StartupFileHdf5.cpp

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/*
 * Copyright 2011-2016 Universiteit Antwerpen
 *
 * Licensed under the EUPL, Version 1.1 or  as soon they will be approved by
 * the European Commission - subsequent versions of the EUPL (the "Licence");
 * You may not use this work except in compliance with the Licence.
 * You may obtain a copy of the Licence at: http://ec.europa.eu/idabc/eupl5
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the Licence is distributed on an "AS IS" basis,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the Licence for the specific language governing
 * permissions and limitations under the Licence.
 */
#include "workspace/StartupFileHdf5.h"

#include "session/SimSession.h"
#include "fileformats/Hdf5File.h"
#include "util/misc/Exception.h"
#include "workspace/MergedPreferences.h"

namespace SimPT_Shell {
namespace Ws {

using namespace std;
using namespace boost::property_tree;
using namespace SimPT_Sim::Util;
using namespace SimShell::Ws;

StartupFileHdf5::StartupFileHdf5(const string& path)
        : StartupFileBase(path),
          m_reverse_index_initialized(false)
{
}

shared_ptr<SimShell::Session::ISession>
StartupFileHdf5::CreateSession(shared_ptr<IProject> proj, std::shared_ptr<IWorkspace> ws) const
{
        shared_ptr<Session::ISession> session;
        auto prefs = MergedPreferences::Create(ws, proj);
        try {
                Hdf5File tissue_file(m_path);
                // may throw
                SimPT_Sim::SimState sim_state = tissue_file.Read();
                session = make_shared<Session::SimSession>(prefs, sim_state);
        }
        catch (exception& e) {
                throw Exception("Could not open \"" + m_path + "\": " + e.what());
        }

        return session;
}

SimPT_Sim::SimState StartupFileHdf5::GetSimState(int timestep) const
{
        if (!m_reverse_index_initialized)
                InitializeReverseIndex();
        try {
                Hdf5File tissue_file(m_path);
                SimPT_Sim::SimState result = tissue_file.Read(m_reverse_index[timestep]);
                tissue_file.Close();
                return result;
        } catch (exception& e) {
                throw Exception("GetSimState(): Could not open \"" + m_path + "\": " + e.what());
        }
}

vector<int> StartupFileHdf5::GetTimeSteps() const
{
        vector<int> result;
        try {
                Hdf5File tissue_file(m_path);
                for (auto& pair : tissue_file.TimeSteps()) {
                        result.push_back(pair.first);
                }
        } catch (exception& e) {
                throw Exception("GetTimeSteps(): Could not open \"" + m_path + "\": " + e.what());
        }
        return result;
}

void StartupFileHdf5::InitializeReverseIndex() const
{
        int i = 0;
        for (int t : GetTimeSteps()) {
                m_reverse_index[t] = i++;
        }
        m_reverse_index_initialized = true;
}

} // namespace
} // namespace