Merge branch 'upstream-Eigen3' into update_eigen_to_master

# By Eigen Upstream * upstream-Eigen3: Eigen3 2023-10-24 (a4f9510a)
InsightSoftwareConsortium · Oct 24, 2023 · f1c48dc · f1c48dc
2 parents 4114b27 + c00ac7c
commit f1c48dc
Show file tree

Hide file tree

Showing 391 changed files with 36,198 additions and 14,951 deletions.
diff --git a/Modules/ThirdParty/Eigen3/src/itkeigen/CMakeLists.txt b/Modules/ThirdParty/Eigen3/src/itkeigen/CMakeLists.txt
diff --git a/Modules/ThirdParty/Eigen3/src/itkeigen/COPYING.MPL2 b/Modules/ThirdParty/Eigen3/src/itkeigen/COPYING.MPL2
@@ -357,7 +357,7 @@ Exhibit A - Source Code Form License Notice
 
   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/.
+  file, You can obtain one at https://mozilla.org/MPL/2.0/.
 
 If it is not possible or desirable to put the notice in a particular
 file, then You may include the notice in a location (such as a LICENSE

diff --git a/Modules/ThirdParty/Eigen3/src/itkeigen/COPYING.README b/Modules/ThirdParty/Eigen3/src/itkeigen/COPYING.README
@@ -2,17 +2,5 @@ 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 BSD or LGPL licenses, whence the other
-COPYING.* files here.
-
-All the LGPL code is either LGPL 2.1-only, or LGPL 2.1-or-later.
-For this reason, the COPYING.LGPL file contains the LGPL 2.1 text.
-
-If you want to guarantee that the Eigen code that you are #including is licensed
-under the MPL2 and possibly more permissive licenses (like BSD), #define this
-preprocessor symbol:
-  EIGEN_MPL2_ONLY
-For example, with most compilers, you could add this to your project CXXFLAGS:
-  -DEIGEN_MPL2_ONLY
-This will cause a compilation error to be generated if you #include any code that is
-LGPL licensed.
+Some files contain third-party code under BSD or other MPL2-compatible licenses,
+whence the other COPYING.* files here.
diff --git a/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/Cholesky b/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/Cholesky
@@ -29,16 +29,14 @@
   * \endcode
   */
 
+// IWYU pragma: begin_exports
 #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/misc/lapacke_helpers.h"
 #include "src/Cholesky/LLT_LAPACKE.h"
 #endif
+// IWYU pragma: end_exports
 
 #include "src/Core/util/ReenableStupidWarnings.h"
 

diff --git a/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/CholmodSupport b/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/CholmodSupport
@@ -22,7 +22,7 @@ extern "C" {
   * This module provides an interface to the Cholmod library which is part of the <a href="http://www.suitesparse.com">suitesparse</a> package.
   * It provides the two following main factorization classes:
   * - class CholmodSupernodalLLT: a supernodal LLT Cholesky factorization.
-  * - class CholmodDecomposiiton: a general L(D)LT Cholesky factorization with automatic or explicit runtime selection of the underlying factorization method (supernodal or simplicial).
+  * - class CholmodDecomposition: a general L(D)LT Cholesky factorization with automatic or explicit runtime selection of the underlying factorization method (supernodal or simplicial).
   *
   * For the sake of completeness, this module also propose the two following classes:
   * - class CholmodSimplicialLLT
@@ -40,7 +40,9 @@ extern "C" {
   *
   */
 
+// IWYU pragma: begin_exports
 #include "src/CholmodSupport/CholmodSupport.h"
+// IWYU pragma: end_exports
 
 #include "src/Core/util/ReenableStupidWarnings.h"
 

diff --git a/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/Core b/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/Core
@@ -8,8 +8,12 @@
 // 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_CORE_H
-#define EIGEN_CORE_H
+#ifndef EIGEN_CORE_MODULE_H
+#define EIGEN_CORE_MODULE_H
+
+#if defined(ITK_EIGEN_MANGLE)
+#define Eigen itkeigen
+#endif
 
 // first thing Eigen does: stop the compiler from reporting useless warnings.
 #include "src/Core/util/DisableStupidWarnings.h"
@@ -34,16 +38,16 @@
   #include <new>
 #endif
 
-// Disable the ipa-cp-clone optimization flag with MinGW 6.x or newer (enabled by default with -O3)
+// 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_AT_LEAST(4,6) && EIGEN_GNUC_AT_MOST(5,5)
+#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.
-#if defined(EIGEN_COMP_ICC) && defined(EIGEN_GPU_COMPILE_PHASE) \
+#if EIGEN_COMP_ICC && defined(EIGEN_GPU_COMPILE_PHASE) \
     && !defined(_OVERRIDE_COMPLEX_SPECIALIZATION_)
 #define _OVERRIDE_COMPLEX_SPECIALIZATION_ 1
 #endif
@@ -67,6 +71,7 @@
 #endif
 
 #ifdef EIGEN_HAS_OPENMP
+#include <atomic>
 #include <omp.h>
 #endif
 
@@ -81,10 +86,9 @@
 #include <cstddef>
 #include <cstdlib>
 #include <cmath>
-#include <cassert>
 #include <functional>
-#include <sstream>
 #ifndef EIGEN_NO_IO
+  #include <sstream>
   #include <iosfwd>
 #endif
 #include <cstring>
@@ -94,14 +98,11 @@
 // for min/max:
 #include <algorithm>
 
-#if EIGEN_HAS_CXX11
 #include <array>
-#endif
+#include <vector>
 
 // for std::is_nothrow_move_assignable
-#ifdef EIGEN_INCLUDE_TYPE_TRAITS
 #include <type_traits>
-#endif
 
 // for outputting debug info
 #ifdef EIGEN_DEBUG_ASSIGN
@@ -159,14 +160,27 @@ using std::ptrdiff_t;
   * \endcode
   */
 
+#ifdef EIGEN_USE_LAPACKE
+  #ifdef EIGEN_USE_MKL
+    #include "mkl_lapacke.h"
+  #else
+    #include "src/misc/lapacke.h"
+  #endif
+#endif
+
+// IWYU pragma: begin_exports
 #include "src/Core/util/Constants.h"
 #include "src/Core/util/Meta.h"
+#include "src/Core/util/Assert.h"
 #include "src/Core/util/ForwardDeclarations.h"
 #include "src/Core/util/StaticAssert.h"
 #include "src/Core/util/XprHelper.h"
 #include "src/Core/util/Memory.h"
 #include "src/Core/util/IntegralConstant.h"
+#include "src/Core/util/Serializer.h"
 #include "src/Core/util/SymbolicIndex.h"
+#include "src/Core/util/EmulateArray.h"
+#include "src/Core/util/MoreMeta.h"
 
 #include "src/Core/NumTraits.h"
 #include "src/Core/MathFunctions.h"
@@ -176,10 +190,12 @@ using std::ptrdiff_t;
 // Generic half float support
 #include "src/Core/arch/Default/Half.h"
 #include "src/Core/arch/Default/BFloat16.h"
-#include "src/Core/arch/Default/TypeCasting.h"
 #include "src/Core/arch/Default/GenericPacketMathFunctionsFwd.h"
 
 #if defined EIGEN_VECTORIZE_AVX512
+  #if defined EIGEN_VECTORIZE_AVX512FP16
+    #include "src/Core/arch/AVX512/PacketMathFP16.h"
+  #endif
   #include "src/Core/arch/SSE/PacketMath.h"
   #include "src/Core/arch/SSE/TypeCasting.h"
   #include "src/Core/arch/SSE/Complex.h"
@@ -192,6 +208,7 @@ using std::ptrdiff_t;
   #include "src/Core/arch/SSE/MathFunctions.h"
   #include "src/Core/arch/AVX/MathFunctions.h"
   #include "src/Core/arch/AVX512/MathFunctions.h"
+  #include "src/Core/arch/AVX512/TrsmKernel.h"
 #elif defined EIGEN_VECTORIZE_AVX
   // Use AVX for floats and doubles, SSE for integers
   #include "src/Core/arch/SSE/PacketMath.h"
@@ -209,6 +226,7 @@ using std::ptrdiff_t;
   #include "src/Core/arch/SSE/Complex.h"
 #elif defined(EIGEN_VECTORIZE_ALTIVEC) || defined(EIGEN_VECTORIZE_VSX)
   #include "src/Core/arch/AltiVec/PacketMath.h"
+  #include "src/Core/arch/AltiVec/TypeCasting.h"
   #include "src/Core/arch/AltiVec/MathFunctions.h"
   #include "src/Core/arch/AltiVec/Complex.h"
 #elif defined EIGEN_VECTORIZE_NEON
@@ -228,6 +246,8 @@ using std::ptrdiff_t;
   #include "src/Core/arch/MSA/PacketMath.h"
   #include "src/Core/arch/MSA/MathFunctions.h"
   #include "src/Core/arch/MSA/Complex.h"
+#elif defined EIGEN_VECTORIZE_HVX
+  #include "src/Core/arch/HVX/PacketMath.h"
 #endif
 
 #if defined EIGEN_VECTORIZE_GPU
@@ -237,7 +257,6 @@ using std::ptrdiff_t;
 #endif
 
 #if defined(EIGEN_USE_SYCL)
-  #include "src/Core/arch/SYCL/SyclMemoryModel.h"
   #include "src/Core/arch/SYCL/InteropHeaders.h"
 #if !defined(EIGEN_DONT_VECTORIZE_SYCL)
   #include "src/Core/arch/SYCL/PacketMath.h"
@@ -257,10 +276,14 @@ using std::ptrdiff_t;
 #include "src/Core/functors/StlFunctors.h"
 #include "src/Core/functors/AssignmentFunctors.h"
 
-// Specialized functors to enable the processing of complex numbers
-// on CUDA devices
-#ifdef EIGEN_CUDACC
-#include "src/Core/arch/CUDA/Complex.h"
+// Specialized functors for GPU.
+#ifdef EIGEN_GPUCC
+#include "src/Core/arch/GPU/Complex.h"
+#endif
+
+// Specializations of vectorized activation functions for NEON.
+#ifdef EIGEN_VECTORIZE_NEON
+#include "src/Core/arch/NEON/UnaryFunctors.h"
 #endif
 
 #include "src/Core/util/IndexedViewHelper.h"
@@ -315,6 +338,7 @@ using std::ptrdiff_t;
 #include "src/Core/DiagonalMatrix.h"
 #include "src/Core/Diagonal.h"
 #include "src/Core/DiagonalProduct.h"
+#include "src/Core/SkewSymmetricMatrix3.h"
 #include "src/Core/Redux.h"
 #include "src/Core/Visitor.h"
 #include "src/Core/Fuzzy.h"
@@ -347,13 +371,20 @@ using std::ptrdiff_t;
 #include "src/Core/CoreIterators.h"
 #include "src/Core/ConditionEstimator.h"
 
-#if defined(EIGEN_VECTORIZE_ALTIVEC) || defined(EIGEN_VECTORIZE_VSX)
+#if defined(EIGEN_VECTORIZE_VSX)
   #include "src/Core/arch/AltiVec/MatrixProduct.h"
 #elif defined EIGEN_VECTORIZE_NEON
   #include "src/Core/arch/NEON/GeneralBlockPanelKernel.h"
 #endif
 
-#include "src/Core/BooleanRedux.h"
+#if defined(EIGEN_VECTORIZE_AVX512)
+  #include "src/Core/arch/AVX512/GemmKernel.h"
+#endif
+
+#if defined(EIGEN_VECTORIZE_HVX)
+  #include "src/Core/arch/HVX/GeneralBlockPanelKernel.h"
+#endif
+
 #include "src/Core/Select.h"
 #include "src/Core/VectorwiseOp.h"
 #include "src/Core/PartialReduxEvaluator.h"
@@ -379,7 +410,8 @@ using std::ptrdiff_t;
 #endif
 
 #include "src/Core/GlobalFunctions.h"
+// IWYU pragma: end_exports
 
 #include "src/Core/util/ReenableStupidWarnings.h"
 
-#endif // EIGEN_CORE_H
+#endif // EIGEN_CORE_MODULE_H
diff --git a/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/Eigenvalues b/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/Eigenvalues
@@ -33,6 +33,8 @@
   */
 
 #include "src/misc/RealSvd2x2.h"
+
+// IWYU pragma: begin_exports
 #include "src/Eigenvalues/Tridiagonalization.h"
 #include "src/Eigenvalues/RealSchur.h"
 #include "src/Eigenvalues/EigenSolver.h"
@@ -54,6 +56,7 @@
 #include "src/Eigenvalues/ComplexSchur_LAPACKE.h"
 #include "src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h"
 #endif
+// IWYU pragma: end_exports
 
 #include "src/Core/util/ReenableStupidWarnings.h"
 

diff --git a/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/Geometry b/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/Geometry
@@ -33,9 +33,9 @@
   * \endcode
   */
 
+// IWYU pragma: begin_exports
 #include "src/Geometry/OrthoMethods.h"
 #include "src/Geometry/EulerAngles.h"
-
 #include "src/Geometry/Homogeneous.h"
 #include "src/Geometry/RotationBase.h"
 #include "src/Geometry/Rotation2D.h"
@@ -53,6 +53,7 @@
 #if (defined EIGEN_VECTORIZE_SSE) || (defined EIGEN_VECTORIZE_NEON)
 #include "src/Geometry/arch/Geometry_SIMD.h"
 #endif
+// IWYU pragma: end_exports
 
 #include "src/Core/util/ReenableStupidWarnings.h"
 

diff --git a/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/Householder b/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/Householder
@@ -20,9 +20,11 @@
   * \endcode
   */
 
+// IWYU pragma: begin_exports
 #include "src/Householder/Householder.h"
 #include "src/Householder/HouseholderSequence.h"
 #include "src/Householder/BlockHouseholder.h"
+// IWYU pragma: end_exports
 
 #include "src/Core/util/ReenableStupidWarnings.h"
 

diff --git a/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/IterativeLinearSolvers b/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/IterativeLinearSolvers
@@ -27,13 +27,14 @@
   *  - DiagonalPreconditioner - also called Jacobi preconditioner, work very well on diagonal dominant matrices.
   *  - IncompleteLUT - incomplete LU factorization with dual thresholding
   *
-  * Such problems can also be solved using the direct sparse decomposition modules: SparseCholesky, CholmodSupport, UmfPackSupport, SuperLUSupport.
+  * Such problems can also be solved using the direct sparse decomposition modules: SparseCholesky, CholmodSupport, UmfPackSupport, SuperLUSupport, AccelerateSupport.
   *
     \code
     #include <Eigen/IterativeLinearSolvers>
     \endcode
   */
 
+// IWYU pragma: begin_exports
 #include "src/IterativeLinearSolvers/SolveWithGuess.h"
 #include "src/IterativeLinearSolvers/IterativeSolverBase.h"
 #include "src/IterativeLinearSolvers/BasicPreconditioners.h"
@@ -42,6 +43,7 @@
 #include "src/IterativeLinearSolvers/BiCGSTAB.h"
 #include "src/IterativeLinearSolvers/IncompleteLUT.h"
 #include "src/IterativeLinearSolvers/IncompleteCholesky.h"
+// IWYU pragma: end_exports
 
 #include "src/Core/util/ReenableStupidWarnings.h"
 

diff --git a/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/Jacobi b/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/Jacobi
@@ -24,7 +24,9 @@
   *  - MatrixBase::applyOnTheRight().
   */
 
+// IWYU pragma: begin_exports
 #include "src/Jacobi/Jacobi.h"
+// IWYU pragma: end_exports
 
 #include "src/Core/util/ReenableStupidWarnings.h"
 

diff --git a/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/LU b/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/LU
@@ -25,14 +25,12 @@
 
 #include "src/misc/Kernel.h"
 #include "src/misc/Image.h"
+
+// IWYU pragma: begin_exports
 #include "src/LU/FullPivLU.h"
 #include "src/LU/PartialPivLU.h"
 #ifdef EIGEN_USE_LAPACKE
-#ifdef EIGEN_USE_MKL
-#include "mkl_lapacke.h"
-#else
-#include "src/misc/lapacke.h"
-#endif
+#include "src/misc/lapacke_helpers.h"
 #include "src/LU/PartialPivLU_LAPACKE.h"
 #endif
 #include "src/LU/Determinant.h"
@@ -41,6 +39,7 @@
 #if defined EIGEN_VECTORIZE_SSE || defined EIGEN_VECTORIZE_NEON
   #include "src/LU/arch/InverseSize4.h"
 #endif
+// IWYU pragma: end_exports
 
 #include "src/Core/util/ReenableStupidWarnings.h"
 

diff --git a/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/MetisSupport b/Modules/ThirdParty/Eigen3/src/itkeigen/Eigen/MetisSupport
@@ -27,8 +27,9 @@ extern "C" {
   * It can be used just as any other built-in method as explained in \link OrderingMethods_Module here. \endlink
   */
 
-
+// IWYU pragma: begin_exports
 #include "src/MetisSupport/MetisSupport.h"
+// IWYU pragma: end_exports
 
 #include "src/Core/util/ReenableStupidWarnings.h"