractChasteRegion<1u>* >& ,std::vector< c_vector<double,3> >& ,std::vector< c_vector<double,3> >& ) const;
#undef COVERAGE_IGNORE //These methods are covered above with DIM=1,2,3 but the instantiations may fail spuriously


// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(HeartConfig)

---