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Merged
anderskaestner merged 14 commits into from
Dec 4, 2025
Merged

Issue19 conan #21

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1c853dc
Compiles until missing libs.
anderskaestner Dec 2, 2025
4e987ae
Builds and runs after manual copy of imagingsuite dependencies
anderskaestner Dec 2, 2025
9d70049
Fixed compile warnings on mac
anderskaestner Dec 3, 2025
abf29b6
Cleaned up build scripts. Added conan build
anderskaestner Dec 3, 2025
fc5cc85
Compiles and runs on windows. Manual copying of dependencies is still…
anderskaestner Dec 3, 2025
c2f68a8
Update pixi.toml
anderskaestner Dec 4, 2025
3d5937b
Update frameworks/ngi/nGIEstimators/CMakeLists.txt
anderskaestner Dec 4, 2025
fd23001
Update frameworks/ngi/nGIFramework/src/nGIProcessor.cpp
anderskaestner Dec 4, 2025
50a2933
Update conanfile.py
anderskaestner Dec 4, 2025
6b31e6f
Update conanfile.py
anderskaestner Dec 4, 2025
656df93
Update CMakeLists.txt
anderskaestner Dec 4, 2025
00b8e99
Update applications/ngitool/CMakeLists.txt
anderskaestner Dec 4, 2025
b8d76ac
Update CMakeLists.txt
anderskaestner Dec 4, 2025
3968da1
Update frameworks/ngi/nGIFramework/CMakeLists.txt
anderskaestner Dec 4, 2025
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283 changes: 126 additions & 157 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
@@ -1,22 +1,19 @@
# define minimum cmake version
cmake_minimum_required(VERSION 3.16 FATAL_ERROR)
cmake_minimum_required(VERSION 3.30 FATAL_ERROR)

#if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
#message(FATAL_ERROR “In-source_build_detected!_Create_a_build_folder_and_call_CMake_there”)
#endif()
# execute_process(
# COMMAND git describe --tags --abbrev=0 | cut -d'v' -f 2
# WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
# OUTPUT_VARIABLE KIPTOOL_VERSION
# OUTPUT_STRIP_TRAILING_WHITESPACE
# )

execute_process(
COMMAND git describe --tags --abbrev=0 | cut -d'v' -f 2
WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
OUTPUT_VARIABLE KIPTOOL_VERSION
OUTPUT_STRIP_TRAILING_WHITESPACE
)
project(nGITool VERSION 1.0 LANGUAGES CXX)

project(nGItool VERSION 1.0 LANGUAGES CXX)
set(CMAKE_FIND_DEBUG_MODE OFF)

# require C++17
if(NOT DEFINED CMAKE_CXX_STANDARD)
set(CMAKE_CXX_STANDARD 20)

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Copilot AI Dec 4, 2025

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Empty conditional block. The if(NOT DEFINED CMAKE_CXX_STANDARD) block on lines 15-17 is empty and serves no purpose. Either set a default C++ standard value inside this block or remove it entirely.

Suggested change
set(CMAKE_CXX_STANDARD 17)

Copilot uses AI. Check for mistakes.
endif(NOT DEFINED CMAKE_CXX_STANDARD)

set(CMAKE_CXX_EXTENSIONS OFF)
Expand All @@ -32,54 +29,127 @@ if(NOT CMAKE_BUILD_TYPE)
)
endif(NOT CMAKE_BUILD_TYPE)

#set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake" )

set(CMAKE_MODULE_PATH "lib" )
# for testing we will need the python interpreter
find_package(PythonInterp REQUIRED)

set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/applications)
set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
file(TO_CMAKE_PATH "$ENV{QTPATH}/lib/cmake/;${CMAKE_BINARY_DIR}/generators" PREFIX_PATH)
file(TO_CMAKE_PATH "${PROJECT_SOURCE_DIR}/cmake/;${CMAKE_BINARY_DIR}/generators" MODULE_PATH)

# Set environment variables so that CMAKE can find the packages
set(CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH} ${PREFIX_PATH})
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${MODULE_PATH})
message("CMAKE_PREFIX_PATH is: ${CMAKE_PREFIX_PATH}")
message("CMAKE_MODULE_PATH is: ${CMAKE_MODULE_PATH}")
message("QTPATH is: $ENV{QTPATH}")
set(CMAKE_FIND_PACKAGE_PREFER_CONFIG TRUE)
find_package(Python3 COMPONENTS Interpreter Development)

find_package(Armadillo REQUIRED)
find_package(pybind11 REQUIRED)
find_package(libxml2 REQUIRED)
find_package(OpenBLAS REQUIRED)
find_package(TIFF REQUIRED)
find_package(FFTW3 REQUIRED)
find_package(cfitsio REQUIRED)
find_package(ZLIB REQUIRED)
find_package(HDF5 REQUIRED)

# Add imagingsuite install path to CMAKE_PREFIX_PATH
set(IMGSUITE_BUILD_DIR "${PROJECT_SOURCE_DIR}/../build-imagingsuite/Release")
list(APPEND CMAKE_PREFIX_PATH "${IMGSUITE_BUILD_DIR}")
list(APPEND CMAKE_PREFIX_PATH "${IMGSUITE_BUILD_DIR}/lib")

# find_package(kipl REQUIRED CONFIG)
# find_package(ModuleConfig REQUIRED CONFIG)
# find_package(ImagingAlgorithms REQUIRED CONFIG)
# find_package(ReaderConfig REQUIRED CONFIG)
# find_package(QtAddons REQUIRED CONFIG)
# find_package(ReaderGUI REQUIRED CONFIG)
# find_package(QtModuleConfigure REQUIRED CONFIG)
# find_package(QtImaging REQUIRED CONFIG)

if (WIN32)
find_package(dirent)
endif()

if (WIN32)
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/Release)
set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib/Release)
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/Release)
elseif (LINUX)
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
elseif (APPLE)
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
include_directories(${CMAKE_LIBRARY_OUTPUT_DIRECTORY})
endif()

if("${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}" VERSION_LESS "3.5")
if("${Python3_VERSION_MAJOR}.${Python3_VERSION_MINOR}" VERSION_LESS "3.5")
message(
FATAL_ERROR
"Python v3 interpreter must be greater than or equal to 3.5. Found ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}"
"Python v3 interpreter must be greater than or equal to 3.5. Found ${Python3_VERSION_MAJOR}.${Python3_VERSION_MINOR}"
)
endif()

if (WIN32)
set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/../build-kiptool) # needs to be fixed

find_package(PythonInterp REQUIRED)
find_package(LibXml2 REQUIRED)
find_package(armadillo REQUIRED)
find_package(ZLIB REQUIRED)
find_package(TIFF REQUIRED)
find_package(FFTW3 REQUIRED)
find_package(OpenBLAS REQUIRED)
find_package(pybind11 REQUIRED)
find_package(cfitsio REQUIRED)
# find_package(Nexus REQUIRED)
# Set path to imagingsuite build/install directory
set(IMAGINGSUITE_INSTALL_DIR "${CMAKE_SOURCE_DIR}/../build-imagingsuite/Release" CACHE PATH "Path to imagingsuite installation")

# Add imagingsuite library path
link_directories("${IMAGINGSUITE_INSTALL_DIR}/lib")

# Add imagingsuite include paths
include_directories(
../imagingsuite/core/kipl/kipl/include
../imagingsuite/core/modules/ModuleConfig/include
../imagingsuite/core/modules/ReaderConfig
../imagingsuite/core/algorithms/ImagingAlgorithms/include
../imagingsuite/GUI/qt/QtAddons
../imagingsuite/GUI/qt/QtImaging
../imagingsuite/GUI/qt/QtModuleConfigure
../imagingsuite/core/modules/ReaderGUI

)
link_directories("${IMGSUITE_BUILD_DIR}/lib")


execute_process(
COMMAND git describe --tag
WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
RESULT_VARIABLE HAVE_GIT_VERSION_INFO
OUTPUT_VARIABLE GIT_VERSION_INFO
OUTPUT_STRIP_TRAILING_WHITESPACE
ERROR_QUIET
)
if(${HAVE_GIT_VERSION_INFO} EQUAL 0)
message(STATUS "Got version from Git: ${GIT_VERSION_INFO}")
add_definitions(-DVERSION="${GIT_VERSION_INFO}")
else()
set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)

# for testing we will need the python interpreter
find_package(PythonInterp REQUIRED)
find_package(LibXml2 REQUIRED)
find_package(Armadillo REQUIRED)
find_package(ZLIB REQUIRED)
find_package(TIFF REQUIRED)
find_package(FFTW REQUIRED)
find_package(LAPACK REQUIRED)
find_package(BLAS REQUIRED)
find_package(pybind11 REQUIRED)
find_package(CFITSIO REQUIRED)
find_package(Nexus REQUIRED)
set(GIT_VERSION_INFO "${PROJECT_VERSION}")
message(WARNING "Could not get version from Git, using project version: ${GIT_VERSION_INFO}")
add_definitions(-DVERSION="${GIT_VERSION_INFO}")
endif()

if(NOT WIN32)
include(CTest)

execute_process(
COMMAND git describe --tag
WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
RESULT_VARIABLE HAVE_GIT_VERSION_INFO
OUTPUT_VARIABLE GIT_VERSION_INFO OUTPUT_STRIP_TRAILING_WHITESPACE
)
if(${HAVE_GIT_VERSION_INFO} EQUAL 0)
message(STATUS "Got version from Git: ${GIT_VERSION_INFO}")
add_definitions(-DIMGSUITE_VERSION="${GIT_VERSION_INFO}")
endif()

if(WIN32)
add_compile_options(
/openmp
/O2
)
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-omit-frame-pointer")
add_compile_options(
-Wall
Expand All @@ -98,20 +168,25 @@ if(NOT WIN32)
$<$<COMPILE_LANGUAGE:CXX>:-Woverloaded-virtual>
$<$<COMPILE_LANGUAGE:CXX>:-fno-operator-names>
)
endif(NOT WIN32)
endif()

set(PYTHONDIR kipl)
set(INCLUDEDIR ${CMAKE_INSTALL_INCLUDEDIR})

set(EXPORT_NAME ${PROJECT_NAME}-targets)

set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
SET(CMAKE_SKIP_BUILD_RPATH FALSE)
SET(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
set(CMAKE_BUILD_RPATH_USE_ORIGIN TRUE)

if(NOT APPLE)
set(CMAKE_INSTALL_RPATH $ORIGIN/../lib)
else()
set(CMAKE_INSTALL_RPATH @loader_path/../Frameworks)
endif()
# turn on testing
enable_testing()

## modules
add_subdirectory(frameworks/ngi/nGIFramework)
Expand All @@ -121,109 +196,3 @@ add_subdirectory(frameworks/ngi/nGIPreprocessing)
## applications
add_subdirectory(applications/nGItool)


if(DYNAMIC_LIB)
# install(
# EXPORT ${EXPORT_NAME}
# DESTINATION "lib/cmake/kipl"
# NAMESPACE kipl::
# )

# include(CMakePackageConfigHelpers)
# configure_package_config_file(
# ${CMAKE_CURRENT_SOURCE_DIR}/cmake/${PROJECT_NAME}-config.cmake.in
# "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config.cmake"
# INSTALL_DESTINATION lib/cmake/kipl
# )
# write_basic_package_version_file(
# "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake"
# VERSION "${CMAKE_PROJECT_VERSION}"
# COMPATIBILITY SameMinorVersion # switch to SameMajorVersion after 1.0
# # release
# )
# install(
# FILES "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config.cmake"
# "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake"
# DESTINATION lib/cmake/kipl
# )
if (LINUX)
print('Linux')
install(FILES
../lib/libkipl.so.1.0.0
../lib/libModuleConfig.so.1.0.0
../lib/libReconFramework.so.1.0.0
../lib/libStdBackProjectors.so.1.0.0
../lib/libFDKBackProjectors.so.1.0.0
../lib/libImagingAlgorithms.so.1.0.0
../lib/libReaderConfig.so.1.0.0
../lib/libNeXus.so.1.0.0
../lib/libhdf5_cpp.so.11
../lib/libNeXusCPP.so.1.0.0
../lib/libhdf5_hl.so.10
../lib/libhdf5.so.10
../lib/libsz.so.2

# /opt/local/lib/libxml2.2.dylib
# /opt/local/lib/libtiff.5.dylib
DESTINATION ${CMAKE_INSTALL_PREFIX}/lib)

execute_process(
COMMAND for f in `ls *.so.1.0.0`; do ln -s $f `basename $f .so.1.0.0`.so.1; done
WORKING_DIRECTORY "${CMAKE_INSTALL_PREFIX}/lib"
)
endif()
if (APPLE)
install(FILES
# ../lib/libkipl.1.0.0.dylib
# ../lib/libModuleConfig.1.0.0.dylib
# ../lib/libReconFramework.1.0.0.dylib
# ../lib/libStdBackProjectors.1.0.0.dylib
# ../lib/libFDKBackProjectors.1.0.0.dylib
# ../lib/libImagingAlgorithms.1.0.0.dylib
# ../lib/libReaderConfig.1.0.0.dylib
# ../imagingsuite/external/mac/lib/libNeXus.1.0.0.dylib
# ../imagingsuite/external/mac/lib//libhdf5_cpp.11.dylib
# ../imagingsuite/external/mac/lib//libNeXusCPP.1.0.0.dylib
# ../imagingsuite/external/mac/lib//libhdf5_hl.10.dylib
# ../imagingsuite/external/mac/lib//libhdf5.10.dylib
# ../imagingsuite/external/mac/lib//libsz.2.dylib
# /opt/local/lib/libxml2.2.dylib
# /opt/local/lib/libtiff.5.dylib
# /opt/local/lib/libfftw3.3.dylib
# /opt/local/lib/libfftw3f.3.dylib
# /opt/local/lib/libcfitsio.dylib
# /opt/local/lib/libarmadillo.10.dylib

DESTINATION ${CMAKE_INSTALL_PREFIX}/lib)

execute_process(
COMMAND for f in `ls *.1.0.0.*`; do ln -s $f `basename $f .1.0.0.dylib`.1.dylib; done
WORKING_DIRECTORY "${CMAKE_INSTALL_PREFIX}/lib"
)
endif()



endif(DYNAMIC_LIB)

# turn on testing
#enable_testing()

message(${CMAKE_CURRENT_SOURCE_DIR})
## define test
#add_test(
# NAME
# testBindAverageImage
# COMMAND
# ${CMAKE_COMMAND} -E env IMAGALG_MODULE_PATH=$<TARGET_FILE_DIR:imagalg>
# ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/UnitTests/python/testBindAverageImage.py
# ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/UnitTests/python/testBindAverageImage.py
#)
#
#add_test(
# NAME
# testBindPolynomialCorrection
# COMMAND
# ${CMAKE_COMMAND} -E env IMAGALG_MODULE_PATH=$<TARGET_FILE_DIR:imagalg>
# ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/UnitTests/python/testBindPolynomialCorrection.py
#)
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