Merge branch 'maint-use-system-eigen-3' into 'master'

MAINT: use system eigen 3

See merge request oddkiva/sara!459

CMakeLists.txt

@@ -61,6 +61,7 @@ sara_dissect_version()
 include(sara_use_ccache)
 
 if(CMAKE_SYSTEM_NAME STREQUAL Emscripten)
+  set(EIGEN3_INCLUDE_DIRECTORY "/usr/include/eigen3")
   set(CMAKE_FIND_ROOT_PATH_MODE_PACKAGE BOTH)
 endif()
 
@@ -89,6 +90,8 @@ if(CMAKE_SYSTEM_NAME STREQUAL iOS)
       /Users/david/GitHub/Apple-Boost-BuildScript/dist/boost.xcframework/ios-arm64/libboost.a
   )
 elseif(NOT CMAKE_SYSTEM_NAME STREQUAL Emscripten)
+  find_package(Eigen3 3.4 REQUIRED NO_MODULE)
+
   find_package(TBB)
 
   # set(Boost_DEBUG ON)

build.py

@@ -383,6 +383,15 @@ def build_emsdk_docker():
         cwd=SARA_SOURCE_DIR,
     ).wait()
 
+    ret = subprocess.Popen(
+        [
+            "docker",
+            "push",
+            f"{sara_emsdk_build_image}:latest",
+        ],
+        cwd=SARA_SOURCE_DIR
+    ).wait()
+
     # Run the docker image.
     ret = subprocess.Popen(
         [

cmake/sara_use_halide.cmake

@@ -85,9 +85,10 @@ function (shakti_halide_library_v2)
   target_include_directories(${generator_NAME}.generator
     PRIVATE
     ${DO_Sara_DIR}/cpp/src
-    ${DO_Sara_ThirdParty_DIR}
-    ${DO_Sara_ThirdParty_DIR}/eigen)
-  target_link_libraries(${generator_NAME}.generator PRIVATE Halide::Generator)
+    ${DO_Sara_ThirdParty_DIR})
+  target_link_libraries(${generator_NAME}.generator
+    PRIVATE Eigen3::Eigen
+            Halide::Generator)
 
   if (generator_HALIDE_TARGET_FEATURES)
     add_halide_library(${generator_NAME}

cpp/drafts/NuScenes/CMakeLists.txt

@@ -1,9 +1,8 @@
 add_library(NuScenes STATIC NuImages.hpp NuImages.cpp NuScenes.hpp NuScenes.cpp)
 target_include_directories(
   NuScenes #
-  PUBLIC ${CMAKE_SOURCE_DIR}/cpp/third-party
-         ${CMAKE_SOURCE_DIR}/cpp/third-party/eigen)
-target_link_libraries(NuScenes PRIVATE Boost::filesystem)
+  PUBLIC ${CMAKE_SOURCE_DIR}/cpp/third-party)
+target_link_libraries(NuScenes PUBLIC Eigen3::Eigen)
 set_property(TARGET NuScenes PROPERTY FOLDER "Datasets/NuScenes")
 
 add_executable(nuimages_cpp_devkit_usage_example

cpp/drafts/NuScenes/NuImages.cpp

@@ -11,16 +11,17 @@
 
 #include <drafts/NuScenes/NuImages.hpp>
 
-#include <boost/filesystem.hpp>
-
 #include <nlohmann/json.hpp>
 
+#include <filesystem>
+
+
+namespace fs = std::filesystem;
+
 
 static auto load_json(const std::string& dataroot, const std::string& version,
                       const std::string& table_name) -> nlohmann::json
 {
-  namespace fs = boost::filesystem;
-
   const auto table_json_filepath =
       fs::path{dataroot} / version / (table_name + ".json");
 
@@ -36,7 +37,7 @@ static auto load_json(const std::string& dataroot, const std::string& version,
 NuImages::NuImages(const std::string& version_,   //
                    const std::string& dataroot_,  //
                    bool verbose_/*,               //
-                                  float map_resolution = 0.1*/)
+                   float map_resolution = 0.1*/)
 : version{version_}
 , dataroot{dataroot_}
 , verbose{verbose_}
@@ -233,7 +234,6 @@ auto NuImages::load_log_table() -> void
 
 auto NuImages::get_data_path(const SampleData& data) const -> std::string
 {
-  namespace fs = boost::filesystem;
   return (fs::path{dataroot} / data.filename).string();
 }
 

cpp/drafts/NuScenes/NuScenes.cpp

@@ -11,16 +11,17 @@
 
 #include <drafts/NuScenes/NuScenes.hpp>
 
-#include <boost/filesystem.hpp>
-
 #include <nlohmann/json.hpp>
 
+#include <filesystem>
+
+
+namespace fs = std::filesystem;
+
 
 static auto load_json(const std::string& dataroot, const std::string& version,
                       const std::string& table_name) -> nlohmann::json
 {
-  namespace fs = boost::filesystem;
-
   const auto table_json_filepath =
       fs::path{dataroot} / version / (table_name + ".json");
 
@@ -257,7 +258,6 @@ auto NuScenes::load_sensor_table() -> void
 
 auto NuScenes::get_data_path(const SampleData& data) const -> std::string
 {
-  namespace fs = boost::filesystem;
   return (fs::path{dataroot} / data.filename).string();
 }
 

cpp/examples/Kalpana/EasyGL/hello_coordinate_systems.cpp

@@ -236,7 +236,7 @@ class App
   {
     // Encode the vertex data in a tensor.
     const auto vertices = make_cube();
-    _num_vertices = vertices.size();
+    _num_vertices = static_cast<GLsizei>(vertices.size());
 
     _vao.generate();
     _vbo.generate();

cpp/examples/Kalpana/EasyGL/hello_square.cpp

@@ -181,7 +181,7 @@ class App
       0, 1, 2,
       2, 3, 0;
     // clang-format on
-    _num_triangle_indices = triangles.size();
+    _num_triangle_indices = static_cast<GLsizei>(triangles.size());
 
     _vao.generate();
     _vbo.generate();

cpp/examples/Kalpana/EasyGL/hello_texture.cpp

@@ -198,7 +198,7 @@ class App
       0, 1, 2,
       2, 3, 0;
     // clang-format on
-    _num_triangle_indices = triangles.size();
+    _num_triangle_indices = static_cast<GLsizei>(triangles.size());
 
     _vao.generate();
 

cpp/examples/Kalpana/EasyGL/hello_transformations.cpp

@@ -229,7 +229,7 @@ class App
       0, 1, 2,
       2, 3, 0;
     // clang-format on
-    _num_triangle_indices = triangles.size();
+    _num_triangle_indices = static_cast<GLsizei>(triangles.size());
 
     _vao.generate();
     // Vertex attributes.

cpp/examples/Shakti/Vulkan/hello_vulkan_image/main.cpp

@@ -332,7 +332,7 @@ class VulkanImageRenderer : public kvk::GraphicsBackend
   auto define_descriptor_set_types() -> void
   {
     const auto num_frames_in_flight = _swapchain.images.size();
-    for (auto i = std::size_t{}; i != num_frames_in_flight; ++i)
+    for (auto i = 0u; i != num_frames_in_flight; ++i)
     {
       // 1. Descriptor set #1: the model-view-projection matrix stack uniform.
       auto buffer_info = VkDescriptorBufferInfo{};

cpp/examples/Shakti/Vulkan/hello_vulkan_triangle/main.cpp

@@ -252,7 +252,7 @@ class VulkanTriangleRenderer : public kvk::GraphicsBackend
           _mvp_dmems[i].map_memory<ModelViewProjectionStack>(1));
     }
 
-    for (auto i = std::size_t{}; i != num_frames_in_flight; ++i)
+    for (auto i = 0u; i != num_frames_in_flight; ++i)
     {
       // 4.a) Register the byte size, the type of buffer which the descriptor
       //      references to.

cpp/src/DO/Sara/Core/EigenExtension.hpp

@@ -25,23 +25,7 @@
 #  define NOMINMAX
 #endif
 
-#if defined(__GNUC__)
-#  pragma GCC diagnostic push
-#  if defined(__has_warning)  // clang
-#    if __has_warning("-Wmaybe-uninitialized")
-#      pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
-#    endif
-#    if __has_warning("-Wconversion")
-#      pragma GCC diagnostic ignored "-Wconversion"
-#    endif
-#  else  // GCC
-#    pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
-#  endif
-#endif
 #include <Eigen/Eigen>
-#if defined(__GNUC__)
-#  pragma GCC diagnostic pop
-#endif
 
 #include <sstream>
 
@@ -137,7 +121,7 @@ namespace Eigen {
 //! @}
 
 
-namespace DO { namespace Sara {
+namespace DO::Sara {
 
   /*!
     @ingroup Core
@@ -217,4 +201,4 @@ namespace DO { namespace Sara {
 
   //! @}
 
-}}  // namespace DO::Sara
+}  // namespace DO::Sara

cpp/src/DO/Sara/ImageIO/Details/Exif.cpp

@@ -91,14 +91,14 @@ namespace DO::Sara {
   auto read_exif_info(EXIFInfo& info, const std::string& file_path) -> bool
   {
     // Read the JPEG file into a buffer
-    FILE* fp = fopen(file_path.c_str(), "rb");
+    const auto fp = fopen(file_path.c_str(), "rb");
     if (!fp)
     {
       std::cout << "Can't open file:" << std::endl << file_path << std::endl;
       return false;
     }
     fseek(fp, 0, SEEK_END);
-    unsigned long fsize = ftell(fp);
+    const auto fsize = static_cast<unsigned long>(ftell(fp));
     rewind(fp);
 
     std::vector<unsigned char> buf(fsize);
@@ -110,7 +110,7 @@ namespace DO::Sara {
     fclose(fp);
 
     // Parse EXIF info.
-    const auto code = info.parseFrom(&buf[0], fsize);
+    const auto code = info.parseFrom(&buf[0], static_cast<unsigned int>(fsize));
 
     return !code;
   }

cpp/src/DO/Sara/KDTree/KDTree.hpp

@@ -22,7 +22,7 @@
 #    if __has_warning("-Wconversion")
 #      pragma GCC diagnostic ignored "-Wconversion"
 #    endif
-#  pragma GCC diagnostic ignored "-Wunused-but-set-variable"
+#    pragma GCC diagnostic ignored "-Wunused-but-set-variable"
 #  endif
 #endif
 #include <flann/flann.hpp>
@@ -59,10 +59,10 @@ namespace DO::Sara {
 
     //! k-NN search for a single query column vector.
     template <int N, int Options, int MaxRows, int MaxCols>
-    void
-    knn_search(const Eigen::Matrix<double, N, 1, Options, MaxRows, MaxCols>& query,
-               int num_nearest_neighbors, std::vector<int>& nn_indices,
-               std::vector<double>& nn_squared_distances)
+    void knn_search(
+        const Eigen::Matrix<double, N, 1, Options, MaxRows, MaxCols>& query,
+        int num_nearest_neighbors, std::vector<int>& nn_indices,
+        std::vector<double>& nn_squared_distances)
     {
       if (static_cast<int>(_row_major_matrix_view.cols) != query.size())
         throw std::runtime_error{"Dimension of query vector do not match "
@@ -93,11 +93,11 @@ namespace DO::Sara {
 
     //! Radius search for a single query column vector.
     template <int N, int Options, int MaxRows, int MaxCols>
-    int
-    radius_search(const Eigen::Matrix<double, N, 1, Options, MaxRows, MaxCols>& query,
-                  double squared_search_radius, std::vector<int>& nn_indices,
-                  std::vector<double>& nn_squared_distances,
-                  int max_num_nearest_neighbors = -1)
+    int radius_search(
+        const Eigen::Matrix<double, N, 1, Options, MaxRows, MaxCols>& query,
+        double squared_search_radius, std::vector<int>& nn_indices,
+        std::vector<double>& nn_squared_distances,
+        int max_num_nearest_neighbors = -1)
     {
       if (static_cast<int>(_row_major_matrix_view.cols) != query.size())
         throw std::runtime_error{"Dimension of query vector do not match "
@@ -110,7 +110,8 @@ namespace DO::Sara {
     }
 
     //! Radius search for a set of of query column vectors.
-    void radius_search(const Eigen::MatrixXd& queries, double squared_search_radius,
+    void radius_search(const Eigen::MatrixXd& queries,
+                       double squared_search_radius,
                        std::vector<std::vector<int>>& nn_indices,
                        std::vector<std::vector<double>>& nn_squared_distances,
                        int max_num_nearest_neighbors = -1);

cpp/src/DO/Sara/NeuralNetworks/Darknet/Layer.cpp

@@ -340,7 +340,8 @@ auto Shortcut::to_output_stream(std::ostream& os) const -> void
   os << "- activation     = " << activation;
 }
 
-auto Shortcut::forward(const TensorView_<float, 4>& fx, const TensorView_<float, 4>& x)
+auto Shortcut::forward_2(const TensorView_<float, 4>& fx,
+                         const TensorView_<float, 4>& x)
     -> const TensorView_<float, 4>&
 {
   output.flat_array() = fx.flat_array() + x.flat_array();

cpp/src/DO/Sara/NeuralNetworks/Darknet/Layer.hpp

@@ -187,8 +187,8 @@ namespace DO::Sara::Darknet {
 
     auto to_output_stream(std::ostream&) const -> void override;
 
-    auto forward(const TensorView_<float, 4>& fx,
-                 const TensorView_<float, 4>& x)
+    auto forward_2(const TensorView_<float, 4>& fx,
+                   const TensorView_<float, 4>& x)
         -> const TensorView_<float, 4>&;
   };
 

cpp/src/DO/Sara/NeuralNetworks/Darknet/Network.hpp

@@ -170,7 +170,7 @@ namespace DO::Sara::Darknet {
                           : shortcut.from;
       const auto& fx = net[i1]->output;
       const auto& x = net[i2]->output;
-      shortcut.forward(fx, x);
+      shortcut.forward_2(fx, x);
 
       if (profile)
         toc("Shortcut");

cpp/src/DO/Sara/UseDOSaraCore.cmake

@@ -7,11 +7,12 @@ if(NOT DO_Sara_Core_ADDED)
 
   target_include_directories(
     DO_Sara_Core #
-    PUBLIC ${CMAKE_SOURCE_DIR}/cpp/third-party/eigen #
+    PUBLIC $<$<PLATFORM_ID:Emscripten>:${EIGEN3_INCLUDE_DIRECTORY}> #
            $<$<NOT:$<PLATFORM_ID:iOS>>:${HDF5_INCLUDE_DIRS}>)
   target_link_libraries(
     DO_Sara_Core #
-    PUBLIC fmt::fmt # This is a deliberate choice.
+    PUBLIC fmt::fmt #
+           $<$<NOT:$<PLATFORM_ID:Emscripten>>:Eigen3::Eigen> #
            $<$<NOT:$<PLATFORM_ID:iOS>>:${HDF5_CXX_LIBRARIES}>)
   target_compile_definitions(
     DO_Sara_Core

cpp/src/DO/Sara/UseDOSaraDisjointSets.cmake

@@ -5,5 +5,6 @@ if (SARA_USE_FROM_SOURCE)
     sara_glob_directory(${DO_Sara_SOURCE_DIR}/DisjointSets)
     sara_create_common_variables("DisjointSets")
     sara_generate_library("DisjointSets")
+    target_link_libraries(DO_Sara_DisjointSets PUBLIC Eigen3::Eigen)
   endif ()
 endif ()

cpp/src/DO/Sara/UseDOSaraFeatureDescriptors.cmake

@@ -12,7 +12,8 @@ if(SARA_USE_FROM_SOURCE)
     endif ()
     target_link_libraries(
       DO_Sara_FeatureDescriptors
-      PUBLIC DO::Sara::Features #
+      PUBLIC Eigen3::Eigen #
+             DO::Sara::Features #
              DO::Sara::ImageProcessing
              $<$<BOOL:${OpenMP_CXX_FOUND}>:OpenMP::OpenMP_CXX>)
   endif()

cpp/src/DO/Sara/UseDOSaraFeatures.cmake

@@ -7,12 +7,10 @@ if (SARA_USE_FROM_SOURCE)
     sara_generate_library("Features")
 
     target_include_directories(DO_Sara_Features
-      PUBLIC
-      ${HDF5_INCLUDE_DIRS})
+      PUBLIC ${HDF5_INCLUDE_DIRS})
     target_link_libraries(DO_Sara_Features
-      PRIVATE
-      DO::Sara::Geometry
-      PUBLIC
-      ${HDF5_LIBRARIES})
+      PRIVATE DO::Sara::Geometry
+      PUBLIC Eigen3::Eigen
+             ${HDF5_LIBRARIES})
   endif ()
 endif ()

cpp/src/DO/Sara/UseDOSaraImageProcessing.cmake

@@ -6,7 +6,10 @@ if(SARA_USE_FROM_SOURCE)
     sara_create_common_variables("ImageProcessing")
     sara_generate_library("ImageProcessing")
 
-    target_link_libraries(DO_Sara_ImageProcessing PRIVATE DO::Sara::Core)
+    target_link_libraries(
+      DO_Sara_ImageProcessing
+      PUBLIC Eigen3::Eigen
+      PRIVATE DO::Sara::Core)
 
     if(SARA_USE_HALIDE)
       target_compile_definitions(DO_Sara_ImageProcessing

cpp/src/DO/Sara/UseDOSaraKDTree.cmake

@@ -11,6 +11,7 @@ if (SARA_USE_FROM_SOURCE)
       $<BUILD_INTERFACE:${DO_Sara_ThirdParty_DIR}/flann/src/cpp>)
     target_link_libraries(DO_Sara_KDTree
       PRIVATE flann_cpp_s
-      PUBLIC $<$<BOOL:${OpenMP_CXX_FOUND}>:OpenMP::OpenMP_CXX>)
+      PUBLIC Eigen3::Eigen
+             $<$<BOOL:${OpenMP_CXX_FOUND}>:OpenMP::OpenMP_CXX>)
   endif ()
 endif ()