Installation

YAGIT requires a C++ compiler that supports C++17. It also requires CMake (3.16 or newer). It works on Linux and Windows. It can be downloaded from https://github.com/DataMedSci/yagit.

YAGIT uses these dependencies:

• GDCM – used for reading DICOM files.

• xsimd – used for vectorization. Used only when GAMMA_VERSION=SIMD or GAMMA_VERSION=THREADS_SIMD.

• GoogleTest – used for unit tests. Used only when BUILD_TESTING=ON.

You can build and install YAGIT using the setup script or by doing it manually.

Setup script installation

To build YAGIT, simply run setup.sh or setup.bat script, depending on your operating system.

On Linux, run:

./setup.sh

On Windows, run:

setup.bat

Note that these scripts will only build the library and not install it by default. To install it, configure the options appropriately in the script file.

For now, the Windows script can install dependencies using only Conan package manager.

Script options

You can freely configure the options that are in the script files. Some of the options are the same as in the CMake YAGIT options section, as they are simply passed to CMake.

Option	Values	Default	Description
BUILD_TYPE	Release, Debug, RelWithDebInfo, MinSizeRel	Release	Build type used in the script by CMake for single-target generators (e.g., Makefile Generators) and by a compiler for multi-target generators (e.g., Visual Studio Generators).
BUILD_SHARED_LIBS	ON, OFF	OFF	Equivalent to the CMake YAGIT option.
INSTALL_DEPENDENCIES	OFF, LOCAL, GLOBAL, CONAN	LOCAL	Method of installing dependencies. Value OFF doesn’t install any dependencies, and it assumes they are already installed system-wide. Value LOCAL installs dependencies locally in the build/deps directory. Value GLOBAL installs dependencies system-wide. It requires admin privileges. Value CONAN installs dependencies using Conan package manager. It requires installed Conan. This option is only available in setup.sh.
GAMMA_VERSION	SEQUENTIAL, THREADS, SIMD, THREADS_SIMD	THREADS	Equivalent to the CMake YAGIT option.
SIMD_EXTENSION	DEFAULT, SSE2, SSE3, SSSE3, SSE4.1, SSE4.2, AVX, AVX2, AVX512, NATIVE	DEFAULT	Equivalent to the CMake YAGIT option.
ENABLE_FMA	ON, OFF	OFF	Equivalent to the CMake YAGIT option.
BUILD_EXAMPLES	ON, OFF	ON	Equivalent to the CMake YAGIT option. Additionally, it runs examples.
BUILD_TESTING	ON, OFF	OFF	Equivalent to the CMake YAGIT option. Additionally, it runs unit tests.
BUILD_PERFORMANCE_TESTING	ON, OFF	OFF	Equivalent to the CMake YAGIT option. Additionally, it runs performance tests.
REF_IMG	—	—	Path to a reference image used in examples and performance tests.
EVAL_IMG	—	—	Path to an evaluated image used in examples and performance tests.
BUILD_DOCUMENTATION	ON, OFF	OFF	Build documentation (docs directory). It requires Doxygen, Python, and libraries listed in docs/requirements.txt.
INSTALL	ON, OFF	OFF	Install YAGIT library.
INSTALL_DIR	—	./yagit	Directory where YAGIT will be installed (only if INSTALL=ON). If this is set to an empty string, then it will be installed system-wide.

Manual installation

If you prefer to perform the installation manually without the script, then follow the commands below to build and install YAGIT on Linux. Before running them, ensure that you have installed the dependencies (e.g., by using a package manager or by building from source).

mkdir build && cd build
cmake .. -DCMAKE_BUILD_TYPE=Release
cmake --build . -j
sudo cmake --install .

If you don’t have admin privileges or you want to install in a specific directory, then use this command:

cmake --install . --prefix <yagit installation path>

CMake YAGIT options

Option	Values	Default	Description
BUILD_SHARED_LIBS	ON, OFF	OFF	Build YAGIT as a shared or static library.
BUILD_EXAMPLES	ON, OFF	OFF	Build examples (examples directory).
BUILD_TESTING	ON, OFF	OFF	Build unit tests (tests/unit directory).
BUILD_PERFORMANCE_TESTING	ON, OFF	OFF	Build performance tests (tests/performance directory).
GAMMA_VERSION	SEQUENTIAL, THREADS, SIMD, THREADS_SIMD	THREADS	Implementation of algorithms calculating the gamma index.
SIMD_EXTENSION	DEFAULT, SSE2, SSE3, SSSE3, SSE4.1, SSE4.2, AVX, AVX2, AVX512, NATIVE	DEFAULT	SIMD instruction set extension. It works only when GAMMA_VERSION is set to SIMD or THREADS_SIMD. Value DEFAULT adds no additional compilation flags. Value NATIVE adds -march=native if a compiler supports it.
ENABLE_FMA	ON, OFF	OFF	Enable fused multiply-add (FMA) when building YAGIT library.

To use these options, pass them to CMake during configuration using -D<option>=<value> (e.g., cmake .. -DGAMMA_VERSION=THREADS_SIMD -DSIMD_EXTENSION=AVX2).

CMake YAGIT integration

Here is an example of adding YAGIT to your CMake project.

find_package(yagit REQUIRED)
add_executable(program program.cpp)
target_link_libraries(program PRIVATE yagit::yagit)

If YAGIT has been installed in a custom location, then you need to set the CMAKE_PREFIX_PATH option to the path of the installed YAGIT. This is necessary for locating the yagitConfig.cmake file.

Including YAGIT

To include the whole YAGIT library in your code, use the line below.

#include <yagit/yagit.hpp>