adding unit test (#16)

* Parallelize phantom creation for improved performance

* update

* update

* Created using Colab

* change cu to cpp in main file

* add warning macro

* rename notebook

* bug fix

* adding unit test

* add scale

* update

.github/workflows/build_cmake.yml

@@ -1,20 +1,18 @@
-name: cmake build
+name: build & test
 
 on:
   push:
-    branches: [ "main", "dev" ]
+    branches: [ "main" ]
   pull_request:
     branches: [ "main" ]
+  workflow_dispatch: # This is the manual trigger
 
 env:
   # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
   BUILD_TYPE: Release
 
 jobs:
   build:
-    # The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
-    # You can convert this to a matrix build if you need cross-platform coverage.
-    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
     runs-on: ubuntu-latest
 
     steps:
@@ -41,4 +39,8 @@ jobs:
     - name: Build
       run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
 
-
+    # Run Unit Tests
+    - name: Run Unit Tests
+      run: |
+        cd ${{github.workspace}}/build/tests
+        ./spinwalk_test

CMakeLists.txt

@@ -2,8 +2,9 @@ cmake_minimum_required(VERSION 3.24)
 message(STATUS "CMake version: ${CMAKE_VERSION}")
 include(CheckLanguage)
 
-set(project "SpinWalk")
-project(${project})
+set(project_exe "SpinWalk_exe")
+set(project_lib "SpinWalk_lib")
+project(${project_exe})
 
 # Find HDF5
 find_package(HDF5 REQUIRED COMPONENTS CXX)
@@ -15,7 +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
@@ -28,6 +29,8 @@ else()
     message("CUDA not found. Compiling without GPU support.")
 endif()
 
+find_package(OpenMP)
+
 set(CMAKE_CXX_STANDARD 20)
 set(CMAKE_CXX_STANDARD_REQUIRED True)
 add_compile_definitions(MINI_CASE_SENSITIVE)
@@ -39,22 +42,21 @@ if(CMAKE_BUILD_TYPE MATCHES Debug)
 endif()
 
 # Add Boost and CUDA include directories
-include_directories(${Boost_INCLUDE_DIRS} ${HDF5_INCLUDE_DIRS} ./include ./src ./src/shapes)
-# Add subfolders
-add_subdirectory(./src/dwi)
-add_subdirectory(./src/phantom)
-add_subdirectory(./src/config)
-add_subdirectory(./src/sim)
+include_directories(${Boost_INCLUDE_DIRS} ${HDF5_INCLUDE_DIRS} ./include ./src)
+# Add modules directory
+add_subdirectory(src/dwi)
+add_subdirectory(src/phantom)
+add_subdirectory(src/config)
+add_subdirectory(src/sim)
 
-# Add the executable
-set(SOURCES ./src/spinwalk.cu ${SUBCOMMAND_PHANTOM} ${SUBCOMMAND_SIM} ${SUBCOMMAND_DWI} ${SUBCOMMAND_CONFIG})
+ # Add the sources files
+set(SOURCE_MODULES ${SUBCOMMAND_PHANTOM} ${SUBCOMMAND_SIM} ${SUBCOMMAND_DWI} ${SUBCOMMAND_CONFIG})
+set(SOURCE_MAIN ./src/spinwalk.cu)
 
-if(CMAKE_CUDA_COMPILER)
-    add_executable(${project} ${SOURCES})
-    target_link_libraries(${project} ${CUDA_LIBRARIES} ${Boost_LIBRARIES} ${HDF5_CXX_LIBRARIES} TBB::tbb)
-else()    
+# change extension of the files if CUDA is not found
+if(NOT  CMAKE_CUDA_COMPILER) 
     set(RENAMED_SOURCES)
-    foreach(OLD_FILE ${SOURCES})
+    foreach(OLD_FILE ${SOURCE_MODULES})
         # Get the file name without extension
         get_filename_component(DIR ${OLD_FILE} DIRECTORY)
         get_filename_component(FILE_NAME_WE ${OLD_FILE} NAME_WE)
@@ -64,15 +66,42 @@ else()
         file(COPY_FILE ${OLD_FILE} ${NEW_FILE})
         list(APPEND RENAMED_SOURCES ${NEW_FILE})
     endforeach()
-    add_executable(${project} ${RENAMED_SOURCES})
-    target_link_libraries(${project} ${Boost_LIBRARIES} ${HDF5_CXX_LIBRARIES} TBB::tbb)
+    set(SOURCE_MODULES ${RENAMED_SOURCES})
+
+    file(COPY_FILE ./src/spinwalk.cu ./src/spinwalk.cpp)
+    set(SOURCE_MAIN ./src/spinwalk.cpp)
 endif()
 
-set_target_properties(${project} PROPERTIES OUTPUT_NAME "spinwalk")
+# Add the executable
+add_library(${project_lib} ${SOURCE_MODULES})
+add_executable(${project_exe} ${SOURCE_MAIN})
 
+# Add the libraries
+if(CMAKE_CUDA_COMPILER)
+    target_link_libraries(${project_lib} ${CUDA_LIBRARIES})
+endif()
+if(OpenMP_CXX_FOUND)
+    message(STATUS "Found OpenMP, adding to target link libraries.")
+    target_link_libraries(${project_lib} OpenMP::OpenMP_CXX)
+else()
+    message(STATUS "OpenMP not found, skipping.")
+endif()
+target_link_libraries(${project_lib} ${Boost_LIBRARIES} ${HDF5_CXX_LIBRARIES} TBB::tbb)
+target_link_libraries(${project_exe} PRIVATE ${project_lib})
+
+# Set the output name
+set_target_properties(${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

README.md

@@ -44,7 +44,7 @@
 ---
 ### Demo
 
-Jupyter notebooks demonstrating the basic functionality of SpinWalk for [BOLD fMRI contrast](./demo/spinwalk_example.ipynb) and [free diffusion](./demo/spinwalk_dwi.ipynb) simulations can be found in the [demo](./demo) folder.
+Jupyter notebooks demonstrating the basic functionality of SpinWalk for [BOLD fMRI contrast](./demo/spinwalk_bold.ipynb) and [free diffusion](./demo/spinwalk_dwi.ipynb) simulations can be found in the [demo](./demo) folder.
 
 Below are example plots generated by SpinWalk, showing BOLD sensitivity as a function of vessel size for Gradient Echo (GRE) and Spin Echo (SE) sequences. Some [literature](#Literature) is provided as a reference to help understand the intended outcomes of these simulations.
 

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

@@ -2,7 +2,7 @@
 #define DEFINITIONS_H
 
 #define VERSION_MAJOR 1
-#define VERSION_MINOR 17
+#define VERSION_MINOR 18
 #define VERSION_PATCH 2
 
 // Helper macros to stringify values
@@ -12,6 +12,7 @@
 #define SPINWALK_VERSION STRINGIFY(VERSION_MAJOR) "." STRINGIFY(VERSION_MINOR) "." STRINGIFY(VERSION_PATCH)
 
 #define ERR_MSG  "\033[1;31mError:\033[0m "
+#define WARN_MSG "\033[1;33mWarning:\033[0m "
 
 // #define MINI_CASE_SENSITIVE
 

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.cpp

@@ -23,15 +23,15 @@ phantom_base::phantom_base()
     m_fov = 0;
     m_resolution = 0;
     m_seed = std::random_device{}();
-    set_blood_parameters(0.273e-6 * 0.4, 0, 10.0);
+    set_parameters(0.273e-6 * 0.4, 0, 10.0);
     set_filename(); 
 }
 
 phantom_base::phantom_base(float fov_um, size_t resolution, float dChi, float Y, float BVF, int32_t seed, std::string filename)
 :phantom_base()
 {
     set_space(fov_um, resolution);
-    set_blood_parameters(dChi, Y, BVF);
+    set_parameters(dChi, Y, BVF);
     set_filename(filename);
     if(seed >= 0)
         m_seed = seed;
@@ -47,11 +47,11 @@ void phantom_base::set_space(float fov_um, size_t resolution)
     this->m_resolution = resolution;
 }
 
-void phantom_base::set_blood_parameters(float dChi, float Y, float BVF)
+void phantom_base::set_parameters(float dChi, float Y, float volume_fraction)
 {
     this->m_dChi = dChi;
     this->m_Y = Y;
-    this->m_BVF = BVF;
+    this->m_volume_fraction = volume_fraction;
     m_calc_fieldmap = Y >= 0;
 }
 
@@ -92,7 +92,7 @@ bool phantom_base::save() const
     // blood volume fraction
     std::vector<size_t> dims_1(1, 1);
     HighFive::DataSet dataset_BVF = file.createDataSet<float>("bvf", HighFive::DataSpace(dims_1));
-    dataset_BVF.write_raw(&m_BVF);
+    dataset_BVF.write_raw(&m_volume_fraction);
 
     return true;
 }

src/phantom/phantom_base.h

@@ -25,16 +25,17 @@ class phantom_base
 {
     public:
         phantom_base();
-        phantom_base(float fov_um, size_t resolution, float dChi, float Y, float BVF, int32_t seed, std::string filename);
+        phantom_base(float fov_um, size_t resolution, float dChi, float Y, float volume_fraction, int32_t seed, std::string filename);
         virtual ~phantom_base();
         void set_space(float fov_um, size_t resolution);
-        void set_blood_parameters(float dChi, float Y, float BVF = 10.0); 
+        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;
         virtual bool generate_mask_fieldmap() = 0;
+        float get_actual_volume_fraction() const {return m_volume_fraction;}
 
         friend std::ostream& operator<<(std::ostream& os, const phantom_base& obj);
 
@@ -44,7 +45,7 @@ class phantom_base
         std::vector<int8_t> m_mask;
         size_t m_resolution;
         float m_fov, m_dChi, m_Y;
-        float m_BVF; // blood volume fraction
+        float m_volume_fraction; // volume fraction
         std::string m_filename;
         float B0[3] = {0.f, 0.f, 1.f};
         bool m_calc_fieldmap;