Jungfraujoch/image_analysis/CMakeLists.txt

# Eigen has to be resolved BEFORE Ceres is added below. Whichever find_package(Eigen3) runs first
# creates the Eigen3::Eigen imported target, and every later one leaves an existing target alone --
# so the first one wins for the whole build, Ceres included. See the guard after Ceres for why that
# matters here.
FIND_PACKAGE(Eigen3 3.4 REQUIRED NO_MODULE)  # provides Eigen3::Eigen

SET(PROVIDE_UNINSTALL_TARGET OFF)
# Force Ceres to build WITHOUT its own CUDA support: Jungfraujoch never uses Ceres' GPU solvers, so
# this just drops unused code and build time (Ceres would otherwise enable CUDA whenever a toolkit is
# found). See the Eigen note in the top-level CMakeLists for the related Windows/cmake history.
SET(USE_CUDA OFF CACHE BOOL "Force Ceres to build without CUDA (Jungfraujoch does not use Ceres' GPU solvers)" FORCE)

# Ceres' sparse and LAPACK back-ends are dead weight here: every Ceres solve in this project picks a
# DENSE solver explicitly (DENSE_QR / DENSE_NORMAL_CHOLESKY / DENSE_SCHUR) and none sets
# dense_linear_algebra_library_type, which defaults to EIGEN -- so no sparse factorization and no
# LAPACK call is ever reachable. Left at their defaults they cost rugnux six shared libraries
# (libopenblas, libmetis, and libgfortran/libquadmath/libgomp/libz behind them), and SuiteSparse
# turns itself on or off depending on what happens to sit on the build host, so two machines build
# different Ceres from the same source. Pinning all three off leaves the results bit-identical.
# EIGENSPARSE stays ON: it keeps a sparse implementation available without an external library.
SET(SUITESPARSE OFF CACHE BOOL "Ceres: no sparse solver is ever selected" FORCE)
SET(LAPACK      OFF CACHE BOOL "Ceres: dense solves go through Eigen, not LAPACK" FORCE)
SET(EIGENMETIS  OFF CACHE BOOL "Ceres: METIS ordering only applies to sparse factorization" FORCE)

# Prevent MKL from being found (guarantees no MKL)
SET(CMAKE_DISABLE_FIND_PACKAGE_MKL TRUE)
SET(CERES_THREADING_MODEL "CXX_THREADS")

# Ceres is the only dependency that needs more than a plain tarball: it carries abseil as a git
# SUBMODULE, so a source archive leaves third_party/abseil-cpp empty. Ceres tests exactly that
# directory and, finding it empty, demands find_package(absl REQUIRED 20240116) instead -- which no
# build image can satisfy (Ubuntu 24.04 still ships 20230802). So populate the two archives
# separately and hand Ceres the tree a submodule checkout would have produced: abseil unpacked into
# third_party/abseil-cpp, and only then the subdirectory added.
#
# Populate-then-add rather than FetchContent_MakeAvailable(ceres), because MakeAvailable populates
# and add_subdirectory()s in one step, leaving no window to fill the submodule -- and the URL
# population clears its source directory, so abseil cannot be put there beforehand.
#
# FetchContent_Populate(<name>) is deprecated from CMake 3.30 (CMP0169) in favour of the
# MakeAvailable that cannot be used here, so ask for the old behaviour rather than let every build
# on a newer CMake print the deprecation.
IF (POLICY CMP0169)
    CMAKE_POLICY(PUSH)
    CMAKE_POLICY(SET CMP0169 OLD)
ENDIF()

FetchContent_Declare(
        ceres
        URL https://github.com/ceres-solver/ceres-solver/archive/0c70ed3a1a2d6ba47c06c7e8b3b040880bc474db.tar.gz
        URL_HASH SHA256=bf0bcc78fae884e59dd893693e52510da7cc6866a7444fdae9ba8f19eae266cd
)
FetchContent_Populate(ceres)

# The exact commit Ceres' submodule points at (abseil lts_2025_01_27), so the tree matches what a
# recursive clone of the pinned Ceres would have checked out.
FetchContent_Declare(
        abseil
        URL https://github.com/abseil/abseil-cpp/archive/9ac7062b1860d895fb5a8cbf58c3e9ef8f674b5f.tar.gz
        URL_HASH SHA256=fd5062972ac6c5575bc8fb6fb1cd6e7c563730be96be4c17b8dcca74a9c5892d
        SOURCE_DIR "${ceres_SOURCE_DIR}/third_party/abseil-cpp"
)
FetchContent_Populate(abseil)

IF (POLICY CMP0169)
    CMAKE_POLICY(POP)
ENDIF()

ADD_SUBDIRECTORY("${ceres_SOURCE_DIR}" "${ceres_BINARY_DIR}" EXCLUDE_FROM_ALL)

# Ceres asks for Eigen with a version RANGE -- find_package(Eigen3 3.3.4...5 NO_MODULE) -- and
# Eigen's own Eigen3ConfigVersion.cmake rejects any range whose two endpoints differ in major
# version. A 3.4 Eigen therefore reports itself INCOMPATIBLE with Ceres' query and the search falls
# through to whatever older Eigen comes next on the prefix path (a distro eigen3-devel, say). Having
# resolved Eigen above, Ceres inherits our Eigen3::Eigen instead, because a generated targets file
# returns early when its targets already exist. (The config package the top-level CMakeLists writes
# for the bundled Eigen answers the range as well, so with it Ceres' own query simply succeeds --
# but an externally provided Eigen still behaves as described.) If that ever stops holding, Ceres compiles against
# one Eigen and the rest of the project against another; the two versions' identically mangled
# template instantiations are then merged at link time -- an ODR violation whose symptom is a crash
# inside Eigen. Refuse to build it.
GET_PROPERTY(CERES_IMPORTED_TARGETS DIRECTORY ${ceres_SOURCE_DIR} PROPERTY IMPORTED_TARGETS)
IF ("Eigen3::Eigen" IN_LIST CERES_IMPORTED_TARGETS)
    MESSAGE(FATAL_ERROR "Ceres created an Eigen3::Eigen of its own instead of using the Eigen this "
            "project resolved. Two Eigen versions in one binary is undefined behaviour. Leave a "
            "single Eigen on the find_package path, or point CMAKE_PREFIX_PATH / Eigen3_DIR at the "
            "one to use.")
ENDIF()

ADD_LIBRARY(JFJochImageAnalysis STATIC
        MXAnalysisWithoutFPGA.cpp
        MXAnalysisWithoutFPGA.h
        MXAnalysisAfterFPGA.h
        MXAnalysisAfterFPGA.cpp
        IndexAndRefine.cpp
        IndexAndRefine.h
        dark_mask_analysis/DarkMaskAnalysis.cpp
        dark_mask_analysis/DarkMaskAnalysis.h
        beam_stop/ShadowFinder.cpp
        beam_stop/ShadowFinder.h
        $<$<BOOL:${JFJOCH_CUDA_AVAILABLE}>:beam_stop/ShadowAccumulatorGPU.cu>
        $<$<BOOL:${JFJOCH_CUDA_AVAILABLE}>:beam_stop/ShadowMaskGPU.cu>
        beam_stop/ShadowAccumulatorGPU.h
        beam_stop/ShadowFinderInternal.h
        beam_stop/ShadowMaskGPU.h
        hot_pixels/HotPixels.cpp
        hot_pixels/HotPixels.h
        hot_pixels/HotPixelsGPU.h
        $<$<BOOL:${JFJOCH_CUDA_AVAILABLE}>:hot_pixels/HotPixelsGPU.cu>
        rotation_indexer/RotationIndexer.cpp
        rotation_indexer/RotationIndexer.h
        WriteReflections.cpp
        WriteReflections.h
        LoadFCalcFromMtz.cpp
        LoadFCalcFromMtz.h
        UpdateReflectionResolution.cpp
        UpdateReflectionResolution.h
        IntegrationOutcome.h
        rotation_indexer/RotationIndexerCounter.cpp
        rotation_indexer/RotationIndexerCounter.h)

ADD_SUBDIRECTORY(spot_finding)
ADD_SUBDIRECTORY(bragg_integration)
ADD_SUBDIRECTORY(bragg_prediction)
ADD_SUBDIRECTORY(indexing)
ADD_SUBDIRECTORY(geom_refinement)
ADD_SUBDIRECTORY(lattice_search)
ADD_SUBDIRECTORY(scale_merge)
ADD_SUBDIRECTORY(image_preprocessing)
ADD_SUBDIRECTORY(azint)
ADD_SUBDIRECTORY(roi)
ADD_SUBDIRECTORY(structure_refinement)

TARGET_LINK_LIBRARIES(JFJochImageAnalysis JFJochAzIntEngine JFJochROIIntegration JFJochImagePreprocessing JFJochBraggPrediction JFJochBraggIntegration JFJochLatticeSearch JFJochIndexing JFJochSpotFinding JFJochCommon JFJochGeomRefinement JFJochScaleMerge JFJochStructureRefinement JFJochRugnuxFiles gemmi)