Merge branch 'dev' into alpha

.github/workflows/build.yml

@@ -4,6 +4,9 @@ on: [push]
 
 env:
   CUDA_BIN: /usr/local/cuda/bin
+  CC: gcc-12
+  CXX: g++-12
+  CUDAHOSTCXX: g++-12
 
 jobs:
   build:
@@ -33,6 +36,7 @@ jobs:
                           libglew-dev \
                           libglfw3-dev \
                           cimg-dev \
+                          g++-12 \
                           wget
         wget http://mirrors.kernel.org/ubuntu/pool/universe/f/flann/libflann-dev_1.9.2+dfsg-1_amd64.deb
         wget http://mirrors.kernel.org/ubuntu/pool/universe/f/flann/libflann1.9_1.9.2+dfsg-1_amd64.deb

README.md

@@ -24,12 +24,17 @@ finally execute:
 
 	./gproshan [mesh_paths.(off,obj,ply)]
 
-### Dependencies (Linux)
-g++ >= 9.4, cuda >= 11.8, cmake >= 3.24, armadillo, eigen3, cgal, suitesparse, openblas, glew, glfw3, cimg, gnuplot, embree >= 3.13
 
-In Ubuntu you can install them with:
+### Dependencies (Linux/MacOS)
+g++ >= 12.3, cuda >= 12.4, cmake >= 3.28, embree >= 4.3, glew, glfw3, armadillo, suitesparse, openblas, flann, cimg
+
+On Ubuntu you can install them with:
+
+	sudo apt install cmake libglew-dev libglfw3-dev libarmadillo-dev libsuitesparse-dev libopenblas-dev libflann-dev cimg-dev
+
+Install Cuda if available to enable Cuda-based modules.
+Export environment variable `OptiX_INSTALL_DIR` with the path to the OptiX library to enable it. 
 
-	sudo apt install cmake libarmadillo-dev libeigen3-dev libcgal-dev libsuitesparse-dev libopenblas-dev libglew-dev libglfw3-dev cimg-dev gnuplot
 
 #### Installing Intel Embree
 

cmake/FindOptiX.cmake

@@ -1,5 +1,5 @@
 #
-# Copyright (c) 2021, NVIDIA CORPORATION. All rights reserved.
+# Copyright (c) 2023, NVIDIA CORPORATION. All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without
 # modification, are permitted provided that the following conditions

cmake/FindSuiteSparse.cmake

@@ -1,8 +1,8 @@
 ## CMake file to locate SuiteSparse and its useful composite projects
-## The first developpement of this file was made fro Windows users who
-## use: 
+## The first development of this file was done by Windows users who
+## used: 
 ##  https://github.com/jlblancoc/suitesparse-metis-for-windows
-## Anyway, it chould be work also on linux (tested on fedora 17 when you installed suitesparse from yum)
+## Anyway, it could work also on linux (tested on fedora 17 when you installed suitesparse from yum)
 ##
 ##
 ## Inputs variables this file can process (variable must be given before find_package(SUITESPARES ...) command) :
@@ -11,7 +11,7 @@
 ##   Note: SuiteSparse lib usually requires linking to a blas and lapack library.
 ##
 ##
-## Help variables this file handle internaly :
+## Help variables this file handle internally :
 ##   * SuiteSparse_SEARCH_LIB_POSTFIX		Is set in cache (as advanced) to look into the right lib/lib64 dir for libraries (user can change)
 ##
 ##
@@ -20,19 +20,19 @@
 ##   * SuiteSparse_INCLUDE_DIRS  			Paths containing SuiteSparse needed headers (depend on which COMPONENTS you gave)
 ##   * SuiteSparse_LIBRARIES     			Absolute paths of SuiteSparse libs found (depend on which COMPONENTS you gave)
 ##   If SuiteSparse_USE_LAPACK_BLAS is set to ON : 
-##   	* SuiteSparse_LAPACK_BLAS_LIBRARIES 	Which contain the libblas and liblapack libraries
+##   	* SuiteSparse_LAPACK_BLAS_LIBRARIES     	Which contain the libblas and liblapack libraries
 ##   	On windows:
-##   		* SuiteSparse_LAPACK_BLAS_DLL		Which contain all requiered binaries for use libblas and liblapack
+##   		* SuiteSparse_LAPACK_BLAS_DLL		Which contain all required binaries for use libblas and liblapack
 ##
 ##
 ## Detailed variables this file provide :
 ##   * SuiteSparse_<UPPPER_CASE_COMPONENT>_FOUND		True if the given component to look for is found (INCLUDE DIR and LIBRARY)
-##   * SuiteSparse_<UPPPER_CASE_COMPONENT>_INCLUDE_DIR	The path directory where we can found all compenent header files
+##   * SuiteSparse_<UPPPER_CASE_COMPONENT>_INCLUDE_DIR  	The path directory where all component header files can be found
 ##   * SuiteSparse_<UPPPER_CASE_COMPONENT>_LIBRARY		The file path to the component library
 ##   Note: If a component is not found, a SuiteSparse_<UPPPER_CASE_COMPONENT>_DIR cache variable is set to allow user set the search directory.
 ##
 ##
-## Possible componnents to find are (maybe some others can be available):
+## Possible components to find are (maybe some others can be available):
 ##   * AMD
 ##   * CAMD
 ##   * COLAMD
@@ -125,13 +125,13 @@ endif()
 ## we can use a generic way to find all of these with simple cmake lines of code
 macro(SuiteSparse_FIND_COMPONENTS )
 
-	## On windows : we absolutly need SuiteSparse_config.h every time for all projects
+	## On windows : we absolutely need SuiteSparse_config.h every time for all projects
 	if(WIN32)
 		list(FIND SuiteSparse_FIND_COMPONENTS "suitesparseconfig" SS_config_index)
 		if(${SS_config_index} MATCHES "-1")
 			list(APPEND SuiteSparse_FIND_COMPONENTS suitesparseconfig)
 			if(SuiteSparse_VERBOSE)
-				message(STATUS "   On windows, we absolutly need SuiteSparse_config.h every time for all projects : add suitesparseconfig component to look for")
+				message(STATUS "   On windows, we absolutely need SuiteSparse_config.h every time for all projects : add suitesparseconfig component to look for")
 			endif()
 		endif()
 	endif()
@@ -292,7 +292,7 @@ macro(SuiteSparse_FIND_COMPONENTS )
 		endif()
 		if(NOT ${componentToCheck})
 			set(SuiteSparse_FOUND OFF)
-			break() ## one component not found is enought to failed
+			break() ## one component not found is enough to failed
 		endif()
 	endforeach()
 endmacro()

gproshanConfig.cmake.in

@@ -2,6 +2,8 @@
 
 include(CMakeFindDependencyMacro)
 
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}")
+
 find_package(CUDAToolkit 12)
 
 find_dependency(embree 4)

include/gproshan/features/descriptor.h

@@ -2,7 +2,8 @@
 #define DESCRIPTOR_H
 
 #include <gproshan/mesh/che.h>
-#include <gproshan/include_arma.h>
+
+#include <armadillo>
 
 
 // geometry processing and shape analysis framework
@@ -15,10 +16,10 @@ class descriptor
 		enum signature { GPS, HKS, WKS };
 
 	private:
-		a_sp_mat L, A;
-		a_vec eigval;
-		a_mat eigvec;
-		a_mat features;
+		arma::sp_mat L, A;
+		arma::vec eigval;
+		arma::mat eigvec;
+		arma::mat features;
 
 	public:
 		descriptor(const signature & sig, const che * mesh, const size_t n_eigs);

include/gproshan/geodesics/heat_method.h

@@ -13,7 +13,6 @@
 #include <gproshan/mesh/che.h>
 
 #include <armadillo>
-#include <cholmod.h>
 
 
 // geometry processing and shape analysis framework
@@ -31,21 +30,10 @@ double heat_method(real_t * dist, const che * mesh, const std::vector<index_t> &
 
 arma::vec compute_divergence(const che * mesh, const arma::vec & u);
 
-/// cholmod Keenan implementation
-/// base on the code https://github.com/larc/dgpdec-course/tree/master/Geodesics
-double solve_positive_definite(arma::mat & x, const arma::sp_mat & A, const arma::mat & b, cholmod_common * context);
-
-cholmod_dense * arma_2_cholmod(const arma::mat & m, cholmod_common * context);
-
-cholmod_sparse * arma_2_cholmod(const arma::sp_mat & m, cholmod_common * context);
 
 #ifdef GPROSHAN_CUDA
 
-///
 double solve_positive_definite_gpu(arma::mat & x, const arma::sp_mat & A, const arma::mat & b);
-
-/// host and device support
-/// https://docs.nvidia.com/cuda/cusolver/index.html#cusolver-lt-t-gt-csrlsvchol
 double solve_positive_definite_cusolver(const int m, const int nnz, const double * hA_values, const int * hA_col_ptrs, const int * hA_row_indices, const double * hb, double * hx, const bool host = 0);
 
 #endif // GPROSHAN_CUDA

include/gproshan/geometry/mat.h

@@ -3,6 +3,10 @@
 
 #include <gproshan/geometry/vec.h>
 
+#ifndef __CUDACC__
+	#include <armadillo>
+#endif // __CUDACC__
+
 
 // geometry processing and shape analysis framework
 namespace gproshan {
@@ -73,26 +77,34 @@ class mat
 		}
 
 		__host_device__
-		static mat<T, N> identity()
+		mat<T, N> t() const
 		{
-			mat<T, N> res;
-			for(index_t i = 0; i < N; ++i)
-				res[i][i] = 1;
-			return res;
+			return transpose(*this);
 		}
 
 		__host_device__
-		static mat<T, N> transpose(const mat<T, N> & m)
+		static mat<T, N> identity()
 		{
 			mat<T, N> res;
 			for(index_t i = 0; i < N; ++i)
-			for(index_t j = 0; j < N; ++j)
-				res[i][j] = m[j][i];
+				res[i][i] = 1;
 			return res;
 		}
 };
 
-///< std std::ostream
+
+template<class T, size_t N>
+__host_device__
+mat<T, N> transpose(const mat<T, N> & m)
+{
+	mat<T, N> res;
+	for(index_t i = 0; i < N; ++i)
+	for(index_t j = 0; j < N; ++j)
+		res[i][j] = m[j][i];
+	return res;
+}
+
+
 template<class T, size_t N>
 std::ostream & operator << (std::ostream & os, const mat<T, N> & m)
 {
@@ -101,7 +113,6 @@ std::ostream & operator << (std::ostream & os, const mat<T, N> & m)
 	return os;
 }
 
-///< std std::istream
 template<class T, size_t N>
 std::istream & operator >> (std::istream & is, mat<T, N> & m)
 {
@@ -111,12 +122,27 @@ std::istream & operator >> (std::istream & is, mat<T, N> & m)
 }
 
 
+#ifndef __CUDACC__
+template<class T, size_t N>
+mat<T, N> inverse(const mat<T, N> & m)
+{
+	mat<T, N> inv;
+	mat<T, N> mt = m.t();
+
+	arma::Mat<T> ainv((T *) &inv, N, N, false, true);
+	arma::Mat<T> amt((T *) &mt, N, N, false, true);
+
+	arma::inv(ainv, amt);
+
+	return inv.t();
+}
+#endif // __CUDACC__
+
+
 using mat2 = mat<real_t, 2>;
 using mat3 = mat<real_t, 3>;
 using mat4 = mat<real_t, 4>;
 
-mat4 inverse(const mat4 & m);
-
 
 } // namespace gproshan
 

include/gproshan/mdict/basis.h

@@ -2,10 +2,11 @@
 #define BASIS_H
 
 #include <gproshan/include.h>
-#include <gproshan/include_arma.h>
 
 #include <fstream>
 
+#include <armadillo>
+
 
 // geometry processing and shape analysis framework
 // mesh dictionary learning and sparse coding namespace
@@ -21,18 +22,18 @@ class basis
 	public:
 		basis(const real_t r, const size_t d);
 		virtual ~basis() = default;
-		virtual void discrete(a_mat & phi, const a_vec & x, const a_vec & y) = 0;
-		virtual void d_discrete(a_mat & phi, const a_vec & x, const a_vec & y, const bool b) = 0;
+		virtual void discrete(arma::fmat & phi, const arma::fvec & x, const arma::fvec & y) = 0;
+		virtual void d_discrete(arma::fmat & phi, const arma::fvec & x, const arma::fvec & y, const bool b) = 0;
 		virtual real_t freq(const index_t idx) = 0;
 		real_t & radio();
 		size_t dim() const;
 		void plot_basis();
-		void plot_atoms(const a_mat & A);
-		void plot_patch(const a_mat & A, const a_mat & xyz, const index_t p);
+		void plot_atoms(const arma::fmat & A);
+		void plot_patch(const arma::fmat & A, const arma::fmat & xyz, const index_t p);
 
 	private:
 		virtual void plot_basis(std::ostream & os) = 0;
-		virtual void plot_atoms(std::ostream & os, const a_vec & A) = 0;
+		virtual void plot_atoms(std::ostream & os, const arma::fvec & A) = 0;
 };
 
 

include/gproshan/mdict/basis_cosine.h

@@ -17,12 +17,12 @@ class basis_cosine: public basis
 
 	public:
 		basis_cosine(const size_t nr, const size_t nf, const real_t r = 0);
-		void discrete(a_mat & phi, const a_vec & x, const a_vec & y);
+		void discrete(arma::fmat & phi, const arma::fvec & x, const arma::fvec & y);
 
 	private:
 		void plot_basis(std::ostream & os);
-		void plot_atoms(std::ostream & os, const a_vec & A);
-		a_vec cosine(const a_vec & x, const a_vec & y, const real_t c, const real_t alpha);
+		void plot_atoms(std::ostream & os, const arma::fvec & A);
+		arma::fvec cosine(const arma::fvec & x, const arma::fvec & y, const real_t c, const real_t alpha);
 		void cosine(std::ostream & os, const real_t c, const real_t alpha);
 };
 

include/gproshan/mdict/basis_dct.h

@@ -16,15 +16,15 @@ class basis_dct: public basis
 
 	public:
 		basis_dct(const size_t n, const real_t r = 1);
-		void discrete(a_mat & phi, const a_vec & x, const a_vec & y);
-		void d_discrete(a_mat & phi, const a_vec & x, const a_vec & y, const bool b);
+		void discrete(arma::fmat & phi, const arma::fvec & x, const arma::fvec & y);
+		void d_discrete(arma::fmat & phi, const arma::fvec & x, const arma::fvec & y, const bool b);
 		real_t freq(const index_t idx);
 
 	private:
 		void plot_basis(std::ostream & os);
-		void plot_atoms(std::ostream & os, const a_vec & A);
-		a_vec dct(const a_vec & x, const a_vec & y, const index_t nx, const index_t ny);
-		a_vec d_dct(const a_vec & x, const a_vec & y, const index_t nx, const index_t ny);
+		void plot_atoms(std::ostream & os, const arma::fvec & A);
+		arma::fvec dct(const arma::fvec & x, const arma::fvec & y, const index_t nx, const index_t ny);
+		arma::fvec d_dct(const arma::fvec & x, const arma::fvec & y, const index_t nx, const index_t ny);
 		void dct(std::ostream & os, const index_t nx, const index_t ny);
 };