soma_projector.h

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/*
 * Copyright (c) 2018:  G-CSC, Goethe University Frankfurt
 * Author: Stephan Grein
 *
 * This file is part of UG4.
 *
 * UG4 is 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):
 *
 * (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"
 *
 * 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.
 */
 
#ifndef __H__UG_cylinder_soma_projector
#define __H__UG_cylinder_soma_projector
 
#include "common/math/misc/math_util.h"
#include "refinement_projector.h"
#include "lib_grid/tools/copy_attachment_handler.h"
#include "lib_grid/global_attachments.h"
 
namespace ug {
 
class SomaProjector : public RefinementProjector {
private:
  Attachment<NeuriteProjector::SurfaceParams> m_aSurfParams;
    Grid::VertexAttachmentAccessor<Attachment<NeuriteProjector::SurfaceParams> > m_aaSurfParams;
    CopyAttachmentHandler<Vertex, Attachment<NeuriteProjector::SurfaceParams> > m_cah;
protected:
    virtual void set_geometry(SPIGeometry3d geometry)
    {
        // call base class method
        RefinementProjector::set_geometry(geometry);
    attach_surf_params();
    }
    virtual void set_geometry(SPIGeometry3d geometry) {…}
public:
    SomaProjector () :
      m_center (0, 0, 0),
      m_axis (0, 0, 1),
      m_soma (0, 0, 0),
      m_somaRad(0)
    {
      typedef Attachment<NeuriteProjector::SurfaceParams> NPSurfParam;
        if (!GlobalAttachments::is_declared("npSurfParams"))
          GlobalAttachments::declare_attachment<NPSurfParam>("npSurfParams", true);
 
    }
    SomaProjector () : {…}
 
    SomaProjector (const vector3& center,
            const vector3& axis,
            const vector3& soma,
            const number& rad) :
 
    m_center (center),
    m_axis (axis),
    m_soma (soma),
    m_somaRad(rad)
  {
      typedef Attachment<NeuriteProjector::SurfaceParams> NPSurfParam;
        if (!GlobalAttachments::is_declared("npSurfParams"))
          GlobalAttachments::declare_attachment<NPSurfParam>("npSurfParams", true);
  }
    SomaProjector (const vector3& center, {…}
 
public:
  SomaProjector (SPIGeometry3d geometry,
          const vector3& center,
          const vector3& axis,
          const vector3& soma,
          const number& rad) :
    RefinementProjector (geometry),
    m_center (center),
    m_axis (axis),
    m_soma (soma),
    m_somaRad(rad)
  {
    attach_surf_params();
  }
  SomaProjector (SPIGeometry3d geometry, {…}
 
 
public:
  virtual ~SomaProjector ()         {}
 
  virtual number new_vertex(Vertex* vrt, Edge* parent)
  {
    return perform_projection(vrt, parent);
  }
  virtual number new_vertex(Vertex* vrt, Edge* parent) {…}
 
  virtual number new_vertex(Vertex* vrt, Face* parent)
  {
    return perform_projection(vrt, parent);
  }
  virtual number new_vertex(Vertex* vrt, Face* parent) {…}
 
  virtual number new_vertex(Vertex* vrt, Volume* parent)
  {
    return perform_projection(vrt, parent);
  }
  virtual number new_vertex(Vertex* vrt, Volume* parent) {…}
 
private:
  void check_attachment() {
    typedef Attachment<NeuriteProjector::SurfaceParams> NPSurfParam;
    if (!GlobalAttachments::is_declared("npSurfParams"))
      GlobalAttachments::declare_attachment<NPSurfParam>("npSurfParams", true);
  }
  void check_attachment() {…}
 
 
  void attach_surf_params() {
    check_attachment();
 
    Grid& grid = this->geometry()->grid();
 
    // make sure attachment was declared
    UG_COND_THROW(!GlobalAttachments::is_declared("npSurfParams"), "GlobalAttachment 'npSurfParams' not declared.");
    m_aSurfParams = GlobalAttachments::attachment<Attachment<NeuriteProjector::SurfaceParams> >("npSurfParams");
 
    // make sure surfaceParams attachment is attached
      UG_COND_THROW(!grid.has_vertex_attachment(m_aSurfParams),
        "No surface parameter attachment for neurite projector attached to grid.");
     m_aaSurfParams.access(grid, m_aSurfParams);
 
    // handle attachment values also on higher grid levels (if required)
    MultiGrid* mg = dynamic_cast<MultiGrid*>(&grid);
    if (mg) {
      SmartPtr<MultiGrid> spMG(mg);
 
      // never destroy the grid from here - we did not create it
        ++(*spMG.refcount_ptr());
 
        // attach copy attachment handler to propagate attachment to higher levels
        m_cah.set_attachment(m_aSurfParams);
        m_cah.set_grid(spMG);
     }
  }
  void attach_surf_params() {…}
 
 
  template <class TElem>
  number perform_projection(Vertex* vrt, TElem* parent)
  {
  //  calculate the new position by linear interpolation and project that point
  //  onto the cylinder.
    typename TElem::ConstVertexArray vrts = parent->vertices();
    size_t numVrts = parent->num_vertices();
 
    if(numVrts == 0){
      set_pos(vrt, vector3(0, 0, 0));
      return 1;
    }
 
    number avDist = 0;
    vector3 parentCenter (0, 0, 0);
 
    for(size_t i = 0; i < numVrts; ++i){
      vector3 p = pos(vrts[i]);
      avDist += DistancePointToRay(p, m_center, m_axis);
      parentCenter += p;
    }
 
    avDist /= (number)numVrts;
    VecScale(parentCenter, parentCenter, 1. / (number)numVrts);
 
    vector3 proj, v;
    ProjectPointToRay(proj, parentCenter, m_center, m_axis);
    VecSubtract(v, parentCenter, proj);
    number len = VecLength(v);
    if(len > SMALL * avDist){ // if avDist is very small, len may be small, too
      VecScale(v, v, avDist/len);
      proj += v;
      set_pos(vrt, proj);
    }
    else
      set_pos(vrt, parentCenter);
 
    if (vertex_at_soma_surf(vrt, parent))
      project_to_soma_surface(vrt, parent);
 
    return 1;
  }
  number perform_projection(Vertex* vrt, TElem* parent) {…}
 
  template <class TElem>
  bool vertex_at_soma_surf(Vertex* vrt, TElem* parent) {
    size_t numSomaVerts = 0;
      size_t nVrt = parent->num_vertices();
      for (size_t i = 0; i < nVrt; ++i) {
         if(m_aaSurfParams[parent->vertex(i)].axial == -1.0) {
           numSomaVerts++;
         }
      }
      return numSomaVerts >= 2;
  }
  bool vertex_at_soma_surf(Vertex* vrt, TElem* parent) {…}
 
  template <class TElem>
  void project_to_soma_surface(Vertex* vrt, TElem* parent) {
    vector3 v0 = this->pos(vrt);
    vector3 P;
    VecSubtract(P, v0, m_soma);
    number Plength = VecLength(P);
    vector3 Q = P;
    VecScale(Q, P, m_somaRad / Plength);
    vector3 R;
    VecAdd(R, Q, m_soma);
    set_pos(vrt, R);
    m_aaSurfParams[vrt].axial = -1;
  }
  void project_to_soma_surface(Vertex* vrt, TElem* parent) {…}
 
 
  friend class boost::serialization::access;
 
  template <class Archive>
  void serialize( Archive& ar, const unsigned int version)
  {
    ar & make_nvp("center", m_center);
    ar & make_nvp("axis", m_axis);
    ar & make_nvp("soma", m_soma);;
    ar & make_nvp("somaRad", m_somaRad);;
    UG_EMPTY_BASE_CLASS_SERIALIZATION(SomaProjector, RefinementProjector);
  }
  void serialize( Archive& ar, const unsigned int version) {…}
 
  vector3 m_center;
  vector3 m_axis;
  vector3 m_soma;
  number m_somaRad;
};
class SomaProjector : public RefinementProjector {…};
 
}// end of namespace
 
#endif  //__H__UG_cylinder_soma_projector