adding unit test

CMakeLists.txt

@@ -2,9 +2,9 @@ cmake_minimum_required(VERSION 3.24)
 message(STATUS "CMake version: ${CMAKE_VERSION}")
 include(CheckLanguage)
 
-set(project "SpinWalk")
-set(project_lib "SpinWalkLib")
-project(${project})
+set(project_exe "SpinWalk_exe")
+set(project_lib "SpinWalk_lib")
+project(${project_exe})
 
 # Find HDF5
 find_package(HDF5 REQUIRED COMPONENTS CXX)
@@ -16,7 +16,7 @@ find_package(TBB REQUIRED)
 if(CMAKE_VERSION VERSION_GREATER "3.30")
     cmake_policy(SET CMP0167 NEW)
 endif()
-find_package(Boost COMPONENTS log log_setup REQUIRED)
+find_package(Boost REQUIRED COMPONENTS log log_setup)
 
 check_language(CUDA)
 # Check for CUDA-capable GPU
@@ -43,11 +43,11 @@ endif()
 
 # Add Boost and CUDA include directories
 include_directories(${Boost_INCLUDE_DIRS} ${HDF5_INCLUDE_DIRS} ./include ./src)
-# Add subfolders
-add_subdirectory(./src/dwi)
-add_subdirectory(./src/phantom)
-add_subdirectory(./src/config)
-add_subdirectory(./src/sim)
+# Add modules directory
+add_subdirectory(src/dwi)
+add_subdirectory(src/phantom)
+add_subdirectory(src/config)
+add_subdirectory(src/sim)
 
  # Add the sources files
 set(SOURCE_MODULES ${SUBCOMMAND_PHANTOM} ${SUBCOMMAND_SIM} ${SUBCOMMAND_DWI} ${SUBCOMMAND_CONFIG})
@@ -74,7 +74,7 @@ endif()
 
 # Add the executable
 add_library(${project_lib} ${SOURCE_MODULES})
-add_executable(${project} ${SOURCE_MAIN})
+add_executable(${project_exe} ${SOURCE_MAIN})
 
 # Add the libraries
 if(CMAKE_CUDA_COMPILER)
@@ -87,18 +87,21 @@ else()
     message(STATUS "OpenMP not found, skipping.")
 endif()
 target_link_libraries(${project_lib} ${Boost_LIBRARIES} ${HDF5_CXX_LIBRARIES} TBB::tbb)
-target_link_libraries(${project} PRIVATE ${project_lib})
+target_link_libraries(${project_exe} PRIVATE ${project_lib})
 
 # Set the output name
-set_target_properties(${project} PROPERTIES OUTPUT_NAME "spinwalk")
+set_target_properties(${project_exe} PROPERTIES OUTPUT_NAME "spinwalk")
 set_target_properties(${project_lib} PROPERTIES OUTPUT_NAME "spinwalk")
 
 
 # Install the executable
 if (UNIX)
-    install(TARGETS ${project} DESTINATION bin) 
+    install(TARGETS ${project_exe} DESTINATION bin) 
     install(TARGETS ${project_lib} DESTINATION lib) 
 endif()
 
+# Add the tests directory
+add_subdirectory(tests)
+
 # cmake ..
 # cmake --build . --config Release

containers/Dockerfile_CPU

@@ -34,8 +34,9 @@ RUN rm -rf ./build && cmake -B ./build && cmake --build ./build --config Release
 # Stage 2: Runtime
 FROM ubuntu:24.04
 USER root
-RUN apt-get update && apt install -y libboost-log1.83.0 libtbb-dev libhdf5-103-1 --no-install-recommends && apt-get clean && apt-get -y autoremove && rm -rf /var/lib/apt/lists/* 
+RUN apt-get update && apt install -y libboost-log1.83.0 libtbb-dev libhdf5-103-1 libomp5 --no-install-recommends && apt-get clean && apt-get -y autoremove && rm -rf /var/lib/apt/lists/* 
 COPY --from=builder /opt/SpinWalk/build/spinwalk /usr/local/bin/
+COPY --from=builder /opt/SpinWalk/build/tests/spinwalk_test /usr/local/bin/
 LABEL org.opencontainers.image.authors="Ali Aghaeifar"
 
 # docker run --rm -it -v /DATA2:/mnt/DATA2 spinwalk_cpu:ubuntu24.04 bash

containers/create_dockers.sh

@@ -4,6 +4,7 @@ SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 pushd "$SCRIPT_DIR" > /dev/null
 
 # docker system prune -a --volumes --force
+docker system prune --force
 
 CUDA_VERSIONS=("12.0.0" "12.2.0" "12.6.3")
 

src/definitions.h

@@ -3,7 +3,7 @@
 
 #define VERSION_MAJOR 1
 #define VERSION_MINOR 18
-#define VERSION_PATCH 1
+#define VERSION_PATCH 2
 
 // Helper macros to stringify values
 #define STRINGIFY_HELPER(x) #x

src/phantom/handler.cpp

@@ -10,14 +10,14 @@ namespace phantom {
         if (args.cylinder){
             std::cout << "Generating cylinder phantom..." << std::endl;
             cylinder cyl(args.fov, args.resolution, args.dchi, args.oxy_level, args.radius, args.volume_fraction, args.orientation, args.seed, args.output);
-            status = status && cyl.run();
+            status = status && cyl.run(true);
         }
         if (args.sphere){
             std::cout << "Generating sphere phantom..." << std::endl;
             sphere sph(args.fov, args.resolution, args.dchi, args.oxy_level, args.radius, args.volume_fraction, args.seed,args.output);
-            status = status && sph.run();
+            status = status && sph.run(true);
         }
         std::cout << "Done." << std::endl;
-        return true;
+        return status;
     }
 }

src/phantom/phantom_base.h

@@ -30,7 +30,7 @@ class phantom_base
         void set_space(float fov_um, size_t resolution);
         void set_parameters(float dChi, float Y, float volume_fraction = 10.0); 
         void set_filename(std::string filename = "shape.h5");      
-        virtual bool run(){return true;}; 
+        virtual bool run(bool write_to_disk) = 0; 
         virtual bool save() const;
         virtual bool create_grid();
         virtual bool generate_shapes() = 0;

src/phantom/phantom_cylinder.cpp

@@ -285,7 +285,7 @@ std::ostream& operator<<(std::ostream& os, const cylinder& obj)
 
 // -------------------------------------------------------------------------- //
 
-bool cylinder::run()
+bool cylinder::run(bool write_to_disk)
 {
     BOOST_LOG_TRIVIAL(info) << *this << std::endl;
     if(create_grid() == false)
@@ -294,8 +294,9 @@ bool cylinder::run()
         return false;
     if(generate_mask_fieldmap() == false)
         return false;
-    if(save() == false)
-        return false;
+    if(write_to_disk)
+        if(save() == false)
+            return false;
     return true;
 }
 

src/phantom/phantom_cylinder.h

@@ -22,7 +22,7 @@ class cylinder : public phantom_base
     cylinder(float fov_um, size_t resolution, float dChi, float Y, float radius_um = 50, float volume_fraction = 10., float orientation = -1.0f, int32_t seed=-1, std::string filename = "shape.h5");
     ~cylinder();
 
-    virtual bool run() override;
+    virtual bool run(bool write_to_disk) override;
     virtual void set_cylinder_parameters(float radius_um = 50, float orientation = -1.0f);    
     virtual bool generate_shapes();
     virtual bool generate_mask_fieldmap();

src/phantom/phantom_sphere.cpp

@@ -208,7 +208,7 @@ std::ostream& operator<<(std::ostream& os, const sphere& obj)
 
 // -------------------------------------------------------------------------- //
 
-bool sphere::run()
+bool sphere::run(bool write_to_disk)
 {
     BOOST_LOG_TRIVIAL(info) << *this << std::endl;
     if(create_grid() == false)
@@ -217,8 +217,9 @@ bool sphere::run()
         return false;
     if(generate_mask_fieldmap() == false)
         return false;
-    if(save() == false)
-        return false;
+    if(write_to_disk)
+        if(save() == false)
+            return false;
     return true;
 }
 

src/phantom/phantom_sphere.h

@@ -22,7 +22,7 @@ class sphere : public phantom_base
     sphere(float fov_um, size_t resolution, float dChi, float Y, float radius_um = 50, float volume_fraction = 10.0, int32_t seed = -1, std::string filename = "shape.h5");
     virtual ~sphere();
 
-    virtual bool run() override;
+    virtual bool run(bool write_to_disk) override;
     virtual void set_sphere_parameters(float radius_um = 50);    
     virtual bool generate_shapes();
     virtual bool generate_mask_fieldmap();

tests/CMakeLists.txt

@@ -0,0 +1,36 @@
+cmake_minimum_required(VERSION 3.24)
+include(CTest)
+
+set(project_test "SpinWalk_test")
+project(${project_test})
+
+# Boost
+if(CMAKE_VERSION VERSION_GREATER "3.30")
+    cmake_policy(SET CMP0167 NEW)
+endif()
+find_package(Boost REQUIRED COMPONENTS unit_test_framework log)
+
+if (NOT Boost_UNIT_TEST_FRAMEWORK_FOUND)
+    message("Boost Unit Test Framework not found. Not compiling tests")
+    return()
+endif ()
+
+if (NOT Boost_USE_STATIC_LIBS)
+    add_definitions(-DBOOST_TEST_DYN_LINK)
+endif()
+
+
+# include_directories(${CMAKE_SOURCE_DIR}/include ${CMAKE_BINARY_DIR}/include ${Boost_INCLUDE_DIR} ${CMAKE_CURRENT_BINARY_DIR})
+include_directories(${Boost_INCLUDE_DIRS})
+
+add_executable(${project_test} test_phantom.cpp test_config.cpp)
+target_link_libraries(${project_test} ${Boost_LIBRARIES} SpinWalk_lib)
+set_target_properties(${project_test} PROPERTIES OUTPUT_NAME "spinwalk_test")
+
+add_test(NAME check COMMAND spinwalk_test)
+
+if (UNIX)
+    install(TARGETS ${project_test} DESTINATION bin) 
+endif()
+
+# spinwalk_test --log_level=test_suite --report_level=short

tests/test_config.cpp

@@ -0,0 +1,34 @@
+#define BOOST_TEST_MODULE "SpinWlkTest"
+#include <boost/test/unit_test.hpp>
+#include <boost/log/core.hpp>
+#include <filesystem>
+
+#include "../src/config/config_generator.h"
+#include "../include/ini.h"
+
+
+BOOST_AUTO_TEST_CASE(config_creation) {
+    boost::log::core::get()->set_logging_enabled(false);
+
+    std::filesystem::path temp_dir = std::filesystem::temp_directory_path();
+    std::filesystem::path temp_file = temp_dir / "gre.ini";
+    std::filesystem::path temp_file_parent = temp_dir / "default_config.ini";
+    std::vector<std::string> phantoms = {"phantom1.h5", "phantom2.h5"};
+    uint32_t timestep_us = 25;
+    uint32_t TE = 12345;
+
+    BOOST_REQUIRE(config::generate_gre(TE, timestep_us, phantoms, temp_file.string()));
+    BOOST_REQUIRE(std::filesystem::exists(temp_file));
+    BOOST_REQUIRE(std::filesystem::exists(temp_file_parent));
+
+    mINI::INIFile file(temp_file.string());
+    mINI::INIStructure ini;
+    BOOST_REQUIRE(file.read(ini));
+    BOOST_CHECK_EQUAL(std::stoi(ini["SCAN_PARAMETERS"]["TE[0]"]), TE);
+    BOOST_CHECK_EQUAL(std::stoi(ini["SCAN_PARAMETERS"]["TIME_STEP"]), timestep_us);
+
+    std::filesystem::remove(temp_file);
+    std::filesystem::remove(temp_file_parent);
+    BOOST_CHECK(!std::filesystem::exists(temp_file));
+    BOOST_CHECK(!std::filesystem::exists(temp_file_parent));
+}

tests/test_phantom.cpp

@@ -0,0 +1,42 @@
+#include <boost/test/unit_test.hpp>
+#include <boost/log/core.hpp>
+
+#include "../src/phantom/phantom_sphere.h"
+#include "../src/phantom/phantom_cylinder.h"
+
+
+BOOST_AUTO_TEST_SUITE(test_phantom_creation)
+
+BOOST_AUTO_TEST_CASE(cylinder_creation) {
+    boost::log::core::get()->set_logging_enabled(false);
+    float diff_margin = 2.f;
+
+    std::vector<float> volume_fraction = {5.0, 10.0};
+    for(const auto &vf : volume_fraction){
+        phantom::cylinder cyl(600, 300, 0.11e-6, -1, -20, vf, 0, 0, "");
+        BOOST_TEST(cyl.run(false));
+        BOOST_TEST(std::abs(cyl.get_actual_volume_fraction() - vf) < diff_margin); 
+    }
+
+    std::vector<float> angles = {5.0, 10.0};
+    float vf = 10.0;
+    for(const auto &a : angles){
+        phantom::cylinder cyl(600, 300, 0.11e-6, -1, -20, vf, 0, a, "");
+        BOOST_TEST(cyl.run(false));
+        BOOST_TEST(std::abs(cyl.get_actual_volume_fraction() - vf) < diff_margin); 
+    }
+}
+
+BOOST_AUTO_TEST_CASE(sphere_creation) {
+    boost::log::core::get()->set_logging_enabled(false);
+    std::vector<float> volume_fraction = {5.0, 10.0};
+    float diff_margin = 2.f;
+    for(const auto &vf : volume_fraction){
+        phantom::sphere sph(600, 300, 0.11e-6, -1, -20, vf, 0, "");
+        BOOST_CHECK(sph.run(false));
+        BOOST_CHECK(std::abs(sph.get_actual_volume_fraction() - vf) < diff_margin); 
+    }
+}
+
+
+BOOST_AUTO_TEST_SUITE_END()