ENH: Pin vendored Eigen3 fork to tagged release 5.0.1 (closes #6239, supersedes #6247)

Modules/ThirdParty/Eigen3/UpdateFromUpstream.sh

@@ -13,7 +13,7 @@ readonly ownership="Eigen Upstream <kwrobot@kitware.com>"
 exact_tree_match=false
 readonly subtree="Modules/ThirdParty/Eigen3/src/itkeigen"
 readonly repo="https://github.com/InsightSoftwareConsortium/eigen"
-readonly tag="for/itk-20260501-879885e1"
+readonly tag="for/itk-eigen-5.0.1"
 readonly paths="
 Eigen/AccelerateSupport
 Eigen/Cholesky

Modules/ThirdParty/Eigen3/src/itkeigen/CMakeLists.txt

@@ -1,3 +1,6 @@
+# SPDX-FileCopyrightText: The Eigen Authors
+# SPDX-License-Identifier: MPL-2.0
+
 # Same version of ITK cmake_minimum_required
 cmake_minimum_required(VERSION 3.16.3)
 
@@ -965,6 +968,10 @@ target_include_directories (eigen_internal SYSTEM INTERFACE
 
 # Export as title case Eigen
 set_target_properties (eigen_internal PROPERTIES EXPORT_NAME Eigen)
+# Issue InsightSoftwareConsortium/ITK#6239: ship eigen_internal in ITKTargets.cmake when building inside ITK.
+if(DEFINED ITK3P_INSTALL_EXPORT_NAME)
+  install (TARGETS eigen_internal EXPORT ${ITK3P_INSTALL_EXPORT_NAME})
+endif()
 install (TARGETS eigen_internal EXPORT ITKInternalEigen3Targets)
 
 set(EIGEN3_TARGETS_FILE ITKInternalEigen3Targets.cmake)

Modules/ThirdParty/Eigen3/src/itkeigen/COPYING.MPL2

@@ -35,7 +35,7 @@ Mozilla Public License Version 2.0
     means any form of the work other than Source Code Form.
 
 1.7. "Larger Work"
-    means a work that combines Covered Software with other material, in
+    means a work that combines Covered Software with other material, in 
     a separate file or files, that is not Covered Software.
 
 1.8. "License"

Modules/ThirdParty/Eigen3/src/itkeigen/COPYING.README

@@ -1,14 +1,6 @@
-Eigen is primarily licensed under the Mozilla Public License 2.0.
-See LICENSE, COPYING.MPL2, and these links:
-  https://www.mozilla.org/MPL/2.0/
-  https://www.mozilla.org/MPL/2.0/FAQ.html
+Eigen is primarily MPL2 licensed. See COPYING.MPL2 and these links:
+  http://www.mozilla.org/MPL/2.0/
+  http://www.mozilla.org/MPL/2.0/FAQ.html
 
-Some files contain third-party code under permissive or otherwise
-MPL2-compatible licenses, hence the other COPYING.* files here. These
-include Apache-2.0, BSD-style notices, the MINPACK license, and the MORSE
-CMake module BSD-style notice in cmake/MORSE-Copyright.txt.
-
-Note that some optional external dependencies (e.g. FFTW, MPFR C++)
-are distributed under different licenses, including the GPL. Refer to
-the individual source files and their respective COPYING files for
-details.
+Some files contain third-party code under BSD or other MPL2-compatible licenses,
+whence the other COPYING.* files here.

Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/Cholesky

@@ -14,6 +14,8 @@
 #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:

Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/CholmodSupport

@@ -26,7 +26,7 @@
  * For the sake of completeness, this module also propose the two following classes:
  * - class CholmodSimplicialLLT
  * - class CholmodSimplicialLDLT
- * Note that these classes do not bring any particular advantage compared to the built-in
+ * Note that these classes does not bring any particular advantage compared to the built-in
  * SimplicialLLT and SimplicialLDLT factorization classes.
  *
  * \code

Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/Core

@@ -36,6 +36,12 @@
 #include <new>
 #endif
 
+// Disable the ipa-cp-clone optimization flag with MinGW 6.x or older (enabled by default with -O3)
+// See http://eigen.tuxfamily.org/bz/show_bug.cgi?id=556 for details.
+#if EIGEN_COMP_MINGW && EIGEN_GNUC_STRICT_LESS_THAN(6, 0, 0)
+#pragma GCC optimize("-fno-ipa-cp-clone")
+#endif
+
 // Prevent ICC from specializing std::complex operators that silently fail
 // on device. This allows us to use our own device-compatible specializations
 // instead.
@@ -47,12 +53,10 @@
 // this include file manages BLAS and MKL related macros
 // and inclusion of their respective header files
 #include "src/Core/util/MKL_support.h"
-#include "src/Core/util/AOCL_Support.h"
-
 
-// EIGEN_HAS_GPU_FP16 is now always true when compiling with CUDA or HIP.
-// Use EIGEN_GPUCC (compile-time) or EIGEN_GPU_COMPILE_PHASE (device phase) instead.
-// TODO: Remove EIGEN_HAS_GPU_BF16 similarly once HIP bf16 guards are cleaned up.
+#if defined(EIGEN_HAS_CUDA_FP16) || defined(EIGEN_HAS_HIP_FP16)
+#define EIGEN_HAS_GPU_FP16
+#endif
 
 #if defined(EIGEN_HAS_CUDA_BF16) || defined(EIGEN_HAS_HIP_BF16)
 #define EIGEN_HAS_GPU_BF16
@@ -67,7 +71,8 @@
 #include <omp.h>
 #endif
 
-#if !EIGEN_COMP_ARM
+// MSVC for windows mobile does not have the errno.h file
+#if !(EIGEN_COMP_MSVC && EIGEN_OS_WINCE) && !EIGEN_COMP_ARM
 #define EIGEN_HAS_ERRNO
 #endif
 
@@ -96,9 +101,6 @@
 // for std::is_nothrow_move_assignable
 #include <type_traits>
 
-// for std::move, std::forward, std::declval
-#include <utility>
-
 // for std::this_thread::yield().
 #if !defined(EIGEN_USE_BLAS) && (defined(EIGEN_HAS_OPENMP) || defined(EIGEN_GEMM_THREADPOOL))
 #include <thread>
@@ -121,18 +123,10 @@
 
 // required for __cpuid, needs to be included after cmath
 // also required for _BitScanReverse on Windows on ARM
-#if EIGEN_COMP_MSVC && (EIGEN_ARCH_i386_OR_x86_64 || EIGEN_ARCH_ARM64)
+#if EIGEN_COMP_MSVC && (EIGEN_ARCH_i386_OR_x86_64 || EIGEN_ARCH_ARM64) && !EIGEN_OS_WINCE
 #include <intrin.h>
 #endif
 
-// Required for querying cache sizes on Linux and macOS.
-#if EIGEN_OS_LINUX
-#include <unistd.h>
-#elif EIGEN_OS_MAC
-#include <sys/types.h>
-#include <sys/sysctl.h>
-#endif
-
 #if defined(EIGEN_USE_SYCL)
 #undef min
 #undef max
@@ -142,6 +136,7 @@
 #include <CL/sycl.hpp>
 #include <map>
 #include <thread>
+#include <utility>
 #ifndef EIGEN_SYCL_LOCAL_THREAD_DIM0
 #define EIGEN_SYCL_LOCAL_THREAD_DIM0 16
 #endif
@@ -150,9 +145,19 @@
 #endif
 #endif
 
+#if defined EIGEN2_SUPPORT_STAGE40_FULL_EIGEN3_STRICTNESS || defined EIGEN2_SUPPORT_STAGE30_FULL_EIGEN3_API || \
+    defined EIGEN2_SUPPORT_STAGE20_RESOLVE_API_CONFLICTS || defined EIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API ||  \
+    defined EIGEN2_SUPPORT
+// This will generate an error message:
+#error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information
+#endif
+
 namespace Eigen {
 
+// we use size_t frequently and we'll never remember to prepend it with std:: every time just to
+// ensure QNX/QCC support
 using std::size_t;
+// gcc 4.6.0 wants std:: for ptrdiff_t
 using std::ptrdiff_t;
 
 }  // namespace Eigen
@@ -170,8 +175,6 @@ using std::ptrdiff_t;
 #ifdef EIGEN_USE_LAPACKE
 #ifdef EIGEN_USE_MKL
 #include "mkl_lapacke.h"
-#elif defined(EIGEN_LAPACKE_SYSTEM)
-#include <lapacke.h>
 #else
 #include "src/misc/lapacke.h"
 #endif
@@ -202,13 +205,6 @@ using std::ptrdiff_t;
 #include "src/Core/arch/Default/BFloat16.h"
 #include "src/Core/arch/Default/GenericPacketMathFunctionsFwd.h"
 
-#if defined(EIGEN_VECTORIZE_GENERIC) && !defined(EIGEN_DONT_VECTORIZE)
-#include "src/Core/arch/clang/PacketMath.h"
-#include "src/Core/arch/clang/TypeCasting.h"
-#include "src/Core/arch/clang/Complex.h"
-#include "src/Core/arch/clang/Reductions.h"
-#include "src/Core/arch/clang/MathFunctions.h"
-#else
 #if defined EIGEN_VECTORIZE_AVX512
 #include "src/Core/arch/SSE/PacketMath.h"
 #include "src/Core/arch/SSE/Reductions.h"
@@ -274,18 +270,6 @@ using std::ptrdiff_t;
 #include "src/Core/arch/SVE/PacketMath.h"
 #include "src/Core/arch/SVE/TypeCasting.h"
 #include "src/Core/arch/SVE/MathFunctions.h"
-#elif defined EIGEN_VECTORIZE_RVV10
-#include "src/Core/arch/RVV10/PacketMath.h"
-#include "src/Core/arch/RVV10/PacketMath4.h"
-#include "src/Core/arch/RVV10/PacketMath2.h"
-#include "src/Core/arch/RVV10/TypeCasting.h"
-#include "src/Core/arch/RVV10/MathFunctions.h"
-#if defined EIGEN_VECTORIZE_RVV10FP16
-#include "src/Core/arch/RVV10/PacketMathFP16.h"
-#endif
-#if defined EIGEN_VECTORIZE_RVV10BF16
-#include "src/Core/arch/RVV10/PacketMathBF16.h"
-#endif
 #elif defined EIGEN_VECTORIZE_ZVECTOR
 #include "src/Core/arch/ZVector/PacketMath.h"
 #include "src/Core/arch/ZVector/MathFunctions.h"
@@ -313,8 +297,6 @@ using std::ptrdiff_t;
 #endif
 #endif
 
-#endif  // #ifndef EIGEN_VECTORIZE_GENERIC
-
 #include "src/Core/arch/Default/Settings.h"
 // This file provides generic implementations valid for scalar as well
 #include "src/Core/arch/Default/GenericPacketMathFunctions.h"
@@ -358,12 +340,13 @@ using std::ptrdiff_t;
 #include "src/Core/DenseStorage.h"
 #include "src/Core/NestByValue.h"
 
+// #include "src/Core/ForceAlignedAccess.h"
+
 #include "src/Core/ReturnByValue.h"
 #include "src/Core/NoAlias.h"
 #include "src/Core/PlainObjectBase.h"
 #include "src/Core/Matrix.h"
 #include "src/Core/Array.h"
-#include "src/Core/StructuredBindings.h"
 #include "src/Core/Fill.h"
 #include "src/Core/CwiseTernaryOp.h"
 #include "src/Core/CwiseBinaryOp.h"
@@ -424,28 +407,23 @@ using std::ptrdiff_t;
 #include "src/Core/CoreIterators.h"
 #include "src/Core/ConditionEstimator.h"
 
-#if !defined(EIGEN_VECTORIZE_GENERIC)
 #if defined(EIGEN_VECTORIZE_VSX)
 #include "src/Core/arch/AltiVec/MatrixProduct.h"
 #elif defined EIGEN_VECTORIZE_NEON
 #include "src/Core/arch/NEON/GeneralBlockPanelKernel.h"
 #elif defined EIGEN_VECTORIZE_LSX
 #include "src/Core/arch/LSX/GeneralBlockPanelKernel.h"
-#elif defined EIGEN_VECTORIZE_RVV10
-#include "src/Core/arch/RVV10/GeneralBlockPanelKernel.h"
 #endif
 
 #if defined(EIGEN_VECTORIZE_AVX512)
 #include "src/Core/arch/AVX512/GemmKernel.h"
 #endif
-#endif
 
 #include "src/Core/Select.h"
 #include "src/Core/VectorwiseOp.h"
 #include "src/Core/PartialReduxEvaluator.h"
 #include "src/Core/Random.h"
 #include "src/Core/Replicate.h"
-#include "src/Core/ConcatOp.h"
 #include "src/Core/Reverse.h"
 #include "src/Core/ArrayWrapper.h"
 #include "src/Core/StlIterators.h"
@@ -465,10 +443,6 @@ using std::ptrdiff_t;
 #include "src/Core/Assign_MKL.h"
 #endif
 
-#ifdef EIGEN_USE_AOCL_VML
-#include "src/Core/Assign_AOCL.h"
-#endif
-
 #include "src/Core/GlobalFunctions.h"
 // IWYU pragma: end_exports
 

Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/Dense

@@ -1,19 +1,7 @@
-// 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_DENSE_MODULE_H
-#define EIGEN_DENSE_MODULE_H
-
 #include "Core"
 #include "LU"
 #include "Cholesky"
 #include "QR"
 #include "SVD"
 #include "Geometry"
 #include "Eigenvalues"
-
-#endif  // EIGEN_DENSE_MODULE_H

Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/Eigen

@@ -1,14 +1,2 @@
-// 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_EIGEN_MODULE_H
-#define EIGEN_EIGEN_MODULE_H
-
 #include "Dense"
 #include "Sparse"
-
-#endif  // EIGEN_EIGEN_MODULE_H

Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/Eigenvalues

@@ -11,13 +11,16 @@
 #include "Core"
 
 #include "Cholesky"
+#include "Jacobi"
+#include "Householder"
 #include "LU"
 #include "Geometry"
-#include "Sparse"  // Needed by ComplexQZ.
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
 /** \defgroup Eigenvalues_Module Eigenvalues module
+ *
+ *
  *
  * This module mainly provides various eigenvalue solvers.
  * This module also provides some MatrixBase methods, including:
@@ -29,6 +32,8 @@
  * \endcode
  */
 
+#include "src/misc/RealSvd2x2.h"
+
 // IWYU pragma: begin_exports
 #include "src/Eigenvalues/Tridiagonalization.h"
 #include "src/Eigenvalues/RealSchur.h"
@@ -39,14 +44,11 @@
 #include "src/Eigenvalues/ComplexSchur.h"
 #include "src/Eigenvalues/ComplexEigenSolver.h"
 #include "src/Eigenvalues/RealQZ.h"
-#include "src/Eigenvalues/ComplexQZ.h"
 #include "src/Eigenvalues/GeneralizedEigenSolver.h"
 #include "src/Eigenvalues/MatrixBaseEigenvalues.h"
 #ifdef EIGEN_USE_LAPACKE
 #ifdef EIGEN_USE_MKL
 #include "mkl_lapacke.h"
-#elif defined(EIGEN_LAPACKE_SYSTEM)
-#include <lapacke.h>
 #else
 #include "src/misc/lapacke.h"
 #endif

Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/Geometry

@@ -12,6 +12,7 @@
 
 #include "SVD"
 #include "LU"
+#include <limits>
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
@@ -47,13 +48,10 @@
 #include "src/Geometry/AlignedBox.h"
 #include "src/Geometry/Umeyama.h"
 
-#ifndef EIGEN_VECTORIZE_GENERIC
-// TODO(rmlarsen): Make these work with generic vectorization if possible.
 // Use the SSE optimized version whenever possible.
 #if (defined EIGEN_VECTORIZE_SSE) || (defined EIGEN_VECTORIZE_NEON)
 #include "src/Geometry/arch/Geometry_SIMD.h"
 #endif
-#endif
 // IWYU pragma: end_exports
 
 #include "src/Core/util/ReenableStupidWarnings.h"

Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/Householder

@@ -22,8 +22,8 @@
 
 // IWYU pragma: begin_exports
 #include "src/Householder/Householder.h"
-#include "src/Householder/BlockHouseholder.h"
 #include "src/Householder/HouseholderSequence.h"
+#include "src/Householder/BlockHouseholder.h"
 // IWYU pragma: end_exports
 
 #include "src/Core/util/ReenableStupidWarnings.h"

Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/KLUSupport

@@ -29,7 +29,7 @@ extern "C" {
  * \endcode
  *
  * In order to use this module, the klu and btf headers must be accessible from the include paths, and your binary must
- * be linked to the klu library and its dependencies. The dependencies depend on how KLU has been compiled. For a
+ * be linked to the klu library and its dependencies. The dependencies depend on how umfpack has been compiled. For a
  * cmake based project, you can use our FindKLU.cmake module to help you in this task.
  *
  */