Merge pull request #55 from ami-iit/conversions

Adds reflection and conversions from common types
ami-iit · Apr 28, 2022 · ed9b196 · ed9b196
2 parents 1555d24 + a94caa1
commit ed9b196
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Showing 25 changed files with 1,040 additions and 70 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -5,8 +5,6 @@ on:
   pull_request:
 
 env:
-  # commit from vcpkg's master branch on 2020/10/06
-  vcpkg_TAG: 76a7e9248fb3c57350b559966dcaa2d52a5e4458
   Catch2_TAG: v2.11.3
 
 jobs:
@@ -16,7 +14,7 @@ jobs:
     strategy:
       matrix:
         build_type: [Release, Debug]
-        os: [ubuntu-latest, windows-latest, macOS-latest]
+        os: [ubuntu-latest, macOS-latest]
       fail-fast: false
 
     steps:
@@ -39,15 +37,6 @@ jobs:
         for apt_file in `grep -lr microsoft /etc/apt/sources.list.d/`; do sudo rm $apt_file; done
 
  
-    # Restore from cache the previously built ports. If "cache miss"
-    # then provision vcpkg, install desired ports, finally cache everything for the next run.
-    - name: Dependencies [Windows]
-      if: matrix.os == 'windows-latest'
-      uses: lukka/run-vcpkg@v6
-      with:
-        vcpkgArguments: '--triplet x64-windows matio catch2'
-        vcpkgGitCommitId: ${{ env.vcpkg_TAG }}
-
     - name: Dependencies [macOS]
       if: matrix.os == 'macOS-latest'
       run: |
@@ -58,7 +47,7 @@ jobs:
       if: matrix.os == 'ubuntu-latest'
       run: |
         sudo apt-get update
-        sudo apt-get install libmatio-dev valgrind
+        sudo apt-get install libmatio-dev valgrind libeigen3-dev
         
     - name: Cache Source-based Dependencies
       id: cache-source-deps
@@ -88,17 +77,6 @@ jobs:
     # CMAKE-BASED PROJECT
     # ===================
 
-    - name: Configure [Windows]
-      # Use bash also on Windows (otherwise cd, mkdir, ... do not work)
-      if: matrix.os == 'windows-latest'
-      shell: bash
-      run: |
-        mkdir -p build
-        cd build
-        cmake -A x64 -DCMAKE_TOOLCHAIN_FILE=${VCPKG_ROOT}/scripts/buildsystems/vcpkg.cmake \
-              -DCMAKE_PREFIX_PATH=${GITHUB_WORKSPACE}/install/deps \
-              -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/install \
-              -DBUILD_TESTING:BOOL=ON ..
 
     - name: Configure [Ubuntu]
       if: matrix.os == 'ubuntu-latest'

diff --git a/.github/workflows/conda-forge-ci.yml b/.github/workflows/conda-forge-ci.yml
@@ -15,7 +15,7 @@ jobs:
     strategy:
       matrix:
         build_type: [Release]
-        os: [ubuntu-latest, windows-latest, macOS-latest]
+        os: [ubuntu-latest, windows-2019, macOS-latest]
       fail-fast: false
 
     steps:
@@ -31,9 +31,9 @@ jobs:
       shell: bash -l {0}
       run: |
         # Compilation related dependencies 
-        mamba install cmake compilers make ninja pkg-config
+        mamba install cmake compilers make ninja pkg-config 
         # Actual dependencies
-        mamba install libmatio catch2
+        mamba install libmatio catch2 eigen
         
     - name: Configure [Linux&macOS]
       if: contains(matrix.os, 'macos') || contains(matrix.os, 'ubuntu')

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unreleased]
 - Using a custom variable in InstallBasicPackageFile to backup the module path: [#47](https://github.com/ami-iit/matio-cpp/pull/47).
 - Added more checks before creating a file: [#49](https://github.com/ami-iit/matio-cpp/pull/49).
+- Added reflection and conversions from common types [#55](https://github.com/ami-iit/matio-cpp/pull/55)
 
 ## [0.1.1] - 2021-03-22
 

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -3,7 +3,7 @@
 # BSD-2-Clause license (https://opensource.org/licenses/BSD-2-Clause).
 
 cmake_minimum_required(VERSION 3.10)
-project(matioCpp VERSION 0.1.1 LANGUAGES CXX)
+project(matioCpp VERSION 0.2.0 LANGUAGES CXX)
 
 # Defines the CMAKE_INSTALL_LIBDIR, CMAKE_INSTALL_BINDIR and many other useful macros.
 # See https://cmake.org/cmake/help/latest/module/GNUInstallDirs.html
@@ -89,6 +89,30 @@ endif()
 
 ## Dependencies
 find_package(MATIO REQUIRED)
+find_package(Eigen3 QUIET)
+
+if (Eigen3_FOUND)
+    set(MATIOCPP_HAS_EIGEN TRUE)
+endif()
+
+# Fetching visit_struct
+include(CMakeDependentOption)
+find_package(visit_struct QUIET)
+cmake_dependent_option(USE_SYSTEM_visit_struct "Use system visit_struct" ON "visit_struct_FOUND" OFF)
+if(USE_SYSTEM_visit_struct)
+     find_package(visit_struct REQUIRED)
+else()
+    include(FetchContent)
+    FetchContent_Declare(visit_struct
+      GIT_REPOSITORY https://github.com/ami-iit/visit_struct
+      GIT_TAG 969fc563477906432a9fcc91addf2c1e13c56f4c)
+
+    FetchContent_GetProperties(visit_struct)
+    if(NOT visit_struct_POPULATED)
+      message(STATUS "Fetching visit_struct...")
+      FetchContent_MakeAvailable(visit_struct)
+    endif()
+endif()
 
 set(MATIOCPP_SRC src/Variable.cpp
                  src/ConversionUtilities.cpp
@@ -98,11 +122,14 @@ set(MATIOCPP_SRC src/Variable.cpp
                  src/CellArray.cpp
                  src/File.cpp
                  src/Struct.cpp
-                 src/StructArray.cpp)
+                 src/StructArray.cpp
+                 src/ExogenousConversions.cpp)
 
 set(MATIOCPP_HDR include/matioCpp/Span.h
                  include/matioCpp/VectorIterator.h
                  include/matioCpp/ConversionUtilities.h
+                 include/matioCpp/ExogenousConversions.h
+                 include/matioCpp/EigenConversions.h
                  include/matioCpp/Variable.h
                  include/matioCpp/ForwardDeclarations.h
                  include/matioCpp/Vector.h
@@ -121,7 +148,10 @@ set(MATIOCPP_TPP include/matioCpp/impl/Vector.tpp
                  include/matioCpp/impl/MultiDimensionalArray.tpp
                  include/matioCpp/impl/Element.tpp
                  include/matioCpp/impl/StructArrayElement.tpp
-                 include/matioCpp/impl/File.tpp)
+                 include/matioCpp/impl/File.tpp
+                 include/matioCpp/impl/EigenConversions.tpp
+                 include/matioCpp/impl/ExogenousConversions.tpp
+                 include/matioCpp/impl/ExogenousConversionHelpers.tpp)
 
 source_group("Template Implementation Files" FILES ${MATIOCPP_TPP})
 
@@ -149,7 +179,13 @@ target_include_directories(matioCpp PUBLIC "$<BUILD_INTERFACE:${CMAKE_CURRENT_SO
                                            "$<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/Autogenerated>"
                                            "$<INSTALL_INTERFACE:$<INSTALL_PREFIX>/${CMAKE_INSTALL_INCLUDEDIR}>")
 
-target_link_libraries(matioCpp PUBLIC MATIO::MATIO)
+target_link_libraries(matioCpp PUBLIC MATIO::MATIO visit_struct::visit_struct)
+list(APPEND MATIOCPP_DEPENDENCIES MATIO visit_struct)
+
+if (Eigen3_FOUND)
+    target_link_libraries(matioCpp PUBLIC Eigen3::Eigen)
+    list(APPEND MATIOCPP_DEPENDENCIES Eigen3)
+endif()
 
 target_compile_features(matioCpp PUBLIC cxx_std_14)
 
@@ -182,7 +218,7 @@ install_basic_package_files(${PROJECT_NAME}
                             COMPATIBILITY AnyNewerVersion
                             VARS_PREFIX ${PROJECT_NAME}
                             NO_CHECK_REQUIRED_COMPONENTS_MACRO
-                            DEPENDENCIES MATIO
+                            DEPENDENCIES ${MATIOCPP_DEPENDENCIES}
                             OVERRIDE_MODULE_PATH ${CMAKE_INSTALL_PREFIX}/share/matioCpp/cmake)
 # Add the uninstall target
 include(AddUninstallTarget)

diff --git a/README.md b/README.md
@@ -20,6 +20,8 @@ The depencies are [``CMake``](https://cmake.org/) (minimum version 3.10) and [``
 - macOS: ``brew install libmatio``
 - Windows, via [``vcpkg``](https://github.com/microsoft/vcpkg): ``vcpkg install --triplet x64-windows matio``
 
+[`Eigen`](https://eigen.tuxfamily.org/index.php) is an optional dependency. If available, some conversions are defined.
+
 For running the tests, it is necessary to install [`Catch2`](https://github.com/catchorg/Catch2). Where supported, [``valgrind``](https://valgrind.org/) can be installed to check for memory leaks.
 
 ## Linux/macOS
@@ -109,6 +111,71 @@ file.write(testString);
 
 ```
 
+It is possibile to convert common types to ``matioCpp`` types with the function ``matioCpp::make_variable``. Examples:
+```c++
+std::vector<double> stdVec = {1.0, 2.0, 3.0, 4.0, 5.0};
+auto toMatioVec = matioCpp::make_variable("test", stdVec);
+
+std::array<float,3> array = {1.0, 2.0, 3.0};
+auto toMatioArray = matioCpp::make_variable("test", array);
+
+int classicalArray[] = {1, 2, 3};
+auto toMatioClassic = matioCpp::make_variable("test", matioCpp::make_span(classicalArray, 3));
+
+std::string string("something");
+auto toMatioString = matioCpp::make_variable("name", string);
+
+std::vector<bool> vecOfBool = {true, false, true};
+auto toVecofBool = matioCpp::make_variable("vecOfBool", vecOfBool);
+
+auto matioDouble = matioCpp::make_variable("double", 5.0);
+
+auto matioBool = matioCpp::make_variable("bool", true);
+
+auto matioInt = matioCpp::make_variable("int", 2);
+
+auto matioChar = matioCpp::make_variable("char", 'f');
+
+std::vector<std::string> stringVector = {"Huey", "Dewey", "Louie"};
+auto matioCell = matioCpp::make_variable("stringVector", stringVector);
+```
+If ``eigen`` is available, it is also possible to convert from and to ``eigen`` types:
+```c++
+matioCpp::Vector<double> vector("vector", 5);                                               
+Eigen::VectorXd eigenVec = matioCpp::to_eigen(vector);                                      
+matioCpp::MultiDimensionalArray<float> matioCppMatrix("matrix"); 
+
+Eigen::MatrixXf toEigenMatrix = matioCpp::to_eigen(matioCppMatrix);
+
+Eigen::Matrix3f eigenMatrix;                                                    
+eigenMatrix << 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0;                     
+auto toMatioMatrix = matioCpp::make_variable("testMatrix", eigenMatrix);        
+Eigen::Vector3i eigenVec;      
+eigenVec << 2, 4, 6;                                                            
+auto toMatioEigenVec = matioCpp::make_variable("testEigen", eigenVec);          
+```
+
+``matioCpp`` also exploits [``visit_struct``](https://github.com/garbageslam/visit_struct) to parse C++ structs into ``matioCpp`` structs. Example:
+```c++
+struct testStruct
+{
+    int i{1};
+    double d{2.0};
+    std::string s{"test"};
+    std::vector<double> stdVec = {1.0, 2.0, 3.0, 4.0, 5.0};
+    int* notSupported = nullptr;
+    std::vector<std::string> stringVector = {"Huey", "Dewey", "Louie"};
+    std::vector<bool> vecOfBool = {true, false, true};
+};
+VISITABLE_STRUCT(testStruct, i, d, s, stdVec, vecOfBool, stringVector);
+
+//----------
+
+testStruct s;
+matioCpp::Struct automaticStruct = matioCpp::make_variable("testStruct", s);
+```
+
+
 # Known Limitations
  - Complex arrays are not yet supported
  - Cannot read timeseries from a ``.mat`` file (this is a ``matio`` limitation https://github.com/tbeu/matio/issues/99)

diff --git a/cmake/Config.h.in b/cmake/Config.h.in
@@ -3,15 +3,20 @@
 // This is an automatically generated file.
 // Please DO NOT edit this file manually.
 
-#ifndef MATIOCPP_CONFIG_H
-#define MATIOCPP_CONFIG_H
 /*
  * Copyright (C) 2020 Fondazione Istituto Italiano di Tecnologia
  *
  * This software may be modified and distributed under the terms of the
  * BSD-2-Clause license (https://opensource.org/licenses/BSD-2-Clause).
  */
 
+#ifndef MATIOCPP_CONFIG_H
+#define MATIOCPP_CONFIG_H
+
 #define MATIOCPP_VER "@PROJECT_VERSION@"
 
+#ifndef MATIOCPP_NO_EIGEN
+#cmakedefine MATIOCPP_HAS_EIGEN
+#endif
+
 #endif // MATIOCPP_CONFIG_H
diff --git a/include/matioCpp/ConversionUtilities.h b/include/matioCpp/ConversionUtilities.h
@@ -46,20 +46,28 @@ template <typename Tp> struct get_type
     static_assert (matioCpp::dependent_false<Tp>::value, "Unsupported type.");
     static_assert (!std::is_same<Tp, bool>::value, "Use matioCpp::Logical instead of bool.");
 };
+
+#ifdef __APPLE__
+using size_t_type = unsigned long;
+#else
+using size_t_type = uint64_t;
+#endif
+
 // specializations
-template <> struct get_type<int8_t>    { using type = int8_t;   static inline ValueType valueType(){return ValueType::INT8;};     static inline std::string toString(){return "int8_t"            ;};};
-template <> struct get_type<uint8_t>   { using type = uint8_t;  static inline ValueType valueType(){return ValueType::UINT8;};    static inline std::string toString(){return "uint8_t"           ;};};
-template <> struct get_type<int16_t>   { using type = int16_t;  static inline ValueType valueType(){return ValueType::INT16;};    static inline std::string toString(){return "int16_t"           ;};};
-template <> struct get_type<uint16_t>  { using type = uint16_t; static inline ValueType valueType(){return ValueType::UINT16;};   static inline std::string toString(){return "uint16_t"          ;};};
-template <> struct get_type<int32_t>   { using type = int32_t;  static inline ValueType valueType(){return ValueType::INT32;};    static inline std::string toString(){return "int32_t"           ;};};
-template <> struct get_type<uint32_t>  { using type = uint32_t; static inline ValueType valueType(){return ValueType::UINT32;};   static inline std::string toString(){return "uint32_t"          ;};};
-template <> struct get_type<float>     { using type = float;    static inline ValueType valueType(){return ValueType::SINGLE;};   static inline std::string toString(){return "float"             ;};};
-template <> struct get_type<double>    { using type = double;   static inline ValueType valueType(){return ValueType::DOUBLE;};   static inline std::string toString(){return "double"            ;};};
-template <> struct get_type<int64_t>   { using type = int64_t;  static inline ValueType valueType(){return ValueType::INT64;};    static inline std::string toString(){return "int64_t"           ;};};
-template <> struct get_type<char>      { using type = char;     static inline ValueType valueType(){return ValueType::UTF8;};     static inline std::string toString(){return "char"              ;};};
-template <> struct get_type<char16_t>  { using type = char16_t; static inline ValueType valueType(){return ValueType::UTF16;};    static inline std::string toString(){return "char16_t"          ;};};
-template <> struct get_type<char32_t>  { using type = char32_t; static inline ValueType valueType(){return ValueType::UTF32;};    static inline std::string toString(){return "char32_t"          ;};};
-template <> struct get_type<Logical>   { using type = uint8_t;  static inline ValueType valueType(){return ValueType::LOGICAL;};  static inline std::string toString(){return "matioCpp::Logical" ;};};
+template <> struct get_type<int8_t>       { using type = int8_t;      static inline ValueType valueType(){return ValueType::INT8;};     static inline std::string toString(){return "int8_t"            ;};};
+template <> struct get_type<uint8_t>      { using type = uint8_t;     static inline ValueType valueType(){return ValueType::UINT8;};    static inline std::string toString(){return "uint8_t"           ;};};
+template <> struct get_type<int16_t>      { using type = int16_t;     static inline ValueType valueType(){return ValueType::INT16;};    static inline std::string toString(){return "int16_t"           ;};};
+template <> struct get_type<uint16_t>     { using type = uint16_t;    static inline ValueType valueType(){return ValueType::UINT16;};   static inline std::string toString(){return "uint16_t"          ;};};
+template <> struct get_type<int32_t>      { using type = int32_t;     static inline ValueType valueType(){return ValueType::INT32;};    static inline std::string toString(){return "int32_t"           ;};};
+template <> struct get_type<uint32_t>     { using type = uint32_t;    static inline ValueType valueType(){return ValueType::UINT32;};   static inline std::string toString(){return "uint32_t"          ;};};
+template <> struct get_type<float>        { using type = float;       static inline ValueType valueType(){return ValueType::SINGLE;};   static inline std::string toString(){return "float"             ;};};
+template <> struct get_type<double>       { using type = double;      static inline ValueType valueType(){return ValueType::DOUBLE;};   static inline std::string toString(){return "double"            ;};};
+template <> struct get_type<int64_t>      { using type = int64_t;     static inline ValueType valueType(){return ValueType::INT64;};    static inline std::string toString(){return "int64_t"           ;};};
+template <> struct get_type<size_t_type>  { using type = size_t_type; static inline ValueType valueType(){return ValueType::UINT64;};   static inline std::string toString(){return "size_t"            ;};};
+template <> struct get_type<char>         { using type = char;        static inline ValueType valueType(){return ValueType::UTF8;};     static inline std::string toString(){return "char"              ;};};
+template <> struct get_type<char16_t>     { using type = char16_t;    static inline ValueType valueType(){return ValueType::UTF16;};    static inline std::string toString(){return "char16_t"          ;};};
+template <> struct get_type<char32_t>     { using type = char32_t;    static inline ValueType valueType(){return ValueType::UTF32;};    static inline std::string toString(){return "char32_t"          ;};};
+template <> struct get_type<Logical>      { using type = uint8_t;     static inline ValueType valueType(){return ValueType::LOGICAL;};  static inline std::string toString(){return "matioCpp::Logical" ;};};
 
 /**
  * @brief Utility meta-function to check if a type is compatible with a std::string
@@ -123,7 +131,7 @@ bool is_convertible_to_primitive_type(matioCpp::ValueType type)
         return std::is_same<T, int64_t>::value;
         break;
     case matioCpp::ValueType::UINT64:
-        return std::is_same<T, uint64_t>::value;
+        return std::is_same<T, size_t_type>::value;
         break;
     case matioCpp::ValueType::UTF8:
         return (std::is_same<T, char>::value || std::is_same<T, uint8_t>::value);