Embed Eigen library

.github/workflows/analysis.yml

@@ -53,7 +53,7 @@ jobs:
             REPORT_PR_CHANGES_ONLY: false
         run: |
             analysis_file="analysis.txt"
-            cppcheck_params="--enable=warning --check-level=exhaustive --inline-suppr --suppress=internalError --suppress=internalAstError --suppress=*:*third-party/eigen/*"
+            cppcheck_params="--enable=warning --check-level=exhaustive --inline-suppr --suppress=internalError --suppress=internalAstError --suppress=*:*third-party/Eigen/*"
             cppcheck -j4 $cppcheck_params --project=$(pwd)/build/compile_commands.json --output-file=$analysis_file
             # Since cppcheck does not support OpenCL and CUDA, we need to check these files separately
             find $(pwd)/reg-lib/cl/. -name "*.cl" -print0 | while IFS= read -r -d '' file; do cppcheck "$file" $cppcheck_params --language=c++ 2>> $analysis_file; done

CMakeLists.txt

@@ -129,12 +129,11 @@ endif(NOT BUILD_ALL_DEP)
 include_directories(${CMAKE_SOURCE_DIR}/reg-io/png)
 include_directories(${PNG_INCLUDE_DIR})
 #-----------------------------------------------------------------------------
+include_directories(${CMAKE_BINARY_DIR})
+include_directories(${CMAKE_SOURCE_DIR}/reg-io)
 include_directories(${CMAKE_SOURCE_DIR}/reg-lib)
 include_directories(${CMAKE_SOURCE_DIR}/reg-lib/cpu)
-include_directories(${CMAKE_SOURCE_DIR}/reg-io)
 include_directories(${CMAKE_SOURCE_DIR}/third-party)
-include_directories(${CMAKE_BINARY_DIR})
-include_directories(${CMAKE_BINARY_DIR}/third-party/eigen)
 #-----------------------------------------------------------------------------
 if(USE_OPENCL)
   # Find the OpenCL package
@@ -203,7 +202,6 @@ if(BUILD_TESTING)
   add_definitions(-DBUILD_TESTS)
 endif(BUILD_TESTING)
 #-----------------------------------------------------------------------------
-add_subdirectory(third-party)
 add_subdirectory(reg-io)
 add_subdirectory(reg-lib)
 add_subdirectory(reg-apps)

niftyreg_build_version.txt

@@ -1 +1 @@
-419
+420

reg-lib/cpu/Maths.cpp

@@ -2,7 +2,7 @@
 
 #include "_reg_tools.h"
 #include "Eigen/Core"
-#include "unsupported/Eigen/MatrixFunctions"
+#include "Eigen/MatrixFunctions"
 
 /* *************************************************************** */
 namespace NiftyReg {

third-party/Eigen/Cholesky

@@ -0,0 +1,46 @@
+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+#ifndef EIGEN_CHOLESKY_MODULE_H
+#define EIGEN_CHOLESKY_MODULE_H
+
+#include "Core"
+#include "Jacobi"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+/** \defgroup Cholesky_Module Cholesky module
+  *
+  *
+  *
+  * This module provides two variants of the Cholesky decomposition for selfadjoint (hermitian) matrices.
+  * Those decompositions are also accessible via the following methods:
+  *  - MatrixBase::llt()
+  *  - MatrixBase::ldlt()
+  *  - SelfAdjointView::llt()
+  *  - SelfAdjointView::ldlt()
+  *
+  * \code
+  * #include <Eigen/Cholesky>
+  * \endcode
+  */
+
+#include "src/Cholesky/LLT.h"
+#include "src/Cholesky/LDLT.h"
+#ifdef EIGEN_USE_LAPACKE
+#ifdef EIGEN_USE_MKL
+#include "mkl_lapacke.h"
+#else
+#include "src/misc/lapacke.h"
+#endif
+#include "src/Cholesky/LLT_LAPACKE.h"
+#endif
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_CHOLESKY_MODULE_H
+/* vim: set filetype=cpp et sw=2 ts=2 ai: */