vm2ug_mpm.h

/*
 * Copyright (c) 2009-2019: G-CSC, Goethe University Frankfurt
 *
 * Author: Stephan Grein
 * Creation date: 2015-06-24
 *
 * This file is part of NeuroBox, which is based on UG4.
 *
 * NeuroBox and UG4 are free software: You can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License version 3
 * (as published by the Free Software Foundation) with the following additional
 * attribution requirements (according to LGPL/GPL v3 §7):
 *
 * (1) The following notice must be displayed in the appropriate legal notices
 * of covered and combined works: "Based on UG4 (www.ug4.org/license)".
 *
 * (2) The following notice must be displayed at a prominent place in the
 * terminal output of covered works: "Based on UG4 (www.ug4.org/license)".
 *
 * (3) The following bibliography is recommended for citation and must be
 * preserved in all covered files:
 * "Reiter, S., Vogel, A., Heppner, I., Rupp, M., and Wittum, G. A massively
 *   parallel geometric multigrid solver on hierarchically distributed grids.
 *   Computing and visualization in science 16, 4 (2013), 151-164"
 * "Vogel, A., Reiter, S., Rupp, M., Nägel, A., and Wittum, G. UG4 -- a novel
 *   flexible software system for simulating PDE based models on high performance
 *   computers. Computing and visualization in science 16, 4 (2013), 165-179"
 * "Stepniewski, M., Breit, M., Hoffer, M. and Queisser, G.
 *   NeuroBox: computational mathematics in multiscale neuroscience.
 *   Computing and visualization in science (2019).
 * "Breit, M. et al. Anatomically detailed and large-scale simulations studying
 *   synapse loss and synchrony using NeuroBox. Front. Neuroanat. 10 (2016), 8"
 *
 * This program 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.
 */

/// guard
#ifndef UG__PLUGINS__MEMBRANE_POTENTIAL_MAPPING__VM2UG_MPM_H
#define UG__PLUGINS__MEMBRANE_POTENTIAL_MAPPING__VM2UG_MPM_H

/// includes
#include "transformator.h"
#include "vm2ug.h"

/*! \defgroup mpm_plugin Membrane Potential Mapping plugin
 * \ingroup plugins_experimental
 * \{
 */
namespace ug {
namespace membrane_potential_mapping {


/*!
 * \brief
 */
template <size_t dim>
class Vm2uGMPM {
		/// private non-static members
		SmartPtr<Mapper<dim, number> > m_mapper;

	public:
		/*!
		 * \brief dtor
		 */
		Vm2uGMPM() : m_mapper(make_sp(new Mapper<dim, number>())) {

		}

		/*!
		 * \brief builds the kd-tree on demand with a file
		 * \param[in] filename
		 * \param[in] delimiter
		 */
		inline void build_tree(const std::string& filename) {
			m_mapper->build_tree(filename);
		}

		/*!
		 * \brief builds the kd-tree on demand without a file
		 * \param[in] points
		 */
		inline void build_tree(const std::vector<std::pair<MathVector<3>, number> >& points) {
			m_mapper->build_tree(points);
		}

		/*!
		 * \brief get's membrane potential for given coordinates x, y and z
		 * \param[in] x
		 * \param[in] y
		 * \param[in] z
		 *
		 * \return \c membrane potential
		 */
		inline number get_vm(number x, number y, number z) {
			return this->get_vm(MathVector<3>(x, y, z));
		}

		/*!
		 * \brief get membrane potential for given vector
		 * \param[in] vec
		 *
		 * \return \c membrane potential
		 */
		inline number get_vm(const MathVector<dim>& vec) {
			return m_mapper->get_data_from_nearest_neighbor(vec);
		}
};

} // end namespace mpm
} // end namespace ug
//<! \}

#endif // UG__PLUGINS__MEMBRANE_POTENTIAL_MAPPING__VM2UG_MPM_H