CMakeLists.txt

cmake_minimum_required(VERSION 3.15)
project(RetinalAnalysis VERSION 1.0.0 LANGUAGES CXX)

# Set C++ standard
set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF)

# Compiler flags
if(CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")
    add_compile_options(-Wall -Wextra -Wpedantic)
endif()

# Include directories
include_directories(${PROJECT_SOURCE_DIR}/src)

# ============================================================================
# SOURCE FILES
# ============================================================================

# Math module sources
set(MATH_SOURCES
    src/math/Vector3.cpp
    src/math/Matrix4.cpp
    src/math/Ray.cpp
    src/math/BoundingBox.cpp
)

# Core module sources
set(CORE_SOURCES
    src/core/Event.h
    src/core/EventBus.h
    src/core/EventBus.cpp
    src/core/ApplicationController.h
    src/core/ApplicationController.cpp
)

# Data module sources
set(DATA_SOURCES
    src/data/ImageVolume.cpp
    src/data/Channel.cpp
    src/data/TimePoint.cpp
    src/data/Dataset.cpp
)

# Camera module sources
set(CAMERA_SOURCES
    src/camera/Camera.cpp
    src/camera/CameraController.cpp
)

# Rendering module sources
set(RENDERING_SOURCES
    src/rendering/Framebuffer.cpp
    src/rendering/TransferFunction.cpp
    src/rendering/RayMarcher.cpp
    src/rendering/VolumeRenderer.cpp
)

# Animation module sources
set(ANIMATION_SOURCES
    src/animation/TimeController.cpp
)

# UI module sources
set(UI_SOURCES
    src/ui/UIManager.h
    src/ui/UIManager.cpp
    src/ui/TimelineWidget.h
    src/ui/ChannelPanel.h
    src/ui/ChannelPanel.cpp
    src/ui/ContrastPanel.h
    src/ui/ContrastPanel.cpp
)

# Window module sources
set(WINDOW_SOURCES
    src/window/Window.h
    src/window/Window.cpp
    src/window/InputManager.h
    src/window/InputManager.cpp
    src/window/RenderLoop.h
    src/window/RenderLoop.cpp
)

# ============================================================================
# LIBRARIES (in dependency order)
# ============================================================================

# Create a library from math sources
add_library(retinal_math ${MATH_SOURCES})
target_include_directories(retinal_math PUBLIC ${PROJECT_SOURCE_DIR}/src)

# Create a library from core sources
add_library(retinal_core ${CORE_SOURCES})
target_include_directories(retinal_core PUBLIC ${PROJECT_SOURCE_DIR}/src)

# Create a library from camera sources
add_library(retinal_camera ${CAMERA_SOURCES})
target_include_directories(retinal_camera PUBLIC ${PROJECT_SOURCE_DIR}/src)
target_link_libraries(retinal_camera retinal_math)

# Create a library from data sources
add_library(retinal_data ${DATA_SOURCES})
target_include_directories(retinal_data PUBLIC ${PROJECT_SOURCE_DIR}/src)
target_link_libraries(retinal_data retinal_math)

# Create a library from rendering sources
add_library(retinal_rendering ${RENDERING_SOURCES})
target_include_directories(retinal_rendering PUBLIC ${PROJECT_SOURCE_DIR}/src)
target_link_libraries(retinal_rendering retinal_math retinal_data retinal_camera)

# Create a library from animation sources
add_library(retinal_animation ${ANIMATION_SOURCES})
target_include_directories(retinal_animation PUBLIC ${PROJECT_SOURCE_DIR}/src)
target_link_libraries(retinal_animation retinal_data retinal_math)

# Create a library from UI sources
add_library(retinal_ui ${UI_SOURCES})
target_include_directories(retinal_ui PUBLIC ${PROJECT_SOURCE_DIR}/src)
target_link_libraries(retinal_ui retinal_core)

# Create a library from window sources
add_library(retinal_window ${WINDOW_SOURCES})
target_include_directories(retinal_window PUBLIC ${PROJECT_SOURCE_DIR}/src)
target_link_libraries(retinal_window retinal_core retinal_rendering retinal_data)

# ============================================================================
# TESTING (requires Google Test)
# ============================================================================

# Option to build tests
option(BUILD_TESTS "Build the test suite" ON)

if(BUILD_TESTS)
    # Find Google Test
    find_package(GTest QUIET)
    
    if(GTest_FOUND)
        enable_testing()
        
        # Math test sources
        set(MATH_TEST_SOURCES
            tests/math/test_Vector3.cpp
            tests/math/test_Matrix4.cpp
            tests/math/test_Ray.cpp
            tests/math/test_BoundingBox.cpp
        )

        # Core test sources
        set(CORE_TEST_SOURCES
            tests/core/test_EventBus.cpp
            tests/core/test_ApplicationController.cpp
        )

        # Data test sources
        set(DATA_TEST_SOURCES
            tests/data/test_ImageVolume.cpp
            tests/data/test_Channel.cpp
            tests/data/test_TimePoint.cpp
            tests/data/test_Dataset.cpp
        )

        # Camera test sources
        set(CAMERA_TEST_SOURCES
            tests/camera/test_Camera.cpp
            tests/camera/test_CameraController.cpp
        )

        # Rendering test sources
        set(RENDERING_TEST_SOURCES
            tests/rendering/test_Framebuffer.cpp
            tests/rendering/test_TransferFunction.cpp
            tests/rendering/test_RayMarcher.cpp
            tests/rendering/test_VolumeRenderer.cpp
        )

        # Animation test sources
        set(ANIMATION_TEST_SOURCES
            tests/animation/test_TimeController.cpp
        )

        # UI test sources
        set(UI_TEST_SOURCES
            tests/ui/test_UIManager.cpp
            tests/ui/test_TimelineWidget.cpp
            tests/ui/test_ChannelPanel.cpp
            tests/ui/test_ContrastPanel.cpp
        )

        # Window test sources
        set(WINDOW_TEST_SOURCES
            tests/window/test_Window.cpp
            tests/window/test_InputManager.cpp
            tests/window/test_RenderLoop.cpp
        )

        # Create math test executable
        add_executable(math_tests ${MATH_TEST_SOURCES})
        target_link_libraries(math_tests 
            retinal_math
            GTest::gtest
            GTest::gtest_main
        )

        # Create core test executable
        add_executable(core_tests ${CORE_TEST_SOURCES})
        target_link_libraries(core_tests 
            retinal_core
            GTest::gtest
            GTest::gtest_main
        )

        # Create camera test executable
        add_executable(camera_tests ${CAMERA_TEST_SOURCES})
        target_link_libraries(camera_tests 
            retinal_camera
            retinal_math
            GTest::gtest
            GTest::gtest_main
        )

        # Create data test executable
        add_executable(data_tests ${DATA_TEST_SOURCES})
        target_link_libraries(data_tests 
            retinal_data
            retinal_math
            GTest::gtest
            GTest::gtest_main
        )

        # Create rendering test executable
        add_executable(rendering_tests ${RENDERING_TEST_SOURCES})
        target_link_libraries(rendering_tests 
            retinal_rendering
            retinal_data
            retinal_camera
            retinal_math
            GTest::gtest
            GTest::gtest_main
        )

        # Create animation test executable
        add_executable(animation_tests ${ANIMATION_TEST_SOURCES})
        target_link_libraries(animation_tests 
            retinal_animation
            retinal_data
            retinal_math
            GTest::gtest
            GTest::gtest_main
        )

        # Create UI test executable
        add_executable(ui_tests ${UI_TEST_SOURCES})
        target_link_libraries(ui_tests 
            retinal_ui
            retinal_core
            retinal_data
            retinal_math
            GTest::gtest
            GTest::gtest_main
        )

        # Create window test executable
        add_executable(window_tests ${WINDOW_TEST_SOURCES})
        target_link_libraries(window_tests 
            retinal_window
            retinal_rendering
            retinal_core
            retinal_data
            retinal_camera
            retinal_math
            GTest::gtest
            GTest::gtest_main
        )

        # Add tests to CTest
        include(GoogleTest)
        gtest_discover_tests(math_tests)
        gtest_discover_tests(core_tests)
        gtest_discover_tests(camera_tests)
        gtest_discover_tests(data_tests)
        gtest_discover_tests(rendering_tests)
        gtest_discover_tests(animation_tests)
        gtest_discover_tests(ui_tests)
        gtest_discover_tests(window_tests)
        
        message(STATUS "Tests will be built with Google Test")
    else()
        message(WARNING "Google Test not found. Tests will not be built.")
        message(WARNING "Install with: brew install googletest")
    endif()
endif()

# ============================================================================
# MAIN EXECUTABLE (placeholder for now)
# ============================================================================

# Uncomment when ready to build main application
# add_executable(retinal_analysis src/main.cpp)
# target_link_libraries(retinal_analysis retinal_math)

# ============================================================================
# INSTALLATION (optional)
# ============================================================================

# install(TARGETS retinal_math DESTINATION lib)
# install(DIRECTORY src/math DESTINATION include FILES_MATCHING PATTERN "*.h")