diff --git a/CMakeLists.txt b/CMakeLists.txt index 13c9dc6..d4e35fa 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -105,7 +105,10 @@ endif() # # VTK -find_package(VTK 5.10 REQUIRED NO_MODULE) +find_package(VTK 6 NO_MODULE) +if(NOT VTK_FOUND) + find_package(VTK 5.10 REQUIRED NO_MODULE) +endif() if(VTK_FOUND) message(STATUS "VTK found ${VTK_DIR}") include(${VTK_USE_FILE}) @@ -135,11 +138,11 @@ endif() # # Eigen -find_package(EIGEN 3.0 REQUIRED) -# -if(EIGEN_FOUND) +find_package(Eigen3 REQUIRED) +if(EIGEN3_FOUND) message(STATUS "eigen found ${EIGEN_DIR} ${EIGEN_INCLUDE_DIR}") - include_directories(${EIGEN_INCLUDE_DIR}) +# include_directories(${EIGEN3_INCLUDE_DIR}) +# include( ${EIGEN3_USE_FILE} ) else() message(STATUS "eigen not found") endif() @@ -178,7 +181,7 @@ endif() # # CGAL -find_package(CGAL 4.3 REQUIRED) +find_package(CGAL REQUIRED) # if(CGAL_FOUND) message( STATUS "CGAL found ${CGAL_DIR}" ) @@ -189,6 +192,15 @@ else() message( STATUS "CGAL not found" ) endif() +# +# GSL +find_package(GSL REQUIRED) +if(GSL_FOUND) + message(STATUS "GSL found ${GSL_DIR}") +else() + message(STATUS "GSL not found") +endif() + # include_directories( SYSTEM ) diff --git a/Fijee/Biophysics/CMakeLists.txt b/Fijee/Biophysics/CMakeLists.txt index 65391bc..ca0898f 100644 --- a/Fijee/Biophysics/CMakeLists.txt +++ b/Fijee/Biophysics/CMakeLists.txt @@ -25,4 +25,4 @@ add_library( FijeeBiophysics ${Fijee_H} ${HEADERS} ${SOURCES} ) # Add FijeeUtils target libraries target_link_libraries( FijeeBiophysics ${Fijee_TARGET_LINK_LIBRARIES} ) # Install -install( TARGETS FijeeBiophysics EXPORT FijeeTargets LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib ) +install( TARGETS FijeeBiophysics EXPORT FijeeTargets LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib ) diff --git a/Fijee/Electrodes/CMakeLists.txt b/Fijee/Electrodes/CMakeLists.txt index efd2c73..510126f 100644 --- a/Fijee/Electrodes/CMakeLists.txt +++ b/Fijee/Electrodes/CMakeLists.txt @@ -25,4 +25,4 @@ add_library( FijeeElectrodes ${Fijee_H} ${HEADERS} ${SOURCES} ) # Add FijeeUtils target libraries target_link_libraries( FijeeElectrodes ${Fijee_TARGET_LINK_LIBRARIES} ) # Install -install( TARGETS FijeeElectrodes EXPORT FijeeTargets LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib ) +install( TARGETS FijeeElectrodes EXPORT FijeeTargets LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib ) diff --git a/Fijee/Finite_element_method_models/CMakeLists.txt b/Fijee/Finite_element_method_models/CMakeLists.txt index 36c2045..69702f8 100644 --- a/Fijee/Finite_element_method_models/CMakeLists.txt +++ b/Fijee/Finite_element_method_models/CMakeLists.txt @@ -49,4 +49,4 @@ add_library( FijeeFEM ${Fijee_H} ${HEADERS} ${UFL_HEADERS} ${SOURCES} ) # Add FijeeUtils target libraries target_link_libraries( FijeeFEM ${Fijee_TARGET_LINK_LIBRARIES} ${DOLFIN_LIBRARIES} ) # Install -install( TARGETS FijeeFEM EXPORT FijeeTargets LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib ) +install( TARGETS FijeeFEM EXPORT FijeeTargets LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib ) diff --git a/Fijee/Finite_element_method_models/Physics.cxx b/Fijee/Finite_element_method_models/Physics.cxx index cbb6240..840008d 100644 --- a/Fijee/Finite_element_method_models/Physics.cxx +++ b/Fijee/Finite_element_method_models/Physics.cxx @@ -81,7 +81,7 @@ Solver::Physics::Physics() std::string facets_collection_xml = (SDEsp::get_instance())->get_files_path_output_(); facets_collection_xml += "mesh_facets_subdomains.xml"; // - mesh_facets_collection_.reset( new MeshValueCollection< std::size_t > (*mesh_, facets_collection_xml) ); + mesh_facets_collection_.reset( new MeshValueCollection< std::size_t > (mesh_, facets_collection_xml) ); // // MeshDataCollection methode diff --git a/Fijee/Finite_element_method_models/SL_direct.cxx b/Fijee/Finite_element_method_models/SL_direct.cxx index 61bdec3..7c01966 100644 --- a/Fijee/Finite_element_method_models/SL_direct.cxx +++ b/Fijee/Finite_element_method_models/SL_direct.cxx @@ -36,13 +36,13 @@ Solver::SL_direct::SL_direct():Physics() { // // Define the function space - V_.reset( new SLD_model::FunctionSpace(*mesh_) ); + V_.reset( new SLD_model::FunctionSpace(mesh_) ); // // Define boundary condition perifery_.reset( new Periphery() ); // Initialize mesh function for boundary domains. We tag the boundaries - boundaries_.reset( new FacetFunction< size_t > (*mesh_) ); + boundaries_.reset( new FacetFunction< size_t > (mesh_) ); boundaries_->set_all(0); perifery_->mark(*boundaries_, 1); @@ -155,6 +155,7 @@ Solver::SL_direct::operator () ( /*Solver::Phi& source, // // // // Define Dirichlet boundary conditions // DirichletBC boundary_conditions(*V, source, perifery); + std::vector> bc; /////////////////////////////////////////////// @@ -163,26 +164,32 @@ Solver::SL_direct::operator () ( /*Solver::Phi& source, // // Define variational forms - SLD_model::BilinearForm a(*V_, *V_); - SLD_model::LinearForm L(*V_); + SLD_model::BilinearForm a(V_, V_); + SLD_model::LinearForm L(V_); // // Anisotropy // Bilinear - a.a_sigma = *sigma_; - a.dx = *domains_; + a.a_sigma = sigma_; + a.dx = domains_; // Linear - L.J_source = source; + L.J_source = std::make_shared(source); // - L.dx = *domains_; - L.ds = *boundaries_; + L.dx = domains_; + L.ds = boundaries_; // // Compute solution Function u(V_); // - LinearVariationalProblem problem(a, L, u); - LinearVariationalSolver solver(problem); +// LinearVariationalProblem problem(a, L, u); +// LinearVariationalSolver solver(problem); + LinearVariationalProblem problem(std::shared_ptr (&a), + std::shared_ptr (&L), + std::shared_ptr (&u), + bc); + LinearVariationalSolver solver( (std::shared_ptr (&problem)) ); + // krylov solver.parameters["linear_solver"] = (SDEsp::get_instance())->get_linear_solver_(); diff --git a/Fijee/Finite_element_method_models/SL_subtraction.cxx b/Fijee/Finite_element_method_models/SL_subtraction.cxx index 9c82e8d..96e0f00 100644 --- a/Fijee/Finite_element_method_models/SL_subtraction.cxx +++ b/Fijee/Finite_element_method_models/SL_subtraction.cxx @@ -46,7 +46,7 @@ Solver::SL_subtraction::SL_subtraction():Physics() // Define boundary condition Periphery perifery; // Initialize mesh function for boundary domains. We tag the boundaries - boundaries_.reset( new FacetFunction< size_t > (*mesh_) ); + boundaries_.reset(new FacetFunction< size_t >(mesh_)); boundaries_->set_all(0); perifery.mark(*boundaries_, 1); @@ -163,7 +163,7 @@ Solver::SL_subtraction::operator () ( /*Solver::Phi& source, // // Anisotropy conductivity // Bilinear form - a_->a_sigma = *sigma_; + a_->a_sigma = sigma_; // a.dx = *domains_; // A_.reset( new Matrix() ); @@ -202,9 +202,9 @@ Solver::SL_subtraction::operator () ( /*Solver::Phi& source, Vector L_; // Linear - L.a_inf = a_inf; - L.a_sigma = *sigma_; - L.Phi_0 = source; + L.a_inf = std::make_shared(a_inf); + L.a_sigma = sigma_; + L.Phi_0 = std::make_shared(source); // // L.dx = *domains_; // L.ds = *boundaries_; diff --git a/Fijee/Finite_element_method_models/Spheres_electric_monopole.cxx b/Fijee/Finite_element_method_models/Spheres_electric_monopole.cxx index aa6b82b..8fdbd01 100644 --- a/Fijee/Finite_element_method_models/Spheres_electric_monopole.cxx +++ b/Fijee/Finite_element_method_models/Spheres_electric_monopole.cxx @@ -295,9 +295,9 @@ Solver::Spheres_electric_monopole::Spheres_electric_monopole(const Spheres_elect r0_values_ = that.r0_values_; // std::copy(that.r_sphere_, that.r_sphere_ + NUM_SPHERES, r_sphere_); - std::copy(that.sigma_, that.sigma_ + NUM_SPHERES, sigma_); + std::copy((double*)that.sigma_, ((double*)that.sigma_) + NUM_SPHERES * 2, (double*)sigma_); // - std::copy(that.nu_, that.nu_ + NUM_ITERATIONS, nu_); + std::copy((double*)that.nu_, ((double*)that.nu_) + NUM_ITERATIONS * NUM_SPHERES, (double*)nu_); std::copy(that.R_coeff_, that.R_coeff_ + NUM_ITERATIONS, R_coeff_); // for ( int n = 0 ; n < NUM_ITERATIONS ; n++ ) @@ -531,9 +531,9 @@ Solver::Spheres_electric_monopole::operator =( const Spheres_electric_monopole& r0_values_ = that.r0_values_; // std::copy(that.r_sphere_, that.r_sphere_ + NUM_SPHERES, r_sphere_); - std::copy(that.sigma_, that.sigma_ + NUM_SPHERES, sigma_); + std::copy((double*)that.sigma_, ((double*)that.sigma_) + NUM_SPHERES * 2, (double*)sigma_); // - std::copy(that.nu_, that.nu_ + NUM_ITERATIONS, nu_); + std::copy((double*)that.nu_, ((double*)that.nu_) + NUM_ITERATIONS * NUM_SPHERES, (double*)nu_); std::copy(that.R_coeff_, that.R_coeff_ + NUM_ITERATIONS, R_coeff_); // for ( int n = 0 ; n < NUM_ITERATIONS ; n++ ) diff --git a/Fijee/Finite_element_method_models/tCS_tACS.cxx b/Fijee/Finite_element_method_models/tCS_tACS.cxx index 028e4bc..7db122a 100644 --- a/Fijee/Finite_element_method_models/tCS_tACS.cxx +++ b/Fijee/Finite_element_method_models/tCS_tACS.cxx @@ -115,6 +115,8 @@ Solver::tCS_tACS::operator () ( /*Solver::Phi& source, // // // // PDE boundary conditions // DirichletBC bc(*V_, *(electrodes_->get_current(0)), *boundaries_, 101); + std::vector> bc; + // // Define variational forms @@ -124,19 +126,25 @@ Solver::tCS_tACS::operator () ( /*Solver::Phi& source, // // Anisotropy // Bilinear - a.a_sigma = *sigma_; + a.a_sigma = sigma_; // a.dx = *domains_; // Linear - L.I = *( electrodes_->get_current(local_sample) ); - L.ds = *boundaries_; + L.I = electrodes_->get_current(local_sample); + L.ds = boundaries_; // // Compute solution - Function u(*V_); - LinearVariationalProblem problem(a, L, u/*, bc*/); - LinearVariationalSolver solver(problem); + Function u(V_); +// LinearVariationalProblem problem(a, L, u, bc); +// LinearVariationalSolver solver(problem); + LinearVariationalProblem problem(std::shared_ptr (&a), + std::shared_ptr (&L), + std::shared_ptr (&u), + bc); + LinearVariationalSolver solver( (std::shared_ptr (&problem)) ); + // krylov solver.parameters["linear_solver"] = (SDEsp::get_instance())->get_linear_solver_(); @@ -257,15 +265,23 @@ Solver::tCS_tACS::operator () ( /*Solver::Phi& source, // Linear - L_field.u = u; - L_field.a_sigma = *sigma_; + L_field.u = std::shared_ptr (&u); + L_field.a_sigma = sigma_; // L.ds = *boundaries_; // // Compute solution - Function J(*V_current_density_); - LinearVariationalProblem problem_field(a_field, L_field, J/*, bc*/); - LinearVariationalSolver solver_field(problem_field); + Function J(V_current_density_); +// LinearVariationalProblem problem_field(a_field, L_field, J/*, bc*/); +// LinearVariationalSolver solver_field(problem_field); + + LinearVariationalProblem problem_field(std::shared_ptr (&a_field), + std::shared_ptr (&L_field), + std::shared_ptr (&J), + bc); + LinearVariationalSolver solver_field( (std::shared_ptr (&problem)) ); + + // krylov solver_field.parameters["linear_solver"] = (SDEsp::get_instance())->get_linear_solver_(); @@ -334,15 +350,22 @@ Solver::tCS_tACS::operator () ( /*Solver::Phi& source, // Linear - L_E.u = u; + L_E.u = std::shared_ptr (&u); // L_Er.a_sigma = *sigma_; // L.ds = *boundaries_; // // Compute solution - Function E(*V_E_); - LinearVariationalProblem problem_E(a_E, L_E, E/*, bc*/); - LinearVariationalSolver solver_E(problem_E); + Function E(V_E_); +// LinearVariationalProblem problem_E(a_E, L_E, E/*, bc*/); +// LinearVariationalSolver solver_E(problem_E); + + LinearVariationalProblem problem_E(std::make_shared (a_E), + std::make_shared (L_E), + std::make_shared (E), + bc); + LinearVariationalSolver solver_E(std::make_shared (problem_E)); + // krylov solver_E.parameters["linear_solver"] = (SDEsp::get_instance())->get_linear_solver_(); diff --git a/Fijee/Finite_element_method_models/tCS_tDCS.cxx b/Fijee/Finite_element_method_models/tCS_tDCS.cxx index 4a9a472..0ac7635 100644 --- a/Fijee/Finite_element_method_models/tCS_tDCS.cxx +++ b/Fijee/Finite_element_method_models/tCS_tDCS.cxx @@ -108,6 +108,7 @@ Solver::tCS_tDCS::operator () ( /*Solver::Phi& source, // // // // PDE boundary conditions // DirichletBC bc(*V_, *(electrodes_->get_current(0)), *boundaries_, 101); + std::vector> bc; // // Define variational forms @@ -117,21 +118,24 @@ Solver::tCS_tDCS::operator () ( /*Solver::Phi& source, // // Anisotropy // Bilinear - a.a_sigma = *sigma_; + a.a_sigma = sigma_; // a.dx = *domains_; // std::cout << electrodes_->get_current(0)->information("T7").get_I_() << std::endl; // Linear - L.I = *(electrodes_->get_current( /*local_sample*/ 0)); - L.ds = *boundaries_; + L.I = electrodes_->get_current( /*local_sample*/ 0); + L.ds = boundaries_; // // Compute solution - Function u(*V_); - LinearVariationalProblem problem(a, L, u/*, bc*/); - LinearVariationalSolver solver(problem); + Function u(V_); + LinearVariationalProblem problem(std::shared_ptr (&a), + std::shared_ptr (&L), + std::shared_ptr (&u), + bc); + LinearVariationalSolver solver( (std::shared_ptr (&problem)) ); // krylov - solver.parameters["linear_solver"] + solver.parameters["linear_solver"] = (SDEsp::get_instance())->get_linear_solver_(); solver.parameters("krylov_solver")["maximum_iterations"] = (SDEsp::get_instance())->get_maximum_iterations_(); @@ -225,15 +229,19 @@ Solver::tCS_tDCS::operator () ( /*Solver::Phi& source, // Linear - L_field.u = u; - L_field.a_sigma = *sigma_; + L_field.u = std::shared_ptr (&u); + L_field.a_sigma = sigma_; // L.ds = *boundaries_; // // Compute solution - Function J(*V_current_density_); - LinearVariationalProblem problem_field(a_field, L_field, J/*, bc*/); - LinearVariationalSolver solver_field(problem_field); + Function J(V_current_density_); +// LinearVariationalProblem problem_field(a_field, L_field, J, bc); + LinearVariationalProblem problem_field(std::make_shared (a_field), + std::make_shared (L_field), + std::make_shared (J), + bc); + LinearVariationalSolver solver_field(std::make_shared(problem_field)); // krylov solver_field.parameters["linear_solver"] = (SDEsp::get_instance())->get_linear_solver_(); @@ -277,15 +285,22 @@ Solver::tCS_tDCS::operator () ( /*Solver::Phi& source, // Linear - L_E.u = u; + L_E.u = std::shared_ptr (&u); // L_Er.a_sigma = *sigma_; // L.ds = *boundaries_; // // Compute solution - Function E(*V_E_); - LinearVariationalProblem problem_E(a_E, L_E, E/*, bc*/); - LinearVariationalSolver solver_E(problem_E); + Function E(V_E_); +// LinearVariationalProblem problem_E(a_E, L_E, E, bc); +// LinearVariationalSolver solver_E(problem_E); + + LinearVariationalProblem problem_E(std::make_shared (a_E), + std::make_shared (L_E), + std::make_shared (E), + bc); + LinearVariationalSolver solver_E(std::make_shared (problem_E)); + // krylov solver_E.parameters["linear_solver"] = (SDEsp::get_instance())->get_linear_solver_(); diff --git a/Fijee/Finite_element_method_models/tCS_tDCS_local_conductivity.cxx b/Fijee/Finite_element_method_models/tCS_tDCS_local_conductivity.cxx index e3883e3..c7766b3 100644 --- a/Fijee/Finite_element_method_models/tCS_tDCS_local_conductivity.cxx +++ b/Fijee/Finite_element_method_models/tCS_tDCS_local_conductivity.cxx @@ -186,7 +186,7 @@ Solver::tCS_tDCS_local_conductivity::operator ()( ) // // // Define Dirichlet boundary conditions // // DirichletBC boundary_conditions(*V, source, perifery); - // + // // Initialize the simplex for( auto vertex = simplex_.begin() ; vertex != simplex_.end() ; vertex++ ) { @@ -218,6 +218,8 @@ Solver::tCS_tDCS_local_conductivity::operator ()( const Eigen::Vector3d& A){retu double Solver::tCS_tDCS_local_conductivity::solve( const Eigen::Vector3d& Vertex ) { + std::vector> bc; + // // Update the conductivity sigma_->conductivity_update( domains_, Vertex ); @@ -234,19 +236,24 @@ Solver::tCS_tDCS_local_conductivity::solve( const Eigen::Vector3d& Vertex ) // // Anisotropy // Bilinear - a.a_sigma = *sigma_; + a.a_sigma = sigma_; // a.dx = *domains_; // Linear - L.I = *(electrodes_->get_current(0)); - L.ds = *boundaries_; + L.I = electrodes_->get_current(0); + L.ds = boundaries_; // // Compute solution - Function u(*V_); - LinearVariationalProblem problem(a, L, u/*, bc*/); - LinearVariationalSolver solver(problem); + Function u(V_); +// LinearVariationalProblem problem(a, L, u/*, bc*/); +// LinearVariationalSolver solver(problem); + LinearVariationalProblem problem(std::shared_ptr (&a), + std::shared_ptr (&L), + std::shared_ptr (&u), + bc); + LinearVariationalSolver solver( (std::shared_ptr (&problem)) ); // krylov solver.parameters["linear_solver"] = (SDEsp::get_instance())->get_linear_solver_(); diff --git a/Fijee/Mesh_rendering/Access_parameters.h b/Fijee/Mesh_rendering/Access_parameters.h index e121efe..0e9051c 100644 --- a/Fijee/Mesh_rendering/Access_parameters.h +++ b/Fijee/Mesh_rendering/Access_parameters.h @@ -61,7 +61,7 @@ typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel; typedef CGAL::Point_with_normal_3 Point_with_normal; -typedef CGAL::Search_traits TreeTraits; +typedef CGAL::Search_traits TreeTraits; typedef CGAL::Orthogonal_k_neighbor_search Neighbor_search; typedef Neighbor_search::iterator NN_iterator; typedef Neighbor_search::Tree Tree; diff --git a/Fijee/Mesh_rendering/Build_dipoles_list_high_density.cxx b/Fijee/Mesh_rendering/Build_dipoles_list_high_density.cxx index 586fc1a..f52b5b5 100644 --- a/Fijee/Mesh_rendering/Build_dipoles_list_high_density.cxx +++ b/Fijee/Mesh_rendering/Build_dipoles_list_high_density.cxx @@ -128,11 +128,11 @@ DBdlhd::Make_list( const std::list< Cell_conductivity >& List_cell_conductivity // Computes average spacing. const unsigned int nb_neighbors = 6; // 1 ring // - FT lh_average_spacing = CGAL::compute_average_spacing(lh_wm_points.begin(), lh_wm_points.end(), + FT lh_average_spacing = CGAL::compute_average_spacing(lh_wm_points.begin(), lh_wm_points.end(), CGAL::Nth_of_tuple_property_map<1,IndexedPointVector>(), nb_neighbors); // - FT rh_average_spacing = CGAL::compute_average_spacing(rh_wm_points.begin(), rh_wm_points.end(), + FT rh_average_spacing = CGAL::compute_average_spacing(rh_wm_points.begin(), rh_wm_points.end(), CGAL::Nth_of_tuple_property_map<1,IndexedPointVector>(), nb_neighbors); // diff --git a/Fijee/Mesh_rendering/Build_dipoles_list_high_density.h b/Fijee/Mesh_rendering/Build_dipoles_list_high_density.h index 6c1e435..b1ed658 100644 --- a/Fijee/Mesh_rendering/Build_dipoles_list_high_density.h +++ b/Fijee/Mesh_rendering/Build_dipoles_list_high_density.h @@ -80,7 +80,7 @@ namespace Domains typedef Dipole_position value_type; typedef const value_type& reference; typedef const High_density_key_type& key_type; - typedef boost::readable_property_map_tag category; + typedef boost::lvalue_property_map_tag category; }; // get function for the property map Point_vector_high_density_map::reference @@ -99,7 +99,7 @@ namespace Domains typedef Dipole_position value_type; typedef const value_type& reference; typedef const Parcellation_key_type& key_type; - typedef boost::readable_property_map_tag category; + typedef boost::lvalue_property_map_tag category; }; // get function for the property map Point_vector_parcellation_map::reference diff --git a/Fijee/Mesh_rendering/Build_dipoles_list_knn.h b/Fijee/Mesh_rendering/Build_dipoles_list_knn.h index 1a4e8fb..de9198e 100644 --- a/Fijee/Mesh_rendering/Build_dipoles_list_knn.h +++ b/Fijee/Mesh_rendering/Build_dipoles_list_knn.h @@ -73,7 +73,7 @@ namespace Domains typedef Dipole_position value_type; typedef const value_type& reference; typedef const Key_type& key_type; - typedef boost::readable_property_map_tag category; + typedef boost::lvalue_property_map_tag category; }; // get function for the property map Point_vector_property_map::reference diff --git a/Fijee/Mesh_rendering/CGAL_image_filtering.h b/Fijee/Mesh_rendering/CGAL_image_filtering.h index 8731742..62f604e 100644 --- a/Fijee/Mesh_rendering/CGAL_image_filtering.h +++ b/Fijee/Mesh_rendering/CGAL_image_filtering.h @@ -328,7 +328,7 @@ namespace Domains // int idx = i + j*256 + k*256*256; // - int value = static_cast( r_im_.labellized_trilinear_interpolation(positions_[idx][0], + int value = static_cast( r_im_.template labellized_trilinear_interpolation(positions_[idx][0], positions_[idx][1], positions_[idx][2], word_type(0)) ); diff --git a/Fijee/Mesh_rendering/CGAL_tools.h b/Fijee/Mesh_rendering/CGAL_tools.h index 672532c..acfe3b6 100644 --- a/Fijee/Mesh_rendering/CGAL_tools.h +++ b/Fijee/Mesh_rendering/CGAL_tools.h @@ -72,7 +72,7 @@ namespace Domains typedef Point_3 value_type; typedef const value_type& reference; typedef const std::tuple< Point_3, int >& key_type; - typedef boost::readable_property_map_tag category; + typedef boost::lvalue_property_map_tag category; }; // get function for the property map Position_property_map::reference diff --git a/Fijee/Mesh_rendering/CMakeLists.txt b/Fijee/Mesh_rendering/CMakeLists.txt index fb60e72..ee735ea 100644 --- a/Fijee/Mesh_rendering/CMakeLists.txt +++ b/Fijee/Mesh_rendering/CMakeLists.txt @@ -35,4 +35,4 @@ add_library( FijeeMesh ${Fijee_H} ${HEADERS} ${SOURCES} ${CUDA_SOURCES_} ) # Add FijeeUtils target libraries target_link_libraries( FijeeMesh ${VTK_LIBRARIES} ${CUDA_LIBRARIES} ) # Install -install( TARGETS FijeeMesh EXPORT FijeeTargets LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib ) +install( TARGETS FijeeMesh EXPORT FijeeTargets LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib ) diff --git a/Fijee/Mesh_rendering/Distance.h b/Fijee/Mesh_rendering/Distance.h index 624af84..69747ce 100644 --- a/Fijee/Mesh_rendering/Distance.h +++ b/Fijee/Mesh_rendering/Distance.h @@ -62,6 +62,8 @@ namespace Domains public: typedef Point_vector Query_item; typedef float FT; +// typedef CGAL::Dynamic_dimension_tag D; + typedef CGAL::Dimension_tag<3> D; private: @@ -100,14 +102,12 @@ namespace Domains float transformed_distance(const Point_vector& P1, const Point_vector& P2) const; /*! */ - template - float min_distance_to_rectangle( const Point_vector&, - const CGAL::Kd_tree_rectangle& ) const; - /*! - */ - template - float max_distance_to_rectangle( const Point_vector&, - const CGAL::Kd_tree_rectangle& ) const; + float min_distance_to_rectangle(const Point& p, + const CGAL::Kd_tree_rectangle& b,std::vector& dists) const; + /*! + */ + float max_distance_to_rectangle(const Point& p, + const CGAL::Kd_tree_rectangle& b,std::vector& dists) const; /*! */ float new_distance( float& Dist, float Old_off, float New_off, @@ -125,64 +125,56 @@ namespace Domains // // // - template - float - Distance::min_distance_to_rectangle( const Point_vector& p, - const CGAL::Kd_tree_rectangle& b) const - { - float - distance(0.0), - h = p.x(); - - // - // - if ( h < b.min_coord(0) ) - distance += ( b.min_coord(0) - h ) * ( b.min_coord(0) - h ); - if ( h > b.max_coord(0) ) - distance += ( h - b.max_coord(0)) * ( h - b.max_coord(0) ); - // - h = p.y(); - if ( h < b.min_coord(1) ) - distance += ( b.min_coord(1) - h ) * ( b.min_coord(1) - h ); - if ( h > b.max_coord(1) ) - distance += ( h - b.max_coord(1) ) * ( h - b.min_coord(1) ); - // - h = p.z(); - if ( h < b.min_coord(2) ) - distance += ( b.min_coord(2) - h ) * ( b.min_coord(2) - h ); - if ( h > b.max_coord(2) ) - distance += ( h - b.max_coord(2) ) * ( h - b.max_coord(2) ); - - // - // - return distance; + float Distance::min_distance_to_rectangle(const Point& p, + const CGAL::Kd_tree_rectangle& b,std::vector& dists) const { + float distance(0.0), h = p.x(); + if (h < b.min_coord(0)){ + dists[0] = (b.min_coord(0)-h); + distance += dists[0]*dists[0]; + } + if (h > b.max_coord(0)){ + dists[0] = (h-b.max_coord(0)); + distance += dists[0]*dists[0]; + } + h=p.y(); + if (h < b.min_coord(1)){ + dists[1] = (b.min_coord(1)-h); + distance += dists[1]*dists[1]; + } + if (h > b.max_coord(1)){ + dists[1] = (h-b.max_coord(1)); + distance += dists[1]*dists[1]; + } + h=p.z(); + if (h < b.min_coord(2)){ + dists[2] = (b.min_coord(2)-h); + distance += dists[2]*dists[2]; + } + if (h > b.max_coord(2)){ + dists[2] = (h-b.max_coord(2)); + distance += dists[2]*dists[2]; + } + return distance; } // // // - template - float - Distance::max_distance_to_rectangle( const Point_vector& p, - const CGAL::Kd_tree_rectangle& b) const - { - float h = p.x(); - // - float d0 = ( h >= ( b.min_coord(0) + b.max_coord(0)) / 2.0 ) ? - ( h - b.min_coord(0) ) * ( h - b.min_coord(0) ) : ( b.max_coord(0) - h ) * ( b.max_coord(0) - h ); - // - h = p.y(); - float d1 = (h >= ( b.min_coord(1) + b.max_coord(1)) / 2.0 ) ? - ( h - b.min_coord(1) ) * ( h - b.min_coord(1) ) : ( b.max_coord(1) - h ) * ( b.max_coord(1) - h ); - // - h = p.z(); - float d2 = ( h >= ( b.min_coord(2) + b.max_coord(2) ) / 2.0 ) ? - ( h - b.min_coord(2) ) * ( h - b.min_coord(2) ) : ( b.max_coord(2) - h ) * ( b.max_coord(2) - h ); + float Distance::max_distance_to_rectangle(const Point& p, + const CGAL::Kd_tree_rectangle& b,std::vector& dists) const { + float h = p.x(); + dists[0] = (h >= (b.min_coord(0)+b.max_coord(0))/2.0) ? + (h-b.min_coord(0)) : (b.max_coord(0)-h); - // - // - return d0 + d1 + d2; + h=p.y(); + dists[1] = (h >= (b.min_coord(1)+b.max_coord(1))/2.0) ? + (h-b.min_coord(1)) : (b.max_coord(1)-h); + h=p.z(); + dists[2] = (h >= (b.min_coord(2)+b.max_coord(2))/2.0) ? + (h-b.min_coord(2)) : (b.max_coord(2)-h); + return dists[0] * dists[0] + dists[1] * dists[1] + dists[2] * dists[2]; } + /*! * \brief Dump values for Distance * diff --git a/Fijee/Mesh_rendering/Head_labeled_domain.cxx b/Fijee/Mesh_rendering/Head_labeled_domain.cxx index a4e4c93..2454312 100644 --- a/Fijee/Mesh_rendering/Head_labeled_domain.cxx +++ b/Fijee/Mesh_rendering/Head_labeled_domain.cxx @@ -332,7 +332,7 @@ Domains_Head_labeled::model_segmentation() SPM_bones.read( (DAp::get_instance())->get_sc4T1_() ); Image_filter spm_bones( SPM_bones, data_position_ ); spm_bones.init( 5 /* % of outliers to remove */, - 85 /* % of the signal */); + 85 /* % of the signal */); // spm_bones.holes_detection(); std::thread bones_thread( std::ref(spm_bones) ); diff --git a/Fijee/Utils/CMakeLists.txt b/Fijee/Utils/CMakeLists.txt index 3b62e02..12faa4c 100644 --- a/Fijee/Utils/CMakeLists.txt +++ b/Fijee/Utils/CMakeLists.txt @@ -28,4 +28,4 @@ add_library( FijeeUtils ${Fijee_H} ${HEADERS} ${SOURCES} ) # Add FijeeUtils target libraries #target_link_libraries( FijeeUtils ${Fijee_TARGET_LINK_LIBRARIES} ) # Install -install( TARGETS FijeeUtils EXPORT FijeeTargets LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib ) +install( TARGETS FijeeUtils EXPORT FijeeTargets LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib ) diff --git a/cmake/modules/FindCGAL.cmake b/cmake/modules/FindCGAL.cmake deleted file mode 100644 index b7cfa5b..0000000 --- a/cmake/modules/FindCGAL.cmake +++ /dev/null @@ -1,91 +0,0 @@ -# -# The following module is based on FindVTK.cmake -# - -# - Find a CGAL installation or binary tree. -# The following variables are set if CGAL is found. If CGAL is not -# found, CGAL_FOUND is set to false. -# -# CGAL_FOUND - Set to true when CGAL is found. -# CGAL_USE_FILE - CMake file to use CGAL. -# - -# Construct consitent error messages for use below. -set(CGAL_DIR_DESCRIPTION "directory containing CGALConfig.cmake. This is either the binary directory where CGAL was configured or PREFIX/lib/CGAL for an installation.") -set(CGAL_DIR_MESSAGE "CGAL not found. Set the CGAL_DIR cmake variable or environment variable to the ${CGAL_DIR_DESCRIPTION}") - -set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS true) - -if ( NOT CGAL_DIR ) - - # Get the system search path as a list. - if(UNIX) - string(REGEX MATCHALL "[^:]+" CGAL_DIR_SEARCH1 "$ENV{PATH}") - else() - string(REGEX REPLACE "\\\\" "/" CGAL_DIR_SEARCH1 "$ENV{PATH}") - endif() - - string(REGEX REPLACE "/;" ";" CGAL_DIR_SEARCH2 "${CGAL_DIR_SEARCH1}") - - # Construct a set of paths relative to the system search path. - set(CGAL_DIR_SEARCH "") - - foreach(dir ${CGAL_DIR_SEARCH2}) - - set(CGAL_DIR_SEARCH ${CGAL_DIR_SEARCH} ${dir}/../lib/CGAL ) - - endforeach() - - - # - # Look for an installation or build tree. - # - find_path(CGAL_DIR CGALConfig.cmake - - # Look for an environment variable CGAL_DIR. - $ENV{CGAL_DIR} - - # Look in places relative to the system executable search path. - ${CGAL_DIR_SEARCH} - - # Look in standard UNIX install locations. - /usr/local/lib/CGAL - /usr/lib/CGAL - - # Read from the CMakeSetup registry entries. It is likely that - # CGAL will have been recently built. - [HKEY_CURRENT_USER\\Software\\Kitware\\CMakeSetup\\Settings\\StartPath;WhereBuild1] - [HKEY_CURRENT_USER\\Software\\Kitware\\CMakeSetup\\Settings\\StartPath;WhereBuild2] - [HKEY_CURRENT_USER\\Software\\Kitware\\CMakeSetup\\Settings\\StartPath;WhereBuild3] - [HKEY_CURRENT_USER\\Software\\Kitware\\CMakeSetup\\Settings\\StartPath;WhereBuild4] - [HKEY_CURRENT_USER\\Software\\Kitware\\CMakeSetup\\Settings\\StartPath;WhereBuild5] - [HKEY_CURRENT_USER\\Software\\Kitware\\CMakeSetup\\Settings\\StartPath;WhereBuild6] - [HKEY_CURRENT_USER\\Software\\Kitware\\CMakeSetup\\Settings\\StartPath;WhereBuild7] - [HKEY_CURRENT_USER\\Software\\Kitware\\CMakeSetup\\Settings\\StartPath;WhereBuild8] - [HKEY_CURRENT_USER\\Software\\Kitware\\CMakeSetup\\Settings\\StartPath;WhereBuild9] - [HKEY_CURRENT_USER\\Software\\Kitware\\CMakeSetup\\Settings\\StartPath;WhereBuild10] - - # Help the user find it if we cannot. - DOC "The ${CGAL_DIR_DESCRIPTION}" - ) - -endif() - -if ( CGAL_DIR ) - - if ( EXISTS "${CGAL_DIR}/CGALConfig.cmake" ) - include( "${CGAL_DIR}/CGALConfig.cmake" ) - set( CGAL_FOUND TRUE ) - endif() - -endif() - -if( NOT CGAL_FOUND) - if(CGAL_FIND_REQUIRED) - MESSAGE(FATAL_ERROR ${CGAL_DIR_MESSAGE}) - else() - if(NOT CGAL_FIND_QUIETLY) - MESSAGE(STATUS ${CGAL_DIR_MESSAGE}) - endif() - endif() -endif() diff --git a/Doc/Doxyfile b/docs/Doxyfile similarity index 100% rename from Doc/Doxyfile rename to docs/Doxyfile diff --git a/Doc/images/.svn/entries b/docs/images/.svn/entries similarity index 100% rename from Doc/images/.svn/entries rename to docs/images/.svn/entries diff --git a/Doc/images/.svn/format b/docs/images/.svn/format similarity index 100% rename from Doc/images/.svn/format rename to docs/images/.svn/format diff --git a/Doc/images/.svn/prop-base/ActivityDiagramme.png.svn-base b/docs/images/.svn/prop-base/ActivityDiagramme.png.svn-base similarity index 100% rename from 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