Merge pull request #2859 from MRtrix3/thirdparty

Improve handling of external dependencies

.github/workflows/checks.yml

@@ -25,7 +25,7 @@ jobs:
     - name: install dependencies
       run: |
          sudo apt-get update
-         sudo apt-get install clang qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build python3-distutils python3-numpy
+         sudo apt-get install clang qt6-base-dev libglvnd-dev zlib1g-dev libfftw3-dev ninja-build python3-distutils python3-numpy
 
     - name: Run sccache-cache
       uses: mozilla-actions/[email protected]
@@ -86,7 +86,7 @@ jobs:
     - name: install dependencies
       run: |
          sudo apt-get update
-         sudo apt-get install g++-9 qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build python3-numpy
+         sudo apt-get install g++-9 qt6-base-dev libglvnd-dev zlib1g-dev libfftw3-dev ninja-build python3-numpy
 
     - name: Run sccache-cache
       uses: mozilla-actions/[email protected]
@@ -208,7 +208,6 @@ jobs:
             ${{env.MINGW_PACKAGE_PREFIX}}-bc
             ${{env.MINGW_PACKAGE_PREFIX}}-cmake
             ${{env.MINGW_PACKAGE_PREFIX}}-diffutils
-            ${{env.MINGW_PACKAGE_PREFIX}}-eigen3
             ${{env.MINGW_PACKAGE_PREFIX}}-fftw
             ${{env.MINGW_PACKAGE_PREFIX}}-gcc
             ${{env.MINGW_PACKAGE_PREFIX}}-ninja
@@ -282,5 +281,4 @@ jobs:
         extensions: 'h,cpp'
         clangFormatVersion: 16
         # Ignore third party headers
-        exclude: './core/file/json.h ./core/file/nifti1.h ./core/file/nifti2.h'
-
+        exclude: './thirdparty ./_deps'

.github/workflows/clang-tidy.yml

@@ -17,7 +17,7 @@ jobs:
     - uses: ZedThree/[email protected]
       id: review
       with:
-        apt_packages: g++,qt6-base-dev,libqt6opengl6-dev,libglvnd-dev,libeigen3-dev,zlib1g-dev,libfftw3-dev,ninja-build
+        apt_packages: g++,qt6-base-dev,libqt6opengl6-dev,libglvnd-dev,zlib1g-dev,libfftw3-dev,ninja-build
         config_file: .clang-tidy
 
     - uses: ZedThree/clang-tidy-review/[email protected]

CMakeLists.txt

@@ -25,6 +25,13 @@ option(MRTRIX_USE_PCH "Use precompiled headers" ON)
 option(MRTRIX_PYTHON_SOFTLINK "Build directory softlink to Python source code rather than copying" ON)
 option(MRTRIX_BUILD_NON_CORE_STATIC "Build MRtrix's non-core code as a static library" OFF)
 
+set(MRTRIX_DEPENDENCIES_DIR "" CACHE PATH
+    "An optional local directory containing thirdparty dependencies:\n \
+    - Eigen3 https://gitlab.com/libeigen/eigen\n \
+    - Json for Modern C++ https://github.com/nlohmann/json\n \
+    - Half https://half.sourceforge.net/\n"
+)
+
 if(MRTRIX_BUILD_TESTS)
     if(CMAKE_VERSION VERSION_GREATER 3.17)
         list(APPEND CMAKE_CTEST_ARGUMENTS "--output-on-failure")
@@ -68,6 +75,7 @@ include(LinkerSetup)
 include(FindFFTW)
 include(CompilerCache)
 include(ECMEnableSanitizers)
+include(Dependencies)
 if(CMAKE_SYSTEM_NAME MATCHES "Darwin")
     include(MacOSBundle)
 endif()

cmake/Dependencies.cmake

@@ -0,0 +1,67 @@
+include(FetchContent)
+
+if(NOT ${MRTRIX_DEPENDENCIES_DIR} STREQUAL "")
+    message(STATUS "Using local dependencies at ${MRTRIX_DEPENDENCIES_DIR}")
+    set(MRTRIX_LOCAL_DEPENDENCIES ON)
+else()
+    set(MRTRIX_LOCAL_DEPENDENCIES OFF)
+endif()
+
+# Eigen
+# We avoid configuring the Eigen library via FetchContent_MakeAvaiable
+# to avoid the verbosity of Eigen's CMake configuration output.
+if(MRTRIX_LOCAL_DEPENDENCIES)
+    set(eigen_url ${MRTRIX_DEPENDENCIES_DIR}/eigen-3.4.0.tar.gz)
+else()
+    set(eigen_url "https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz")
+endif()
+
+FetchContent_Declare(
+    eigen3
+    DOWNLOAD_EXTRACT_TIMESTAMP ON
+    URL ${eigen_url}
+)
+FetchContent_GetProperties(Eigen3)
+if(NOT eigen3_POPULATED)
+    FetchContent_Populate(Eigen3)
+    add_library(Eigen3 INTERFACE)
+    add_library(Eigen3::Eigen ALIAS Eigen3)
+    target_include_directories(Eigen3 INTERFACE "${eigen3_SOURCE_DIR}")
+endif()
+
+# Json for Modern C++
+if(MRTRIX_LOCAL_DEPENDENCIES)
+    set(json_url ${MRTRIX_DEPENDENCIES_DIR}/json.tar.xz)
+else()
+    set(json_url "https://github.com/nlohmann/json/releases/download/v3.11.3/json.tar.xz")
+endif()
+FetchContent_Declare(
+    json
+    DOWNLOAD_EXTRACT_TIMESTAMP ON
+    URL ${json_url}
+)
+FetchContent_MakeAvailable(json)
+
+
+# Half-precision floating-point library
+if(MRTRIX_LOCAL_DEPENDENCIES)
+    set(half_url ${MRTRIX_DEPENDENCIES_DIR}/half-2.1.0.zip)
+else()
+    set(half_url "https://sourceforge.net/projects/half/files/half/2.1.0/half-2.1.0.zip/download")
+endif()
+FetchContent_Declare(
+    half
+    DOWNLOAD_EXTRACT_TIMESTAMP ON
+    URL ${half_url}
+)
+FetchContent_MakeAvailable(half)
+
+add_library(half INTERFACE)
+add_library(half::half ALIAS half)
+target_include_directories(half INTERFACE "${half_SOURCE_DIR}/include")
+
+
+# Nifti headers
+add_library(nifti INTERFACE)
+add_library(nifti::nifti ALIAS nifti)
+target_include_directories(nifti INTERFACE "${PROJECT_SOURCE_DIR}/thirdparty/nifti")

cmd/CMakeLists.txt

@@ -9,8 +9,7 @@ if(MRTRIX_USE_PCH)
     file(GENERATE OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/pch_cmd.cpp CONTENT "int main(){}")
     add_executable(pch_cmd ${CMAKE_CURRENT_BINARY_DIR}/pch_cmd.cpp)
     target_include_directories(pch_cmd PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/../core)
-    find_package(Eigen3 REQUIRED)
-    target_link_libraries(pch_cmd PRIVATE Eigen3::Eigen mrtrix::common)
+    target_link_libraries(pch_cmd PRIVATE Eigen3::Eigen half::half mrtrix::common)
     target_precompile_headers(pch_cmd PRIVATE
         [["app.h"]]
         [["image.h"]]

cmd/mrinfo.cpp

@@ -19,13 +19,14 @@
 
 #include "command.h"
 #include "dwi/gradient.h"
-#include "file/json.h"
 #include "file/json_utils.h"
 #include "header.h"
 #include "image_io/pipe.h"
 #include "phase_encoding.h"
 #include "types.h"
 
+#include <nlohmann/json.hpp>
+
 using namespace MR;
 using namespace App;
 

core/CMakeLists.txt

@@ -2,16 +2,12 @@ include(CheckSymbolExists)
 
 file(GLOB_RECURSE CORE_SRCS *.cpp *.h)
 
-find_package(Eigen3 REQUIRED NO_MODULE)
 find_package(ZLIB REQUIRED)
 find_package(FFTW REQUIRED)
 find_package(Git QUIET)
 find_package(Threads REQUIRED)
 find_package(PNG QUIET)
 
-# The find modules for Eigen3, and PNG don't log the location
-# of the libraries, so we do it manually here
-message(STATUS "Found Eigen3: ${EIGEN3_INCLUDE_DIR}")
 if(PNG_FOUND)
     message(STATUS "Found PNG: ${PNG_LIBRARIES}")
 endif()
@@ -90,6 +86,9 @@ target_link_libraries(mrtrix-core PUBLIC
     mrtrix::common
     Threads::Threads
     ${FFTW_LIBRARIES}
+    nlohmann_json::nlohmann_json
+    nifti::nifti
+    half::half
 )
 
 target_include_directories(mrtrix-core PUBLIC