diff --git a/.gitignore b/.gitignore index fa89656d94..180323acaa 100644 --- a/.gitignore +++ b/.gitignore @@ -22,5 +22,4 @@ applications/*/CMakeLists.txt tools/build/cmake_files/MakeContainers.cmake Files.cmake .DS_Store -modules/npctransport/ .#* diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000000..1906e7587b --- /dev/null +++ b/.gitmodules @@ -0,0 +1,6 @@ +[submodule "modules/npctransport"] + path = modules/npctransport + url = https://github.com/salilab/npctransport.git +[submodule "components/pathway_mapping"] + path = components/pathway_mapping + url = https://github.com/salilab/pathway_mapping.git diff --git a/.travis.yml b/.travis.yml index d957f62ac8..12da131dc7 100644 --- a/.travis.yml +++ b/.travis.yml @@ -48,7 +48,7 @@ git: before_install: - sudo apt-get update -qq - - sudo apt-get install -qq libboost$BOOST-all-dev swig libhdf5-serial-dev + - sudo apt-get install -qq libboost$BOOST-all-dev swig libhdf5-serial-dev libeigen3-dev - ./setup_git.py script: diff --git a/CMakeLists.txt b/CMakeLists.txt index 561fbdf909..093a3740ca 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -64,9 +64,7 @@ cmake_policy(SET CMP0017 NEW) endif(POLICY CMP0017) # Don't set MACOSX_RPATH by default -if(POLICY CMP0042) -cmake_policy(SET CMP0042 OLD) -endif(POLICY CMP0042) +set(CMAKE_MACOSX_RPATH 0) # Stop cmake warning about files in the build directory it didn't create # (see issue #909) @@ -277,6 +275,12 @@ if(NOT IMP_STATIC) find_package(OpenMP3) endif() +find_package(Eigen3 3.0 REQUIRED) +# Add Eigen3 to 'system' include path. Amongst other things, this will suppress +# many compiler warnings about Eigen code which a) clutter the output and +# b) we're not going to fix, since Eigen isn't our code. +include_directories(SYSTEM ${EIGEN3_INCLUDE_DIR}) + add_custom_target("IMP-version" COMMAND ${CMAKE_SOURCE_DIR}/tools/build/make_version.py --source=${CMAKE_SOURCE_DIR} WORKING_DIRECTORY ${CMAKE_BINARY_DIR} diff --git a/ChangeLog.md b/ChangeLog.md index 560b17c466..1ba0d42ac0 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -1,6 +1,47 @@ ChangeLog {#changelog} ========= +# 2.9.0 - 2018-07-02 # {#changelog_2_9_0} +- [Eigen](https://eigen.tuxfamily.org/) is now required to build IMP. +- The Windows .exe IMP installer no longer supports Python 2.6. Python 2.7, + 3.4, 3.5, and 3.6 are supported by this installer. +- A binary package is now provided for Ubuntu 18.04 LTS, Bionic Beaver. +- The IMP::atom::setup_as_rigid_body() function has been removed. + Use IMP::atom::create_rigid_body() instead. +- Constructors for IMP::container classes, IMP::core::BallMover, + IMP::core::RigidBodyMover, and IMP::core::IncrementalScoringFunction taking + a RigidBody or Particles have been removed. Use constructors taking + ParticleIndexes instead. +- The IMP::core::ConnectivityRestraint::get_connected_pairs() method has been + removed. Use get_connected_index_pairs() instead. +- The stats() profiling method has been removed from + IMP::isd::GaussianProcessInterpolationRestraint and + IMP::isd::MultivariateFNormalSufficient. Use a third party package (such as + gperftools) for profiling instead. +- Scores in IMP.saxs (and FoXS) now use the chi-square value rather than chi. +- New applications of IMP are now available: + - [Modeling of the entire yeast nuclear pore complex](https://salilab.org/npc2018), as well as + [modeling of the flexible FG regions](https://salilab.org/npc_fg_2018) and + modeling of the individual [Nup133](https://salilab.org/nup133), + [Nup82](https://salilab.org/nup82), and + [Pom152](https://salilab.org/pom152) subcomplexes. + - [Modeling of the Ecm29-proteasome complex](https://salilab.org/ecm29) +- The new modules IMP::npc and IMP::npctransport provide specialized + restraints and other functionality for modeling static nuclear pore complex + structures and transport through these structures, respectively, although + may also be useful for other modeling applications. +- IMP's mmCIF support for deposition of models in + [PDB-Dev](https://pdb-dev.wwpdb.org/), in the IMP::pmi and IMP::mmcif modules, + now utilizes the [python-ihm](https://github.com/ihmwg/python-ihm) library, + a copy of which is included with IMP. +- RMF files now store additional metadata, such as the primary sequence of + each chain, software used, information on each restraint (such as fit values), + and provenance (classes derived from IMP::core::Provenance) that describes + transformations of the system, such as initial input from a PDB file, + sampling, clustering, and filtering. +- The new experimental IMP::mmcif module allows generating basic mmCIF files + directly from an IMP::Model and/or RMF files. + # 2.8.0 - 2017-08-16 # {#changelog_2_8_0} - New applications of IMP are now available: - [Modeling of the yeast Spindle Pole Body core](https://salilab.org/spb/) @@ -32,7 +73,7 @@ ChangeLog {#changelog} - Memory and CPU performance improvements across the code, particularly in IMP::pmi. - Preview of mmCIF support for deposition of integrative models in - [PDB-dev](https://pdb-dev.rcsb.rutgers.edu/). See the IMP::pmi::mmcif + [PDB-Dev](https://pdb-dev.wwpdb.org/). See the IMP::pmi::mmcif module for more details. - This will be the last release that includes packages for RedHat Enterprise Linux 5 (and variants, such as CentOS 5), since RHEL 5 has reached end @@ -50,7 +91,7 @@ ChangeLog {#changelog} Use IMP::core::create_rigid_body() instead. - IMP::test:TempDir and IMP::test::RunInTempDir are deprecated in favor of similar functions that work as Python context managers - (IMP::test::temporary_directory() and IMP::Test::temporary_working_directory() + (IMP::test::temporary_directory() and IMP::test::temporary_working_directory() respectively). # 2.6.2 - 2016-05-25 # {#changelog_2_6_2} diff --git a/README.md b/README.md index 612e5a57ee..c50c7387c8 100644 --- a/README.md +++ b/README.md @@ -31,7 +31,7 @@ new shell. Copyright and License information ================================= -IMP is Copyright 2007-2017 IMP Inventors. The IMP Inventors are +IMP is Copyright 2007-2018 IMP Inventors. The IMP Inventors are Andrej Sali, Ben Webb, Daniel Russel, Keren Lasker, Dina Schneidman, Javier Velázquez-Muriel, Friedrich Förster, Elina Tjioe, Hao Fan, Seung Joong Kim, Yannick Spill, Riccardo Pellarin. diff --git a/VERSION b/VERSION index 834f262953..c8e38b6140 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -2.8.0 +2.9.0 diff --git a/components/README.md b/components/README.md new file mode 100644 index 0000000000..5d1d561f25 --- /dev/null +++ b/components/README.md @@ -0,0 +1,2 @@ +This directory contains additional components for integrative modeling +that are not IMP modules. diff --git a/components/pathway_mapping b/components/pathway_mapping new file mode 160000 index 0000000000..81911e5637 --- /dev/null +++ b/components/pathway_mapping @@ -0,0 +1 @@ +Subproject commit 81911e56376be53df97ff5d9f5de019388a1da91 diff --git a/doc/manual/biosystem.md b/doc/manual/biosystem.md index 76c3048059..c428f2d3d3 100644 --- a/doc/manual/biosystem.md +++ b/doc/manual/biosystem.md @@ -23,13 +23,19 @@ We recommend the following contents for your repository (see the for an example): - subdirectories containing - - your modeling protocol (generally one or more Python scripts) + - your modeling protocol (generally one or more Python scripts). - input files (e.g. PDB files, EM density maps, lists of crosslinks), - especially if these files aren't in a database somewhere already + especially if these files aren't in a database somewhere already. + If these inputs are derived in some fashion (e.g. you use a PDB file as + input that's a comparative model or docking result, or you use an EM map + that's been segmented) then this needs to be described somewhere, with + links to the original unmodified files (e.g. PDB IDs for templates of any + comparative models, alignment files, Modeller scripts). - outputs (trajectories, clusters, analysis). Where this isn't possible due to size, we can host the larger files, such as trajectories, elsewhere (e.g. as a dataset in [Zenodo](https://zenodo.org)) and link to them - from the repository. + from the repository. Aim to keep the repository below 1GB in size so that + it's manageable. - a top-level `%README.md` file describing the system and explaining how to run the protocol. - a top-level `LICENSE` file with the license for the data files and scripts. diff --git a/doc/manual/cnmultifit_groel.dox b/doc/manual/cnmultifit_groel.dox index 0fad83131d..123a5ce98e 100644 --- a/doc/manual/cnmultifit_groel.dox +++ b/doc/manual/cnmultifit_groel.dox @@ -97,7 +97,7 @@ It also generates a file multifit.output that shows the transformation needed to place the subunit in the density. The optional --chimera parameter requests the same transformation -output in a \external{http://www.cgl.ucsf.edu/chimera/,Chimera}-compatible +output in a \external{https://www.cgl.ucsf.edu/chimera/,Chimera}-compatible format. To generate PDB files from the Chimera output file, use: \code{.sh} diff --git a/doc/manual/design.md b/doc/manual/design.md index 6ba543e2bc..001b4c72cb 100644 --- a/doc/manual/design.md +++ b/doc/manual/design.md @@ -17,7 +17,7 @@ The next parts of the manual will cover the use of the various parts of - [Chimera tools/web services](@ref web_services): we provide a number of web services that use %IMP at [https://salilab.org/](https://salilab.org). Additionally, - the [UCSF Chimera](http://www.cgl.ucsf.edu/chimera/) software includes + the [UCSF Chimera](https://www.cgl.ucsf.edu/chimera/) software includes several tools that use %IMP. These are the simplest to use because they do not require an %IMP installation. diff --git a/doc/manual/eigen.md b/doc/manual/eigen.md deleted file mode 100644 index b42cedf087..0000000000 --- a/doc/manual/eigen.md +++ /dev/null @@ -1,34 +0,0 @@ -Eigen {#eigen} -===== - -We ship a copy of Eigen. To patch an updated version, first commit the unpatched version and then patch it by running all of these. More clever approaches are welcome. - - sed -i.old "s#namespace Eigen#namespace IMP_Eigen#g" `find modules/algebra/include/eigen3 -type f` - sed -i.old "s#,Eigen::#,IMP_Eigen::#g" `find modules/algebra/include/eigen3 -type f` - sed -i.old "s# Eigen::# IMP_Eigen::#g" `find modules/algebra/include/eigen3 -type f` - sed -i.old "s#(Eigen::#(IMP_Eigen::#g" `find modules/algebra/include/eigen3 -type f` - sed -i.old "s#{Eigen::#{IMP_Eigen::#g" `find modules/algebra/include/eigen3 -type f` - sed -i.old "s#=Eigen::#=IMP_Eigen::#g" `find modules/algebra/include/eigen3 -type f` - sed -i.old "s#EIGEN#>IMP_EIGEN#g" `find modules/algebra/include/eigen3 -type f` - sed -i.old "s#\!Eigen#\!IMP_Eigen#g" `find modules/algebra/include/eigen3 -type f` - sed -i.old "s#\*Eigen#*IMP_Eigen#g" `find modules/algebra/include/eigen3 -type f` - sed -i.old "s#=EIGEN#=IMP_EIGEN#g" `find modules/algebra/include/eigen3 -type f` - sed -i.old "s#ei_declare_aligned_stack_constructed_variable#imp_ei_declare_aligned_stack_constructed_variable#g" `find modules/algebra/include/eigen3 -type f` - sed -i.old "s#\!Eigen::#\!IMP_Eigen::#g" `find modules/algebra/include/eigen3 -type f` - sed -i.old "s#eigen_assert#imp_eigen_assert#g" `find modules/algebra/include/eigen3 -type f` - sed -i.old "s#eigen_internal_assert#imp_eigen_internal_assert#g" `find modules/algebra/include/eigen3 -type f` - sed -i.old "s#eigen_plain_assert#imp_eigen_plain_assert#g" `find modules/algebra/include/eigen3 -type f` - -in addition, the following commits introduced some modifications to the code -- `26a1f70d5faef3f` -- `5c0b9b7b57dbf97` - -Eigen headers can be found at `IMP/algebra/eigen3`. diff --git a/doc/manual/installation.md b/doc/manual/installation.md index cecbacf6c3..e82471bc6e 100644 --- a/doc/manual/installation.md +++ b/doc/manual/installation.md @@ -24,6 +24,7 @@ In order to build %IMP from source, you will need: - [CMake](https://cmake.org) (2.8 or later) - [Boost](http://www.boost.org) (1.41 or later) +- [Eigen](https://eigen.tuxfamily.org/) (3.0 or later) - [HDF5](https://support.hdfgroup.org/HDF5/) (1.8 or later; 1.10 should also work) - [Python](https://www.python.org) (2.6 or later, or any version of Python 3) @@ -41,7 +42,7 @@ will not build, and some will not function optimally. nonbonded lists. - [Google perf tools](\ref perf): needed only for profiling %IMP code. - [ANN](\ref ANN): certain data structures will be faster if it is available. -- [GSL](\ref GSL): needed to use the IMP.gsl module. +- [GSL](\ref GSL) (1.13 or later): needed to use the IMP.gsl module. - [OpenCV](\ref OpenCV) (2.1 or later): needed to use the IMP.em2d module or the [idock](@ref idock_pcsk9) and [emagefit](@ref emagefit_3sfd) command line tools. @@ -50,6 +51,8 @@ will not build, and some will not function optimally. - [libTAU](https://integrativemodeling.org/libTAU.html): needed to use the IMP.cnmultifit module or the [cnmultifit](@ref cnmultifit_groel) command line tool. +- [Protobuf](https://github.com/google/protobuf): needed to use the + IMP.npctransport module. - An [MPI](@ref IMP::mpi) library is needed to use the IMP.mpi module. - The [numpy, scipy](http://www.scipy.org/scipylib/download.html), [scikit-learn](http://scikit-learn.org/stable/install.html), @@ -80,7 +83,7 @@ such as brew tap homebrew/science brew tap salilab/salilab - brew install boost gmp google-perftools cgal graphviz gsl cmake doxygen hdf5 swig fftw mpfr opencv libtau + brew install boost gmp google-perftools cgal graphviz gsl cmake doxygen hdf5 swig fftw mpfr opencv libtau eigen to install everything %IMP finds useful (or that you will want for installing various useful Python libs that %IMP finds useful). On older Macs, you may also need to `brew install git` if you want to use git (newer Macs include git). - [Macports](http://www.macports.org/) If you use MacPorts, you must add `/opt/local/bin` to your path (either by modifying your shell's diff --git a/doc/manual/licenses.md b/doc/manual/licenses.md index 3ddde55fa9..e57a67ed12 100644 --- a/doc/manual/licenses.md +++ b/doc/manual/licenses.md @@ -1,7 +1,7 @@ Copyright and licenses {#licenses} ====================== -%IMP is Copyright 2007-2017 %IMP Inventors. The %IMP Inventors are +%IMP is Copyright 2007-2018 %IMP Inventors. The %IMP Inventors are Andrej Sali, Ben Webb, Daniel Russel, Keren Lasker, Dina Schneidman, Javier Velázquez-Muriel, Friedrich Förster, Elina Tjioe, Hao Fan, Seung Joong Kim, Yannick Spill, Riccardo Pellarin. diff --git a/doc/manual/mainpage.dox b/doc/manual/mainpage.dox index 283af1fb4b..252c1056b2 100644 --- a/doc/manual/mainpage.dox +++ b/doc/manual/mainpage.dox @@ -93,7 +93,6 @@ complex might want to skip ahead to - [Close pairs lists](@ref close_pairs) - [RMF](@ref rmf) - [Building](@ref building) - - [Eigen](@ref eigen) - [git submodules and subtrees](@ref subtree) - [Copyright and licenses](@ref licenses) diff --git a/doc/manual/multi_foxs.dox b/doc/manual/multi_foxs.dox index 8c5da457fe..6f9f431021 100644 --- a/doc/manual/multi_foxs.dox +++ b/doc/manual/multi_foxs.dox @@ -33,10 +33,10 @@ print(IMP.multi_foxs.get_example_path('rpa'))'. \section multi_foxs_calc Calculation The structure of the RPA in complex with ssDNA is available in the -\external{http://www.pdb.org,RCSB Protein Data Bank (PDB)} as code -\external{http://www.pdb.org/pdb/explore/explore.do?structureId=1JMC,1jmc} +\external{https://www.rcsb.org/,RCSB Protein Data Bank (PDB)} as code +\external{https://www.rcsb.org/structure/1JMC,1jmc} (file 1jmc.pdb), the unbound RPA structures are available as code -\external{http://www.pdb.org/pdb/explore/explore.do?structureId=1FGU,1fgu} +\external{https://www.rcsb.org/structure/1FGU,1fgu} (file 1fguA.pdb, 1fguB.pdb), while the SAXS profile is given in the weighted.dat file. The SAXS profile was simulated from the 3 structures with the following weights: \verbatim diff --git a/doc/manual/multifit_3sfd.dox b/doc/manual/multifit_3sfd.dox index ad5e94ee85..90c0d56a69 100644 --- a/doc/manual/multifit_3sfd.dox +++ b/doc/manual/multifit_3sfd.dox @@ -118,7 +118,7 @@ each Gaussian. For example, with 50 residues per Gaussian, a 170-residue protein should use 3 Gaussians and a 260-residue protein should use 5 Gaussians.) The reduced representation is written out as a PDB file containing fake CA atoms, where each CA corresponds to a single anchor point, -and also as a \external{http://www.cgl.ucsf.edu/chimera/,Chimera} cmm file. +and also as a \external{https://www.cgl.ucsf.edu/chimera/,Chimera} cmm file. \section multifit_3sfd_fit_fft Fit each protein to the map diff --git a/doc/manual/rnapolii_stalk.dox b/doc/manual/rnapolii_stalk.dox index 1761963bb5..915a8db5ae 100644 --- a/doc/manual/rnapolii_stalk.dox +++ b/doc/manual/rnapolii_stalk.dox @@ -32,7 +32,7 @@ packages installed in addition to [IMP itself](@ref installation): - [Chimera](https://www.cgl.ucsf.edu/chimera/download.html) for visualization of results -(If you are using [Anaconda Python](https://store.continuum.io/cshop/anaconda/), +(If you are using [Anaconda Python](https://www.anaconda.com/download/), you can get the Python packages above by simply running `conda install numpy scipy scikit-learn matplotlib`. On a Mac you can get them using the diff --git a/doc/manual/web_services.md b/doc/manual/web_services.md index d912766e59..83ae2fdaec 100644 --- a/doc/manual/web_services.md +++ b/doc/manual/web_services.md @@ -6,11 +6,11 @@ They are the simplest to use because they do not require an %IMP installation. # Chimera tools -The [UCSF Chimera](http://www.cgl.ucsf.edu/chimera/) software includes +The [UCSF Chimera](https://www.cgl.ucsf.edu/chimera/) software includes several tools that use %IMP: - - [Small-Angle X-Ray Profile](http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/saxs/saxs.html): calculate a theoretical small-angle X-ray scattering (SAXS) profile from a set of atoms - - [MultiFit](http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multifit/multifit.html): perform simultaneous rigid fitting of multiple atomic-resolution structures into density maps at resolutions as low as 25 Å. + - [Small-Angle X-Ray Profile](https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/saxs/saxs.html): calculate a theoretical small-angle X-ray scattering (SAXS) profile from a set of atoms + - [MultiFit](https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multifit/multifit.html): perform simultaneous rigid fitting of multiple atomic-resolution structures into density maps at resolutions as low as 25 Å. In addition, UCSF Chimera is able to read [RMF files](https://integrativemodeling.org/rmf/) generated by %IMP. diff --git a/modules/algebra/README.md b/modules/algebra/README.md index d96488fbed..db34b5dfa8 100644 --- a/modules/algebra/README.md +++ b/modules/algebra/README.md @@ -58,9 +58,6 @@ straightforward, it is not available as a package for common platforms. In addition, ANN must be built as a shared library rather than a static library. -# Eigen # {#Eigen} -We ship a copy of Eigen as part of IMP as Eigen support varies quite considerably across platforms and it is header-only and so easy to ship. Our version of Eigen has been patched to move everything to the `IMP_Eigen` namespace and preprocessor symbols to start with `IMP_EIGEN_` so that things do not conflict with system installs of Eigen. - # Info _Author(s)_: Daniel Russel, Keren Lasker, Ben Webb, Javier Angel Velázquez-Muriel diff --git a/modules/algebra/benchmark/benchmark_grid_traversal.cpp b/modules/algebra/benchmark/benchmark_grid_traversal.cpp index 1edc69b13a..76e59dfd14 100644 --- a/modules/algebra/benchmark/benchmark_grid_traversal.cpp +++ b/modules/algebra/benchmark/benchmark_grid_traversal.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/algebra/benchmark/benchmark_knn.cpp b/modules/algebra/benchmark/benchmark_knn.cpp index e27df9707d..3a0a4f1f67 100644 --- a/modules/algebra/benchmark/benchmark_knn.cpp +++ b/modules/algebra/benchmark/benchmark_knn.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. */ #include diff --git a/modules/algebra/benchmark/benchmark_rotate.cpp b/modules/algebra/benchmark/benchmark_rotate.cpp index afa3471ff0..d8acf139af 100644 --- a/modules/algebra/benchmark/benchmark_rotate.cpp +++ b/modules/algebra/benchmark/benchmark_rotate.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/algebra/benchmark/benchmark_surface.cpp b/modules/algebra/benchmark/benchmark_surface.cpp index 2e8ea3a743..5d0c12777f 100644 --- a/modules/algebra/benchmark/benchmark_surface.cpp +++ b/modules/algebra/benchmark/benchmark_surface.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. */ #include diff --git a/modules/algebra/examples/grid.cpp b/modules/algebra/examples/grid.cpp index 95b074348d..446ad98f22 100644 --- a/modules/algebra/examples/grid.cpp +++ b/modules/algebra/examples/grid.cpp @@ -2,7 +2,7 @@ * \example grid.cpp * \brief Show some of the basics of using a grid from C++. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/algebra/include/BoundingBoxD.h b/modules/algebra/include/BoundingBoxD.h index 6b606e284d..ce778538ec 100644 --- a/modules/algebra/include/BoundingBoxD.h +++ b/modules/algebra/include/BoundingBoxD.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/BoundingBoxD.h \brief A bounding box in D dimensions. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Cone3D.h b/modules/algebra/include/Cone3D.h index 33f50452a2..5c5714d306 100644 --- a/modules/algebra/include/Cone3D.h +++ b/modules/algebra/include/Cone3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/Cone3D.h * \brief Represent a cone in 3D. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_CONE_3D_H diff --git a/modules/algebra/include/Cylinder3D.h b/modules/algebra/include/Cylinder3D.h index ea30659218..12685bc510 100644 --- a/modules/algebra/include/Cylinder3D.h +++ b/modules/algebra/include/Cylinder3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/Cylinder3D.h * \brief Represent a cylinder in 3D. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_CYLINDER_3D_H diff --git a/modules/algebra/include/Ellipsoid3D.h b/modules/algebra/include/Ellipsoid3D.h index 5a1d23c531..89fd5d16ac 100644 --- a/modules/algebra/include/Ellipsoid3D.h +++ b/modules/algebra/include/Ellipsoid3D.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/Ellipsoid3D.h \brief Simple 3D ellipsoid class. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Gaussian3D.h b/modules/algebra/include/Gaussian3D.h index 69dfef7a13..cda9e93b38 100644 --- a/modules/algebra/include/Gaussian3D.h +++ b/modules/algebra/include/Gaussian3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/Gaussian3D.h * \brief Gaussian shape * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ @@ -14,7 +14,7 @@ #include "ReferenceFrame3D.h" #include #include -#include +#include IMPALGEBRA_BEGIN_NAMESPACE @@ -44,11 +44,11 @@ IMP_VALUES(Gaussian3D, Gaussian3Ds); /** Return the covariance matrix from a given set of standard deviations in the passed reference frame. */ -IMPALGEBRAEXPORT IMP_Eigen::Matrix3d get_covariance(const Gaussian3D &g); +IMPALGEBRAEXPORT Eigen::Matrix3d get_covariance(const Gaussian3D &g); //! Return a Gaussian centered at the origin from a covariance matrix. IMPALGEBRAEXPORT Gaussian3D -get_gaussian_from_covariance(const IMP_Eigen::Matrix3d &covariance, +get_gaussian_from_covariance(const Eigen::Matrix3d &covariance, const Vector3D ¢er); //! Rasterize the Gaussians to a grid. diff --git a/modules/algebra/include/GeometricPrimitiveD.h b/modules/algebra/include/GeometricPrimitiveD.h index 5e14b16d8c..7b37c70c5f 100644 --- a/modules/algebra/include/GeometricPrimitiveD.h +++ b/modules/algebra/include/GeometricPrimitiveD.h @@ -2,7 +2,7 @@ * \file IMP/algebra/GeometricPrimitiveD.h * \brief Base class for geometric types. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/GridD.h b/modules/algebra/include/GridD.h index 9022cc2949..06f3ea88a5 100644 --- a/modules/algebra/include/GridD.h +++ b/modules/algebra/include/GridD.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/GridD.h \brief A class to represent a voxel grid. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Line3D.h b/modules/algebra/include/Line3D.h index c4b7867013..ccd0e6c7a4 100644 --- a/modules/algebra/include/Line3D.h +++ b/modules/algebra/include/Line3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/Line3D.h * \brief Simple implementation of lines in 3D * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_LINE_3D_H diff --git a/modules/algebra/include/LinearFit.h b/modules/algebra/include/LinearFit.h index c5254d65a5..e802205ea4 100644 --- a/modules/algebra/include/LinearFit.h +++ b/modules/algebra/include/LinearFit.h @@ -2,7 +2,7 @@ * \file IMP/algebra/LinearFit.h * \brief Linear fit of data points * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/ParabolicFit.h b/modules/algebra/include/ParabolicFit.h index 1c4e041fdc..e6442f2f6d 100644 --- a/modules/algebra/include/ParabolicFit.h +++ b/modules/algebra/include/ParabolicFit.h @@ -2,7 +2,7 @@ * \file IMP/algebra/ParabolicFit.h * \brief Fit data with parabola * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Plane3D.h b/modules/algebra/include/Plane3D.h index 9c7b1707aa..15f55f9948 100644 --- a/modules/algebra/include/Plane3D.h +++ b/modules/algebra/include/Plane3D.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/Plane3D.h \brief Simple 3D plane class. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/ReferenceFrame3D.h b/modules/algebra/include/ReferenceFrame3D.h index 0fbc51a3cf..9ca5a3a3eb 100644 --- a/modules/algebra/include/ReferenceFrame3D.h +++ b/modules/algebra/include/ReferenceFrame3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/ReferenceFrame3D.h * \brief A reference frame in 3D. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Reflection3D.h b/modules/algebra/include/Reflection3D.h index 3b433d9731..b557158c88 100644 --- a/modules/algebra/include/Reflection3D.h +++ b/modules/algebra/include/Reflection3D.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/Reflection3D.h \brief Reflect about a plane in 3D. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Rotation2D.h b/modules/algebra/include/Rotation2D.h index 1825c507ca..3b28dd90df 100644 --- a/modules/algebra/include/Rotation2D.h +++ b/modules/algebra/include/Rotation2D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/Rotation2D.h * \brief Represent a rotation in 2D space. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_ROTATION_2D_H diff --git a/modules/algebra/include/Rotation3D.h b/modules/algebra/include/Rotation3D.h index 03efcd6930..949214ee21 100644 --- a/modules/algebra/include/Rotation3D.h +++ b/modules/algebra/include/Rotation3D.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/Rotation3D.h \brief Simple 3D rotation class. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ @@ -13,7 +13,7 @@ #include "utility.h" #include "constants.h" #include "GeometricPrimitiveD.h" -#include +#include #include #include @@ -332,7 +332,7 @@ IMPALGEBRAEXPORT Rotation3D /** \see Rotation3D */ -IMPALGEBRAEXPORT Rotation3D get_rotation_from_matrix(IMP_Eigen::Matrix3d m); +IMPALGEBRAEXPORT Rotation3D get_rotation_from_matrix(Eigen::Matrix3d m); //! Pick a rotation at random from all possible rotations /** \see Rotation3D */ diff --git a/modules/algebra/include/Segment3D.h b/modules/algebra/include/Segment3D.h index 76109be1c8..a9ca6547d8 100644 --- a/modules/algebra/include/Segment3D.h +++ b/modules/algebra/include/Segment3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/Segment3D.h * \brief Simple implementation of segments in 3D * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_SEGMENT_3D_H diff --git a/modules/algebra/include/Sphere3D.h b/modules/algebra/include/Sphere3D.h index 04f905a724..cc89b072e0 100644 --- a/modules/algebra/include/Sphere3D.h +++ b/modules/algebra/include/Sphere3D.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/Sphere3D.h \brief Simple 3D sphere class. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/SphereD.h b/modules/algebra/include/SphereD.h index 80c95baa41..d5baa2d686 100644 --- a/modules/algebra/include/SphereD.h +++ b/modules/algebra/include/SphereD.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/SphereD.h \brief Simple 3D sphere class. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/SpherePatch3D.h b/modules/algebra/include/SpherePatch3D.h index 5629a3b03a..8da5804fea 100644 --- a/modules/algebra/include/SpherePatch3D.h +++ b/modules/algebra/include/SpherePatch3D.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/SpherePatch3D.h \brief Simple 3D sphere patch class. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/SphericalVector3D.h b/modules/algebra/include/SphericalVector3D.h index 24215e4250..392c3ac890 100644 --- a/modules/algebra/include/SphericalVector3D.h +++ b/modules/algebra/include/SphericalVector3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/SphericalVector3D.h * \brief Stores and converts spherical coordinates * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_SPHERICAL_VECTOR_3D_H @@ -27,7 +27,7 @@ IMPALGEBRA_BEGIN_NAMESPACE \geometry */ class IMPALGEBRAEXPORT SphericalVector3D : public GeometricPrimitiveD<3> { - bool check(double r, double theta, double psi); + bool check(double r, double theta, double psi) const; public: SphericalVector3D() {}; @@ -65,7 +65,7 @@ class IMPALGEBRAEXPORT SphericalVector3D : public GeometricPrimitiveD<3> { } //! Returns a vector with the Cartesian coordinates - Vector3D get_cartesian_coordinates(); + Vector3D get_cartesian_coordinates() const; IMP_SHOWABLE_INLINE(SphericalVector3D, out << v_[0] << " , " << v_[1] << " , " << v_[2]); diff --git a/modules/algebra/include/Torus3D.h b/modules/algebra/include/Torus3D.h index 9e63dc920b..eca416aca6 100644 --- a/modules/algebra/include/Torus3D.h +++ b/modules/algebra/include/Torus3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/Torus3D.h * \brief Represent a torus in 3D. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_TORUS_3D_H diff --git a/modules/algebra/include/Transformation2D.h b/modules/algebra/include/Transformation2D.h index 6eb24cacde..1470c7c031 100644 --- a/modules/algebra/include/Transformation2D.h +++ b/modules/algebra/include/Transformation2D.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/Transformation2D.h * \brief 2D transformations. - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Transformation3D.h b/modules/algebra/include/Transformation3D.h index ea961afe4a..e021d691d8 100644 --- a/modules/algebra/include/Transformation3D.h +++ b/modules/algebra/include/Transformation3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/Transformation3D.h * \brief Simple 3D transformation class. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Triangle3D.h b/modules/algebra/include/Triangle3D.h index 3167ddb600..5de5cb4c6f 100644 --- a/modules/algebra/include/Triangle3D.h +++ b/modules/algebra/include/Triangle3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/Triangle3D.h * \brief Represent a triangle in 3D * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_TRIANGLE_3D_H diff --git a/modules/algebra/include/Vector2D.h b/modules/algebra/include/Vector2D.h index f81f383d1d..291cf9d758 100644 --- a/modules/algebra/include/Vector2D.h +++ b/modules/algebra/include/Vector2D.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/Vector2D.h \brief Simple 2D vector class. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Vector3D.h b/modules/algebra/include/Vector3D.h index 00a3e79e4a..43c073eef2 100644 --- a/modules/algebra/include/Vector3D.h +++ b/modules/algebra/include/Vector3D.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/Vector3D.h \brief Simple 3D vector class. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/VectorBaseD.h b/modules/algebra/include/VectorBaseD.h index 17956903df..1f744116c9 100644 --- a/modules/algebra/include/VectorBaseD.h +++ b/modules/algebra/include/VectorBaseD.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/VectorBaseD.h \brief Simple D vector class. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ @@ -227,18 +227,22 @@ class VectorBaseD : public GeometricPrimitiveD { */ template inline VT get_unit_vector(VT vt) { - const double tiny_double = 1e-12; + static const double tiny_double = + 256.0 * std::numeric_limits::epsilon(); double mag = vt.get_magnitude(); if (mag > tiny_double) { - return vt / mag; + VT ret_value= vt/mag; + IMP_USAGE_CHECK(std::abs(ret_value.get_magnitude() - 1.0) < 256.0 * tiny_double, + "returned vector is not unit vector"); + return ret_value; } else { // avoid division by zero - return random unit v // NOTE: (1) avoids vector_generators / SphereD to prevent recursiveness // (2) D might be -1, so use get_dimension() - boost::variate_generator > - generator(IMP::random_number_generator, - ::boost::normal_distribution<>(0, 1.0)); + static boost::variate_generator > + generator(IMP::random_number_generator, + ::boost::normal_distribution<>(0, 1.0)); for (unsigned int i = 0; i < vt.get_dimension(); ++i) { vt[i] = generator(); } diff --git a/modules/algebra/include/VectorD.h b/modules/algebra/include/VectorD.h index 83c59dc212..f50b6ba6ec 100644 --- a/modules/algebra/include/VectorD.h +++ b/modules/algebra/include/VectorD.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/VectorD.h \brief Simple D vector class. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/algebra_macros.h b/modules/algebra/include/algebra_macros.h index 0404049046..ba781744e6 100644 --- a/modules/algebra/include/algebra_macros.h +++ b/modules/algebra/include/algebra_macros.h @@ -2,7 +2,7 @@ * \file IMP/algebra/algebra_macros.h * \brief Various helper macros. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/connolly_surface.h b/modules/algebra/include/connolly_surface.h index 6d5ada7e20..5803ad84b8 100644 --- a/modules/algebra/include/connolly_surface.h +++ b/modules/algebra/include/connolly_surface.h @@ -2,7 +2,7 @@ * \file IMP/algebra/connolly_surface.h * \brief Generate surface for a set of atoms. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/constants.h b/modules/algebra/include/constants.h index 4c583072cb..1ba84713cf 100644 --- a/modules/algebra/include/constants.h +++ b/modules/algebra/include/constants.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/constants.h \brief Various useful constants. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/distance.h b/modules/algebra/include/distance.h index 836c02a01d..7916a1b149 100644 --- a/modules/algebra/include/distance.h +++ b/modules/algebra/include/distance.h @@ -2,7 +2,7 @@ * \file IMP/algebra/distance.h * \brief Distance metrics. * - * Copyright 2007-2017 IMP Inventors. All rights reserved. + * Copyright 2007-2018 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/eigen3/Eigen/Array b/modules/algebra/include/eigen3/Eigen/Array deleted file mode 100644 index 3c6ef277fc..0000000000 --- a/modules/algebra/include/eigen3/Eigen/Array +++ /dev/null @@ -1,11 +0,0 @@ -#ifndef IMP_EIGEN_ARRAY_MODULE_H -#define IMP_EIGEN_ARRAY_MODULE_H - -// include Core first to handle Eigen2 support macros -#include "Core" - -#ifndef IMP_EIGEN2_SUPPORT - #error The Eigen/Array header does no longer exist in Eigen3. All that functionality has moved to Eigen/Core. -#endif - -#endif // IMP_EIGEN_ARRAY_MODULE_H diff --git a/modules/algebra/include/eigen3/Eigen/Cholesky b/modules/algebra/include/eigen3/Eigen/Cholesky deleted file mode 100644 index 858bf5128d..0000000000 --- a/modules/algebra/include/eigen3/Eigen/Cholesky +++ /dev/null @@ -1,32 +0,0 @@ -#ifndef IMP_EIGEN_CHOLESKY_MODULE_H -#define IMP_EIGEN_CHOLESKY_MODULE_H - -#include "Core" - -#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 accessible via the following MatrixBase methods: - * - MatrixBase::llt(), - * - MatrixBase::ldlt() - * - * \code - * #include - * \endcode - */ - -#include "src/misc/Solve.h" -#include "src/Cholesky/LLT.h" -#include "src/Cholesky/LDLT.h" -#ifdef IMP_EIGEN_USE_LAPACKE -#include "src/Cholesky/LLT_MKL.h" -#endif - -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif // IMP_EIGEN_CHOLESKY_MODULE_H -/* vim: set filetype=cpp et sw=2 ts=2 ai: */ diff --git a/modules/algebra/include/eigen3/Eigen/CholmodSupport b/modules/algebra/include/eigen3/Eigen/CholmodSupport deleted file mode 100644 index cba956c3be..0000000000 --- a/modules/algebra/include/eigen3/Eigen/CholmodSupport +++ /dev/null @@ -1,45 +0,0 @@ -#ifndef IMP_EIGEN_CHOLMODSUPPORT_MODULE_H -#define IMP_EIGEN_CHOLMODSUPPORT_MODULE_H - -#include "SparseCore" - -#include "src/Core/util/DisableStupidWarnings.h" - -extern "C" { - #include -} - -/** \ingroup Support_modules - * \defgroup CholmodSupport_Module CholmodSupport module - * - * This module provides an interface to the Cholmod library which is part of the suitesparse 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). - * - * For the sake of completeness, this module also propose the two following classes: - * - class CholmodSimplicialLLT - * - class CholmodSimplicialLDLT - * Note that these classes does not bring any particular advantage compared to the built-in - * SimplicialLLT and SimplicialLDLT factorization classes. - * - * \code - * #include - * \endcode - * - * In order to use this module, the cholmod headers must be accessible from the include paths, and your binary must be linked to the cholmod library and its dependencies. - * The dependencies depend on how cholmod has been compiled. - * For a cmake based project, you can use our FindCholmod.cmake module to help you in this task. - * - */ - -#include "src/misc/Solve.h" -#include "src/misc/SparseSolve.h" - -#include "src/CholmodSupport/CholmodSupport.h" - - -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif // IMP_EIGEN_CHOLMODSUPPORT_MODULE_H - diff --git a/modules/algebra/include/eigen3/Eigen/Core b/modules/algebra/include/eigen3/Eigen/Core deleted file mode 100644 index 2fe64f6c79..0000000000 --- a/modules/algebra/include/eigen3/Eigen/Core +++ /dev/null @@ -1,376 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008 Gael Guennebaud -// Copyright (C) 2007-2011 Benoit Jacob -// -// 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 IMP_EIGEN_CORE_H -#define IMP_EIGEN_CORE_H - -// first thing Eigen does: stop the compiler from committing suicide -#include "src/Core/util/DisableStupidWarnings.h" - -// then include this file where all our macros are defined. It's really important to do it first because -// it's where we do all the alignment settings (platform detection and honoring the user's will if he -// defined e.g. IMP_EIGEN_DONT_ALIGN) so it needs to be done before we do anything with vectorization. -#include "src/Core/util/Macros.h" - -// Disable the ipa-cp-clone optimization flag with MinGW 6.x or newer (enabled by default with -O3) -// See http://eigen.tuxfamily.org/bz/show_bug.cgi?id=556 for details. -#if defined(__MINGW32__) && IMP_EIGEN_GNUC_AT_LEAST(4,6) - #pragma GCC optimize ("-fno-ipa-cp-clone") -#endif - -#include - -// this include file manages BLAS and MKL related macros -// and inclusion of their respective header files -#include "src/Core/util/MKL_support.h" - -// if alignment is disabled, then disable vectorization. Note: IMP_EIGEN_ALIGN is the proper check, it takes into -// account both the user's will (IMP_EIGEN_DONT_ALIGN) and our own platform checks -#if !IMP_EIGEN_ALIGN - #ifndef IMP_EIGEN_DONT_VECTORIZE - #define IMP_EIGEN_DONT_VECTORIZE - #endif -#endif - -#ifdef _MSC_VER - #include // for _aligned_malloc -- need it regardless of whether vectorization is enabled - #if (_MSC_VER >= 1500) // 2008 or later - // Remember that usage of defined() in a #define is undefined by the standard. - // a user reported that in 64-bit mode, MSVC doesn't care to define _M_IX86_FP. - #if (defined(_M_IX86_FP) && (_M_IX86_FP >= 2)) || defined(_M_X64) - #define IMP_EIGEN_SSE2_ON_MSVC_2008_OR_LATER - #endif - #endif -#else - // Remember that usage of defined() in a #define is undefined by the standard - #if (defined __SSE2__) && ( (!defined __GNUC__) || (defined __INTEL_COMPILER) || IMP_EIGEN_GNUC_AT_LEAST(4,2) ) - #define IMP_EIGEN_SSE2_ON_NON_MSVC_BUT_NOT_OLD_GCC - #endif -#endif - -#ifndef IMP_EIGEN_DONT_VECTORIZE - - #if defined (IMP_EIGEN_SSE2_ON_NON_MSVC_BUT_NOT_OLD_GCC) || defined(IMP_EIGEN_SSE2_ON_MSVC_2008_OR_LATER) - - // Defines symbols for compile-time detection of which instructions are - // used. - // IMP_EIGEN_VECTORIZE_YY is defined if and only if the instruction set YY is used - #define IMP_EIGEN_VECTORIZE - #define IMP_EIGEN_VECTORIZE_SSE - #define IMP_EIGEN_VECTORIZE_SSE2 - - // Detect sse3/ssse3/sse4: - // gcc and icc defines __SSE3__, ... - // there is no way to know about this on msvc. You can define IMP_EIGEN_VECTORIZE_SSE* if you - // want to force the use of those instructions with msvc. - #ifdef __SSE3__ - #define IMP_EIGEN_VECTORIZE_SSE3 - #endif - #ifdef __SSSE3__ - #define IMP_EIGEN_VECTORIZE_SSSE3 - #endif - #ifdef __SSE4_1__ - #define IMP_EIGEN_VECTORIZE_SSE4_1 - #endif - #ifdef __SSE4_2__ - #define IMP_EIGEN_VECTORIZE_SSE4_2 - #endif - - // include files - - // This extern "C" works around a MINGW-w64 compilation issue - // https://sourceforge.net/tracker/index.php?func=detail&aid=3018394&group_id=202880&atid=983354 - // In essence, intrin.h is included by windows.h and also declares intrinsics (just as emmintrin.h etc. below do). - // However, intrin.h uses an extern "C" declaration, and g++ thus complains of duplicate declarations - // with conflicting linkage. The linkage for intrinsics doesn't matter, but at that stage the compiler doesn't know; - // so, to avoid compile errors when windows.h is included after Eigen/Core, ensure intrinsics are extern "C" here too. - // notice that since these are C headers, the extern "C" is theoretically needed anyways. - extern "C" { - // In theory we should only include immintrin.h and not the other *mmintrin.h header files directly. - // Doing so triggers some issues with ICC. However old gcc versions seems to not have this file, thus: - #if defined(__INTEL_COMPILER) && __INTEL_COMPILER >= 1110 - #include - #else - #include - #include - #ifdef IMP_EIGEN_VECTORIZE_SSE3 - #include - #endif - #ifdef IMP_EIGEN_VECTORIZE_SSSE3 - #include - #endif - #ifdef IMP_EIGEN_VECTORIZE_SSE4_1 - #include - #endif - #ifdef IMP_EIGEN_VECTORIZE_SSE4_2 - #include - #endif - #endif - } // end extern "C" - #elif defined __ALTIVEC__ - #define IMP_EIGEN_VECTORIZE - #define IMP_EIGEN_VECTORIZE_ALTIVEC - #include - // We need to #undef all these ugly tokens defined in - // => use __vector instead of vector - #undef bool - #undef vector - #undef pixel - #elif defined __ARM_NEON - #define IMP_EIGEN_VECTORIZE - #define IMP_EIGEN_VECTORIZE_NEON - #include - #endif -#endif - -#if (defined _OPENMP) && (!defined IMP_EIGEN_DONT_PARALLELIZE) - #define IMP_EIGEN_HAS_OPENMP -#endif - -#ifdef IMP_EIGEN_HAS_OPENMP -#include -#endif - -// MSVC for windows mobile does not have the errno.h file -#if !(defined(_MSC_VER) && defined(_WIN32_WCE)) && !defined(__ARMCC_VERSION) -#define IMP_EIGEN_HAS_ERRNO -#endif - -#ifdef IMP_EIGEN_HAS_ERRNO -#include -#endif -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include // for CHAR_BIT -// for min/max: -#include - -// for outputting debug info -#ifdef IMP_EIGEN_DEBUG_ASSIGN -#include -#endif - -// required for __cpuid, needs to be included after cmath -#if defined(_MSC_VER) && (defined(_M_IX86)||defined(_M_X64)) && (!defined(_WIN32_WCE)) - #include -#endif - -#if defined(_CPPUNWIND) || defined(__EXCEPTIONS) - #define IMP_EIGEN_EXCEPTIONS -#endif - -#ifdef IMP_EIGEN_EXCEPTIONS - #include -#endif - -/** \brief Namespace containing all symbols from the %Eigen library. */ -namespace IMP_Eigen { - -inline static const char *SimdInstructionSetsInUse(void) { -#if defined(IMP_EIGEN_VECTORIZE_SSE4_2) - return "SSE, SSE2, SSE3, SSSE3, SSE4.1, SSE4.2"; -#elif defined(IMP_EIGEN_VECTORIZE_SSE4_1) - return "SSE, SSE2, SSE3, SSSE3, SSE4.1"; -#elif defined(IMP_EIGEN_VECTORIZE_SSSE3) - return "SSE, SSE2, SSE3, SSSE3"; -#elif defined(IMP_EIGEN_VECTORIZE_SSE3) - return "SSE, SSE2, SSE3"; -#elif defined(IMP_EIGEN_VECTORIZE_SSE2) - return "SSE, SSE2"; -#elif defined(IMP_EIGEN_VECTORIZE_ALTIVEC) - return "AltiVec"; -#elif defined(IMP_EIGEN_VECTORIZE_NEON) - return "ARM NEON"; -#else - return "None"; -#endif -} - -} // end namespace IMP_Eigen - -#define STAGE10_FULL_EIGEN2_API 10 -#define STAGE20_RESOLVE_API_CONFLICTS 20 -#define STAGE30_FULL_EIGEN3_API 30 -#define STAGE40_FULL_EIGEN3_STRICTNESS 40 -#define STAGE99_NO_EIGEN2_SUPPORT 99 - -#if defined IMP_EIGEN2_SUPPORT_STAGE40_FULL_EIGEN3_STRICTNESS - #define IMP_EIGEN2_SUPPORT - #define IMP_EIGEN2_SUPPORT_STAGE STAGE40_FULL_EIGEN3_STRICTNESS -#elif defined IMP_EIGEN2_SUPPORT_STAGE30_FULL_EIGEN3_API - #define IMP_EIGEN2_SUPPORT - #define IMP_EIGEN2_SUPPORT_STAGE STAGE30_FULL_EIGEN3_API -#elif defined IMP_EIGEN2_SUPPORT_STAGE20_RESOLVE_API_CONFLICTS - #define IMP_EIGEN2_SUPPORT - #define IMP_EIGEN2_SUPPORT_STAGE STAGE20_RESOLVE_API_CONFLICTS -#elif defined IMP_EIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API - #define IMP_EIGEN2_SUPPORT - #define IMP_EIGEN2_SUPPORT_STAGE STAGE10_FULL_EIGEN2_API -#elif defined IMP_EIGEN2_SUPPORT - // default to stage 3, that's what it's always meant - #define IMP_EIGEN2_SUPPORT_STAGE30_FULL_EIGEN3_API - #define IMP_EIGEN2_SUPPORT_STAGE STAGE30_FULL_EIGEN3_API -#else - #define IMP_EIGEN2_SUPPORT_STAGE STAGE99_NO_EIGEN2_SUPPORT -#endif - -#ifdef IMP_EIGEN2_SUPPORT -#undef minor -#endif - -// we use size_t frequently and we'll never remember to prepend it with std:: everytime just to -// ensure QNX/QCC support -using std::size_t; -// gcc 4.6.0 wants std:: for ptrdiff_t -using std::ptrdiff_t; - -/** \defgroup Core_Module Core module - * This is the main module of Eigen providing dense matrix and vector support - * (both fixed and dynamic size) with all the features corresponding to a BLAS library - * and much more... - * - * \code - * #include - * \endcode - */ - -#include "src/Core/util/Constants.h" -#include "src/Core/util/ForwardDeclarations.h" -#include "src/Core/util/Meta.h" -#include "src/Core/util/StaticAssert.h" -#include "src/Core/util/XprHelper.h" -#include "src/Core/util/Memory.h" - -#include "src/Core/NumTraits.h" -#include "src/Core/MathFunctions.h" -#include "src/Core/GenericPacketMath.h" - -#if defined IMP_EIGEN_VECTORIZE_SSE - #include "src/Core/arch/SSE/PacketMath.h" - #include "src/Core/arch/SSE/MathFunctions.h" - #include "src/Core/arch/SSE/Complex.h" -#elif defined IMP_EIGEN_VECTORIZE_ALTIVEC - #include "src/Core/arch/AltiVec/PacketMath.h" - #include "src/Core/arch/AltiVec/Complex.h" -#elif defined IMP_EIGEN_VECTORIZE_NEON - #include "src/Core/arch/NEON/PacketMath.h" - #include "src/Core/arch/NEON/Complex.h" -#endif - -#include "src/Core/arch/Default/Settings.h" - -#include "src/Core/Functors.h" -#include "src/Core/DenseCoeffsBase.h" -#include "src/Core/DenseBase.h" -#include "src/Core/MatrixBase.h" -#include "src/Core/EigenBase.h" - -#ifndef IMP_EIGEN_PARSED_BY_DOXYGEN // work around Doxygen bug triggered by Assign.h r814874 - // at least confirmed with Doxygen 1.5.5 and 1.5.6 - #include "src/Core/Assign.h" -#endif - -#include "src/Core/util/BlasUtil.h" -#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/CwiseBinaryOp.h" -#include "src/Core/CwiseUnaryOp.h" -#include "src/Core/CwiseNullaryOp.h" -#include "src/Core/CwiseUnaryView.h" -#include "src/Core/SelfCwiseBinaryOp.h" -#include "src/Core/Dot.h" -#include "src/Core/StableNorm.h" -#include "src/Core/MapBase.h" -#include "src/Core/Stride.h" -#include "src/Core/Map.h" -#include "src/Core/Block.h" -#include "src/Core/VectorBlock.h" -#include "src/Core/Ref.h" -#include "src/Core/Transpose.h" -#include "src/Core/DiagonalMatrix.h" -#include "src/Core/Diagonal.h" -#include "src/Core/DiagonalProduct.h" -#include "src/Core/PermutationMatrix.h" -#include "src/Core/Transpositions.h" -#include "src/Core/Redux.h" -#include "src/Core/Visitor.h" -#include "src/Core/Fuzzy.h" -#include "src/Core/IO.h" -#include "src/Core/Swap.h" -#include "src/Core/CommaInitializer.h" -#include "src/Core/Flagged.h" -#include "src/Core/ProductBase.h" -#include "src/Core/GeneralProduct.h" -#include "src/Core/TriangularMatrix.h" -#include "src/Core/SelfAdjointView.h" -#include "src/Core/products/GeneralBlockPanelKernel.h" -#include "src/Core/products/Parallelizer.h" -#include "src/Core/products/CoeffBasedProduct.h" -#include "src/Core/products/GeneralMatrixVector.h" -#include "src/Core/products/GeneralMatrixMatrix.h" -#include "src/Core/SolveTriangular.h" -#include "src/Core/products/GeneralMatrixMatrixTriangular.h" -#include "src/Core/products/SelfadjointMatrixVector.h" -#include "src/Core/products/SelfadjointMatrixMatrix.h" -#include "src/Core/products/SelfadjointProduct.h" -#include "src/Core/products/SelfadjointRank2Update.h" -#include "src/Core/products/TriangularMatrixVector.h" -#include "src/Core/products/TriangularMatrixMatrix.h" -#include "src/Core/products/TriangularSolverMatrix.h" -#include "src/Core/products/TriangularSolverVector.h" -#include "src/Core/BandMatrix.h" -#include "src/Core/CoreIterators.h" - -#include "src/Core/BooleanRedux.h" -#include "src/Core/Select.h" -#include "src/Core/VectorwiseOp.h" -#include "src/Core/Random.h" -#include "src/Core/Replicate.h" -#include "src/Core/Reverse.h" -#include "src/Core/ArrayBase.h" -#include "src/Core/ArrayWrapper.h" - -#ifdef IMP_EIGEN_USE_BLAS -#include "src/Core/products/GeneralMatrixMatrix_MKL.h" -#include "src/Core/products/GeneralMatrixVector_MKL.h" -#include "src/Core/products/GeneralMatrixMatrixTriangular_MKL.h" -#include "src/Core/products/SelfadjointMatrixMatrix_MKL.h" -#include "src/Core/products/SelfadjointMatrixVector_MKL.h" -#include "src/Core/products/TriangularMatrixMatrix_MKL.h" -#include "src/Core/products/TriangularMatrixVector_MKL.h" -#include "src/Core/products/TriangularSolverMatrix_MKL.h" -#endif // IMP_EIGEN_USE_BLAS - -#ifdef IMP_EIGEN_USE_MKL_VML -#include "src/Core/Assign_MKL.h" -#endif - -#include "src/Core/GlobalFunctions.h" - -#include "src/Core/util/ReenableStupidWarnings.h" - -#ifdef IMP_EIGEN2_SUPPORT -#include "Eigen2Support" -#endif - -#endif // IMP_EIGEN_CORE_H diff --git a/modules/algebra/include/eigen3/Eigen/Dense b/modules/algebra/include/eigen3/Eigen/Dense deleted file mode 100644 index 5768910bd8..0000000000 --- a/modules/algebra/include/eigen3/Eigen/Dense +++ /dev/null @@ -1,7 +0,0 @@ -#include "Core" -#include "LU" -#include "Cholesky" -#include "QR" -#include "SVD" -#include "Geometry" -#include "Eigenvalues" diff --git a/modules/algebra/include/eigen3/Eigen/Eigen b/modules/algebra/include/eigen3/Eigen/Eigen deleted file mode 100644 index 19b40ea4e7..0000000000 --- a/modules/algebra/include/eigen3/Eigen/Eigen +++ /dev/null @@ -1,2 +0,0 @@ -#include "Dense" -//#include "Sparse" diff --git a/modules/algebra/include/eigen3/Eigen/Eigen2Support b/modules/algebra/include/eigen3/Eigen/Eigen2Support deleted file mode 100644 index dc606f3fac..0000000000 --- a/modules/algebra/include/eigen3/Eigen/Eigen2Support +++ /dev/null @@ -1,95 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2009 Gael Guennebaud -// -// 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 IMP_EIGEN2SUPPORT_H -#define IMP_EIGEN2SUPPORT_H - -#if (!defined(IMP_EIGEN2_SUPPORT)) || (!defined(IMP_EIGEN_CORE_H)) -#error Eigen2 support must be enabled by defining IMP_EIGEN2_SUPPORT before including any Eigen header -#endif - -#ifndef IMP_EIGEN_NO_EIGEN2_DEPRECATED_WARNING - -#if defined(__GNUC__) || defined(__INTEL_COMPILER) || defined(__clang__) -#warning "Eigen2 support is deprecated in Eigen 3.2.x and it will be removed in Eigen 3.3. (Define IMP_EIGEN_NO_EIGEN2_DEPRECATED_WARNING to disable this warning)" -#else -#pragma message ("Eigen2 support is deprecated in Eigen 3.2.x and it will be removed in Eigen 3.3. (Define IMP_EIGEN_NO_EIGEN2_DEPRECATED_WARNING to disable this warning)") -#endif - -#endif // IMP_EIGEN_NO_EIGEN2_DEPRECATED_WARNING - -#include "src/Core/util/DisableStupidWarnings.h" - -/** \ingroup Support_modules - * \defgroup Eigen2Support_Module Eigen2 support module - * - * \warning Eigen2 support is deprecated in Eigen 3.2.x and it will be removed in Eigen 3.3. - * - * This module provides a couple of deprecated functions improving the compatibility with Eigen2. - * - * To use it, define IMP_EIGEN2_SUPPORT before including any Eigen header - * \code - * #define IMP_EIGEN2_SUPPORT - * \endcode - * - */ - -#include "src/Eigen2Support/Macros.h" -#include "src/Eigen2Support/Memory.h" -#include "src/Eigen2Support/Meta.h" -#include "src/Eigen2Support/Lazy.h" -#include "src/Eigen2Support/Cwise.h" -#include "src/Eigen2Support/CwiseOperators.h" -#include "src/Eigen2Support/TriangularSolver.h" -#include "src/Eigen2Support/Block.h" -#include "src/Eigen2Support/VectorBlock.h" -#include "src/Eigen2Support/Minor.h" -#include "src/Eigen2Support/MathFunctions.h" - - -#include "src/Core/util/ReenableStupidWarnings.h" - -// Eigen2 used to include iostream -#include - -#define IMP_EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, SizeSuffix) \ -using IMP_Eigen::Matrix##SizeSuffix##TypeSuffix; \ -using IMP_Eigen::Vector##SizeSuffix##TypeSuffix; \ -using IMP_Eigen::RowVector##SizeSuffix##TypeSuffix; - -#define IMP_EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE(TypeSuffix) \ -IMP_EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, 2) \ -IMP_EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, 3) \ -IMP_EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, 4) \ -IMP_EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, X) \ - -#define IMP_EIGEN_USING_MATRIX_TYPEDEFS \ -IMP_EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE(i) \ -IMP_EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE(f) \ -IMP_EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE(d) \ -IMP_EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE(cf) \ -IMP_EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE(cd) - -#define USING_PART_OF_NAMESPACE_EIGEN \ -IMP_EIGEN_USING_MATRIX_TYPEDEFS \ -using IMP_Eigen::Matrix; \ -using IMP_Eigen::MatrixBase; \ -using IMP_Eigen::ei_random; \ -using IMP_Eigen::ei_real; \ -using IMP_Eigen::ei_imag; \ -using IMP_Eigen::ei_conj; \ -using IMP_Eigen::ei_abs; \ -using IMP_Eigen::ei_abs2; \ -using IMP_Eigen::ei_sqrt; \ -using IMP_Eigen::ei_exp; \ -using IMP_Eigen::ei_log; \ -using IMP_Eigen::ei_sin; \ -using IMP_Eigen::ei_cos; - -#endif // IMP_EIGEN2SUPPORT_H diff --git a/modules/algebra/include/eigen3/Eigen/Eigenvalues b/modules/algebra/include/eigen3/Eigen/Eigenvalues deleted file mode 100644 index 3ff0d27dba..0000000000 --- a/modules/algebra/include/eigen3/Eigen/Eigenvalues +++ /dev/null @@ -1,48 +0,0 @@ -#ifndef IMP_EIGEN_EIGENVALUES_MODULE_H -#define IMP_EIGEN_EIGENVALUES_MODULE_H - -#include "Core" - -#include "src/Core/util/DisableStupidWarnings.h" - -#include "Cholesky" -#include "Jacobi" -#include "Householder" -#include "LU" -#include "Geometry" - -/** \defgroup Eigenvalues_Module Eigenvalues module - * - * - * - * This module mainly provides various eigenvalue solvers. - * This module also provides some MatrixBase methods, including: - * - MatrixBase::eigenvalues(), - * - MatrixBase::operatorNorm() - * - * \code - * #include - * \endcode - */ - -#include "src/Eigenvalues/Tridiagonalization.h" -#include "src/Eigenvalues/RealSchur.h" -#include "src/Eigenvalues/EigenSolver.h" -#include "src/Eigenvalues/SelfAdjointEigenSolver.h" -#include "src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h" -#include "src/Eigenvalues/HessenbergDecomposition.h" -#include "src/Eigenvalues/ComplexSchur.h" -#include "src/Eigenvalues/ComplexEigenSolver.h" -#include "src/Eigenvalues/RealQZ.h" -#include "src/Eigenvalues/GeneralizedEigenSolver.h" -#include "src/Eigenvalues/MatrixBaseEigenvalues.h" -#ifdef IMP_EIGEN_USE_LAPACKE -#include "src/Eigenvalues/RealSchur_MKL.h" -#include "src/Eigenvalues/ComplexSchur_MKL.h" -#include "src/Eigenvalues/SelfAdjointEigenSolver_MKL.h" -#endif - -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif // IMP_EIGEN_EIGENVALUES_MODULE_H -/* vim: set filetype=cpp et sw=2 ts=2 ai: */ diff --git a/modules/algebra/include/eigen3/Eigen/Geometry b/modules/algebra/include/eigen3/Eigen/Geometry deleted file mode 100644 index 38e3479811..0000000000 --- a/modules/algebra/include/eigen3/Eigen/Geometry +++ /dev/null @@ -1,63 +0,0 @@ -#ifndef IMP_EIGEN_GEOMETRY_MODULE_H -#define IMP_EIGEN_GEOMETRY_MODULE_H - -#include "Core" - -#include "src/Core/util/DisableStupidWarnings.h" - -#include "SVD" -#include "LU" -#include - -#ifndef M_PI -#define M_PI 3.14159265358979323846 -#endif - -/** \defgroup Geometry_Module Geometry module - * - * - * - * This module provides support for: - * - fixed-size homogeneous transformations - * - translation, scaling, 2D and 3D rotations - * - quaternions - * - \ref MatrixBase::cross() "cross product" - * - \ref MatrixBase::unitOrthogonal() "orthognal vector generation" - * - some linear components: parametrized-lines and hyperplanes - * - * \code - * #include - * \endcode - */ - -#include "src/Geometry/OrthoMethods.h" -#include "src/Geometry/EulerAngles.h" - -#if IMP_EIGEN2_SUPPORT_STAGE > STAGE20_RESOLVE_API_CONFLICTS - #include "src/Geometry/Homogeneous.h" - #include "src/Geometry/RotationBase.h" - #include "src/Geometry/Rotation2D.h" - #include "src/Geometry/Quaternion.h" - #include "src/Geometry/AngleAxis.h" - #include "src/Geometry/Transform.h" - #include "src/Geometry/Translation.h" - #include "src/Geometry/Scaling.h" - #include "src/Geometry/Hyperplane.h" - #include "src/Geometry/ParametrizedLine.h" - #include "src/Geometry/AlignedBox.h" - #include "src/Geometry/Umeyama.h" - - #if defined IMP_EIGEN_VECTORIZE_SSE - #include "src/Geometry/arch/Geometry_SSE.h" - #endif -#endif - -#ifdef IMP_EIGEN2_SUPPORT -#include "src/Eigen2Support/Geometry/All.h" -#endif - -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif // IMP_EIGEN_GEOMETRY_MODULE_H -/* vim: set filetype=cpp et sw=2 ts=2 ai: */ - diff --git a/modules/algebra/include/eigen3/Eigen/Householder b/modules/algebra/include/eigen3/Eigen/Householder deleted file mode 100644 index 775a037e6b..0000000000 --- a/modules/algebra/include/eigen3/Eigen/Householder +++ /dev/null @@ -1,23 +0,0 @@ -#ifndef IMP_EIGEN_HOUSEHOLDER_MODULE_H -#define IMP_EIGEN_HOUSEHOLDER_MODULE_H - -#include "Core" - -#include "src/Core/util/DisableStupidWarnings.h" - -/** \defgroup Householder_Module Householder module - * This module provides Householder transformations. - * - * \code - * #include - * \endcode - */ - -#include "src/Householder/Householder.h" -#include "src/Householder/HouseholderSequence.h" -#include "src/Householder/BlockHouseholder.h" - -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif // IMP_EIGEN_HOUSEHOLDER_MODULE_H -/* vim: set filetype=cpp et sw=2 ts=2 ai: */ diff --git a/modules/algebra/include/eigen3/Eigen/IterativeLinearSolvers b/modules/algebra/include/eigen3/Eigen/IterativeLinearSolvers deleted file mode 100644 index 6ea17f3862..0000000000 --- a/modules/algebra/include/eigen3/Eigen/IterativeLinearSolvers +++ /dev/null @@ -1,40 +0,0 @@ -#ifndef IMP_EIGEN_ITERATIVELINEARSOLVERS_MODULE_H -#define IMP_EIGEN_ITERATIVELINEARSOLVERS_MODULE_H - -#include "SparseCore" -#include "OrderingMethods" - -#include "src/Core/util/DisableStupidWarnings.h" - -/** - * \defgroup IterativeLinearSolvers_Module IterativeLinearSolvers module - * - * This module currently provides iterative methods to solve problems of the form \c A \c x = \c b, where \c A is a squared matrix, usually very large and sparse. - * Those solvers are accessible via the following classes: - * - ConjugateGradient for selfadjoint (hermitian) matrices, - * - BiCGSTAB for general square matrices. - * - * These iterative solvers are associated with some preconditioners: - * - IdentityPreconditioner - not really useful - * - DiagonalPreconditioner - also called JAcobi preconditioner, work very well on diagonal dominant matrices. - * - IncompleteILUT - incomplete LU factorization with dual thresholding - * - * Such problems can also be solved using the direct sparse decomposition modules: SparseCholesky, CholmodSupport, UmfPackSupport, SuperLUSupport. - * - * \code - * #include - * \endcode - */ - -#include "src/misc/Solve.h" -#include "src/misc/SparseSolve.h" - -#include "src/IterativeLinearSolvers/IterativeSolverBase.h" -#include "src/IterativeLinearSolvers/BasicPreconditioners.h" -#include "src/IterativeLinearSolvers/ConjugateGradient.h" -#include "src/IterativeLinearSolvers/BiCGSTAB.h" -#include "src/IterativeLinearSolvers/IncompleteLUT.h" - -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif // IMP_EIGEN_ITERATIVELINEARSOLVERS_MODULE_H diff --git a/modules/algebra/include/eigen3/Eigen/Jacobi b/modules/algebra/include/eigen3/Eigen/Jacobi deleted file mode 100644 index 2ec621160a..0000000000 --- a/modules/algebra/include/eigen3/Eigen/Jacobi +++ /dev/null @@ -1,26 +0,0 @@ -#ifndef IMP_EIGEN_JACOBI_MODULE_H -#define IMP_EIGEN_JACOBI_MODULE_H - -#include "Core" - -#include "src/Core/util/DisableStupidWarnings.h" - -/** \defgroup Jacobi_Module Jacobi module - * This module provides Jacobi and Givens rotations. - * - * \code - * #include - * \endcode - * - * In addition to listed classes, it defines the two following MatrixBase methods to apply a Jacobi or Givens rotation: - * - MatrixBase::applyOnTheLeft() - * - MatrixBase::applyOnTheRight(). - */ - -#include "src/Jacobi/Jacobi.h" - -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif // IMP_EIGEN_JACOBI_MODULE_H -/* vim: set filetype=cpp et sw=2 ts=2 ai: */ - diff --git a/modules/algebra/include/eigen3/Eigen/LU b/modules/algebra/include/eigen3/Eigen/LU deleted file mode 100644 index d2f3301998..0000000000 --- a/modules/algebra/include/eigen3/Eigen/LU +++ /dev/null @@ -1,41 +0,0 @@ -#ifndef IMP_EIGEN_LU_MODULE_H -#define IMP_EIGEN_LU_MODULE_H - -#include "Core" - -#include "src/Core/util/DisableStupidWarnings.h" - -/** \defgroup LU_Module LU module - * This module includes %LU decomposition and related notions such as matrix inversion and determinant. - * This module defines the following MatrixBase methods: - * - MatrixBase::inverse() - * - MatrixBase::determinant() - * - * \code - * #include - * \endcode - */ - -#include "src/misc/Solve.h" -#include "src/misc/Kernel.h" -#include "src/misc/Image.h" -#include "src/LU/FullPivLU.h" -#include "src/LU/PartialPivLU.h" -#ifdef IMP_EIGEN_USE_LAPACKE -#include "src/LU/PartialPivLU_MKL.h" -#endif -#include "src/LU/Determinant.h" -#include "src/LU/Inverse.h" - -#if defined IMP_EIGEN_VECTORIZE_SSE - #include "src/LU/arch/Inverse_SSE.h" -#endif - -#ifdef IMP_EIGEN2_SUPPORT - #include "src/Eigen2Support/LU.h" -#endif - -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif // IMP_EIGEN_LU_MODULE_H -/* vim: set filetype=cpp et sw=2 ts=2 ai: */ diff --git a/modules/algebra/include/eigen3/Eigen/LeastSquares b/modules/algebra/include/eigen3/Eigen/LeastSquares deleted file mode 100644 index 71ab5b4b44..0000000000 --- a/modules/algebra/include/eigen3/Eigen/LeastSquares +++ /dev/null @@ -1,32 +0,0 @@ -#ifndef IMP_EIGEN_REGRESSION_MODULE_H -#define IMP_EIGEN_REGRESSION_MODULE_H - -#ifndef IMP_EIGEN2_SUPPORT -#error LeastSquares is only available in Eigen2 support mode (define IMP_EIGEN2_SUPPORT) -#endif - -// exclude from normal eigen3-only documentation -#ifdef IMP_EIGEN2_SUPPORT - -#include "Core" - -#include "src/Core/util/DisableStupidWarnings.h" - -#include "Eigenvalues" -#include "Geometry" - -/** \defgroup LeastSquares_Module LeastSquares module - * This module provides linear regression and related features. - * - * \code - * #include - * \endcode - */ - -#include "src/Eigen2Support/LeastSquares.h" - -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif // IMP_EIGEN2_SUPPORT - -#endif // IMP_EIGEN_REGRESSION_MODULE_H diff --git a/modules/algebra/include/eigen3/Eigen/MetisSupport b/modules/algebra/include/eigen3/Eigen/MetisSupport deleted file mode 100644 index 540f1c08a6..0000000000 --- a/modules/algebra/include/eigen3/Eigen/MetisSupport +++ /dev/null @@ -1,28 +0,0 @@ -#ifndef IMP_EIGEN_METISSUPPORT_MODULE_H -#define IMP_EIGEN_METISSUPPORT_MODULE_H - -#include "SparseCore" - -#include "src/Core/util/DisableStupidWarnings.h" - -extern "C" { -#include -} - - -/** \ingroup Support_modules - * \defgroup MetisSupport_Module MetisSupport module - * - * \code - * #include - * \endcode - * This module defines an interface to the METIS reordering package (http://glaros.dtc.umn.edu/gkhome/views/metis). - * It can be used just as any other built-in method as explained in \link OrderingMethods_Module here. \endlink - */ - - -#include "src/MetisSupport/MetisSupport.h" - -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif // IMP_EIGEN_METISSUPPORT_MODULE_H diff --git a/modules/algebra/include/eigen3/Eigen/OrderingMethods b/modules/algebra/include/eigen3/Eigen/OrderingMethods deleted file mode 100644 index 406e273cb5..0000000000 --- a/modules/algebra/include/eigen3/Eigen/OrderingMethods +++ /dev/null @@ -1,66 +0,0 @@ -#ifndef IMP_EIGEN_ORDERINGMETHODS_MODULE_H -#define IMP_EIGEN_ORDERINGMETHODS_MODULE_H - -#include "SparseCore" - -#include "src/Core/util/DisableStupidWarnings.h" - -/** - * \defgroup OrderingMethods_Module OrderingMethods module - * - * This module is currently for internal use only - * - * It defines various built-in and external ordering methods for sparse matrices. - * They are typically used to reduce the number of elements during - * the sparse matrix decomposition (LLT, LU, QR). - * Precisely, in a preprocessing step, a permutation matrix P is computed using - * those ordering methods and applied to the columns of the matrix. - * Using for instance the sparse Cholesky decomposition, it is expected that - * the nonzeros elements in LLT(A*P) will be much smaller than that in LLT(A). - * - * - * Usage : - * \code - * #include - * \endcode - * - * A simple usage is as a template parameter in the sparse decomposition classes : - * - * \code - * SparseLU > solver; - * \endcode - * - * \code - * SparseQR > solver; - * \endcode - * - * It is possible as well to call directly a particular ordering method for your own purpose, - * \code - * AMDOrdering ordering; - * PermutationMatrix perm; - * SparseMatrix A; - * //Fill the matrix ... - * - * ordering(A, perm); // Call AMD - * \endcode - * - * \note Some of these methods (like AMD or METIS), need the sparsity pattern - * of the input matrix to be symmetric. When the matrix is structurally unsymmetric, - * Eigen computes internally the pattern of \f$A^T*A\f$ before calling the method. - * If your matrix is already symmetric (at leat in structure), you can avoid that - * by calling the method with a SelfAdjointView type. - * - * \code - * // Call the ordering on the pattern of the lower triangular matrix A - * ordering(A.selfadjointView(), perm); - * \endcode - */ - -#ifndef IMP_EIGEN_MPL2_ONLY -#include "src/OrderingMethods/Amd.h" -#endif - -#include "src/OrderingMethods/Ordering.h" -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif // IMP_EIGEN_ORDERINGMETHODS_MODULE_H diff --git a/modules/algebra/include/eigen3/Eigen/PaStiXSupport b/modules/algebra/include/eigen3/Eigen/PaStiXSupport deleted file mode 100644 index fb3a1df521..0000000000 --- a/modules/algebra/include/eigen3/Eigen/PaStiXSupport +++ /dev/null @@ -1,46 +0,0 @@ -#ifndef IMP_EIGEN_PASTIXSUPPORT_MODULE_H -#define IMP_EIGEN_PASTIXSUPPORT_MODULE_H - -#include "SparseCore" - -#include "src/Core/util/DisableStupidWarnings.h" - -#include -extern "C" { -#include -#include -} - -#ifdef complex -#undef complex -#endif - -/** \ingroup Support_modules - * \defgroup PaStiXSupport_Module PaStiXSupport module - * - * This module provides an interface to the PaSTiX library. - * PaSTiX is a general \b supernodal, \b parallel and \b opensource sparse solver. - * It provides the two following main factorization classes: - * - class PastixLLT : a supernodal, parallel LLt Cholesky factorization. - * - class PastixLDLT: a supernodal, parallel LDLt Cholesky factorization. - * - class PastixLU : a supernodal, parallel LU factorization (optimized for a symmetric pattern). - * - * \code - * #include - * \endcode - * - * In order to use this module, the PaSTiX headers must be accessible from the include paths, and your binary must be linked to the PaSTiX library and its dependencies. - * The dependencies depend on how PaSTiX has been compiled. - * For a cmake based project, you can use our FindPaSTiX.cmake module to help you in this task. - * - */ - -#include "src/misc/Solve.h" -#include "src/misc/SparseSolve.h" - -#include "src/PaStiXSupport/PaStiXSupport.h" - - -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif // IMP_EIGEN_PASTIXSUPPORT_MODULE_H diff --git a/modules/algebra/include/eigen3/Eigen/PardisoSupport b/modules/algebra/include/eigen3/Eigen/PardisoSupport deleted file mode 100644 index 3e5a48433c..0000000000 --- a/modules/algebra/include/eigen3/Eigen/PardisoSupport +++ /dev/null @@ -1,30 +0,0 @@ -#ifndef IMP_EIGEN_PARDISOSUPPORT_MODULE_H -#define IMP_EIGEN_PARDISOSUPPORT_MODULE_H - -#include "SparseCore" - -#include "src/Core/util/DisableStupidWarnings.h" - -#include - -#include - -/** \ingroup Support_modules - * \defgroup PardisoSupport_Module PardisoSupport module - * - * This module brings support for the Intel(R) MKL PARDISO direct sparse solvers. - * - * \code - * #include - * \endcode - * - * In order to use this module, the MKL headers must be accessible from the include paths, and your binary must be linked to the MKL library and its dependencies. - * See this \ref TopicUsingIntelMKL "page" for more information on MKL-Eigen integration. - * - */ - -#include "src/PardisoSupport/PardisoSupport.h" - -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif // IMP_EIGEN_PARDISOSUPPORT_MODULE_H diff --git a/modules/algebra/include/eigen3/Eigen/QR b/modules/algebra/include/eigen3/Eigen/QR deleted file mode 100644 index c3849c74d3..0000000000 --- a/modules/algebra/include/eigen3/Eigen/QR +++ /dev/null @@ -1,45 +0,0 @@ -#ifndef IMP_EIGEN_QR_MODULE_H -#define IMP_EIGEN_QR_MODULE_H - -#include "Core" - -#include "src/Core/util/DisableStupidWarnings.h" - -#include "Cholesky" -#include "Jacobi" -#include "Householder" - -/** \defgroup QR_Module QR module - * - * - * - * This module provides various QR decompositions - * This module also provides some MatrixBase methods, including: - * - MatrixBase::qr(), - * - * \code - * #include - * \endcode - */ - -#include "src/misc/Solve.h" -#include "src/QR/HouseholderQR.h" -#include "src/QR/FullPivHouseholderQR.h" -#include "src/QR/ColPivHouseholderQR.h" -#ifdef IMP_EIGEN_USE_LAPACKE -#include "src/QR/HouseholderQR_MKL.h" -#include "src/QR/ColPivHouseholderQR_MKL.h" -#endif - -#ifdef IMP_EIGEN2_SUPPORT -#include "src/Eigen2Support/QR.h" -#endif - -#include "src/Core/util/ReenableStupidWarnings.h" - -#ifdef IMP_EIGEN2_SUPPORT -#include "Eigenvalues" -#endif - -#endif // IMP_EIGEN_QR_MODULE_H -/* vim: set filetype=cpp et sw=2 ts=2 ai: */ diff --git a/modules/algebra/include/eigen3/Eigen/QtAlignedMalloc b/modules/algebra/include/eigen3/Eigen/QtAlignedMalloc deleted file mode 100644 index 6bcd1c4d68..0000000000 --- a/modules/algebra/include/eigen3/Eigen/QtAlignedMalloc +++ /dev/null @@ -1,34 +0,0 @@ - -#ifndef IMP_EIGEN_QTMALLOC_MODULE_H -#define IMP_EIGEN_QTMALLOC_MODULE_H - -#include "Core" - -#if (!IMP_EIGEN_MALLOC_ALREADY_ALIGNED) - -#include "src/Core/util/DisableStupidWarnings.h" - -void *qMalloc(size_t size) -{ - return IMP_Eigen::internal::aligned_malloc(size); -} - -void qFree(void *ptr) -{ - IMP_Eigen::internal::aligned_free(ptr); -} - -void *qRealloc(void *ptr, size_t size) -{ - void* newPtr = IMP_Eigen::internal::aligned_malloc(size); - memcpy(newPtr, ptr, size); - IMP_Eigen::internal::aligned_free(ptr); - return newPtr; -} - -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif - -#endif // IMP_EIGEN_QTMALLOC_MODULE_H -/* vim: set filetype=cpp et sw=2 ts=2 ai: */ diff --git a/modules/algebra/include/eigen3/Eigen/SPQRSupport b/modules/algebra/include/eigen3/Eigen/SPQRSupport deleted file mode 100644 index c7dec27f91..0000000000 --- a/modules/algebra/include/eigen3/Eigen/SPQRSupport +++ /dev/null @@ -1,29 +0,0 @@ -#ifndef IMP_EIGEN_SPQRSUPPORT_MODULE_H -#define IMP_EIGEN_SPQRSUPPORT_MODULE_H - -#include "SparseCore" - -#include "src/Core/util/DisableStupidWarnings.h" - -#include "SuiteSparseQR.hpp" - -/** \ingroup Support_modules - * \defgroup SPQRSupport_Module SuiteSparseQR module - * - * This module provides an interface to the SPQR library, which is part of the suitesparse package. - * - * \code - * #include - * \endcode - * - * In order to use this module, the SPQR headers must be accessible from the include paths, and your binary must be linked to the SPQR library and its dependencies (Cholmod, AMD, COLAMD,...). - * For a cmake based project, you can use our FindSPQR.cmake and FindCholmod.Cmake modules - * - */ - -#include "src/misc/Solve.h" -#include "src/misc/SparseSolve.h" -#include "src/CholmodSupport/CholmodSupport.h" -#include "src/SPQRSupport/SuiteSparseQRSupport.h" - -#endif diff --git a/modules/algebra/include/eigen3/Eigen/SVD b/modules/algebra/include/eigen3/Eigen/SVD deleted file mode 100644 index b3141521d5..0000000000 --- a/modules/algebra/include/eigen3/Eigen/SVD +++ /dev/null @@ -1,37 +0,0 @@ -#ifndef IMP_EIGEN_SVD_MODULE_H -#define IMP_EIGEN_SVD_MODULE_H - -#include "QR" -#include "Householder" -#include "Jacobi" - -#include "src/Core/util/DisableStupidWarnings.h" - -/** \defgroup SVD_Module SVD module - * - * - * - * This module provides SVD decomposition for matrices (both real and complex). - * This decomposition is accessible via the following MatrixBase method: - * - MatrixBase::jacobiSvd() - * - * \code - * #include - * \endcode - */ - -#include "src/misc/Solve.h" -#include "src/SVD/JacobiSVD.h" -#if defined(IMP_EIGEN_USE_LAPACKE) && !defined(IMP_EIGEN_USE_LAPACKE_STRICT) -#include "src/SVD/JacobiSVD_MKL.h" -#endif -#include "src/SVD/UpperBidiagonalization.h" - -#ifdef IMP_EIGEN2_SUPPORT -#include "src/Eigen2Support/SVD.h" -#endif - -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif // IMP_EIGEN_SVD_MODULE_H -/* vim: set filetype=cpp et sw=2 ts=2 ai: */ diff --git a/modules/algebra/include/eigen3/Eigen/Sparse b/modules/algebra/include/eigen3/Eigen/Sparse deleted file mode 100644 index 484ec8f1fe..0000000000 --- a/modules/algebra/include/eigen3/Eigen/Sparse +++ /dev/null @@ -1,27 +0,0 @@ -#ifndef IMP_EIGEN_SPARSE_MODULE_H -#define IMP_EIGEN_SPARSE_MODULE_H - -/** \defgroup Sparse_Module Sparse meta-module - * - * Meta-module including all related modules: - * - \ref SparseCore_Module - * - \ref OrderingMethods_Module - * - \ref SparseCholesky_Module - * - \ref SparseLU_Module - * - \ref SparseQR_Module - * - \ref IterativeLinearSolvers_Module - * - * \code - * #include - * \endcode - */ - -#include "SparseCore" -#include "OrderingMethods" -#include "SparseCholesky" -#include "SparseLU" -#include "SparseQR" -#include "IterativeLinearSolvers" - -#endif // IMP_EIGEN_SPARSE_MODULE_H - diff --git a/modules/algebra/include/eigen3/Eigen/SparseCholesky b/modules/algebra/include/eigen3/Eigen/SparseCholesky deleted file mode 100644 index e124da8a9d..0000000000 --- a/modules/algebra/include/eigen3/Eigen/SparseCholesky +++ /dev/null @@ -1,47 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008-2013 Gael Guennebaud -// -// 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 IMP_EIGEN_SPARSECHOLESKY_MODULE_H -#define IMP_EIGEN_SPARSECHOLESKY_MODULE_H - -#include "SparseCore" -#include "OrderingMethods" - -#include "src/Core/util/DisableStupidWarnings.h" - -/** - * \defgroup SparseCholesky_Module SparseCholesky module - * - * This module currently provides two variants of the direct sparse Cholesky decomposition for selfadjoint (hermitian) matrices. - * Those decompositions are accessible via the following classes: - * - SimplicialLLt, - * - SimplicialLDLt - * - * Such problems can also be solved using the ConjugateGradient solver from the IterativeLinearSolvers module. - * - * \code - * #include - * \endcode - */ - -#ifdef IMP_EIGEN_MPL2_ONLY -#error The SparseCholesky module has nothing to offer in MPL2 only mode -#endif - -#include "src/misc/Solve.h" -#include "src/misc/SparseSolve.h" -#include "src/SparseCholesky/SimplicialCholesky.h" - -#ifndef IMP_EIGEN_MPL2_ONLY -#include "src/SparseCholesky/SimplicialCholesky_impl.h" -#endif - -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif // IMP_EIGEN_SPARSECHOLESKY_MODULE_H diff --git a/modules/algebra/include/eigen3/Eigen/SparseCore b/modules/algebra/include/eigen3/Eigen/SparseCore deleted file mode 100644 index d7ff286de4..0000000000 --- a/modules/algebra/include/eigen3/Eigen/SparseCore +++ /dev/null @@ -1,64 +0,0 @@ -#ifndef IMP_EIGEN_SPARSECORE_MODULE_H -#define IMP_EIGEN_SPARSECORE_MODULE_H - -#include "Core" - -#include "src/Core/util/DisableStupidWarnings.h" - -#include -#include -#include -#include -#include - -/** - * \defgroup SparseCore_Module SparseCore module - * - * This module provides a sparse matrix representation, and basic associated matrix manipulations - * and operations. - * - * See the \ref TutorialSparse "Sparse tutorial" - * - * \code - * #include - * \endcode - * - * This module depends on: Core. - */ - -namespace IMP_Eigen { - -/** The type used to identify a general sparse storage. */ -struct Sparse {}; - -} - -#include "src/SparseCore/SparseUtil.h" -#include "src/SparseCore/SparseMatrixBase.h" -#include "src/SparseCore/CompressedStorage.h" -#include "src/SparseCore/AmbiVector.h" -#include "src/SparseCore/SparseMatrix.h" -#include "src/SparseCore/MappedSparseMatrix.h" -#include "src/SparseCore/SparseVector.h" -#include "src/SparseCore/SparseBlock.h" -#include "src/SparseCore/SparseTranspose.h" -#include "src/SparseCore/SparseCwiseUnaryOp.h" -#include "src/SparseCore/SparseCwiseBinaryOp.h" -#include "src/SparseCore/SparseDot.h" -#include "src/SparseCore/SparsePermutation.h" -#include "src/SparseCore/SparseRedux.h" -#include "src/SparseCore/SparseFuzzy.h" -#include "src/SparseCore/ConservativeSparseSparseProduct.h" -#include "src/SparseCore/SparseSparseProductWithPruning.h" -#include "src/SparseCore/SparseProduct.h" -#include "src/SparseCore/SparseDenseProduct.h" -#include "src/SparseCore/SparseDiagonalProduct.h" -#include "src/SparseCore/SparseTriangularView.h" -#include "src/SparseCore/SparseSelfAdjointView.h" -#include "src/SparseCore/TriangularSolver.h" -#include "src/SparseCore/SparseView.h" - -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif // IMP_EIGEN_SPARSECORE_MODULE_H - diff --git a/modules/algebra/include/eigen3/Eigen/SparseLU b/modules/algebra/include/eigen3/Eigen/SparseLU deleted file mode 100644 index b85403ead3..0000000000 --- a/modules/algebra/include/eigen3/Eigen/SparseLU +++ /dev/null @@ -1,49 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2012 Désiré Nuentsa-Wakam -// Copyright (C) 2012 Gael Guennebaud -// -// 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 IMP_EIGEN_SPARSELU_MODULE_H -#define IMP_EIGEN_SPARSELU_MODULE_H - -#include "SparseCore" - -/** - * \defgroup SparseLU_Module SparseLU module - * This module defines a supernodal factorization of general sparse matrices. - * The code is fully optimized for supernode-panel updates with specialized kernels. - * Please, see the documentation of the SparseLU class for more details. - */ - -#include "src/misc/Solve.h" -#include "src/misc/SparseSolve.h" - -// Ordering interface -#include "OrderingMethods" - -#include "src/SparseLU/SparseLU_gemm_kernel.h" - -#include "src/SparseLU/SparseLU_Structs.h" -#include "src/SparseLU/SparseLU_SupernodalMatrix.h" -#include "src/SparseLU/SparseLUImpl.h" -#include "src/SparseCore/SparseColEtree.h" -#include "src/SparseLU/SparseLU_Memory.h" -#include "src/SparseLU/SparseLU_heap_relax_snode.h" -#include "src/SparseLU/SparseLU_relax_snode.h" -#include "src/SparseLU/SparseLU_pivotL.h" -#include "src/SparseLU/SparseLU_panel_dfs.h" -#include "src/SparseLU/SparseLU_kernel_bmod.h" -#include "src/SparseLU/SparseLU_panel_bmod.h" -#include "src/SparseLU/SparseLU_column_dfs.h" -#include "src/SparseLU/SparseLU_column_bmod.h" -#include "src/SparseLU/SparseLU_copy_to_ucol.h" -#include "src/SparseLU/SparseLU_pruneL.h" -#include "src/SparseLU/SparseLU_Utils.h" -#include "src/SparseLU/SparseLU.h" - -#endif // IMP_EIGEN_SPARSELU_MODULE_H diff --git a/modules/algebra/include/eigen3/Eigen/SparseQR b/modules/algebra/include/eigen3/Eigen/SparseQR deleted file mode 100644 index 3253ebd5de..0000000000 --- a/modules/algebra/include/eigen3/Eigen/SparseQR +++ /dev/null @@ -1,33 +0,0 @@ -#ifndef IMP_EIGEN_SPARSEQR_MODULE_H -#define IMP_EIGEN_SPARSEQR_MODULE_H - -#include "SparseCore" -#include "OrderingMethods" -#include "src/Core/util/DisableStupidWarnings.h" - -/** \defgroup SparseQR_Module SparseQR module - * \brief Provides QR decomposition for sparse matrices - * - * This module provides a simplicial version of the left-looking Sparse QR decomposition. - * The columns of the input matrix should be reordered to limit the fill-in during the - * decomposition. Built-in methods (COLAMD, AMD) or external methods (METIS) can be used to this end. - * See the \link OrderingMethods_Module OrderingMethods\endlink module for the list - * of built-in and external ordering methods. - * - * \code - * #include - * \endcode - * - * - */ - -#include "src/misc/Solve.h" -#include "src/misc/SparseSolve.h" - -#include "OrderingMethods" -#include "src/SparseCore/SparseColEtree.h" -#include "src/SparseQR/SparseQR.h" - -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif diff --git a/modules/algebra/include/eigen3/Eigen/StdDeque b/modules/algebra/include/eigen3/Eigen/StdDeque deleted file mode 100644 index 90a8d873bd..0000000000 --- a/modules/algebra/include/eigen3/Eigen/StdDeque +++ /dev/null @@ -1,27 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2009 Gael Guennebaud -// Copyright (C) 2009 Hauke Heibel -// -// 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 IMP_EIGEN_STDDEQUE_MODULE_H -#define IMP_EIGEN_STDDEQUE_MODULE_H - -#include "Core" -#include - -#if (defined(_MSC_VER) && defined(_WIN64)) /* MSVC auto aligns in 64 bit builds */ - -#define IMP_EIGEN_DEFINE_STL_DEQUE_SPECIALIZATION(...) - -#else - -#include "src/StlSupport/StdDeque.h" - -#endif - -#endif // IMP_EIGEN_STDDEQUE_MODULE_H diff --git a/modules/algebra/include/eigen3/Eigen/StdList b/modules/algebra/include/eigen3/Eigen/StdList deleted file mode 100644 index 1655a1ccf0..0000000000 --- a/modules/algebra/include/eigen3/Eigen/StdList +++ /dev/null @@ -1,26 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2009 Hauke Heibel -// -// 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 IMP_EIGEN_STDLIST_MODULE_H -#define IMP_EIGEN_STDLIST_MODULE_H - -#include "Core" -#include - -#if (defined(_MSC_VER) && defined(_WIN64)) /* MSVC auto aligns in 64 bit builds */ - -#define IMP_EIGEN_DEFINE_STL_LIST_SPECIALIZATION(...) - -#else - -#include "src/StlSupport/StdList.h" - -#endif - -#endif // IMP_EIGEN_STDLIST_MODULE_H diff --git a/modules/algebra/include/eigen3/Eigen/StdVector b/modules/algebra/include/eigen3/Eigen/StdVector deleted file mode 100644 index 7986d6ccf7..0000000000 --- a/modules/algebra/include/eigen3/Eigen/StdVector +++ /dev/null @@ -1,27 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2009 Gael Guennebaud -// Copyright (C) 2009 Hauke Heibel -// -// 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 IMP_EIGEN_STDVECTOR_MODULE_H -#define IMP_EIGEN_STDVECTOR_MODULE_H - -#include "Core" -#include - -#if (defined(_MSC_VER) && defined(_WIN64)) /* MSVC auto aligns in 64 bit builds */ - -#define IMP_EIGEN_DEFINE_STL_VECTOR_SPECIALIZATION(...) - -#else - -#include "src/StlSupport/StdVector.h" - -#endif - -#endif // IMP_EIGEN_STDVECTOR_MODULE_H diff --git a/modules/algebra/include/eigen3/Eigen/SuperLUSupport b/modules/algebra/include/eigen3/Eigen/SuperLUSupport deleted file mode 100644 index 0d309fc4bf..0000000000 --- a/modules/algebra/include/eigen3/Eigen/SuperLUSupport +++ /dev/null @@ -1,59 +0,0 @@ -#ifndef IMP_EIGEN_SUPERLUSUPPORT_MODULE_H -#define IMP_EIGEN_SUPERLUSUPPORT_MODULE_H - -#include "SparseCore" - -#include "src/Core/util/DisableStupidWarnings.h" - -#ifdef EMPTY -#define IMP_EIGEN_EMPTY_WAS_ALREADY_DEFINED -#endif - -typedef int int_t; -#include -#include -#include - -// slu_util.h defines a preprocessor token named EMPTY which is really polluting, -// so we remove it in favor of a SUPERLU_EMPTY token. -// If EMPTY was already defined then we don't undef it. - -#if defined(IMP_EIGEN_EMPTY_WAS_ALREADY_DEFINED) -# undef IMP_EIGEN_EMPTY_WAS_ALREADY_DEFINED -#elif defined(EMPTY) -# undef EMPTY -#endif - -#define SUPERLU_EMPTY (-1) - -namespace IMP_Eigen { struct SluMatrix; } - -/** \ingroup Support_modules - * \defgroup SuperLUSupport_Module SuperLUSupport module - * - * This module provides an interface to the SuperLU library. - * It provides the following factorization class: - * - class SuperLU: a supernodal sequential LU factorization. - * - class SuperILU: a supernodal sequential incomplete LU factorization (to be used as a preconditioner for iterative methods). - * - * \warning When including this module, you have to use SUPERLU_EMPTY instead of EMPTY which is no longer defined because it is too polluting. - * - * \code - * #include - * \endcode - * - * In order to use this module, the superlu headers must be accessible from the include paths, and your binary must be linked to the superlu library and its dependencies. - * The dependencies depend on how superlu has been compiled. - * For a cmake based project, you can use our FindSuperLU.cmake module to help you in this task. - * - */ - -#include "src/misc/Solve.h" -#include "src/misc/SparseSolve.h" - -#include "src/SuperLUSupport/SuperLUSupport.h" - - -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif // IMP_EIGEN_SUPERLUSUPPORT_MODULE_H diff --git a/modules/algebra/include/eigen3/Eigen/UmfPackSupport b/modules/algebra/include/eigen3/Eigen/UmfPackSupport deleted file mode 100644 index 94ec636f2d..0000000000 --- a/modules/algebra/include/eigen3/Eigen/UmfPackSupport +++ /dev/null @@ -1,36 +0,0 @@ -#ifndef IMP_EIGEN_UMFPACKSUPPORT_MODULE_H -#define IMP_EIGEN_UMFPACKSUPPORT_MODULE_H - -#include "SparseCore" - -#include "src/Core/util/DisableStupidWarnings.h" - -extern "C" { -#include -} - -/** \ingroup Support_modules - * \defgroup UmfPackSupport_Module UmfPackSupport module - * - * This module provides an interface to the UmfPack library which is part of the suitesparse package. - * It provides the following factorization class: - * - class UmfPackLU: a multifrontal sequential LU factorization. - * - * \code - * #include - * \endcode - * - * In order to use this module, the umfpack headers must be accessible from the include paths, and your binary must be linked to the umfpack library and its dependencies. - * The dependencies depend on how umfpack has been compiled. - * For a cmake based project, you can use our FindUmfPack.cmake module to help you in this task. - * - */ - -#include "src/misc/Solve.h" -#include "src/misc/SparseSolve.h" - -#include "src/UmfPackSupport/UmfPackSupport.h" - -#include "src/Core/util/ReenableStupidWarnings.h" - -#endif // IMP_EIGEN_UMFPACKSUPPORT_MODULE_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Cholesky/LDLT.h b/modules/algebra/include/eigen3/Eigen/src/Cholesky/LDLT.h deleted file mode 100644 index f9b7a37d10..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Cholesky/LDLT.h +++ /dev/null @@ -1,611 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008-2011 Gael Guennebaud -// Copyright (C) 2009 Keir Mierle -// Copyright (C) 2009 Benoit Jacob -// Copyright (C) 2011 Timothy E. Holy -// -// 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 IMP_EIGEN_LDLT_H -#define IMP_EIGEN_LDLT_H - -namespace IMP_Eigen { - -namespace internal { - template struct LDLT_Traits; - - // PositiveSemiDef means positive semi-definite and non-zero; same for NegativeSemiDef - enum SignMatrix { PositiveSemiDef, NegativeSemiDef, ZeroSign, Indefinite }; -} - -/** \ingroup Cholesky_Module - * - * \class LDLT - * - * \brief Robust Cholesky decomposition of a matrix with pivoting - * - * \param MatrixType the type of the matrix of which to compute the LDL^T Cholesky decomposition - * \param UpLo the triangular part that will be used for the decompositon: Lower (default) or Upper. - * The other triangular part won't be read. - * - * Perform a robust Cholesky decomposition of a positive semidefinite or negative semidefinite - * matrix \f$ A \f$ such that \f$ A = P^TLDL^*P \f$, where P is a permutation matrix, L - * is lower triangular with a unit diagonal and D is a diagonal matrix. - * - * The decomposition uses pivoting to ensure stability, so that L will have - * zeros in the bottom right rank(A) - n submatrix. Avoiding the square root - * on D also stabilizes the computation. - * - * Remember that Cholesky decompositions are not rank-revealing. Also, do not use a Cholesky - * decomposition to determine whether a system of equations has a solution. - * - * \sa MatrixBase::ldlt(), class LLT - */ -template class LDLT -{ - public: - typedef _MatrixType MatrixType; - enum { - RowsAtCompileTime = MatrixType::RowsAtCompileTime, - ColsAtCompileTime = MatrixType::ColsAtCompileTime, - Options = MatrixType::Options & ~RowMajorBit, // these are the options for the TmpMatrixType, we need a ColMajor matrix here! - MaxRowsAtCompileTime = MatrixType::MaxRowsAtCompileTime, - MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime, - UpLo = _UpLo - }; - typedef typename MatrixType::Scalar Scalar; - typedef typename NumTraits::Real RealScalar; - typedef typename MatrixType::Index Index; - typedef Matrix TmpMatrixType; - - typedef Transpositions TranspositionType; - typedef PermutationMatrix PermutationType; - - typedef internal::LDLT_Traits Traits; - - /** \brief Default Constructor. - * - * The default constructor is useful in cases in which the user intends to - * perform decompositions via LDLT::compute(const MatrixType&). - */ - LDLT() - : m_matrix(), - m_transpositions(), - m_sign(internal::ZeroSign), - m_isInitialized(false) - {} - - /** \brief Default Constructor with memory preallocation - * - * Like the default constructor but with preallocation of the internal data - * according to the specified problem \a size. - * \sa LDLT() - */ - LDLT(Index size) - : m_matrix(size, size), - m_transpositions(size), - m_temporary(size), - m_sign(internal::ZeroSign), - m_isInitialized(false) - {} - - /** \brief Constructor with decomposition - * - * This calculates the decomposition for the input \a matrix. - * \sa LDLT(Index size) - */ - LDLT(const MatrixType& matrix) - : m_matrix(matrix.rows(), matrix.cols()), - m_transpositions(matrix.rows()), - m_temporary(matrix.rows()), - m_sign(internal::ZeroSign), - m_isInitialized(false) - { - compute(matrix); - } - - /** Clear any existing decomposition - * \sa rankUpdate(w,sigma) - */ - void setZero() - { - m_isInitialized = false; - } - - /** \returns a view of the upper triangular matrix U */ - inline typename Traits::MatrixU matrixU() const - { - imp_eigen_assert(m_isInitialized && "LDLT is not initialized."); - return Traits::getU(m_matrix); - } - - /** \returns a view of the lower triangular matrix L */ - inline typename Traits::MatrixL matrixL() const - { - imp_eigen_assert(m_isInitialized && "LDLT is not initialized."); - return Traits::getL(m_matrix); - } - - /** \returns the permutation matrix P as a transposition sequence. - */ - inline const TranspositionType& transpositionsP() const - { - imp_eigen_assert(m_isInitialized && "LDLT is not initialized."); - return m_transpositions; - } - - /** \returns the coefficients of the diagonal matrix D */ - inline Diagonal vectorD() const - { - imp_eigen_assert(m_isInitialized && "LDLT is not initialized."); - return m_matrix.diagonal(); - } - - /** \returns true if the matrix is positive (semidefinite) */ - inline bool isPositive() const - { - imp_eigen_assert(m_isInitialized && "LDLT is not initialized."); - return m_sign == internal::PositiveSemiDef || m_sign == internal::ZeroSign; - } - - #ifdef IMP_EIGEN2_SUPPORT - inline bool isPositiveDefinite() const - { - return isPositive(); - } - #endif - - /** \returns true if the matrix is negative (semidefinite) */ - inline bool isNegative(void) const - { - imp_eigen_assert(m_isInitialized && "LDLT is not initialized."); - return m_sign == internal::NegativeSemiDef || m_sign == internal::ZeroSign; - } - - /** \returns a solution x of \f$ A x = b \f$ using the current decomposition of A. - * - * This function also supports in-place solves using the syntax x = decompositionObject.solve(x) . - * - * \note_about_checking_solutions - * - * More precisely, this method solves \f$ A x = b \f$ using the decomposition \f$ A = P^T L D L^* P \f$ - * by solving the systems \f$ P^T y_1 = b \f$, \f$ L y_2 = y_1 \f$, \f$ D y_3 = y_2 \f$, - * \f$ L^* y_4 = y_3 \f$ and \f$ P x = y_4 \f$ in succession. If the matrix \f$ A \f$ is singular, then - * \f$ D \f$ will also be singular (all the other matrices are invertible). In that case, the - * least-square solution of \f$ D y_3 = y_2 \f$ is computed. This does not mean that this function - * computes the least-square solution of \f$ A x = b \f$ is \f$ A \f$ is singular. - * - * \sa MatrixBase::ldlt() - */ - template - inline const internal::solve_retval - solve(const MatrixBase& b) const - { - imp_eigen_assert(m_isInitialized && "LDLT is not initialized."); - imp_eigen_assert(m_matrix.rows()==b.rows() - && "LDLT::solve(): invalid number of rows of the right hand side matrix b"); - return internal::solve_retval(*this, b.derived()); - } - - #ifdef IMP_EIGEN2_SUPPORT - template - bool solve(const MatrixBase& b, ResultType *result) const - { - *result = this->solve(b); - return true; - } - #endif - - template - bool solveInPlace(MatrixBase &bAndX) const; - - LDLT& compute(const MatrixType& matrix); - - template - LDLT& rankUpdate(const MatrixBase& w, const RealScalar& alpha=1); - - /** \returns the internal LDLT decomposition matrix - * - * TODO: document the storage layout - */ - inline const MatrixType& matrixLDLT() const - { - imp_eigen_assert(m_isInitialized && "LDLT is not initialized."); - return m_matrix; - } - - MatrixType reconstructedMatrix() const; - - inline Index rows() const { return m_matrix.rows(); } - inline Index cols() const { return m_matrix.cols(); } - - /** \brief Reports whether previous computation was successful. - * - * \returns \c Success if computation was succesful, - * \c NumericalIssue if the matrix.appears to be negative. - */ - ComputationInfo info() const - { - imp_eigen_assert(m_isInitialized && "LDLT is not initialized."); - return Success; - } - - protected: - - static void check_template_parameters() - { - IMP_EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar); - } - - /** \internal - * Used to compute and store the Cholesky decomposition A = L D L^* = U^* D U. - * The strict upper part is used during the decomposition, the strict lower - * part correspond to the coefficients of L (its diagonal is equal to 1 and - * is not stored), and the diagonal entries correspond to D. - */ - MatrixType m_matrix; - TranspositionType m_transpositions; - TmpMatrixType m_temporary; - internal::SignMatrix m_sign; - bool m_isInitialized; -}; - -namespace internal { - -template struct ldlt_inplace; - -template<> struct ldlt_inplace -{ - template - static bool unblocked(MatrixType& mat, TranspositionType& transpositions, Workspace& temp, SignMatrix& sign) - { - using std::abs; - typedef typename MatrixType::Scalar Scalar; - typedef typename MatrixType::RealScalar RealScalar; - typedef typename MatrixType::Index Index; - imp_eigen_assert(mat.rows()==mat.cols()); - const Index size = mat.rows(); - - if (size <= 1) - { - transpositions.setIdentity(); - if (numext::real(mat.coeff(0,0)) > 0) sign = PositiveSemiDef; - else if (numext::real(mat.coeff(0,0)) < 0) sign = NegativeSemiDef; - else sign = ZeroSign; - return true; - } - - for (Index k = 0; k < size; ++k) - { - // Find largest diagonal element - Index index_of_biggest_in_corner; - mat.diagonal().tail(size-k).cwiseAbs().maxCoeff(&index_of_biggest_in_corner); - index_of_biggest_in_corner += k; - - transpositions.coeffRef(k) = index_of_biggest_in_corner; - if(k != index_of_biggest_in_corner) - { - // apply the transposition while taking care to consider only - // the lower triangular part - Index s = size-index_of_biggest_in_corner-1; // trailing size after the biggest element - mat.row(k).head(k).swap(mat.row(index_of_biggest_in_corner).head(k)); - mat.col(k).tail(s).swap(mat.col(index_of_biggest_in_corner).tail(s)); - std::swap(mat.coeffRef(k,k),mat.coeffRef(index_of_biggest_in_corner,index_of_biggest_in_corner)); - for(int i=k+1;i::IsComplex) - mat.coeffRef(index_of_biggest_in_corner,k) = numext::conj(mat.coeff(index_of_biggest_in_corner,k)); - } - - // partition the matrix: - // A00 | - | - - // lu = A10 | A11 | - - // A20 | A21 | A22 - Index rs = size - k - 1; - Block A21(mat,k+1,k,rs,1); - Block A10(mat,k,0,1,k); - Block A20(mat,k+1,0,rs,k); - - if(k>0) - { - temp.head(k) = mat.diagonal().real().head(k).asDiagonal() * A10.adjoint(); - mat.coeffRef(k,k) -= (A10 * temp.head(k)).value(); - if(rs>0) - A21.noalias() -= A20 * temp.head(k); - } - - // In some previous versions of Eigen (e.g., 3.2.1), the scaling was omitted if the pivot - // was smaller than the cutoff value. However, soince LDLT is not rank-revealing - // we should only make sure we do not introduce INF or NaN values. - // LAPACK also uses 0 as the cutoff value. - RealScalar realAkk = numext::real(mat.coeffRef(k,k)); - if((rs>0) && (abs(realAkk) > RealScalar(0))) - A21 /= realAkk; - - if (sign == PositiveSemiDef) { - if (realAkk < 0) sign = Indefinite; - } else if (sign == NegativeSemiDef) { - if (realAkk > 0) sign = Indefinite; - } else if (sign == ZeroSign) { - if (realAkk > 0) sign = PositiveSemiDef; - else if (realAkk < 0) sign = NegativeSemiDef; - } - } - - return true; - } - - // Reference for the algorithm: Davis and Hager, "Multiple Rank - // Modifications of a Sparse Cholesky Factorization" (Algorithm 1) - // Trivial rearrangements of their computations (Timothy E. Holy) - // allow their algorithm to work for rank-1 updates even if the - // original matrix is not of full rank. - // Here only rank-1 updates are implemented, to reduce the - // requirement for intermediate storage and improve accuracy - template - static bool updateInPlace(MatrixType& mat, MatrixBase& w, const typename MatrixType::RealScalar& sigma=1) - { - using numext::isfinite; - typedef typename MatrixType::Scalar Scalar; - typedef typename MatrixType::RealScalar RealScalar; - typedef typename MatrixType::Index Index; - - const Index size = mat.rows(); - imp_eigen_assert(mat.cols() == size && w.size()==size); - - RealScalar alpha = 1; - - // Apply the update - for (Index j = 0; j < size; j++) - { - // Check for termination due to an original decomposition of low-rank - if (!(isfinite)(alpha)) - break; - - // Update the diagonal terms - RealScalar dj = numext::real(mat.coeff(j,j)); - Scalar wj = w.coeff(j); - RealScalar swj2 = sigma*numext::abs2(wj); - RealScalar gamma = dj*alpha + swj2; - - mat.coeffRef(j,j) += swj2/alpha; - alpha += swj2/dj; - - - // Update the terms of L - Index rs = size-j-1; - w.tail(rs) -= wj * mat.col(j).tail(rs); - if(gamma != 0) - mat.col(j).tail(rs) += (sigma*numext::conj(wj)/gamma)*w.tail(rs); - } - return true; - } - - template - static bool update(MatrixType& mat, const TranspositionType& transpositions, Workspace& tmp, const WType& w, const typename MatrixType::RealScalar& sigma=1) - { - // Apply the permutation to the input w - tmp = transpositions * w; - - return ldlt_inplace::updateInPlace(mat,tmp,sigma); - } -}; - -template<> struct ldlt_inplace -{ - template - static IMP_EIGEN_STRONG_INLINE bool unblocked(MatrixType& mat, TranspositionType& transpositions, Workspace& temp, SignMatrix& sign) - { - Transpose matt(mat); - return ldlt_inplace::unblocked(matt, transpositions, temp, sign); - } - - template - static IMP_EIGEN_STRONG_INLINE bool update(MatrixType& mat, TranspositionType& transpositions, Workspace& tmp, WType& w, const typename MatrixType::RealScalar& sigma=1) - { - Transpose matt(mat); - return ldlt_inplace::update(matt, transpositions, tmp, w.conjugate(), sigma); - } -}; - -template struct LDLT_Traits -{ - typedef const TriangularView MatrixL; - typedef const TriangularView MatrixU; - static inline MatrixL getL(const MatrixType& m) { return m; } - static inline MatrixU getU(const MatrixType& m) { return m.adjoint(); } -}; - -template struct LDLT_Traits -{ - typedef const TriangularView MatrixL; - typedef const TriangularView MatrixU; - static inline MatrixL getL(const MatrixType& m) { return m.adjoint(); } - static inline MatrixU getU(const MatrixType& m) { return m; } -}; - -} // end namespace internal - -/** Compute / recompute the LDLT decomposition A = L D L^* = U^* D U of \a matrix - */ -template -LDLT& LDLT::compute(const MatrixType& a) -{ - check_template_parameters(); - - imp_eigen_assert(a.rows()==a.cols()); - const Index size = a.rows(); - - m_matrix = a; - - m_transpositions.resize(size); - m_isInitialized = false; - m_temporary.resize(size); - m_sign = internal::ZeroSign; - - internal::ldlt_inplace::unblocked(m_matrix, m_transpositions, m_temporary, m_sign); - - m_isInitialized = true; - return *this; -} - -/** Update the LDLT decomposition: given A = L D L^T, efficiently compute the decomposition of A + sigma w w^T. - * \param w a vector to be incorporated into the decomposition. - * \param sigma a scalar, +1 for updates and -1 for "downdates," which correspond to removing previously-added column vectors. Optional; default value is +1. - * \sa setZero() - */ -template -template -LDLT& LDLT::rankUpdate(const MatrixBase& w, const typename LDLT::RealScalar& sigma) -{ - const Index size = w.rows(); - if (m_isInitialized) - { - imp_eigen_assert(m_matrix.rows()==size); - } - else - { - m_matrix.resize(size,size); - m_matrix.setZero(); - m_transpositions.resize(size); - for (Index i = 0; i < size; i++) - m_transpositions.coeffRef(i) = i; - m_temporary.resize(size); - m_sign = sigma>=0 ? internal::PositiveSemiDef : internal::NegativeSemiDef; - m_isInitialized = true; - } - - internal::ldlt_inplace::update(m_matrix, m_transpositions, m_temporary, w, sigma); - - return *this; -} - -namespace internal { -template -struct solve_retval, Rhs> - : solve_retval_base, Rhs> -{ - typedef LDLT<_MatrixType,_UpLo> LDLTType; - IMP_EIGEN_MAKE_SOLVE_HELPERS(LDLTType,Rhs) - - template void evalTo(Dest& dst) const - { - imp_eigen_assert(rhs().rows() == dec().matrixLDLT().rows()); - // dst = P b - dst = dec().transpositionsP() * rhs(); - - // dst = L^-1 (P b) - dec().matrixL().solveInPlace(dst); - - // dst = D^-1 (L^-1 P b) - // more precisely, use pseudo-inverse of D (see bug 241) - using std::abs; - using std::max; - typedef typename LDLTType::MatrixType MatrixType; - typedef typename LDLTType::RealScalar RealScalar; - const typename Diagonal::RealReturnType vectorD(dec().vectorD()); - // In some previous versions, tolerance was set to the max of 1/highest and the maximal diagonal entry * epsilon - // as motivated by LAPACK's xGELSS: - // RealScalar tolerance = (max)(vectorD.array().abs().maxCoeff() *NumTraits::epsilon(),RealScalar(1) / NumTraits::highest()); - // However, LDLT is not rank revealing, and so adjusting the tolerance wrt to the highest - // diagonal element is not well justified and to numerical issues in some cases. - // Moreover, Lapack's xSYTRS routines use 0 for the tolerance. - RealScalar tolerance = RealScalar(1) / NumTraits::highest(); - - for (Index i = 0; i < vectorD.size(); ++i) { - if(abs(vectorD(i)) > tolerance) - dst.row(i) /= vectorD(i); - else - dst.row(i).setZero(); - } - - // dst = L^-T (D^-1 L^-1 P b) - dec().matrixU().solveInPlace(dst); - - // dst = P^-1 (L^-T D^-1 L^-1 P b) = A^-1 b - dst = dec().transpositionsP().transpose() * dst; - } -}; -} - -/** \internal use x = ldlt_object.solve(x); - * - * This is the \em in-place version of solve(). - * - * \param bAndX represents both the right-hand side matrix b and result x. - * - * \returns true always! If you need to check for existence of solutions, use another decomposition like LU, QR, or SVD. - * - * This version avoids a copy when the right hand side matrix b is not - * needed anymore. - * - * \sa LDLT::solve(), MatrixBase::ldlt() - */ -template -template -bool LDLT::solveInPlace(MatrixBase &bAndX) const -{ - imp_eigen_assert(m_isInitialized && "LDLT is not initialized."); - imp_eigen_assert(m_matrix.rows() == bAndX.rows()); - - bAndX = this->solve(bAndX); - - return true; -} - -/** \returns the matrix represented by the decomposition, - * i.e., it returns the product: P^T L D L^* P. - * This function is provided for debug purpose. */ -template -MatrixType LDLT::reconstructedMatrix() const -{ - imp_eigen_assert(m_isInitialized && "LDLT is not initialized."); - const Index size = m_matrix.rows(); - MatrixType res(size,size); - - // P - res.setIdentity(); - res = transpositionsP() * res; - // L^* P - res = matrixU() * res; - // D(L^*P) - res = vectorD().real().asDiagonal() * res; - // L(DL^*P) - res = matrixL() * res; - // P^T (LDL^*P) - res = transpositionsP().transpose() * res; - - return res; -} - -/** \cholesky_module - * \returns the Cholesky decomposition with full pivoting without square root of \c *this - */ -template -inline const LDLT::PlainObject, UpLo> -SelfAdjointView::ldlt() const -{ - return LDLT(m_matrix); -} - -/** \cholesky_module - * \returns the Cholesky decomposition with full pivoting without square root of \c *this - */ -template -inline const LDLT::PlainObject> -MatrixBase::ldlt() const -{ - return LDLT(derived()); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_LDLT_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Cholesky/LLT.h b/modules/algebra/include/eigen3/Eigen/src/Cholesky/LLT.h deleted file mode 100644 index b6f10aec1e..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Cholesky/LLT.h +++ /dev/null @@ -1,498 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008 Gael Guennebaud -// -// 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 IMP_EIGEN_LLT_H -#define IMP_EIGEN_LLT_H - -namespace IMP_Eigen { - -namespace internal{ -template struct LLT_Traits; -} - -/** \ingroup Cholesky_Module - * - * \class LLT - * - * \brief Standard Cholesky decomposition (LL^T) of a matrix and associated features - * - * \param MatrixType the type of the matrix of which we are computing the LL^T Cholesky decomposition - * \param UpLo the triangular part that will be used for the decompositon: Lower (default) or Upper. - * The other triangular part won't be read. - * - * This class performs a LL^T Cholesky decomposition of a symmetric, positive definite - * matrix A such that A = LL^* = U^*U, where L is lower triangular. - * - * While the Cholesky decomposition is particularly useful to solve selfadjoint problems like D^*D x = b, - * for that purpose, we recommend the Cholesky decomposition without square root which is more stable - * and even faster. Nevertheless, this standard Cholesky decomposition remains useful in many other - * situations like generalised eigen problems with hermitian matrices. - * - * Remember that Cholesky decompositions are not rank-revealing. This LLT decomposition is only stable on positive definite matrices, - * use LDLT instead for the semidefinite case. Also, do not use a Cholesky decomposition to determine whether a system of equations - * has a solution. - * - * Example: \include LLT_example.cpp - * Output: \verbinclude LLT_example.out - * - * \sa MatrixBase::llt(), class LDLT - */ - /* HEY THIS DOX IS DISABLED BECAUSE THERE's A BUG EITHER HERE OR IN LDLT ABOUT THAT (OR BOTH) - * Note that during the decomposition, only the upper triangular part of A is considered. Therefore, - * the strict lower part does not have to store correct values. - */ -template class LLT -{ - public: - typedef _MatrixType MatrixType; - enum { - RowsAtCompileTime = MatrixType::RowsAtCompileTime, - ColsAtCompileTime = MatrixType::ColsAtCompileTime, - Options = MatrixType::Options, - MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime - }; - typedef typename MatrixType::Scalar Scalar; - typedef typename NumTraits::Real RealScalar; - typedef typename MatrixType::Index Index; - - enum { - PacketSize = internal::packet_traits::size, - AlignmentMask = int(PacketSize)-1, - UpLo = _UpLo - }; - - typedef internal::LLT_Traits Traits; - - /** - * \brief Default Constructor. - * - * The default constructor is useful in cases in which the user intends to - * perform decompositions via LLT::compute(const MatrixType&). - */ - LLT() : m_matrix(), m_isInitialized(false) {} - - /** \brief Default Constructor with memory preallocation - * - * Like the default constructor but with preallocation of the internal data - * according to the specified problem \a size. - * \sa LLT() - */ - LLT(Index size) : m_matrix(size, size), - m_isInitialized(false) {} - - LLT(const MatrixType& matrix) - : m_matrix(matrix.rows(), matrix.cols()), - m_isInitialized(false) - { - compute(matrix); - } - - /** \returns a view of the upper triangular matrix U */ - inline typename Traits::MatrixU matrixU() const - { - imp_eigen_assert(m_isInitialized && "LLT is not initialized."); - return Traits::getU(m_matrix); - } - - /** \returns a view of the lower triangular matrix L */ - inline typename Traits::MatrixL matrixL() const - { - imp_eigen_assert(m_isInitialized && "LLT is not initialized."); - return Traits::getL(m_matrix); - } - - /** \returns the solution x of \f$ A x = b \f$ using the current decomposition of A. - * - * Since this LLT class assumes anyway that the matrix A is invertible, the solution - * theoretically exists and is unique regardless of b. - * - * Example: \include LLT_solve.cpp - * Output: \verbinclude LLT_solve.out - * - * \sa solveInPlace(), MatrixBase::llt() - */ - template - inline const internal::solve_retval - solve(const MatrixBase& b) const - { - imp_eigen_assert(m_isInitialized && "LLT is not initialized."); - imp_eigen_assert(m_matrix.rows()==b.rows() - && "LLT::solve(): invalid number of rows of the right hand side matrix b"); - return internal::solve_retval(*this, b.derived()); - } - - #ifdef IMP_EIGEN2_SUPPORT - template - bool solve(const MatrixBase& b, ResultType *result) const - { - *result = this->solve(b); - return true; - } - - bool isPositiveDefinite() const { return true; } - #endif - - template - void solveInPlace(MatrixBase &bAndX) const; - - LLT& compute(const MatrixType& matrix); - - /** \returns the LLT decomposition matrix - * - * TODO: document the storage layout - */ - inline const MatrixType& matrixLLT() const - { - imp_eigen_assert(m_isInitialized && "LLT is not initialized."); - return m_matrix; - } - - MatrixType reconstructedMatrix() const; - - - /** \brief Reports whether previous computation was successful. - * - * \returns \c Success if computation was succesful, - * \c NumericalIssue if the matrix.appears to be negative. - */ - ComputationInfo info() const - { - imp_eigen_assert(m_isInitialized && "LLT is not initialized."); - return m_info; - } - - inline Index rows() const { return m_matrix.rows(); } - inline Index cols() const { return m_matrix.cols(); } - - template - LLT rankUpdate(const VectorType& vec, const RealScalar& sigma = 1); - - protected: - - static void check_template_parameters() - { - IMP_EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar); - } - - /** \internal - * Used to compute and store L - * The strict upper part is not used and even not initialized. - */ - MatrixType m_matrix; - bool m_isInitialized; - ComputationInfo m_info; -}; - -namespace internal { - -template struct llt_inplace; - -template -static typename MatrixType::Index llt_rank_update_lower(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) -{ - using std::sqrt; - typedef typename MatrixType::Scalar Scalar; - typedef typename MatrixType::RealScalar RealScalar; - typedef typename MatrixType::Index Index; - typedef typename MatrixType::ColXpr ColXpr; - typedef typename internal::remove_all::type ColXprCleaned; - typedef typename ColXprCleaned::SegmentReturnType ColXprSegment; - typedef Matrix TempVectorType; - typedef typename TempVectorType::SegmentReturnType TempVecSegment; - - Index n = mat.cols(); - imp_eigen_assert(mat.rows()==n && vec.size()==n); - - TempVectorType temp; - - if(sigma>0) - { - // This version is based on Givens rotations. - // It is faster than the other one below, but only works for updates, - // i.e., for sigma > 0 - temp = sqrt(sigma) * vec; - - for(Index i=0; i g; - g.makeGivens(mat(i,i), -temp(i), &mat(i,i)); - - Index rs = n-i-1; - if(rs>0) - { - ColXprSegment x(mat.col(i).tail(rs)); - TempVecSegment y(temp.tail(rs)); - apply_rotation_in_the_plane(x, y, g); - } - } - } - else - { - temp = vec; - RealScalar beta = 1; - for(Index j=0; j struct llt_inplace -{ - typedef typename NumTraits::Real RealScalar; - template - static typename MatrixType::Index unblocked(MatrixType& mat) - { - using std::sqrt; - typedef typename MatrixType::Index Index; - - imp_eigen_assert(mat.rows()==mat.cols()); - const Index size = mat.rows(); - for(Index k = 0; k < size; ++k) - { - Index rs = size-k-1; // remaining size - - Block A21(mat,k+1,k,rs,1); - Block A10(mat,k,0,1,k); - Block A20(mat,k+1,0,rs,k); - - RealScalar x = numext::real(mat.coeff(k,k)); - if (k>0) x -= A10.squaredNorm(); - if (x<=RealScalar(0)) - return k; - mat.coeffRef(k,k) = x = sqrt(x); - if (k>0 && rs>0) A21.noalias() -= A20 * A10.adjoint(); - if (rs>0) A21 /= x; - } - return -1; - } - - template - static typename MatrixType::Index blocked(MatrixType& m) - { - typedef typename MatrixType::Index Index; - imp_eigen_assert(m.rows()==m.cols()); - Index size = m.rows(); - if(size<32) - return unblocked(m); - - Index blockSize = size/8; - blockSize = (blockSize/16)*16; - blockSize = (std::min)((std::max)(blockSize,Index(8)), Index(128)); - - for (Index k=0; k A11(m,k, k, bs,bs); - Block A21(m,k+bs,k, rs,bs); - Block A22(m,k+bs,k+bs,rs,rs); - - Index ret; - if((ret=unblocked(A11))>=0) return k+ret; - if(rs>0) A11.adjoint().template triangularView().template solveInPlace(A21); - if(rs>0) A22.template selfadjointView().rankUpdate(A21,-1); // bottleneck - } - return -1; - } - - template - static typename MatrixType::Index rankUpdate(MatrixType& mat, const VectorType& vec, const RealScalar& sigma) - { - return IMP_Eigen::internal::llt_rank_update_lower(mat, vec, sigma); - } -}; - -template struct llt_inplace -{ - typedef typename NumTraits::Real RealScalar; - - template - static IMP_EIGEN_STRONG_INLINE typename MatrixType::Index unblocked(MatrixType& mat) - { - Transpose matt(mat); - return llt_inplace::unblocked(matt); - } - template - static IMP_EIGEN_STRONG_INLINE typename MatrixType::Index blocked(MatrixType& mat) - { - Transpose matt(mat); - return llt_inplace::blocked(matt); - } - template - static typename MatrixType::Index rankUpdate(MatrixType& mat, const VectorType& vec, const RealScalar& sigma) - { - Transpose matt(mat); - return llt_inplace::rankUpdate(matt, vec.conjugate(), sigma); - } -}; - -template struct LLT_Traits -{ - typedef const TriangularView MatrixL; - typedef const TriangularView MatrixU; - static inline MatrixL getL(const MatrixType& m) { return m; } - static inline MatrixU getU(const MatrixType& m) { return m.adjoint(); } - static bool inplace_decomposition(MatrixType& m) - { return llt_inplace::blocked(m)==-1; } -}; - -template struct LLT_Traits -{ - typedef const TriangularView MatrixL; - typedef const TriangularView MatrixU; - static inline MatrixL getL(const MatrixType& m) { return m.adjoint(); } - static inline MatrixU getU(const MatrixType& m) { return m; } - static bool inplace_decomposition(MatrixType& m) - { return llt_inplace::blocked(m)==-1; } -}; - -} // end namespace internal - -/** Computes / recomputes the Cholesky decomposition A = LL^* = U^*U of \a matrix - * - * \returns a reference to *this - * - * Example: \include TutorialLinAlgComputeTwice.cpp - * Output: \verbinclude TutorialLinAlgComputeTwice.out - */ -template -LLT& LLT::compute(const MatrixType& a) -{ - check_template_parameters(); - - imp_eigen_assert(a.rows()==a.cols()); - const Index size = a.rows(); - m_matrix.resize(size, size); - m_matrix = a; - - m_isInitialized = true; - bool ok = Traits::inplace_decomposition(m_matrix); - m_info = ok ? Success : NumericalIssue; - - return *this; -} - -/** Performs a rank one update (or dowdate) of the current decomposition. - * If A = LL^* before the rank one update, - * then after it we have LL^* = A + sigma * v v^* where \a v must be a vector - * of same dimension. - */ -template -template -LLT<_MatrixType,_UpLo> LLT<_MatrixType,_UpLo>::rankUpdate(const VectorType& v, const RealScalar& sigma) -{ - IMP_EIGEN_STATIC_ASSERT_VECTOR_ONLY(VectorType); - imp_eigen_assert(v.size()==m_matrix.cols()); - imp_eigen_assert(m_isInitialized); - if(internal::llt_inplace::rankUpdate(m_matrix,v,sigma)>=0) - m_info = NumericalIssue; - else - m_info = Success; - - return *this; -} - -namespace internal { -template -struct solve_retval, Rhs> - : solve_retval_base, Rhs> -{ - typedef LLT<_MatrixType,UpLo> LLTType; - IMP_EIGEN_MAKE_SOLVE_HELPERS(LLTType,Rhs) - - template void evalTo(Dest& dst) const - { - dst = rhs(); - dec().solveInPlace(dst); - } -}; -} - -/** \internal use x = llt_object.solve(x); - * - * This is the \em in-place version of solve(). - * - * \param bAndX represents both the right-hand side matrix b and result x. - * - * \returns true always! If you need to check for existence of solutions, use another decomposition like LU, QR, or SVD. - * - * This version avoids a copy when the right hand side matrix b is not - * needed anymore. - * - * \sa LLT::solve(), MatrixBase::llt() - */ -template -template -void LLT::solveInPlace(MatrixBase &bAndX) const -{ - imp_eigen_assert(m_isInitialized && "LLT is not initialized."); - imp_eigen_assert(m_matrix.rows()==bAndX.rows()); - matrixL().solveInPlace(bAndX); - matrixU().solveInPlace(bAndX); -} - -/** \returns the matrix represented by the decomposition, - * i.e., it returns the product: L L^*. - * This function is provided for debug purpose. */ -template -MatrixType LLT::reconstructedMatrix() const -{ - imp_eigen_assert(m_isInitialized && "LLT is not initialized."); - return matrixL() * matrixL().adjoint().toDenseMatrix(); -} - -/** \cholesky_module - * \returns the LLT decomposition of \c *this - */ -template -inline const LLT::PlainObject> -MatrixBase::llt() const -{ - return LLT(derived()); -} - -/** \cholesky_module - * \returns the LLT decomposition of \c *this - */ -template -inline const LLT::PlainObject, UpLo> -SelfAdjointView::llt() const -{ - return LLT(m_matrix); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_LLT_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Cholesky/LLT_MKL.h b/modules/algebra/include/eigen3/Eigen/src/Cholesky/LLT_MKL.h deleted file mode 100644 index 27de322a8a..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Cholesky/LLT_MKL.h +++ /dev/null @@ -1,102 +0,0 @@ -/* - Copyright (c) 2011, Intel Corporation. All rights reserved. - - Redistribution and use in source and binary forms, with or without modification, - are permitted provided that the following conditions are met: - - * Redistributions of source code must retain the above copyright notice, this - list of conditions and the following disclaimer. - * Redistributions in binary form must reproduce the above copyright notice, - this list of conditions and the following disclaimer in the documentation - and/or other materials provided with the distribution. - * Neither the name of Intel Corporation nor the names of its contributors may - be used to endorse or promote products derived from this software without - specific prior written permission. - - THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND - ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED - WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE - DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR - ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES - (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; - LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON - ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS - SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - - ******************************************************************************** - * Content : Eigen bindings to Intel(R) MKL - * LLt decomposition based on LAPACKE_?potrf function. - ******************************************************************************** -*/ - -#ifndef IMP_EIGEN_LLT_MKL_H -#define IMP_EIGEN_LLT_MKL_H - -#include "Eigen/src/Core/util/MKL_support.h" -#include - -namespace IMP_Eigen { - -namespace internal { - -template struct mkl_llt; - -#define IMP_EIGEN_MKL_LLT(EIGTYPE, MKLTYPE, MKLPREFIX) \ -template<> struct mkl_llt \ -{ \ - template \ - static inline typename MatrixType::Index potrf(MatrixType& m, char uplo) \ - { \ - lapack_int matrix_order; \ - lapack_int size, lda, info, StorageOrder; \ - EIGTYPE* a; \ - imp_eigen_assert(m.rows()==m.cols()); \ - /* Set up parameters for ?potrf */ \ - size = m.rows(); \ - StorageOrder = MatrixType::Flags&RowMajorBit?RowMajor:ColMajor; \ - matrix_order = StorageOrder==RowMajor ? LAPACK_ROW_MAJOR : LAPACK_COL_MAJOR; \ - a = &(m.coeffRef(0,0)); \ - lda = m.outerStride(); \ -\ - info = LAPACKE_##MKLPREFIX##potrf( matrix_order, uplo, size, (MKLTYPE*)a, lda ); \ - info = (info==0) ? -1 : info>0 ? info-1 : size; \ - return info; \ - } \ -}; \ -template<> struct llt_inplace \ -{ \ - template \ - static typename MatrixType::Index blocked(MatrixType& m) \ - { \ - return mkl_llt::potrf(m, 'L'); \ - } \ - template \ - static typename MatrixType::Index rankUpdate(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) \ - { return IMP_Eigen::internal::llt_rank_update_lower(mat, vec, sigma); } \ -}; \ -template<> struct llt_inplace \ -{ \ - template \ - static typename MatrixType::Index blocked(MatrixType& m) \ - { \ - return mkl_llt::potrf(m, 'U'); \ - } \ - template \ - static typename MatrixType::Index rankUpdate(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) \ - { \ - Transpose matt(mat); \ - return llt_inplace::rankUpdate(matt, vec.conjugate(), sigma); \ - } \ -}; - -IMP_EIGEN_MKL_LLT(double, double, d) -IMP_EIGEN_MKL_LLT(float, float, s) -IMP_EIGEN_MKL_LLT(dcomplex, MKL_Complex16, z) -IMP_EIGEN_MKL_LLT(scomplex, MKL_Complex8, c) - -} // end namespace internal - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_LLT_MKL_H diff --git a/modules/algebra/include/eigen3/Eigen/src/CholmodSupport/CholmodSupport.h b/modules/algebra/include/eigen3/Eigen/src/CholmodSupport/CholmodSupport.h deleted file mode 100644 index 6952159b96..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/CholmodSupport/CholmodSupport.h +++ /dev/null @@ -1,607 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008-2010 Gael Guennebaud -// -// 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 IMP_EIGEN_CHOLMODSUPPORT_H -#define IMP_EIGEN_CHOLMODSUPPORT_H - -namespace IMP_Eigen { - -namespace internal { - -template -void cholmod_configure_matrix(CholmodType& mat) -{ - if (internal::is_same::value) - { - mat.xtype = CHOLMOD_REAL; - mat.dtype = CHOLMOD_SINGLE; - } - else if (internal::is_same::value) - { - mat.xtype = CHOLMOD_REAL; - mat.dtype = CHOLMOD_DOUBLE; - } - else if (internal::is_same >::value) - { - mat.xtype = CHOLMOD_COMPLEX; - mat.dtype = CHOLMOD_SINGLE; - } - else if (internal::is_same >::value) - { - mat.xtype = CHOLMOD_COMPLEX; - mat.dtype = CHOLMOD_DOUBLE; - } - else - { - imp_eigen_assert(false && "Scalar type not supported by CHOLMOD"); - } -} - -} // namespace internal - -/** Wraps the Eigen sparse matrix \a mat into a Cholmod sparse matrix object. - * Note that the data are shared. - */ -template -cholmod_sparse viewAsCholmod(SparseMatrix<_Scalar,_Options,_Index>& mat) -{ - cholmod_sparse res; - res.nzmax = mat.nonZeros(); - res.nrow = mat.rows();; - res.ncol = mat.cols(); - res.p = mat.outerIndexPtr(); - res.i = mat.innerIndexPtr(); - res.x = mat.valuePtr(); - res.z = 0; - res.sorted = 1; - if(mat.isCompressed()) - { - res.packed = 1; - res.nz = 0; - } - else - { - res.packed = 0; - res.nz = mat.innerNonZeroPtr(); - } - - res.dtype = 0; - res.stype = -1; - - if (internal::is_same<_Index,int>::value) - { - res.itype = CHOLMOD_INT; - } - else if (internal::is_same<_Index,SuiteSparse_long>::value) - { - res.itype = CHOLMOD_LONG; - } - else - { - imp_eigen_assert(false && "Index type not supported yet"); - } - - // setup res.xtype - internal::cholmod_configure_matrix<_Scalar>(res); - - res.stype = 0; - - return res; -} - -template -const cholmod_sparse viewAsCholmod(const SparseMatrix<_Scalar,_Options,_Index>& mat) -{ - cholmod_sparse res = viewAsCholmod(mat.const_cast_derived()); - return res; -} - -/** Returns a view of the Eigen sparse matrix \a mat as Cholmod sparse matrix. - * The data are not copied but shared. */ -template -cholmod_sparse viewAsCholmod(const SparseSelfAdjointView, UpLo>& mat) -{ - cholmod_sparse res = viewAsCholmod(mat.matrix().const_cast_derived()); - - if(UpLo==Upper) res.stype = 1; - if(UpLo==Lower) res.stype = -1; - - return res; -} - -/** Returns a view of the Eigen \b dense matrix \a mat as Cholmod dense matrix. - * The data are not copied but shared. */ -template -cholmod_dense viewAsCholmod(MatrixBase& mat) -{ - IMP_EIGEN_STATIC_ASSERT((internal::traits::Flags&RowMajorBit)==0,THIS_METHOD_IS_ONLY_FOR_COLUMN_MAJOR_MATRICES); - typedef typename Derived::Scalar Scalar; - - cholmod_dense res; - res.nrow = mat.rows(); - res.ncol = mat.cols(); - res.nzmax = res.nrow * res.ncol; - res.d = Derived::IsVectorAtCompileTime ? mat.derived().size() : mat.derived().outerStride(); - res.x = (void*)(mat.derived().data()); - res.z = 0; - - internal::cholmod_configure_matrix(res); - - return res; -} - -/** Returns a view of the Cholmod sparse matrix \a cm as an Eigen sparse matrix. - * The data are not copied but shared. */ -template -MappedSparseMatrix viewAsEigen(cholmod_sparse& cm) -{ - return MappedSparseMatrix - (cm.nrow, cm.ncol, static_cast(cm.p)[cm.ncol], - static_cast(cm.p), static_cast(cm.i),static_cast(cm.x) ); -} - -enum CholmodMode { - CholmodAuto, CholmodSimplicialLLt, CholmodSupernodalLLt, CholmodLDLt -}; - - -/** \ingroup CholmodSupport_Module - * \class CholmodBase - * \brief The base class for the direct Cholesky factorization of Cholmod - * \sa class CholmodSupernodalLLT, class CholmodSimplicialLDLT, class CholmodSimplicialLLT - */ -template -class CholmodBase : internal::noncopyable -{ - public: - typedef _MatrixType MatrixType; - enum { UpLo = _UpLo }; - typedef typename MatrixType::Scalar Scalar; - typedef typename MatrixType::RealScalar RealScalar; - typedef MatrixType CholMatrixType; - typedef typename MatrixType::Index Index; - - public: - - CholmodBase() - : m_cholmodFactor(0), m_info(Success), m_isInitialized(false) - { - m_shiftOffset[0] = m_shiftOffset[1] = RealScalar(0.0); - cholmod_start(&m_cholmod); - } - - CholmodBase(const MatrixType& matrix) - : m_cholmodFactor(0), m_info(Success), m_isInitialized(false) - { - m_shiftOffset[0] = m_shiftOffset[1] = RealScalar(0.0); - cholmod_start(&m_cholmod); - compute(matrix); - } - - ~CholmodBase() - { - if(m_cholmodFactor) - cholmod_free_factor(&m_cholmodFactor, &m_cholmod); - cholmod_finish(&m_cholmod); - } - - inline Index cols() const { return m_cholmodFactor->n; } - inline Index rows() const { return m_cholmodFactor->n; } - - Derived& derived() { return *static_cast(this); } - const Derived& derived() const { return *static_cast(this); } - - /** \brief Reports whether previous computation was successful. - * - * \returns \c Success if computation was succesful, - * \c NumericalIssue if the matrix.appears to be negative. - */ - ComputationInfo info() const - { - imp_eigen_assert(m_isInitialized && "Decomposition is not initialized."); - return m_info; - } - - /** Computes the sparse Cholesky decomposition of \a matrix */ - Derived& compute(const MatrixType& matrix) - { - analyzePattern(matrix); - factorize(matrix); - return derived(); - } - - /** \returns the solution x of \f$ A x = b \f$ using the current decomposition of A. - * - * \sa compute() - */ - template - inline const internal::solve_retval - solve(const MatrixBase& b) const - { - imp_eigen_assert(m_isInitialized && "LLT is not initialized."); - imp_eigen_assert(rows()==b.rows() - && "CholmodDecomposition::solve(): invalid number of rows of the right hand side matrix b"); - return internal::solve_retval(*this, b.derived()); - } - - /** \returns the solution x of \f$ A x = b \f$ using the current decomposition of A. - * - * \sa compute() - */ - template - inline const internal::sparse_solve_retval - solve(const SparseMatrixBase& b) const - { - imp_eigen_assert(m_isInitialized && "LLT is not initialized."); - imp_eigen_assert(rows()==b.rows() - && "CholmodDecomposition::solve(): invalid number of rows of the right hand side matrix b"); - return internal::sparse_solve_retval(*this, b.derived()); - } - - /** Performs a symbolic decomposition on the sparsity pattern of \a matrix. - * - * This function is particularly useful when solving for several problems having the same structure. - * - * \sa factorize() - */ - void analyzePattern(const MatrixType& matrix) - { - if(m_cholmodFactor) - { - cholmod_free_factor(&m_cholmodFactor, &m_cholmod); - m_cholmodFactor = 0; - } - cholmod_sparse A = viewAsCholmod(matrix.template selfadjointView()); - m_cholmodFactor = cholmod_analyze(&A, &m_cholmod); - - this->m_isInitialized = true; - this->m_info = Success; - m_analysisIsOk = true; - m_factorizationIsOk = false; - } - - /** Performs a numeric decomposition of \a matrix - * - * The given matrix must have the same sparsity pattern as the matrix on which the symbolic decomposition has been performed. - * - * \sa analyzePattern() - */ - void factorize(const MatrixType& matrix) - { - imp_eigen_assert(m_analysisIsOk && "You must first call analyzePattern()"); - cholmod_sparse A = viewAsCholmod(matrix.template selfadjointView()); - cholmod_factorize_p(&A, m_shiftOffset, 0, 0, m_cholmodFactor, &m_cholmod); - - // If the factorization failed, minor is the column at which it did. On success minor == n. - this->m_info = (m_cholmodFactor->minor == m_cholmodFactor->n ? Success : NumericalIssue); - m_factorizationIsOk = true; - } - - /** Returns a reference to the Cholmod's configuration structure to get a full control over the performed operations. - * See the Cholmod user guide for details. */ - cholmod_common& cholmod() { return m_cholmod; } - - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - /** \internal */ - template - void _solve(const MatrixBase &b, MatrixBase &dest) const - { - imp_eigen_assert(m_factorizationIsOk && "The decomposition is not in a valid state for solving, you must first call either compute() or symbolic()/numeric()"); - const Index size = m_cholmodFactor->n; - IMP_EIGEN_UNUSED_VARIABLE(size); - imp_eigen_assert(size==b.rows()); - - // note: cd stands for Cholmod Dense - Rhs& b_ref(b.const_cast_derived()); - cholmod_dense b_cd = viewAsCholmod(b_ref); - cholmod_dense* x_cd = cholmod_solve(CHOLMOD_A, m_cholmodFactor, &b_cd, &m_cholmod); - if(!x_cd) - { - this->m_info = NumericalIssue; - } - // TODO optimize this copy by swapping when possible (be careful with alignment, etc.) - dest = Matrix::Map(reinterpret_cast(x_cd->x),b.rows(),b.cols()); - cholmod_free_dense(&x_cd, &m_cholmod); - } - - /** \internal */ - template - void _solve(const SparseMatrix &b, SparseMatrix &dest) const - { - imp_eigen_assert(m_factorizationIsOk && "The decomposition is not in a valid state for solving, you must first call either compute() or symbolic()/numeric()"); - const Index size = m_cholmodFactor->n; - IMP_EIGEN_UNUSED_VARIABLE(size); - imp_eigen_assert(size==b.rows()); - - // note: cs stands for Cholmod Sparse - cholmod_sparse b_cs = viewAsCholmod(b); - cholmod_sparse* x_cs = cholmod_spsolve(CHOLMOD_A, m_cholmodFactor, &b_cs, &m_cholmod); - if(!x_cs) - { - this->m_info = NumericalIssue; - } - // TODO optimize this copy by swapping when possible (be careful with alignment, etc.) - dest = viewAsEigen(*x_cs); - cholmod_free_sparse(&x_cs, &m_cholmod); - } - #endif // IMP_EIGEN_PARSED_BY_DOXYGEN - - - /** Sets the shift parameter that will be used to adjust the diagonal coefficients during the numerical factorization. - * - * During the numerical factorization, an offset term is added to the diagonal coefficients:\n - * \c d_ii = \a offset + \c d_ii - * - * The default is \a offset=0. - * - * \returns a reference to \c *this. - */ - Derived& setShift(const RealScalar& offset) - { - m_shiftOffset[0] = offset; - return derived(); - } - - template - void dumpMemory(Stream& /*s*/) - {} - - protected: - mutable cholmod_common m_cholmod; - cholmod_factor* m_cholmodFactor; - RealScalar m_shiftOffset[2]; - mutable ComputationInfo m_info; - bool m_isInitialized; - int m_factorizationIsOk; - int m_analysisIsOk; -}; - -/** \ingroup CholmodSupport_Module - * \class CholmodSimplicialLLT - * \brief A simplicial direct Cholesky (LLT) factorization and solver based on Cholmod - * - * This class allows to solve for A.X = B sparse linear problems via a simplicial LL^T Cholesky factorization - * using the Cholmod library. - * This simplicial variant is equivalent to Eigen's built-in SimplicialLLT class. Therefore, it has little practical interest. - * The sparse matrix A must be selfadjoint and positive definite. The vectors or matrices - * X and B can be either dense or sparse. - * - * \tparam _MatrixType the type of the sparse matrix A, it must be a SparseMatrix<> - * \tparam _UpLo the triangular part that will be used for the computations. It can be Lower - * or Upper. Default is Lower. - * - * This class supports all kind of SparseMatrix<>: row or column major; upper, lower, or both; compressed or non compressed. - * - * \sa \ref TutorialSparseDirectSolvers, class CholmodSupernodalLLT, class SimplicialLLT - */ -template -class CholmodSimplicialLLT : public CholmodBase<_MatrixType, _UpLo, CholmodSimplicialLLT<_MatrixType, _UpLo> > -{ - typedef CholmodBase<_MatrixType, _UpLo, CholmodSimplicialLLT> Base; - using Base::m_cholmod; - - public: - - typedef _MatrixType MatrixType; - - CholmodSimplicialLLT() : Base() { init(); } - - CholmodSimplicialLLT(const MatrixType& matrix) : Base() - { - init(); - Base::compute(matrix); - } - - ~CholmodSimplicialLLT() {} - protected: - void init() - { - m_cholmod.final_asis = 0; - m_cholmod.supernodal = CHOLMOD_SIMPLICIAL; - m_cholmod.final_ll = 1; - } -}; - - -/** \ingroup CholmodSupport_Module - * \class CholmodSimplicialLDLT - * \brief A simplicial direct Cholesky (LDLT) factorization and solver based on Cholmod - * - * This class allows to solve for A.X = B sparse linear problems via a simplicial LDL^T Cholesky factorization - * using the Cholmod library. - * This simplicial variant is equivalent to Eigen's built-in SimplicialLDLT class. Therefore, it has little practical interest. - * The sparse matrix A must be selfadjoint and positive definite. The vectors or matrices - * X and B can be either dense or sparse. - * - * \tparam _MatrixType the type of the sparse matrix A, it must be a SparseMatrix<> - * \tparam _UpLo the triangular part that will be used for the computations. It can be Lower - * or Upper. Default is Lower. - * - * This class supports all kind of SparseMatrix<>: row or column major; upper, lower, or both; compressed or non compressed. - * - * \sa \ref TutorialSparseDirectSolvers, class CholmodSupernodalLLT, class SimplicialLDLT - */ -template -class CholmodSimplicialLDLT : public CholmodBase<_MatrixType, _UpLo, CholmodSimplicialLDLT<_MatrixType, _UpLo> > -{ - typedef CholmodBase<_MatrixType, _UpLo, CholmodSimplicialLDLT> Base; - using Base::m_cholmod; - - public: - - typedef _MatrixType MatrixType; - - CholmodSimplicialLDLT() : Base() { init(); } - - CholmodSimplicialLDLT(const MatrixType& matrix) : Base() - { - init(); - Base::compute(matrix); - } - - ~CholmodSimplicialLDLT() {} - protected: - void init() - { - m_cholmod.final_asis = 1; - m_cholmod.supernodal = CHOLMOD_SIMPLICIAL; - } -}; - -/** \ingroup CholmodSupport_Module - * \class CholmodSupernodalLLT - * \brief A supernodal Cholesky (LLT) factorization and solver based on Cholmod - * - * This class allows to solve for A.X = B sparse linear problems via a supernodal LL^T Cholesky factorization - * using the Cholmod library. - * This supernodal variant performs best on dense enough problems, e.g., 3D FEM, or very high order 2D FEM. - * The sparse matrix A must be selfadjoint and positive definite. The vectors or matrices - * X and B can be either dense or sparse. - * - * \tparam _MatrixType the type of the sparse matrix A, it must be a SparseMatrix<> - * \tparam _UpLo the triangular part that will be used for the computations. It can be Lower - * or Upper. Default is Lower. - * - * This class supports all kind of SparseMatrix<>: row or column major; upper, lower, or both; compressed or non compressed. - * - * \sa \ref TutorialSparseDirectSolvers - */ -template -class CholmodSupernodalLLT : public CholmodBase<_MatrixType, _UpLo, CholmodSupernodalLLT<_MatrixType, _UpLo> > -{ - typedef CholmodBase<_MatrixType, _UpLo, CholmodSupernodalLLT> Base; - using Base::m_cholmod; - - public: - - typedef _MatrixType MatrixType; - - CholmodSupernodalLLT() : Base() { init(); } - - CholmodSupernodalLLT(const MatrixType& matrix) : Base() - { - init(); - Base::compute(matrix); - } - - ~CholmodSupernodalLLT() {} - protected: - void init() - { - m_cholmod.final_asis = 1; - m_cholmod.supernodal = CHOLMOD_SUPERNODAL; - } -}; - -/** \ingroup CholmodSupport_Module - * \class CholmodDecomposition - * \brief A general Cholesky factorization and solver based on Cholmod - * - * This class allows to solve for A.X = B sparse linear problems via a LL^T or LDL^T Cholesky factorization - * using the Cholmod library. The sparse matrix A must be selfadjoint and positive definite. The vectors or matrices - * X and B can be either dense or sparse. - * - * This variant permits to change the underlying Cholesky method at runtime. - * On the other hand, it does not provide access to the result of the factorization. - * The default is to let Cholmod automatically choose between a simplicial and supernodal factorization. - * - * \tparam _MatrixType the type of the sparse matrix A, it must be a SparseMatrix<> - * \tparam _UpLo the triangular part that will be used for the computations. It can be Lower - * or Upper. Default is Lower. - * - * This class supports all kind of SparseMatrix<>: row or column major; upper, lower, or both; compressed or non compressed. - * - * \sa \ref TutorialSparseDirectSolvers - */ -template -class CholmodDecomposition : public CholmodBase<_MatrixType, _UpLo, CholmodDecomposition<_MatrixType, _UpLo> > -{ - typedef CholmodBase<_MatrixType, _UpLo, CholmodDecomposition> Base; - using Base::m_cholmod; - - public: - - typedef _MatrixType MatrixType; - - CholmodDecomposition() : Base() { init(); } - - CholmodDecomposition(const MatrixType& matrix) : Base() - { - init(); - Base::compute(matrix); - } - - ~CholmodDecomposition() {} - - void setMode(CholmodMode mode) - { - switch(mode) - { - case CholmodAuto: - m_cholmod.final_asis = 1; - m_cholmod.supernodal = CHOLMOD_AUTO; - break; - case CholmodSimplicialLLt: - m_cholmod.final_asis = 0; - m_cholmod.supernodal = CHOLMOD_SIMPLICIAL; - m_cholmod.final_ll = 1; - break; - case CholmodSupernodalLLt: - m_cholmod.final_asis = 1; - m_cholmod.supernodal = CHOLMOD_SUPERNODAL; - break; - case CholmodLDLt: - m_cholmod.final_asis = 1; - m_cholmod.supernodal = CHOLMOD_SIMPLICIAL; - break; - default: - break; - } - } - protected: - void init() - { - m_cholmod.final_asis = 1; - m_cholmod.supernodal = CHOLMOD_AUTO; - } -}; - -namespace internal { - -template -struct solve_retval, Rhs> - : solve_retval_base, Rhs> -{ - typedef CholmodBase<_MatrixType,_UpLo,Derived> Dec; - IMP_EIGEN_MAKE_SOLVE_HELPERS(Dec,Rhs) - - template void evalTo(Dest& dst) const - { - dec()._solve(rhs(),dst); - } -}; - -template -struct sparse_solve_retval, Rhs> - : sparse_solve_retval_base, Rhs> -{ - typedef CholmodBase<_MatrixType,_UpLo,Derived> Dec; - IMP_EIGEN_MAKE_SPARSE_SOLVE_HELPERS(Dec,Rhs) - - template void evalTo(Dest& dst) const - { - dec()._solve(rhs(),dst); - } -}; - -} // end namespace internal - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_CHOLMODSUPPORT_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/Array.h b/modules/algebra/include/eigen3/Eigen/src/Core/Array.h deleted file mode 100644 index 66be197bd4..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/Array.h +++ /dev/null @@ -1,323 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2009 Gael Guennebaud -// -// 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 IMP_EIGEN_ARRAY_H -#define IMP_EIGEN_ARRAY_H - -namespace IMP_Eigen { - -/** \class Array - * \ingroup Core_Module - * - * \brief General-purpose arrays with easy API for coefficient-wise operations - * - * The %Array class is very similar to the Matrix class. It provides - * general-purpose one- and two-dimensional arrays. The difference between the - * %Array and the %Matrix class is primarily in the API: the API for the - * %Array class provides easy access to coefficient-wise operations, while the - * API for the %Matrix class provides easy access to linear-algebra - * operations. - * - * This class can be extended with the help of the plugin mechanism described on the page - * \ref TopicCustomizingEigen by defining the preprocessor symbol \c IMP_EIGEN_ARRAY_PLUGIN. - * - * \sa \ref TutorialArrayClass, \ref TopicClassHierarchy - */ -namespace internal { -template -struct traits > : traits > -{ - typedef ArrayXpr XprKind; - typedef ArrayBase > XprBase; -}; -} - -template -class Array - : public PlainObjectBase > -{ - public: - - typedef PlainObjectBase Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(Array) - - enum { Options = _Options }; - typedef typename Base::PlainObject PlainObject; - - protected: - template - friend struct internal::conservative_resize_like_impl; - - using Base::m_storage; - - public: - - using Base::base; - using Base::coeff; - using Base::coeffRef; - - /** - * The usage of - * using Base::operator=; - * fails on MSVC. Since the code below is working with GCC and MSVC, we skipped - * the usage of 'using'. This should be done only for operator=. - */ - template - IMP_EIGEN_STRONG_INLINE Array& operator=(const EigenBase &other) - { - return Base::operator=(other); - } - - /** Copies the value of the expression \a other into \c *this with automatic resizing. - * - * *this might be resized to match the dimensions of \a other. If *this was a null matrix (not already initialized), - * it will be initialized. - * - * Note that copying a row-vector into a vector (and conversely) is allowed. - * The resizing, if any, is then done in the appropriate way so that row-vectors - * remain row-vectors and vectors remain vectors. - */ - template - IMP_EIGEN_STRONG_INLINE Array& operator=(const ArrayBase& other) - { - return Base::_set(other); - } - - /** This is a special case of the templated operator=. Its purpose is to - * prevent a default operator= from hiding the templated operator=. - */ - IMP_EIGEN_STRONG_INLINE Array& operator=(const Array& other) - { - return Base::_set(other); - } - - /** Default constructor. - * - * For fixed-size matrices, does nothing. - * - * For dynamic-size matrices, creates an empty matrix of size 0. Does not allocate any array. Such a matrix - * is called a null matrix. This constructor is the unique way to create null matrices: resizing - * a matrix to 0 is not supported. - * - * \sa resize(Index,Index) - */ - IMP_EIGEN_STRONG_INLINE Array() : Base() - { - Base::_check_template_params(); - IMP_EIGEN_INITIALIZE_COEFFS_IF_THAT_OPTION_IS_ENABLED - } - -#ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - // FIXME is it still needed ?? - /** \internal */ - Array(internal::constructor_without_unaligned_array_assert) - : Base(internal::constructor_without_unaligned_array_assert()) - { - Base::_check_template_params(); - IMP_EIGEN_INITIALIZE_COEFFS_IF_THAT_OPTION_IS_ENABLED - } -#endif - -#ifdef IMP_EIGEN_HAVE_RVALUE_REFERENCES - Array(Array&& other) - : Base(std::move(other)) - { - Base::_check_template_params(); - if (RowsAtCompileTime!=Dynamic && ColsAtCompileTime!=Dynamic) - Base::_set_noalias(other); - } - Array& operator=(Array&& other) - { - other.swap(*this); - return *this; - } -#endif - - /** Constructs a vector or row-vector with given dimension. \only_for_vectors - * - * Note that this is only useful for dynamic-size vectors. For fixed-size vectors, - * it is redundant to pass the dimension here, so it makes more sense to use the default - * constructor Matrix() instead. - */ - IMP_EIGEN_STRONG_INLINE explicit Array(Index dim) - : Base(dim, RowsAtCompileTime == 1 ? 1 : dim, ColsAtCompileTime == 1 ? 1 : dim) - { - Base::_check_template_params(); - IMP_EIGEN_STATIC_ASSERT_VECTOR_ONLY(Array) - imp_eigen_assert(dim >= 0); - imp_eigen_assert(SizeAtCompileTime == Dynamic || SizeAtCompileTime == dim); - IMP_EIGEN_INITIALIZE_COEFFS_IF_THAT_OPTION_IS_ENABLED - } - - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - template - IMP_EIGEN_STRONG_INLINE Array(const T0& val0, const T1& val1) - { - Base::_check_template_params(); - this->template _init2(val0, val1); - } - #else - /** constructs an uninitialized matrix with \a rows rows and \a cols columns. - * - * This is useful for dynamic-size matrices. For fixed-size matrices, - * it is redundant to pass these parameters, so one should use the default constructor - * Matrix() instead. */ - Array(Index rows, Index cols); - /** constructs an initialized 2D vector with given coefficients */ - Array(const Scalar& val0, const Scalar& val1); - #endif - - /** constructs an initialized 3D vector with given coefficients */ - IMP_EIGEN_STRONG_INLINE Array(const Scalar& val0, const Scalar& val1, const Scalar& val2) - { - Base::_check_template_params(); - IMP_EIGEN_STATIC_ASSERT_VECTOR_SPECIFIC_SIZE(Array, 3) - m_storage.data()[0] = val0; - m_storage.data()[1] = val1; - m_storage.data()[2] = val2; - } - /** constructs an initialized 4D vector with given coefficients */ - IMP_EIGEN_STRONG_INLINE Array(const Scalar& val0, const Scalar& val1, const Scalar& val2, const Scalar& val3) - { - Base::_check_template_params(); - IMP_EIGEN_STATIC_ASSERT_VECTOR_SPECIFIC_SIZE(Array, 4) - m_storage.data()[0] = val0; - m_storage.data()[1] = val1; - m_storage.data()[2] = val2; - m_storage.data()[3] = val3; - } - - explicit Array(const Scalar *data); - - /** Constructor copying the value of the expression \a other */ - template - IMP_EIGEN_STRONG_INLINE Array(const ArrayBase& other) - : Base(other.rows() * other.cols(), other.rows(), other.cols()) - { - Base::_check_template_params(); - Base::_set_noalias(other); - } - /** Copy constructor */ - IMP_EIGEN_STRONG_INLINE Array(const Array& other) - : Base(other.rows() * other.cols(), other.rows(), other.cols()) - { - Base::_check_template_params(); - Base::_set_noalias(other); - } - /** Copy constructor with in-place evaluation */ - template - IMP_EIGEN_STRONG_INLINE Array(const ReturnByValue& other) - { - Base::_check_template_params(); - Base::resize(other.rows(), other.cols()); - other.evalTo(*this); - } - - /** \sa MatrixBase::operator=(const EigenBase&) */ - template - IMP_EIGEN_STRONG_INLINE Array(const EigenBase &other) - : Base(other.derived().rows() * other.derived().cols(), other.derived().rows(), other.derived().cols()) - { - Base::_check_template_params(); - Base::_resize_to_match(other); - *this = other; - } - - /** Override MatrixBase::swap() since for dynamic-sized matrices of same type it is enough to swap the - * data pointers. - */ - template - void swap(ArrayBase const & other) - { this->_swap(other.derived()); } - - inline Index innerStride() const { return 1; } - inline Index outerStride() const { return this->innerSize(); } - - #ifdef IMP_EIGEN_ARRAY_PLUGIN - #include IMP_EIGEN_ARRAY_PLUGIN - #endif - - private: - - template - friend struct internal::matrix_swap_impl; -}; - -/** \defgroup arraytypedefs Global array typedefs - * \ingroup Core_Module - * - * Eigen defines several typedef shortcuts for most common 1D and 2D array types. - * - * The general patterns are the following: - * - * \c ArrayRowsColsType where \c Rows and \c Cols can be \c 2,\c 3,\c 4 for fixed size square matrices or \c X for dynamic size, - * and where \c Type can be \c i for integer, \c f for float, \c d for double, \c cf for complex float, \c cd - * for complex double. - * - * For example, \c Array33d is a fixed-size 3x3 array type of doubles, and \c ArrayXXf is a dynamic-size matrix of floats. - * - * There are also \c ArraySizeType which are self-explanatory. For example, \c Array4cf is - * a fixed-size 1D array of 4 complex floats. - * - * \sa class Array - */ - -#define IMP_EIGEN_MAKE_ARRAY_TYPEDEFS(Type, TypeSuffix, Size, SizeSuffix) \ -/** \ingroup arraytypedefs */ \ -typedef Array Array##SizeSuffix##SizeSuffix##TypeSuffix; \ -/** \ingroup arraytypedefs */ \ -typedef Array Array##SizeSuffix##TypeSuffix; - -#define IMP_EIGEN_MAKE_ARRAY_FIXED_TYPEDEFS(Type, TypeSuffix, Size) \ -/** \ingroup arraytypedefs */ \ -typedef Array Array##Size##X##TypeSuffix; \ -/** \ingroup arraytypedefs */ \ -typedef Array Array##X##Size##TypeSuffix; - -#define IMP_EIGEN_MAKE_ARRAY_TYPEDEFS_ALL_SIZES(Type, TypeSuffix) \ -IMP_EIGEN_MAKE_ARRAY_TYPEDEFS(Type, TypeSuffix, 2, 2) \ -IMP_EIGEN_MAKE_ARRAY_TYPEDEFS(Type, TypeSuffix, 3, 3) \ -IMP_EIGEN_MAKE_ARRAY_TYPEDEFS(Type, TypeSuffix, 4, 4) \ -IMP_EIGEN_MAKE_ARRAY_TYPEDEFS(Type, TypeSuffix, Dynamic, X) \ -IMP_EIGEN_MAKE_ARRAY_FIXED_TYPEDEFS(Type, TypeSuffix, 2) \ -IMP_EIGEN_MAKE_ARRAY_FIXED_TYPEDEFS(Type, TypeSuffix, 3) \ -IMP_EIGEN_MAKE_ARRAY_FIXED_TYPEDEFS(Type, TypeSuffix, 4) - -IMP_EIGEN_MAKE_ARRAY_TYPEDEFS_ALL_SIZES(int, i) -IMP_EIGEN_MAKE_ARRAY_TYPEDEFS_ALL_SIZES(float, f) -IMP_EIGEN_MAKE_ARRAY_TYPEDEFS_ALL_SIZES(double, d) -IMP_EIGEN_MAKE_ARRAY_TYPEDEFS_ALL_SIZES(std::complex, cf) -IMP_EIGEN_MAKE_ARRAY_TYPEDEFS_ALL_SIZES(std::complex, cd) - -#undef IMP_EIGEN_MAKE_ARRAY_TYPEDEFS_ALL_SIZES -#undef IMP_EIGEN_MAKE_ARRAY_TYPEDEFS - -#undef IMP_EIGEN_MAKE_ARRAY_TYPEDEFS_LARGE - -#define IMP_EIGEN_USING_ARRAY_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, SizeSuffix) \ -using IMP_Eigen::Matrix##SizeSuffix##TypeSuffix; \ -using IMP_Eigen::Vector##SizeSuffix##TypeSuffix; \ -using IMP_Eigen::RowVector##SizeSuffix##TypeSuffix; - -#define IMP_EIGEN_USING_ARRAY_TYPEDEFS_FOR_TYPE(TypeSuffix) \ -IMP_EIGEN_USING_ARRAY_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, 2) \ -IMP_EIGEN_USING_ARRAY_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, 3) \ -IMP_EIGEN_USING_ARRAY_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, 4) \ -IMP_EIGEN_USING_ARRAY_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, X) \ - -#define IMP_EIGEN_USING_ARRAY_TYPEDEFS \ -IMP_EIGEN_USING_ARRAY_TYPEDEFS_FOR_TYPE(i) \ -IMP_EIGEN_USING_ARRAY_TYPEDEFS_FOR_TYPE(f) \ -IMP_EIGEN_USING_ARRAY_TYPEDEFS_FOR_TYPE(d) \ -IMP_EIGEN_USING_ARRAY_TYPEDEFS_FOR_TYPE(cf) \ -IMP_EIGEN_USING_ARRAY_TYPEDEFS_FOR_TYPE(cd) - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_ARRAY_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/ArrayBase.h b/modules/algebra/include/eigen3/Eigen/src/Core/ArrayBase.h deleted file mode 100644 index e06009d26d..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/ArrayBase.h +++ /dev/null @@ -1,226 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2009 Gael Guennebaud -// -// 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 IMP_EIGEN_ARRAYBASE_H -#define IMP_EIGEN_ARRAYBASE_H - -namespace IMP_Eigen { - -template class MatrixWrapper; - -/** \class ArrayBase - * \ingroup Core_Module - * - * \brief Base class for all 1D and 2D array, and related expressions - * - * An array is similar to a dense vector or matrix. While matrices are mathematical - * objects with well defined linear algebra operators, an array is just a collection - * of scalar values arranged in a one or two dimensionnal fashion. As the main consequence, - * all operations applied to an array are performed coefficient wise. Furthermore, - * arrays support scalar math functions of the c++ standard library (e.g., std::sin(x)), and convenient - * constructors allowing to easily write generic code working for both scalar values - * and arrays. - * - * This class is the base that is inherited by all array expression types. - * - * \tparam Derived is the derived type, e.g., an array or an expression type. - * - * This class can be extended with the help of the plugin mechanism described on the page - * \ref TopicCustomizingEigen by defining the preprocessor symbol \c IMP_EIGEN_ARRAYBASE_PLUGIN. - * - * \sa class MatrixBase, \ref TopicClassHierarchy - */ -template class ArrayBase - : public DenseBase -{ - public: -#ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - /** The base class for a given storage type. */ - typedef ArrayBase StorageBaseType; - - typedef ArrayBase Eigen_BaseClassForSpecializationOfGlobalMathFuncImpl; - - typedef typename internal::traits::StorageKind StorageKind; - typedef typename internal::traits::Index Index; - typedef typename internal::traits::Scalar Scalar; - typedef typename internal::packet_traits::type PacketScalar; - typedef typename NumTraits::Real RealScalar; - - typedef DenseBase Base; - using Base::operator*; - using Base::RowsAtCompileTime; - using Base::ColsAtCompileTime; - using Base::SizeAtCompileTime; - using Base::MaxRowsAtCompileTime; - using Base::MaxColsAtCompileTime; - using Base::MaxSizeAtCompileTime; - using Base::IsVectorAtCompileTime; - using Base::Flags; - using Base::CoeffReadCost; - - using Base::derived; - using Base::const_cast_derived; - using Base::rows; - using Base::cols; - using Base::size; - using Base::coeff; - using Base::coeffRef; - using Base::lazyAssign; - using Base::operator=; - using Base::operator+=; - using Base::operator-=; - using Base::operator*=; - using Base::operator/=; - - typedef typename Base::CoeffReturnType CoeffReturnType; - -#endif // not IMP_EIGEN_PARSED_BY_DOXYGEN - -#ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - /** \internal the plain matrix type corresponding to this expression. Note that is not necessarily - * exactly the return type of eval(): in the case of plain matrices, the return type of eval() is a const - * reference to a matrix, not a matrix! It is however guaranteed that the return type of eval() is either - * PlainObject or const PlainObject&. - */ - typedef Array::Scalar, - internal::traits::RowsAtCompileTime, - internal::traits::ColsAtCompileTime, - AutoAlign | (internal::traits::Flags&RowMajorBit ? RowMajor : ColMajor), - internal::traits::MaxRowsAtCompileTime, - internal::traits::MaxColsAtCompileTime - > PlainObject; - - - /** \internal Represents a matrix with all coefficients equal to one another*/ - typedef CwiseNullaryOp,Derived> ConstantReturnType; -#endif // not IMP_EIGEN_PARSED_BY_DOXYGEN - -#define IMP_EIGEN_CURRENT_STORAGE_BASE_CLASS IMP_Eigen::ArrayBase -# include "../plugins/CommonCwiseUnaryOps.h" -# include "../plugins/MatrixCwiseUnaryOps.h" -# include "../plugins/ArrayCwiseUnaryOps.h" -# include "../plugins/CommonCwiseBinaryOps.h" -# include "../plugins/MatrixCwiseBinaryOps.h" -# include "../plugins/ArrayCwiseBinaryOps.h" -# ifdef IMP_EIGEN_ARRAYBASE_PLUGIN -# include IMP_EIGEN_ARRAYBASE_PLUGIN -# endif -#undef IMP_EIGEN_CURRENT_STORAGE_BASE_CLASS - - /** Special case of the template operator=, in order to prevent the compiler - * from generating a default operator= (issue hit with g++ 4.1) - */ - Derived& operator=(const ArrayBase& other) - { - return internal::assign_selector::run(derived(), other.derived()); - } - - Derived& operator+=(const Scalar& scalar) - { return *this = derived() + scalar; } - Derived& operator-=(const Scalar& scalar) - { return *this = derived() - scalar; } - - template - Derived& operator+=(const ArrayBase& other); - template - Derived& operator-=(const ArrayBase& other); - - template - Derived& operator*=(const ArrayBase& other); - - template - Derived& operator/=(const ArrayBase& other); - - public: - ArrayBase& array() { return *this; } - const ArrayBase& array() const { return *this; } - - /** \returns an \link IMP_Eigen::MatrixBase Matrix \endlink expression of this array - * \sa MatrixBase::array() */ - MatrixWrapper matrix() { return derived(); } - const MatrixWrapper matrix() const { return derived(); } - -// template -// inline void evalTo(Dest& dst) const { dst = matrix(); } - - protected: - ArrayBase() : Base() {} - - private: - explicit ArrayBase(Index); - ArrayBase(Index,Index); - template explicit ArrayBase(const ArrayBase&); - protected: - // mixing arrays and matrices is not legal - template Derived& operator+=(const MatrixBase& ) - {IMP_EIGEN_STATIC_ASSERT(std::ptrdiff_t(sizeof(typename OtherDerived::Scalar))==-1,YOU_CANNOT_MIX_ARRAYS_AND_MATRICES); return *this;} - // mixing arrays and matrices is not legal - template Derived& operator-=(const MatrixBase& ) - {IMP_EIGEN_STATIC_ASSERT(std::ptrdiff_t(sizeof(typename OtherDerived::Scalar))==-1,YOU_CANNOT_MIX_ARRAYS_AND_MATRICES); return *this;} -}; - -/** replaces \c *this by \c *this - \a other. - * - * \returns a reference to \c *this - */ -template -template -IMP_EIGEN_STRONG_INLINE Derived & -ArrayBase::operator-=(const ArrayBase &other) -{ - SelfCwiseBinaryOp, Derived, OtherDerived> tmp(derived()); - tmp = other.derived(); - return derived(); -} - -/** replaces \c *this by \c *this + \a other. - * - * \returns a reference to \c *this - */ -template -template -IMP_EIGEN_STRONG_INLINE Derived & -ArrayBase::operator+=(const ArrayBase& other) -{ - SelfCwiseBinaryOp, Derived, OtherDerived> tmp(derived()); - tmp = other.derived(); - return derived(); -} - -/** replaces \c *this by \c *this * \a other coefficient wise. - * - * \returns a reference to \c *this - */ -template -template -IMP_EIGEN_STRONG_INLINE Derived & -ArrayBase::operator*=(const ArrayBase& other) -{ - SelfCwiseBinaryOp, Derived, OtherDerived> tmp(derived()); - tmp = other.derived(); - return derived(); -} - -/** replaces \c *this by \c *this / \a other coefficient wise. - * - * \returns a reference to \c *this - */ -template -template -IMP_EIGEN_STRONG_INLINE Derived & -ArrayBase::operator/=(const ArrayBase& other) -{ - SelfCwiseBinaryOp, Derived, OtherDerived> tmp(derived()); - tmp = other.derived(); - return derived(); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_ARRAYBASE_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/ArrayWrapper.h b/modules/algebra/include/eigen3/Eigen/src/Core/ArrayWrapper.h deleted file mode 100644 index bb5f92a641..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/ArrayWrapper.h +++ /dev/null @@ -1,264 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2009-2010 Gael Guennebaud -// -// 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 IMP_EIGEN_ARRAYWRAPPER_H -#define IMP_EIGEN_ARRAYWRAPPER_H - -namespace IMP_Eigen { - -/** \class ArrayWrapper - * \ingroup Core_Module - * - * \brief Expression of a mathematical vector or matrix as an array object - * - * This class is the return type of MatrixBase::array(), and most of the time - * this is the only way it is use. - * - * \sa MatrixBase::array(), class MatrixWrapper - */ - -namespace internal { -template -struct traits > - : public traits::type > -{ - typedef ArrayXpr XprKind; - // Let's remove NestByRefBit - enum { - Flags0 = traits::type >::Flags, - Flags = Flags0 & ~NestByRefBit - }; -}; -} - -template -class ArrayWrapper : public ArrayBase > -{ - public: - typedef ArrayBase Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(ArrayWrapper) - IMP_EIGEN_INHERIT_ASSIGNMENT_OPERATORS(ArrayWrapper) - - typedef typename internal::conditional< - internal::is_lvalue::value, - Scalar, - const Scalar - >::type ScalarWithConstIfNotLvalue; - - typedef typename internal::nested::type NestedExpressionType; - - inline ArrayWrapper(ExpressionType& matrix) : m_expression(matrix) {} - - inline Index rows() const { return m_expression.rows(); } - inline Index cols() const { return m_expression.cols(); } - inline Index outerStride() const { return m_expression.outerStride(); } - inline Index innerStride() const { return m_expression.innerStride(); } - - inline ScalarWithConstIfNotLvalue* data() { return m_expression.const_cast_derived().data(); } - inline const Scalar* data() const { return m_expression.data(); } - - inline CoeffReturnType coeff(Index rowId, Index colId) const - { - return m_expression.coeff(rowId, colId); - } - - inline Scalar& coeffRef(Index rowId, Index colId) - { - return m_expression.const_cast_derived().coeffRef(rowId, colId); - } - - inline const Scalar& coeffRef(Index rowId, Index colId) const - { - return m_expression.const_cast_derived().coeffRef(rowId, colId); - } - - inline CoeffReturnType coeff(Index index) const - { - return m_expression.coeff(index); - } - - inline Scalar& coeffRef(Index index) - { - return m_expression.const_cast_derived().coeffRef(index); - } - - inline const Scalar& coeffRef(Index index) const - { - return m_expression.const_cast_derived().coeffRef(index); - } - - template - inline const PacketScalar packet(Index rowId, Index colId) const - { - return m_expression.template packet(rowId, colId); - } - - template - inline void writePacket(Index rowId, Index colId, const PacketScalar& val) - { - m_expression.const_cast_derived().template writePacket(rowId, colId, val); - } - - template - inline const PacketScalar packet(Index index) const - { - return m_expression.template packet(index); - } - - template - inline void writePacket(Index index, const PacketScalar& val) - { - m_expression.const_cast_derived().template writePacket(index, val); - } - - template - inline void evalTo(Dest& dst) const { dst = m_expression; } - - const typename internal::remove_all::type& - nestedExpression() const - { - return m_expression; - } - - /** Forwards the resizing request to the nested expression - * \sa DenseBase::resize(Index) */ - void resize(Index newSize) { m_expression.const_cast_derived().resize(newSize); } - /** Forwards the resizing request to the nested expression - * \sa DenseBase::resize(Index,Index)*/ - void resize(Index nbRows, Index nbCols) { m_expression.const_cast_derived().resize(nbRows,nbCols); } - - protected: - NestedExpressionType m_expression; -}; - -/** \class MatrixWrapper - * \ingroup Core_Module - * - * \brief Expression of an array as a mathematical vector or matrix - * - * This class is the return type of ArrayBase::matrix(), and most of the time - * this is the only way it is use. - * - * \sa MatrixBase::matrix(), class ArrayWrapper - */ - -namespace internal { -template -struct traits > - : public traits::type > -{ - typedef MatrixXpr XprKind; - // Let's remove NestByRefBit - enum { - Flags0 = traits::type >::Flags, - Flags = Flags0 & ~NestByRefBit - }; -}; -} - -template -class MatrixWrapper : public MatrixBase > -{ - public: - typedef MatrixBase > Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(MatrixWrapper) - IMP_EIGEN_INHERIT_ASSIGNMENT_OPERATORS(MatrixWrapper) - - typedef typename internal::conditional< - internal::is_lvalue::value, - Scalar, - const Scalar - >::type ScalarWithConstIfNotLvalue; - - typedef typename internal::nested::type NestedExpressionType; - - inline MatrixWrapper(ExpressionType& a_matrix) : m_expression(a_matrix) {} - - inline Index rows() const { return m_expression.rows(); } - inline Index cols() const { return m_expression.cols(); } - inline Index outerStride() const { return m_expression.outerStride(); } - inline Index innerStride() const { return m_expression.innerStride(); } - - inline ScalarWithConstIfNotLvalue* data() { return m_expression.const_cast_derived().data(); } - inline const Scalar* data() const { return m_expression.data(); } - - inline CoeffReturnType coeff(Index rowId, Index colId) const - { - return m_expression.coeff(rowId, colId); - } - - inline Scalar& coeffRef(Index rowId, Index colId) - { - return m_expression.const_cast_derived().coeffRef(rowId, colId); - } - - inline const Scalar& coeffRef(Index rowId, Index colId) const - { - return m_expression.derived().coeffRef(rowId, colId); - } - - inline CoeffReturnType coeff(Index index) const - { - return m_expression.coeff(index); - } - - inline Scalar& coeffRef(Index index) - { - return m_expression.const_cast_derived().coeffRef(index); - } - - inline const Scalar& coeffRef(Index index) const - { - return m_expression.const_cast_derived().coeffRef(index); - } - - template - inline const PacketScalar packet(Index rowId, Index colId) const - { - return m_expression.template packet(rowId, colId); - } - - template - inline void writePacket(Index rowId, Index colId, const PacketScalar& val) - { - m_expression.const_cast_derived().template writePacket(rowId, colId, val); - } - - template - inline const PacketScalar packet(Index index) const - { - return m_expression.template packet(index); - } - - template - inline void writePacket(Index index, const PacketScalar& val) - { - m_expression.const_cast_derived().template writePacket(index, val); - } - - const typename internal::remove_all::type& - nestedExpression() const - { - return m_expression; - } - - /** Forwards the resizing request to the nested expression - * \sa DenseBase::resize(Index) */ - void resize(Index newSize) { m_expression.const_cast_derived().resize(newSize); } - /** Forwards the resizing request to the nested expression - * \sa DenseBase::resize(Index,Index)*/ - void resize(Index nbRows, Index nbCols) { m_expression.const_cast_derived().resize(nbRows,nbCols); } - - protected: - NestedExpressionType m_expression; -}; - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_ARRAYWRAPPER_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/Assign.h b/modules/algebra/include/eigen3/Eigen/src/Core/Assign.h deleted file mode 100644 index b6b6663be1..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/Assign.h +++ /dev/null @@ -1,590 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2007 Michael Olbrich -// Copyright (C) 2006-2010 Benoit Jacob -// Copyright (C) 2008 Gael Guennebaud -// -// 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 IMP_EIGEN_ASSIGN_H -#define IMP_EIGEN_ASSIGN_H - -namespace IMP_Eigen { - -namespace internal { - -/*************************************************************************** -* Part 1 : the logic deciding a strategy for traversal and unrolling * -***************************************************************************/ - -template -struct assign_traits -{ -public: - enum { - DstIsAligned = Derived::Flags & AlignedBit, - DstHasDirectAccess = Derived::Flags & DirectAccessBit, - SrcIsAligned = OtherDerived::Flags & AlignedBit, - JointAlignment = bool(DstIsAligned) && bool(SrcIsAligned) ? Aligned : Unaligned - }; - -private: - enum { - InnerSize = int(Derived::IsVectorAtCompileTime) ? int(Derived::SizeAtCompileTime) - : int(Derived::Flags)&RowMajorBit ? int(Derived::ColsAtCompileTime) - : int(Derived::RowsAtCompileTime), - InnerMaxSize = int(Derived::IsVectorAtCompileTime) ? int(Derived::MaxSizeAtCompileTime) - : int(Derived::Flags)&RowMajorBit ? int(Derived::MaxColsAtCompileTime) - : int(Derived::MaxRowsAtCompileTime), - MaxSizeAtCompileTime = Derived::SizeAtCompileTime, - PacketSize = packet_traits::size - }; - - enum { - StorageOrdersAgree = (int(Derived::IsRowMajor) == int(OtherDerived::IsRowMajor)), - MightVectorize = StorageOrdersAgree - && (int(Derived::Flags) & int(OtherDerived::Flags) & ActualPacketAccessBit), - MayInnerVectorize = MightVectorize && int(InnerSize)!=Dynamic && int(InnerSize)%int(PacketSize)==0 - && int(DstIsAligned) && int(SrcIsAligned), - MayLinearize = StorageOrdersAgree && (int(Derived::Flags) & int(OtherDerived::Flags) & LinearAccessBit), - MayLinearVectorize = MightVectorize && MayLinearize && DstHasDirectAccess - && (DstIsAligned || MaxSizeAtCompileTime == Dynamic), - /* If the destination isn't aligned, we have to do runtime checks and we don't unroll, - so it's only good for large enough sizes. */ - MaySliceVectorize = MightVectorize && DstHasDirectAccess - && (int(InnerMaxSize)==Dynamic || int(InnerMaxSize)>=3*PacketSize) - /* slice vectorization can be slow, so we only want it if the slices are big, which is - indicated by InnerMaxSize rather than InnerSize, think of the case of a dynamic block - in a fixed-size matrix */ - }; - -public: - enum { - Traversal = int(MayInnerVectorize) ? int(InnerVectorizedTraversal) - : int(MayLinearVectorize) ? int(LinearVectorizedTraversal) - : int(MaySliceVectorize) ? int(SliceVectorizedTraversal) - : int(MayLinearize) ? int(LinearTraversal) - : int(DefaultTraversal), - Vectorized = int(Traversal) == InnerVectorizedTraversal - || int(Traversal) == LinearVectorizedTraversal - || int(Traversal) == SliceVectorizedTraversal - }; - -private: - enum { - UnrollingLimit = IMP_EIGEN_UNROLLING_LIMIT * (Vectorized ? int(PacketSize) : 1), - MayUnrollCompletely = int(Derived::SizeAtCompileTime) != Dynamic - && int(OtherDerived::CoeffReadCost) != Dynamic - && int(Derived::SizeAtCompileTime) * int(OtherDerived::CoeffReadCost) <= int(UnrollingLimit), - MayUnrollInner = int(InnerSize) != Dynamic - && int(OtherDerived::CoeffReadCost) != Dynamic - && int(InnerSize) * int(OtherDerived::CoeffReadCost) <= int(UnrollingLimit) - }; - -public: - enum { - Unrolling = (int(Traversal) == int(InnerVectorizedTraversal) || int(Traversal) == int(DefaultTraversal)) - ? ( - int(MayUnrollCompletely) ? int(CompleteUnrolling) - : int(MayUnrollInner) ? int(InnerUnrolling) - : int(NoUnrolling) - ) - : int(Traversal) == int(LinearVectorizedTraversal) - ? ( bool(MayUnrollCompletely) && bool(DstIsAligned) ? int(CompleteUnrolling) : int(NoUnrolling) ) - : int(Traversal) == int(LinearTraversal) - ? ( bool(MayUnrollCompletely) ? int(CompleteUnrolling) : int(NoUnrolling) ) - : int(NoUnrolling) - }; - -#ifdef IMP_EIGEN_DEBUG_ASSIGN - static void debug() - { - IMP_EIGEN_DEBUG_VAR(DstIsAligned) - IMP_EIGEN_DEBUG_VAR(SrcIsAligned) - IMP_EIGEN_DEBUG_VAR(JointAlignment) - IMP_EIGEN_DEBUG_VAR(InnerSize) - IMP_EIGEN_DEBUG_VAR(InnerMaxSize) - IMP_EIGEN_DEBUG_VAR(PacketSize) - IMP_EIGEN_DEBUG_VAR(StorageOrdersAgree) - IMP_EIGEN_DEBUG_VAR(MightVectorize) - IMP_EIGEN_DEBUG_VAR(MayLinearize) - IMP_EIGEN_DEBUG_VAR(MayInnerVectorize) - IMP_EIGEN_DEBUG_VAR(MayLinearVectorize) - IMP_EIGEN_DEBUG_VAR(MaySliceVectorize) - IMP_EIGEN_DEBUG_VAR(Traversal) - IMP_EIGEN_DEBUG_VAR(UnrollingLimit) - IMP_EIGEN_DEBUG_VAR(MayUnrollCompletely) - IMP_EIGEN_DEBUG_VAR(MayUnrollInner) - IMP_EIGEN_DEBUG_VAR(Unrolling) - } -#endif -}; - -/*************************************************************************** -* Part 2 : meta-unrollers -***************************************************************************/ - -/************************ -*** Default traversal *** -************************/ - -template -struct assign_DefaultTraversal_CompleteUnrolling -{ - enum { - outer = Index / Derived1::InnerSizeAtCompileTime, - inner = Index % Derived1::InnerSizeAtCompileTime - }; - - static IMP_EIGEN_STRONG_INLINE void run(Derived1 &dst, const Derived2 &src) - { - dst.copyCoeffByOuterInner(outer, inner, src); - assign_DefaultTraversal_CompleteUnrolling::run(dst, src); - } -}; - -template -struct assign_DefaultTraversal_CompleteUnrolling -{ - static IMP_EIGEN_STRONG_INLINE void run(Derived1 &, const Derived2 &) {} -}; - -template -struct assign_DefaultTraversal_InnerUnrolling -{ - static IMP_EIGEN_STRONG_INLINE void run(Derived1 &dst, const Derived2 &src, typename Derived1::Index outer) - { - dst.copyCoeffByOuterInner(outer, Index, src); - assign_DefaultTraversal_InnerUnrolling::run(dst, src, outer); - } -}; - -template -struct assign_DefaultTraversal_InnerUnrolling -{ - static IMP_EIGEN_STRONG_INLINE void run(Derived1 &, const Derived2 &, typename Derived1::Index) {} -}; - -/*********************** -*** Linear traversal *** -***********************/ - -template -struct assign_LinearTraversal_CompleteUnrolling -{ - static IMP_EIGEN_STRONG_INLINE void run(Derived1 &dst, const Derived2 &src) - { - dst.copyCoeff(Index, src); - assign_LinearTraversal_CompleteUnrolling::run(dst, src); - } -}; - -template -struct assign_LinearTraversal_CompleteUnrolling -{ - static IMP_EIGEN_STRONG_INLINE void run(Derived1 &, const Derived2 &) {} -}; - -/************************** -*** Inner vectorization *** -**************************/ - -template -struct assign_innervec_CompleteUnrolling -{ - enum { - outer = Index / Derived1::InnerSizeAtCompileTime, - inner = Index % Derived1::InnerSizeAtCompileTime, - JointAlignment = assign_traits::JointAlignment - }; - - static IMP_EIGEN_STRONG_INLINE void run(Derived1 &dst, const Derived2 &src) - { - dst.template copyPacketByOuterInner(outer, inner, src); - assign_innervec_CompleteUnrolling::size, Stop>::run(dst, src); - } -}; - -template -struct assign_innervec_CompleteUnrolling -{ - static IMP_EIGEN_STRONG_INLINE void run(Derived1 &, const Derived2 &) {} -}; - -template -struct assign_innervec_InnerUnrolling -{ - static IMP_EIGEN_STRONG_INLINE void run(Derived1 &dst, const Derived2 &src, typename Derived1::Index outer) - { - dst.template copyPacketByOuterInner(outer, Index, src); - assign_innervec_InnerUnrolling::size, Stop>::run(dst, src, outer); - } -}; - -template -struct assign_innervec_InnerUnrolling -{ - static IMP_EIGEN_STRONG_INLINE void run(Derived1 &, const Derived2 &, typename Derived1::Index) {} -}; - -/*************************************************************************** -* Part 3 : implementation of all cases -***************************************************************************/ - -template::Traversal, - int Unrolling = assign_traits::Unrolling, - int Version = Specialized> -struct assign_impl; - -/************************ -*** Default traversal *** -************************/ - -template -struct assign_impl -{ - static inline void run(Derived1 &, const Derived2 &) { } -}; - -template -struct assign_impl -{ - typedef typename Derived1::Index Index; - static inline void run(Derived1 &dst, const Derived2 &src) - { - const Index innerSize = dst.innerSize(); - const Index outerSize = dst.outerSize(); - for(Index outer = 0; outer < outerSize; ++outer) - for(Index inner = 0; inner < innerSize; ++inner) - dst.copyCoeffByOuterInner(outer, inner, src); - } -}; - -template -struct assign_impl -{ - static IMP_EIGEN_STRONG_INLINE void run(Derived1 &dst, const Derived2 &src) - { - assign_DefaultTraversal_CompleteUnrolling - ::run(dst, src); - } -}; - -template -struct assign_impl -{ - typedef typename Derived1::Index Index; - static IMP_EIGEN_STRONG_INLINE void run(Derived1 &dst, const Derived2 &src) - { - const Index outerSize = dst.outerSize(); - for(Index outer = 0; outer < outerSize; ++outer) - assign_DefaultTraversal_InnerUnrolling - ::run(dst, src, outer); - } -}; - -/*********************** -*** Linear traversal *** -***********************/ - -template -struct assign_impl -{ - typedef typename Derived1::Index Index; - static inline void run(Derived1 &dst, const Derived2 &src) - { - const Index size = dst.size(); - for(Index i = 0; i < size; ++i) - dst.copyCoeff(i, src); - } -}; - -template -struct assign_impl -{ - static IMP_EIGEN_STRONG_INLINE void run(Derived1 &dst, const Derived2 &src) - { - assign_LinearTraversal_CompleteUnrolling - ::run(dst, src); - } -}; - -/************************** -*** Inner vectorization *** -**************************/ - -template -struct assign_impl -{ - typedef typename Derived1::Index Index; - static inline void run(Derived1 &dst, const Derived2 &src) - { - const Index innerSize = dst.innerSize(); - const Index outerSize = dst.outerSize(); - const Index packetSize = packet_traits::size; - for(Index outer = 0; outer < outerSize; ++outer) - for(Index inner = 0; inner < innerSize; inner+=packetSize) - dst.template copyPacketByOuterInner(outer, inner, src); - } -}; - -template -struct assign_impl -{ - static IMP_EIGEN_STRONG_INLINE void run(Derived1 &dst, const Derived2 &src) - { - assign_innervec_CompleteUnrolling - ::run(dst, src); - } -}; - -template -struct assign_impl -{ - typedef typename Derived1::Index Index; - static IMP_EIGEN_STRONG_INLINE void run(Derived1 &dst, const Derived2 &src) - { - const Index outerSize = dst.outerSize(); - for(Index outer = 0; outer < outerSize; ++outer) - assign_innervec_InnerUnrolling - ::run(dst, src, outer); - } -}; - -/*************************** -*** Linear vectorization *** -***************************/ - -template -struct unaligned_assign_impl -{ - template - static IMP_EIGEN_STRONG_INLINE void run(const Derived&, OtherDerived&, typename Derived::Index, typename Derived::Index) {} -}; - -template <> -struct unaligned_assign_impl -{ - // MSVC must not inline this functions. If it does, it fails to optimize the - // packet access path. -#ifdef _MSC_VER - template - static IMP_EIGEN_DONT_INLINE void run(const Derived& src, OtherDerived& dst, typename Derived::Index start, typename Derived::Index end) -#else - template - static IMP_EIGEN_STRONG_INLINE void run(const Derived& src, OtherDerived& dst, typename Derived::Index start, typename Derived::Index end) -#endif - { - for (typename Derived::Index index = start; index < end; ++index) - dst.copyCoeff(index, src); - } -}; - -template -struct assign_impl -{ - typedef typename Derived1::Index Index; - static IMP_EIGEN_STRONG_INLINE void run(Derived1 &dst, const Derived2 &src) - { - const Index size = dst.size(); - typedef packet_traits PacketTraits; - enum { - packetSize = PacketTraits::size, - dstAlignment = PacketTraits::AlignedOnScalar ? Aligned : int(assign_traits::DstIsAligned) , - srcAlignment = assign_traits::JointAlignment - }; - const Index alignedStart = assign_traits::DstIsAligned ? 0 - : internal::first_aligned(&dst.coeffRef(0), size); - const Index alignedEnd = alignedStart + ((size-alignedStart)/packetSize)*packetSize; - - unaligned_assign_impl::DstIsAligned!=0>::run(src,dst,0,alignedStart); - - for(Index index = alignedStart; index < alignedEnd; index += packetSize) - { - dst.template copyPacket(index, src); - } - - unaligned_assign_impl<>::run(src,dst,alignedEnd,size); - } -}; - -template -struct assign_impl -{ - typedef typename Derived1::Index Index; - static IMP_EIGEN_STRONG_INLINE void run(Derived1 &dst, const Derived2 &src) - { - enum { size = Derived1::SizeAtCompileTime, - packetSize = packet_traits::size, - alignedSize = (size/packetSize)*packetSize }; - - assign_innervec_CompleteUnrolling::run(dst, src); - assign_DefaultTraversal_CompleteUnrolling::run(dst, src); - } -}; - -/************************** -*** Slice vectorization *** -***************************/ - -template -struct assign_impl -{ - typedef typename Derived1::Index Index; - static inline void run(Derived1 &dst, const Derived2 &src) - { - typedef typename Derived1::Scalar Scalar; - typedef packet_traits PacketTraits; - enum { - packetSize = PacketTraits::size, - alignable = PacketTraits::AlignedOnScalar, - dstIsAligned = assign_traits::DstIsAligned, - dstAlignment = alignable ? Aligned : int(dstIsAligned), - srcAlignment = assign_traits::JointAlignment - }; - const Scalar *dst_ptr = &dst.coeffRef(0,0); - if((!bool(dstIsAligned)) && (size_t(dst_ptr) % sizeof(Scalar))>0) - { - // the pointer is not aligend-on scalar, so alignment is not possible - return assign_impl::run(dst, src); - } - const Index packetAlignedMask = packetSize - 1; - const Index innerSize = dst.innerSize(); - const Index outerSize = dst.outerSize(); - const Index alignedStep = alignable ? (packetSize - dst.outerStride() % packetSize) & packetAlignedMask : 0; - Index alignedStart = ((!alignable) || bool(dstIsAligned)) ? 0 : internal::first_aligned(dst_ptr, innerSize); - - for(Index outer = 0; outer < outerSize; ++outer) - { - const Index alignedEnd = alignedStart + ((innerSize-alignedStart) & ~packetAlignedMask); - // do the non-vectorizable part of the assignment - for(Index inner = 0; inner(outer, inner, src); - - // do the non-vectorizable part of the assignment - for(Index inner = alignedEnd; inner((alignedStart+alignedStep)%packetSize, innerSize); - } - } -}; - -} // end namespace internal - -/*************************************************************************** -* Part 4 : implementation of DenseBase methods -***************************************************************************/ - -template -template -IMP_EIGEN_STRONG_INLINE Derived& DenseBase - ::lazyAssign(const DenseBase& other) -{ - enum{ - SameType = internal::is_same::value - }; - - IMP_EIGEN_STATIC_ASSERT_LVALUE(Derived) - IMP_EIGEN_STATIC_ASSERT_SAME_MATRIX_SIZE(Derived,OtherDerived) - IMP_EIGEN_STATIC_ASSERT(SameType,YOU_MIXED_DIFFERENT_NUMERIC_TYPES__YOU_NEED_TO_USE_THE_CAST_METHOD_OF_MATRIXBASE_TO_CAST_NUMERIC_TYPES_EXPLICITLY) - -#ifdef IMP_EIGEN_DEBUG_ASSIGN - internal::assign_traits::debug(); -#endif - imp_eigen_assert(rows() == other.rows() && cols() == other.cols()); - internal::assign_impl::Traversal) - : int(InvalidTraversal)>::run(derived(),other.derived()); -#ifndef IMP_EIGEN_NO_DEBUG - checkTransposeAliasing(other.derived()); -#endif - return derived(); -} - -namespace internal { - -template::Flags) & EvalBeforeAssigningBit) != 0, - bool NeedToTranspose = ((int(Derived::RowsAtCompileTime) == 1 && int(OtherDerived::ColsAtCompileTime) == 1) - | // FIXME | instead of || to please GCC 4.4.0 stupid warning "suggest parentheses around &&". - // revert to || as soon as not needed anymore. - (int(Derived::ColsAtCompileTime) == 1 && int(OtherDerived::RowsAtCompileTime) == 1)) - && int(Derived::SizeAtCompileTime) != 1> -struct assign_selector; - -template -struct assign_selector { - static IMP_EIGEN_STRONG_INLINE Derived& run(Derived& dst, const OtherDerived& other) { return dst.lazyAssign(other.derived()); } - template - static IMP_EIGEN_STRONG_INLINE Derived& evalTo(ActualDerived& dst, const ActualOtherDerived& other) { other.evalTo(dst); return dst; } -}; -template -struct assign_selector { - static IMP_EIGEN_STRONG_INLINE Derived& run(Derived& dst, const OtherDerived& other) { return dst.lazyAssign(other.eval()); } -}; -template -struct assign_selector { - static IMP_EIGEN_STRONG_INLINE Derived& run(Derived& dst, const OtherDerived& other) { return dst.lazyAssign(other.transpose()); } - template - static IMP_EIGEN_STRONG_INLINE Derived& evalTo(ActualDerived& dst, const ActualOtherDerived& other) { Transpose dstTrans(dst); other.evalTo(dstTrans); return dst; } -}; -template -struct assign_selector { - static IMP_EIGEN_STRONG_INLINE Derived& run(Derived& dst, const OtherDerived& other) { return dst.lazyAssign(other.transpose().eval()); } -}; - -} // end namespace internal - -template -template -IMP_EIGEN_STRONG_INLINE Derived& DenseBase::operator=(const DenseBase& other) -{ - return internal::assign_selector::run(derived(), other.derived()); -} - -template -IMP_EIGEN_STRONG_INLINE Derived& DenseBase::operator=(const DenseBase& other) -{ - return internal::assign_selector::run(derived(), other.derived()); -} - -template -IMP_EIGEN_STRONG_INLINE Derived& MatrixBase::operator=(const MatrixBase& other) -{ - return internal::assign_selector::run(derived(), other.derived()); -} - -template -template -IMP_EIGEN_STRONG_INLINE Derived& MatrixBase::operator=(const DenseBase& other) -{ - return internal::assign_selector::run(derived(), other.derived()); -} - -template -template -IMP_EIGEN_STRONG_INLINE Derived& MatrixBase::operator=(const EigenBase& other) -{ - return internal::assign_selector::evalTo(derived(), other.derived()); -} - -template -template -IMP_EIGEN_STRONG_INLINE Derived& MatrixBase::operator=(const ReturnByValue& other) -{ - return internal::assign_selector::evalTo(derived(), other.derived()); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_ASSIGN_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/Assign_MKL.h b/modules/algebra/include/eigen3/Eigen/src/Core/Assign_MKL.h deleted file mode 100644 index 6a9078b1f8..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/Assign_MKL.h +++ /dev/null @@ -1,224 +0,0 @@ -/* - Copyright (c) 2011, Intel Corporation. All rights reserved. - - Redistribution and use in source and binary forms, with or without modification, - are permitted provided that the following conditions are met: - - * Redistributions of source code must retain the above copyright notice, this - list of conditions and the following disclaimer. - * Redistributions in binary form must reproduce the above copyright notice, - this list of conditions and the following disclaimer in the documentation - and/or other materials provided with the distribution. - * Neither the name of Intel Corporation nor the names of its contributors may - be used to endorse or promote products derived from this software without - specific prior written permission. - - THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND - ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED - WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE - DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR - ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES - (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; - LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON - ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS - SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - - ******************************************************************************** - * Content : Eigen bindings to Intel(R) MKL - * MKL VML support for coefficient-wise unary Eigen expressions like a=b.sin() - ******************************************************************************** -*/ - -#ifndef IMP_EIGEN_ASSIGN_VML_H -#define IMP_EIGEN_ASSIGN_VML_H - -namespace IMP_Eigen { - -namespace internal { - -template struct vml_call -{ enum { IsSupported = 0 }; }; - -template -class vml_assign_traits -{ - private: - enum { - DstHasDirectAccess = Dst::Flags & DirectAccessBit, - SrcHasDirectAccess = Src::Flags & DirectAccessBit, - - StorageOrdersAgree = (int(Dst::IsRowMajor) == int(Src::IsRowMajor)), - InnerSize = int(Dst::IsVectorAtCompileTime) ? int(Dst::SizeAtCompileTime) - : int(Dst::Flags)&RowMajorBit ? int(Dst::ColsAtCompileTime) - : int(Dst::RowsAtCompileTime), - InnerMaxSize = int(Dst::IsVectorAtCompileTime) ? int(Dst::MaxSizeAtCompileTime) - : int(Dst::Flags)&RowMajorBit ? int(Dst::MaxColsAtCompileTime) - : int(Dst::MaxRowsAtCompileTime), - MaxSizeAtCompileTime = Dst::SizeAtCompileTime, - - MightEnableVml = vml_call::IsSupported && StorageOrdersAgree && DstHasDirectAccess && SrcHasDirectAccess - && Src::InnerStrideAtCompileTime==1 && Dst::InnerStrideAtCompileTime==1, - MightLinearize = MightEnableVml && (int(Dst::Flags) & int(Src::Flags) & LinearAccessBit), - VmlSize = MightLinearize ? MaxSizeAtCompileTime : InnerMaxSize, - LargeEnough = VmlSize==Dynamic || VmlSize>=IMP_EIGEN_MKL_VML_THRESHOLD, - MayEnableVml = MightEnableVml && LargeEnough, - MayLinearize = MayEnableVml && MightLinearize - }; - public: - enum { - Traversal = MayLinearize ? LinearVectorizedTraversal - : MayEnableVml ? InnerVectorizedTraversal - : DefaultTraversal - }; -}; - -template::Traversal > -struct vml_assign_impl - : assign_impl,Traversal,Unrolling,BuiltIn> -{ -}; - -template -struct vml_assign_impl -{ - typedef typename Derived1::Scalar Scalar; - typedef typename Derived1::Index Index; - static inline void run(Derived1& dst, const CwiseUnaryOp& src) - { - // in case we want to (or have to) skip VML at runtime we can call: - // assign_impl,Traversal,Unrolling,BuiltIn>::run(dst,src); - const Index innerSize = dst.innerSize(); - const Index outerSize = dst.outerSize(); - for(Index outer = 0; outer < outerSize; ++outer) { - const Scalar *src_ptr = src.IsRowMajor ? &(src.nestedExpression().coeffRef(outer,0)) : - &(src.nestedExpression().coeffRef(0, outer)); - Scalar *dst_ptr = dst.IsRowMajor ? &(dst.coeffRef(outer,0)) : &(dst.coeffRef(0, outer)); - vml_call::run(src.functor(), innerSize, src_ptr, dst_ptr ); - } - } -}; - -template -struct vml_assign_impl -{ - static inline void run(Derived1& dst, const CwiseUnaryOp& src) - { - // in case we want to (or have to) skip VML at runtime we can call: - // assign_impl,Traversal,Unrolling,BuiltIn>::run(dst,src); - vml_call::run(src.functor(), dst.size(), src.nestedExpression().data(), dst.data() ); - } -}; - -// Macroses - -#define IMP_EIGEN_MKL_VML_SPECIALIZE_ASSIGN(TRAVERSAL,UNROLLING) \ - template \ - struct assign_impl, TRAVERSAL, UNROLLING, Specialized> { \ - static inline void run(Derived1 &dst, const IMP_Eigen::CwiseUnaryOp &src) { \ - vml_assign_impl::run(dst, src); \ - } \ - }; - -IMP_EIGEN_MKL_VML_SPECIALIZE_ASSIGN(DefaultTraversal,NoUnrolling) -IMP_EIGEN_MKL_VML_SPECIALIZE_ASSIGN(DefaultTraversal,CompleteUnrolling) -IMP_EIGEN_MKL_VML_SPECIALIZE_ASSIGN(DefaultTraversal,InnerUnrolling) -IMP_EIGEN_MKL_VML_SPECIALIZE_ASSIGN(LinearTraversal,NoUnrolling) -IMP_EIGEN_MKL_VML_SPECIALIZE_ASSIGN(LinearTraversal,CompleteUnrolling) -IMP_EIGEN_MKL_VML_SPECIALIZE_ASSIGN(InnerVectorizedTraversal,NoUnrolling) -IMP_EIGEN_MKL_VML_SPECIALIZE_ASSIGN(InnerVectorizedTraversal,CompleteUnrolling) -IMP_EIGEN_MKL_VML_SPECIALIZE_ASSIGN(InnerVectorizedTraversal,InnerUnrolling) -IMP_EIGEN_MKL_VML_SPECIALIZE_ASSIGN(LinearVectorizedTraversal,CompleteUnrolling) -IMP_EIGEN_MKL_VML_SPECIALIZE_ASSIGN(LinearVectorizedTraversal,NoUnrolling) -IMP_EIGEN_MKL_VML_SPECIALIZE_ASSIGN(SliceVectorizedTraversal,NoUnrolling) - - -#if !defined (IMP_EIGEN_FAST_MATH) || (IMP_EIGEN_FAST_MATH != 1) -#define IMP_EIGEN_MKL_VML_MODE VML_HA -#else -#define IMP_EIGEN_MKL_VML_MODE VML_LA -#endif - -#define IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALL(IMP_EIGENOP, VMLOP, IMP_EIGENTYPE, VMLTYPE) \ - template<> struct vml_call< scalar_##EIGENOP##_op > { \ - enum { IsSupported = 1 }; \ - static inline void run( const scalar_##EIGENOP##_op& /*func*/, \ - int size, const IMP_EIGENTYPE* src, IMP_EIGENTYPE* dst) { \ - VMLOP(size, (const VMLTYPE*)src, (VMLTYPE*)dst); \ - } \ - }; - -#define IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALL_LA(IMP_EIGENOP, VMLOP, IMP_EIGENTYPE, VMLTYPE) \ - template<> struct vml_call< scalar_##EIGENOP##_op > { \ - enum { IsSupported = 1 }; \ - static inline void run( const scalar_##EIGENOP##_op& /*func*/, \ - int size, const IMP_EIGENTYPE* src, IMP_EIGENTYPE* dst) { \ - MKL_INT64 vmlMode = IMP_EIGEN_MKL_VML_MODE; \ - VMLOP(size, (const VMLTYPE*)src, (VMLTYPE*)dst, vmlMode); \ - } \ - }; - -#define IMP_EIGEN_MKL_VML_DECLARE_POW_CALL(IMP_EIGENOP, VMLOP, IMP_EIGENTYPE, VMLTYPE) \ - template<> struct vml_call< scalar_##EIGENOP##_op > { \ - enum { IsSupported = 1 }; \ - static inline void run( const scalar_##EIGENOP##_op& func, \ - int size, const IMP_EIGENTYPE* src, IMP_EIGENTYPE* dst) { \ - IMP_EIGENTYPE exponent = func.m_exponent; \ - MKL_INT64 vmlMode = IMP_EIGEN_MKL_VML_MODE; \ - VMLOP(&size, (const VMLTYPE*)src, (const VMLTYPE*)&exponent, \ - (VMLTYPE*)dst, &vmlMode); \ - } \ - }; - -#define IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALLS_REAL(IMP_EIGENOP, VMLOP) \ - IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALL(IMP_EIGENOP, vs##VMLOP, float, float) \ - IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALL(IMP_EIGENOP, vd##VMLOP, double, double) - -#define IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALLS_COMPLEX(IMP_EIGENOP, VMLOP) \ - IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALL(IMP_EIGENOP, vc##VMLOP, scomplex, MKL_Complex8) \ - IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALL(IMP_EIGENOP, vz##VMLOP, dcomplex, MKL_Complex16) - -#define IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALLS(IMP_EIGENOP, VMLOP) \ - IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALLS_REAL(IMP_EIGENOP, VMLOP) \ - IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALLS_COMPLEX(IMP_EIGENOP, VMLOP) - - -#define IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALLS_REAL_LA(IMP_EIGENOP, VMLOP) \ - IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALL_LA(IMP_EIGENOP, vms##VMLOP, float, float) \ - IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALL_LA(IMP_EIGENOP, vmd##VMLOP, double, double) - -#define IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALLS_COMPLEX_LA(IMP_EIGENOP, VMLOP) \ - IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALL_LA(IMP_EIGENOP, vmc##VMLOP, scomplex, MKL_Complex8) \ - IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALL_LA(IMP_EIGENOP, vmz##VMLOP, dcomplex, MKL_Complex16) - -#define IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALLS_LA(IMP_EIGENOP, VMLOP) \ - IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALLS_REAL_LA(IMP_EIGENOP, VMLOP) \ - IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALLS_COMPLEX_LA(IMP_EIGENOP, VMLOP) - - -IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALLS_LA(sin, Sin) -IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALLS_LA(asin, Asin) -IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALLS_LA(cos, Cos) -IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALLS_LA(acos, Acos) -IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALLS_LA(tan, Tan) -//EIGEN_MKL_VML_DECLARE_UNARY_CALLS(abs, Abs) -IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALLS_LA(exp, Exp) -IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALLS_LA(log, Ln) -IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALLS_LA(sqrt, Sqrt) - -IMP_EIGEN_MKL_VML_DECLARE_UNARY_CALLS_REAL(square, Sqr) - -// The vm*powx functions are not avaibale in the windows version of MKL. -#ifndef _WIN32 -IMP_EIGEN_MKL_VML_DECLARE_POW_CALL(pow, vmspowx_, float, float) -IMP_EIGEN_MKL_VML_DECLARE_POW_CALL(pow, vmdpowx_, double, double) -IMP_EIGEN_MKL_VML_DECLARE_POW_CALL(pow, vmcpowx_, scomplex, MKL_Complex8) -IMP_EIGEN_MKL_VML_DECLARE_POW_CALL(pow, vmzpowx_, dcomplex, MKL_Complex16) -#endif - -} // end namespace internal - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_ASSIGN_VML_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/BandMatrix.h b/modules/algebra/include/eigen3/Eigen/src/Core/BandMatrix.h deleted file mode 100644 index 8625481d32..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/BandMatrix.h +++ /dev/null @@ -1,334 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2009 Gael Guennebaud -// -// 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 IMP_EIGEN_BANDMATRIX_H -#define IMP_EIGEN_BANDMATRIX_H - -namespace IMP_Eigen { - -namespace internal { - -template -class BandMatrixBase : public EigenBase -{ - public: - - enum { - Flags = internal::traits::Flags, - CoeffReadCost = internal::traits::CoeffReadCost, - RowsAtCompileTime = internal::traits::RowsAtCompileTime, - ColsAtCompileTime = internal::traits::ColsAtCompileTime, - MaxRowsAtCompileTime = internal::traits::MaxRowsAtCompileTime, - MaxColsAtCompileTime = internal::traits::MaxColsAtCompileTime, - Supers = internal::traits::Supers, - Subs = internal::traits::Subs, - Options = internal::traits::Options - }; - typedef typename internal::traits::Scalar Scalar; - typedef Matrix DenseMatrixType; - typedef typename DenseMatrixType::Index Index; - typedef typename internal::traits::CoefficientsType CoefficientsType; - typedef EigenBase Base; - - protected: - enum { - DataRowsAtCompileTime = ((Supers!=Dynamic) && (Subs!=Dynamic)) - ? 1 + Supers + Subs - : Dynamic, - SizeAtCompileTime = IMP_EIGEN_SIZE_MIN_PREFER_DYNAMIC(RowsAtCompileTime,ColsAtCompileTime) - }; - - public: - - using Base::derived; - using Base::rows; - using Base::cols; - - /** \returns the number of super diagonals */ - inline Index supers() const { return derived().supers(); } - - /** \returns the number of sub diagonals */ - inline Index subs() const { return derived().subs(); } - - /** \returns an expression of the underlying coefficient matrix */ - inline const CoefficientsType& coeffs() const { return derived().coeffs(); } - - /** \returns an expression of the underlying coefficient matrix */ - inline CoefficientsType& coeffs() { return derived().coeffs(); } - - /** \returns a vector expression of the \a i -th column, - * only the meaningful part is returned. - * \warning the internal storage must be column major. */ - inline Block col(Index i) - { - IMP_EIGEN_STATIC_ASSERT((Options&RowMajor)==0,THIS_METHOD_IS_ONLY_FOR_COLUMN_MAJOR_MATRICES); - Index start = 0; - Index len = coeffs().rows(); - if (i<=supers()) - { - start = supers()-i; - len = (std::min)(rows(),std::max(0,coeffs().rows() - (supers()-i))); - } - else if (i>=rows()-subs()) - len = std::max(0,coeffs().rows() - (i + 1 - rows() + subs())); - return Block(coeffs(), start, i, len, 1); - } - - /** \returns a vector expression of the main diagonal */ - inline Block diagonal() - { return Block(coeffs(),supers(),0,1,(std::min)(rows(),cols())); } - - /** \returns a vector expression of the main diagonal (const version) */ - inline const Block diagonal() const - { return Block(coeffs(),supers(),0,1,(std::min)(rows(),cols())); } - - template struct DiagonalIntReturnType { - enum { - ReturnOpposite = (Options&SelfAdjoint) && (((Index)>0 && Supers==0) || ((Index)<0 && Subs==0)), - Conjugate = ReturnOpposite && NumTraits::IsComplex, - ActualIndex = ReturnOpposite ? -Index : Index, - DiagonalSize = (RowsAtCompileTime==Dynamic || ColsAtCompileTime==Dynamic) - ? Dynamic - : (ActualIndex<0 - ? IMP_EIGEN_SIZE_MIN_PREFER_DYNAMIC(ColsAtCompileTime, RowsAtCompileTime + ActualIndex) - : IMP_EIGEN_SIZE_MIN_PREFER_DYNAMIC(RowsAtCompileTime, ColsAtCompileTime - ActualIndex)) - }; - typedef Block BuildType; - typedef typename internal::conditional,BuildType >, - BuildType>::type Type; - }; - - /** \returns a vector expression of the \a N -th sub or super diagonal */ - template inline typename DiagonalIntReturnType::Type diagonal() - { - return typename DiagonalIntReturnType::BuildType(coeffs(), supers()-N, (std::max)(0,N), 1, diagonalLength(N)); - } - - /** \returns a vector expression of the \a N -th sub or super diagonal */ - template inline const typename DiagonalIntReturnType::Type diagonal() const - { - return typename DiagonalIntReturnType::BuildType(coeffs(), supers()-N, (std::max)(0,N), 1, diagonalLength(N)); - } - - /** \returns a vector expression of the \a i -th sub or super diagonal */ - inline Block diagonal(Index i) - { - imp_eigen_assert((i<0 && -i<=subs()) || (i>=0 && i<=supers())); - return Block(coeffs(), supers()-i, std::max(0,i), 1, diagonalLength(i)); - } - - /** \returns a vector expression of the \a i -th sub or super diagonal */ - inline const Block diagonal(Index i) const - { - imp_eigen_assert((i<0 && -i<=subs()) || (i>=0 && i<=supers())); - return Block(coeffs(), supers()-i, std::max(0,i), 1, diagonalLength(i)); - } - - template inline void evalTo(Dest& dst) const - { - dst.resize(rows(),cols()); - dst.setZero(); - dst.diagonal() = diagonal(); - for (Index i=1; i<=supers();++i) - dst.diagonal(i) = diagonal(i); - for (Index i=1; i<=subs();++i) - dst.diagonal(-i) = diagonal(-i); - } - - DenseMatrixType toDenseMatrix() const - { - DenseMatrixType res(rows(),cols()); - evalTo(res); - return res; - } - - protected: - - inline Index diagonalLength(Index i) const - { return i<0 ? (std::min)(cols(),rows()+i) : (std::min)(rows(),cols()-i); } -}; - -/** - * \class BandMatrix - * \ingroup Core_Module - * - * \brief Represents a rectangular matrix with a banded storage - * - * \param _Scalar Numeric type, i.e. float, double, int - * \param Rows Number of rows, or \b Dynamic - * \param Cols Number of columns, or \b Dynamic - * \param Supers Number of super diagonal - * \param Subs Number of sub diagonal - * \param _Options A combination of either \b #RowMajor or \b #ColMajor, and of \b #SelfAdjoint - * The former controls \ref TopicStorageOrders "storage order", and defaults to - * column-major. The latter controls whether the matrix represents a selfadjoint - * matrix in which case either Supers of Subs have to be null. - * - * \sa class TridiagonalMatrix - */ - -template -struct traits > -{ - typedef _Scalar Scalar; - typedef Dense StorageKind; - typedef DenseIndex Index; - enum { - CoeffReadCost = NumTraits::ReadCost, - RowsAtCompileTime = _Rows, - ColsAtCompileTime = _Cols, - MaxRowsAtCompileTime = _Rows, - MaxColsAtCompileTime = _Cols, - Flags = LvalueBit, - Supers = _Supers, - Subs = _Subs, - Options = _Options, - DataRowsAtCompileTime = ((Supers!=Dynamic) && (Subs!=Dynamic)) ? 1 + Supers + Subs : Dynamic - }; - typedef Matrix CoefficientsType; -}; - -template -class BandMatrix : public BandMatrixBase > -{ - public: - - typedef typename internal::traits::Scalar Scalar; - typedef typename internal::traits::Index Index; - typedef typename internal::traits::CoefficientsType CoefficientsType; - - inline BandMatrix(Index rows=Rows, Index cols=Cols, Index supers=Supers, Index subs=Subs) - : m_coeffs(1+supers+subs,cols), - m_rows(rows), m_supers(supers), m_subs(subs) - { - } - - /** \returns the number of columns */ - inline Index rows() const { return m_rows.value(); } - - /** \returns the number of rows */ - inline Index cols() const { return m_coeffs.cols(); } - - /** \returns the number of super diagonals */ - inline Index supers() const { return m_supers.value(); } - - /** \returns the number of sub diagonals */ - inline Index subs() const { return m_subs.value(); } - - inline const CoefficientsType& coeffs() const { return m_coeffs; } - inline CoefficientsType& coeffs() { return m_coeffs; } - - protected: - - CoefficientsType m_coeffs; - internal::variable_if_dynamic m_rows; - internal::variable_if_dynamic m_supers; - internal::variable_if_dynamic m_subs; -}; - -template -class BandMatrixWrapper; - -template -struct traits > -{ - typedef typename _CoefficientsType::Scalar Scalar; - typedef typename _CoefficientsType::StorageKind StorageKind; - typedef typename _CoefficientsType::Index Index; - enum { - CoeffReadCost = internal::traits<_CoefficientsType>::CoeffReadCost, - RowsAtCompileTime = _Rows, - ColsAtCompileTime = _Cols, - MaxRowsAtCompileTime = _Rows, - MaxColsAtCompileTime = _Cols, - Flags = LvalueBit, - Supers = _Supers, - Subs = _Subs, - Options = _Options, - DataRowsAtCompileTime = ((Supers!=Dynamic) && (Subs!=Dynamic)) ? 1 + Supers + Subs : Dynamic - }; - typedef _CoefficientsType CoefficientsType; -}; - -template -class BandMatrixWrapper : public BandMatrixBase > -{ - public: - - typedef typename internal::traits::Scalar Scalar; - typedef typename internal::traits::CoefficientsType CoefficientsType; - typedef typename internal::traits::Index Index; - - inline BandMatrixWrapper(const CoefficientsType& coeffs, Index rows=_Rows, Index cols=_Cols, Index supers=_Supers, Index subs=_Subs) - : m_coeffs(coeffs), - m_rows(rows), m_supers(supers), m_subs(subs) - { - IMP_EIGEN_UNUSED_VARIABLE(cols); - //internal::assert(coeffs.cols()==cols() && (supers()+subs()+1)==coeffs.rows()); - } - - /** \returns the number of columns */ - inline Index rows() const { return m_rows.value(); } - - /** \returns the number of rows */ - inline Index cols() const { return m_coeffs.cols(); } - - /** \returns the number of super diagonals */ - inline Index supers() const { return m_supers.value(); } - - /** \returns the number of sub diagonals */ - inline Index subs() const { return m_subs.value(); } - - inline const CoefficientsType& coeffs() const { return m_coeffs; } - - protected: - - const CoefficientsType& m_coeffs; - internal::variable_if_dynamic m_rows; - internal::variable_if_dynamic m_supers; - internal::variable_if_dynamic m_subs; -}; - -/** - * \class TridiagonalMatrix - * \ingroup Core_Module - * - * \brief Represents a tridiagonal matrix with a compact banded storage - * - * \param _Scalar Numeric type, i.e. float, double, int - * \param Size Number of rows and cols, or \b Dynamic - * \param _Options Can be 0 or \b SelfAdjoint - * - * \sa class BandMatrix - */ -template -class TridiagonalMatrix : public BandMatrix -{ - typedef BandMatrix Base; - typedef typename Base::Index Index; - public: - TridiagonalMatrix(Index size = Size) : Base(size,size,Options&SelfAdjoint?0:1,1) {} - - inline typename Base::template DiagonalIntReturnType<1>::Type super() - { return Base::template diagonal<1>(); } - inline const typename Base::template DiagonalIntReturnType<1>::Type super() const - { return Base::template diagonal<1>(); } - inline typename Base::template DiagonalIntReturnType<-1>::Type sub() - { return Base::template diagonal<-1>(); } - inline const typename Base::template DiagonalIntReturnType<-1>::Type sub() const - { return Base::template diagonal<-1>(); } - protected: -}; - -} // end namespace internal - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_BANDMATRIX_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/Block.h b/modules/algebra/include/eigen3/Eigen/src/Core/Block.h deleted file mode 100644 index 4893c31224..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/Block.h +++ /dev/null @@ -1,406 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008 Gael Guennebaud -// Copyright (C) 2006-2010 Benoit Jacob -// -// 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 IMP_EIGEN_BLOCK_H -#define IMP_EIGEN_BLOCK_H - -namespace IMP_Eigen { - -/** \class Block - * \ingroup Core_Module - * - * \brief Expression of a fixed-size or dynamic-size block - * - * \param XprType the type of the expression in which we are taking a block - * \param BlockRows the number of rows of the block we are taking at compile time (optional) - * \param BlockCols the number of columns of the block we are taking at compile time (optional) - * - * This class represents an expression of either a fixed-size or dynamic-size block. It is the return - * type of DenseBase::block(Index,Index,Index,Index) and DenseBase::block(Index,Index) and - * most of the time this is the only way it is used. - * - * However, if you want to directly maniputate block expressions, - * for instance if you want to write a function returning such an expression, you - * will need to use this class. - * - * Here is an example illustrating the dynamic case: - * \include class_Block.cpp - * Output: \verbinclude class_Block.out - * - * \note Even though this expression has dynamic size, in the case where \a XprType - * has fixed size, this expression inherits a fixed maximal size which means that evaluating - * it does not cause a dynamic memory allocation. - * - * Here is an example illustrating the fixed-size case: - * \include class_FixedBlock.cpp - * Output: \verbinclude class_FixedBlock.out - * - * \sa DenseBase::block(Index,Index,Index,Index), DenseBase::block(Index,Index), class VectorBlock - */ - -namespace internal { -template -struct traits > : traits -{ - typedef typename traits::Scalar Scalar; - typedef typename traits::StorageKind StorageKind; - typedef typename traits::XprKind XprKind; - typedef typename nested::type XprTypeNested; - typedef typename remove_reference::type _XprTypeNested; - enum{ - MatrixRows = traits::RowsAtCompileTime, - MatrixCols = traits::ColsAtCompileTime, - RowsAtCompileTime = MatrixRows == 0 ? 0 : BlockRows, - ColsAtCompileTime = MatrixCols == 0 ? 0 : BlockCols, - MaxRowsAtCompileTime = BlockRows==0 ? 0 - : RowsAtCompileTime != Dynamic ? int(RowsAtCompileTime) - : int(traits::MaxRowsAtCompileTime), - MaxColsAtCompileTime = BlockCols==0 ? 0 - : ColsAtCompileTime != Dynamic ? int(ColsAtCompileTime) - : int(traits::MaxColsAtCompileTime), - XprTypeIsRowMajor = (int(traits::Flags)&RowMajorBit) != 0, - IsDense = is_same::value, - IsRowMajor = (IsDense&&MaxRowsAtCompileTime==1&&MaxColsAtCompileTime!=1) ? 1 - : (IsDense&&MaxColsAtCompileTime==1&&MaxRowsAtCompileTime!=1) ? 0 - : XprTypeIsRowMajor, - HasSameStorageOrderAsXprType = (IsRowMajor == XprTypeIsRowMajor), - InnerSize = IsRowMajor ? int(ColsAtCompileTime) : int(RowsAtCompileTime), - InnerStrideAtCompileTime = HasSameStorageOrderAsXprType - ? int(inner_stride_at_compile_time::ret) - : int(outer_stride_at_compile_time::ret), - OuterStrideAtCompileTime = HasSameStorageOrderAsXprType - ? int(outer_stride_at_compile_time::ret) - : int(inner_stride_at_compile_time::ret), - MaskPacketAccessBit = (InnerSize == Dynamic || (InnerSize % packet_traits::size) == 0) - && (InnerStrideAtCompileTime == 1) - ? PacketAccessBit : 0, - MaskAlignedBit = (InnerPanel && (OuterStrideAtCompileTime!=Dynamic) && (((OuterStrideAtCompileTime * int(sizeof(Scalar))) % 16) == 0)) ? AlignedBit : 0, - FlagsLinearAccessBit = (RowsAtCompileTime == 1 || ColsAtCompileTime == 1 || (InnerPanel && (traits::Flags&LinearAccessBit))) ? LinearAccessBit : 0, - FlagsLvalueBit = is_lvalue::value ? LvalueBit : 0, - FlagsRowMajorBit = IsRowMajor ? RowMajorBit : 0, - Flags0 = traits::Flags & ( (HereditaryBits & ~RowMajorBit) | - DirectAccessBit | - MaskPacketAccessBit | - MaskAlignedBit), - Flags = Flags0 | FlagsLinearAccessBit | FlagsLvalueBit | FlagsRowMajorBit - }; -}; - -template::ret> class BlockImpl_dense; - -} // end namespace internal - -template class BlockImpl; - -template class Block - : public BlockImpl::StorageKind> -{ - typedef BlockImpl::StorageKind> Impl; - public: - //typedef typename Impl::Base Base; - typedef Impl Base; - IMP_EIGEN_GENERIC_PUBLIC_INTERFACE(Block) - IMP_EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Block) - - /** Column or Row constructor - */ - inline Block(XprType& xpr, Index i) : Impl(xpr,i) - { - imp_eigen_assert( (i>=0) && ( - ((BlockRows==1) && (BlockCols==XprType::ColsAtCompileTime) && i= 0 && BlockRows >= 1 && a_startRow + BlockRows <= xpr.rows() - && a_startCol >= 0 && BlockCols >= 1 && a_startCol + BlockCols <= xpr.cols()); - } - - /** Dynamic-size constructor - */ - inline Block(XprType& xpr, - Index a_startRow, Index a_startCol, - Index blockRows, Index blockCols) - : Impl(xpr, a_startRow, a_startCol, blockRows, blockCols) - { - imp_eigen_assert((RowsAtCompileTime==Dynamic || RowsAtCompileTime==blockRows) - && (ColsAtCompileTime==Dynamic || ColsAtCompileTime==blockCols)); - imp_eigen_assert(a_startRow >= 0 && blockRows >= 0 && a_startRow <= xpr.rows() - blockRows - && a_startCol >= 0 && blockCols >= 0 && a_startCol <= xpr.cols() - blockCols); - } -}; - -// The generic default implementation for dense block simplu forward to the internal::BlockImpl_dense -// that must be specialized for direct and non-direct access... -template -class BlockImpl - : public internal::BlockImpl_dense -{ - typedef internal::BlockImpl_dense Impl; - typedef typename XprType::Index Index; - public: - typedef Impl Base; - IMP_EIGEN_INHERIT_ASSIGNMENT_OPERATORS(BlockImpl) - inline BlockImpl(XprType& xpr, Index i) : Impl(xpr,i) {} - inline BlockImpl(XprType& xpr, Index a_startRow, Index a_startCol) : Impl(xpr, a_startRow, a_startCol) {} - inline BlockImpl(XprType& xpr, Index a_startRow, Index a_startCol, Index blockRows, Index blockCols) - : Impl(xpr, a_startRow, a_startCol, blockRows, blockCols) {} -}; - -namespace internal { - -/** \internal Internal implementation of dense Blocks in the general case. */ -template class BlockImpl_dense - : public internal::dense_xpr_base >::type -{ - typedef Block BlockType; - public: - - typedef typename internal::dense_xpr_base::type Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(BlockType) - IMP_EIGEN_INHERIT_ASSIGNMENT_OPERATORS(BlockImpl_dense) - - class InnerIterator; - - /** Column or Row constructor - */ - inline BlockImpl_dense(XprType& xpr, Index i) - : m_xpr(xpr), - // It is a row if and only if BlockRows==1 and BlockCols==XprType::ColsAtCompileTime, - // and it is a column if and only if BlockRows==XprType::RowsAtCompileTime and BlockCols==1, - // all other cases are invalid. - // The case a 1x1 matrix seems ambiguous, but the result is the same anyway. - m_startRow( (BlockRows==1) && (BlockCols==XprType::ColsAtCompileTime) ? i : 0), - m_startCol( (BlockRows==XprType::RowsAtCompileTime) && (BlockCols==1) ? i : 0), - m_blockRows(BlockRows==1 ? 1 : xpr.rows()), - m_blockCols(BlockCols==1 ? 1 : xpr.cols()) - {} - - /** Fixed-size constructor - */ - inline BlockImpl_dense(XprType& xpr, Index a_startRow, Index a_startCol) - : m_xpr(xpr), m_startRow(a_startRow), m_startCol(a_startCol), - m_blockRows(BlockRows), m_blockCols(BlockCols) - {} - - /** Dynamic-size constructor - */ - inline BlockImpl_dense(XprType& xpr, - Index a_startRow, Index a_startCol, - Index blockRows, Index blockCols) - : m_xpr(xpr), m_startRow(a_startRow), m_startCol(a_startCol), - m_blockRows(blockRows), m_blockCols(blockCols) - {} - - inline Index rows() const { return m_blockRows.value(); } - inline Index cols() const { return m_blockCols.value(); } - - inline Scalar& coeffRef(Index rowId, Index colId) - { - IMP_EIGEN_STATIC_ASSERT_LVALUE(XprType) - return m_xpr.const_cast_derived() - .coeffRef(rowId + m_startRow.value(), colId + m_startCol.value()); - } - - inline const Scalar& coeffRef(Index rowId, Index colId) const - { - return m_xpr.derived() - .coeffRef(rowId + m_startRow.value(), colId + m_startCol.value()); - } - - IMP_EIGEN_STRONG_INLINE const CoeffReturnType coeff(Index rowId, Index colId) const - { - return m_xpr.coeff(rowId + m_startRow.value(), colId + m_startCol.value()); - } - - inline Scalar& coeffRef(Index index) - { - IMP_EIGEN_STATIC_ASSERT_LVALUE(XprType) - return m_xpr.const_cast_derived() - .coeffRef(m_startRow.value() + (RowsAtCompileTime == 1 ? 0 : index), - m_startCol.value() + (RowsAtCompileTime == 1 ? index : 0)); - } - - inline const Scalar& coeffRef(Index index) const - { - return m_xpr.const_cast_derived() - .coeffRef(m_startRow.value() + (RowsAtCompileTime == 1 ? 0 : index), - m_startCol.value() + (RowsAtCompileTime == 1 ? index : 0)); - } - - inline const CoeffReturnType coeff(Index index) const - { - return m_xpr - .coeff(m_startRow.value() + (RowsAtCompileTime == 1 ? 0 : index), - m_startCol.value() + (RowsAtCompileTime == 1 ? index : 0)); - } - - template - inline PacketScalar packet(Index rowId, Index colId) const - { - return m_xpr.template packet - (rowId + m_startRow.value(), colId + m_startCol.value()); - } - - template - inline void writePacket(Index rowId, Index colId, const PacketScalar& val) - { - m_xpr.const_cast_derived().template writePacket - (rowId + m_startRow.value(), colId + m_startCol.value(), val); - } - - template - inline PacketScalar packet(Index index) const - { - return m_xpr.template packet - (m_startRow.value() + (RowsAtCompileTime == 1 ? 0 : index), - m_startCol.value() + (RowsAtCompileTime == 1 ? index : 0)); - } - - template - inline void writePacket(Index index, const PacketScalar& val) - { - m_xpr.const_cast_derived().template writePacket - (m_startRow.value() + (RowsAtCompileTime == 1 ? 0 : index), - m_startCol.value() + (RowsAtCompileTime == 1 ? index : 0), val); - } - - #ifdef IMP_EIGEN_PARSED_BY_DOXYGEN - /** \sa MapBase::data() */ - inline const Scalar* data() const; - inline Index innerStride() const; - inline Index outerStride() const; - #endif - - const typename internal::remove_all::type& nestedExpression() const - { - return m_xpr; - } - - Index startRow() const - { - return m_startRow.value(); - } - - Index startCol() const - { - return m_startCol.value(); - } - - protected: - - const typename XprType::Nested m_xpr; - const internal::variable_if_dynamic m_startRow; - const internal::variable_if_dynamic m_startCol; - const internal::variable_if_dynamic m_blockRows; - const internal::variable_if_dynamic m_blockCols; -}; - -/** \internal Internal implementation of dense Blocks in the direct access case.*/ -template -class BlockImpl_dense - : public MapBase > -{ - typedef Block BlockType; - public: - - typedef MapBase Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(BlockType) - IMP_EIGEN_INHERIT_ASSIGNMENT_OPERATORS(BlockImpl_dense) - - /** Column or Row constructor - */ - inline BlockImpl_dense(XprType& xpr, Index i) - : Base(internal::const_cast_ptr(&xpr.coeffRef( - (BlockRows==1) && (BlockCols==XprType::ColsAtCompileTime) ? i : 0, - (BlockRows==XprType::RowsAtCompileTime) && (BlockCols==1) ? i : 0)), - BlockRows==1 ? 1 : xpr.rows(), - BlockCols==1 ? 1 : xpr.cols()), - m_xpr(xpr) - { - init(); - } - - /** Fixed-size constructor - */ - inline BlockImpl_dense(XprType& xpr, Index startRow, Index startCol) - : Base(internal::const_cast_ptr(&xpr.coeffRef(startRow,startCol))), m_xpr(xpr) - { - init(); - } - - /** Dynamic-size constructor - */ - inline BlockImpl_dense(XprType& xpr, - Index startRow, Index startCol, - Index blockRows, Index blockCols) - : Base(internal::const_cast_ptr(&xpr.coeffRef(startRow,startCol)), blockRows, blockCols), - m_xpr(xpr) - { - init(); - } - - const typename internal::remove_all::type& nestedExpression() const - { - return m_xpr; - } - - /** \sa MapBase::innerStride() */ - inline Index innerStride() const - { - return internal::traits::HasSameStorageOrderAsXprType - ? m_xpr.innerStride() - : m_xpr.outerStride(); - } - - /** \sa MapBase::outerStride() */ - inline Index outerStride() const - { - return m_outerStride; - } - - #ifndef __SUNPRO_CC - // FIXME sunstudio is not friendly with the above friend... - // META-FIXME there is no 'friend' keyword around here. Is this obsolete? - protected: - #endif - - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - /** \internal used by allowAligned() */ - inline BlockImpl_dense(XprType& xpr, const Scalar* data, Index blockRows, Index blockCols) - : Base(data, blockRows, blockCols), m_xpr(xpr) - { - init(); - } - #endif - - protected: - void init() - { - m_outerStride = internal::traits::HasSameStorageOrderAsXprType - ? m_xpr.outerStride() - : m_xpr.innerStride(); - } - - typename XprType::Nested m_xpr; - Index m_outerStride; -}; - -} // end namespace internal - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_BLOCK_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/BooleanRedux.h b/modules/algebra/include/eigen3/Eigen/src/Core/BooleanRedux.h deleted file mode 100644 index c8d06a2688..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/BooleanRedux.h +++ /dev/null @@ -1,154 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008 Gael Guennebaud -// -// 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 IMP_EIGEN_ALLANDANY_H -#define IMP_EIGEN_ALLANDANY_H - -namespace IMP_Eigen { - -namespace internal { - -template -struct all_unroller -{ - enum { - col = (UnrollCount-1) / Derived::RowsAtCompileTime, - row = (UnrollCount-1) % Derived::RowsAtCompileTime - }; - - static inline bool run(const Derived &mat) - { - return all_unroller::run(mat) && mat.coeff(row, col); - } -}; - -template -struct all_unroller -{ - static inline bool run(const Derived &/*mat*/) { return true; } -}; - -template -struct all_unroller -{ - static inline bool run(const Derived &) { return false; } -}; - -template -struct any_unroller -{ - enum { - col = (UnrollCount-1) / Derived::RowsAtCompileTime, - row = (UnrollCount-1) % Derived::RowsAtCompileTime - }; - - static inline bool run(const Derived &mat) - { - return any_unroller::run(mat) || mat.coeff(row, col); - } -}; - -template -struct any_unroller -{ - static inline bool run(const Derived & /*mat*/) { return false; } -}; - -template -struct any_unroller -{ - static inline bool run(const Derived &) { return false; } -}; - -} // end namespace internal - -/** \returns true if all coefficients are true - * - * Example: \include MatrixBase_all.cpp - * Output: \verbinclude MatrixBase_all.out - * - * \sa any(), Cwise::operator<() - */ -template -inline bool DenseBase::all() const -{ - enum { - unroll = SizeAtCompileTime != Dynamic - && CoeffReadCost != Dynamic - && NumTraits::AddCost != Dynamic - && SizeAtCompileTime * (CoeffReadCost + NumTraits::AddCost) <= IMP_EIGEN_UNROLLING_LIMIT - }; - if(unroll) - return internal::all_unroller::run(derived()); - else - { - for(Index j = 0; j < cols(); ++j) - for(Index i = 0; i < rows(); ++i) - if (!coeff(i, j)) return false; - return true; - } -} - -/** \returns true if at least one coefficient is true - * - * \sa all() - */ -template -inline bool DenseBase::any() const -{ - enum { - unroll = SizeAtCompileTime != Dynamic - && CoeffReadCost != Dynamic - && NumTraits::AddCost != Dynamic - && SizeAtCompileTime * (CoeffReadCost + NumTraits::AddCost) <= IMP_EIGEN_UNROLLING_LIMIT - }; - if(unroll) - return internal::any_unroller::run(derived()); - else - { - for(Index j = 0; j < cols(); ++j) - for(Index i = 0; i < rows(); ++i) - if (coeff(i, j)) return true; - return false; - } -} - -/** \returns the number of coefficients which evaluate to true - * - * \sa all(), any() - */ -template -inline typename DenseBase::Index DenseBase::count() const -{ - return derived().template cast().template cast().sum(); -} - -/** \returns true is \c *this contains at least one Not A Number (NaN). - * - * \sa allFinite() - */ -template -inline bool DenseBase::hasNaN() const -{ - return !((derived().array()==derived().array()).all()); -} - -/** \returns true if \c *this contains only finite numbers, i.e., no NaN and no +/-INF values. - * - * \sa hasNaN() - */ -template -inline bool DenseBase::allFinite() const -{ - return !((derived()-derived()).hasNaN()); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_ALLANDANY_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/CommaInitializer.h b/modules/algebra/include/eigen3/Eigen/src/Core/CommaInitializer.h deleted file mode 100644 index e0bc616a80..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/CommaInitializer.h +++ /dev/null @@ -1,157 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008 Gael Guennebaud -// Copyright (C) 2006-2008 Benoit Jacob -// -// 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 IMP_EIGEN_COMMAINITIALIZER_H -#define IMP_EIGEN_COMMAINITIALIZER_H - -namespace IMP_Eigen { - -/** \class CommaInitializer - * \ingroup Core_Module - * - * \brief Helper class used by the comma initializer operator - * - * This class is internally used to implement the comma initializer feature. It is - * the return type of MatrixBase::operator<<, and most of the time this is the only - * way it is used. - * - * \sa \ref MatrixBaseCommaInitRef "MatrixBase::operator<<", CommaInitializer::finished() - */ -template -struct CommaInitializer -{ - typedef typename XprType::Scalar Scalar; - typedef typename XprType::Index Index; - - inline CommaInitializer(XprType& xpr, const Scalar& s) - : m_xpr(xpr), m_row(0), m_col(1), m_currentBlockRows(1) - { - m_xpr.coeffRef(0,0) = s; - } - - template - inline CommaInitializer(XprType& xpr, const DenseBase& other) - : m_xpr(xpr), m_row(0), m_col(other.cols()), m_currentBlockRows(other.rows()) - { - m_xpr.block(0, 0, other.rows(), other.cols()) = other; - } - - /* Copy/Move constructor which transfers ownership. This is crucial in - * absence of return value optimization to avoid assertions during destruction. */ - // FIXME in C++11 mode this could be replaced by a proper RValue constructor - inline CommaInitializer(const CommaInitializer& o) - : m_xpr(o.m_xpr), m_row(o.m_row), m_col(o.m_col), m_currentBlockRows(o.m_currentBlockRows) { - // Mark original object as finished. In absence of R-value references we need to const_cast: - const_cast(o).m_row = m_xpr.rows(); - const_cast(o).m_col = m_xpr.cols(); - const_cast(o).m_currentBlockRows = 0; - } - - /* inserts a scalar value in the target matrix */ - CommaInitializer& operator,(const Scalar& s) - { - if (m_col==m_xpr.cols()) - { - m_row+=m_currentBlockRows; - m_col = 0; - m_currentBlockRows = 1; - imp_eigen_assert(m_row - CommaInitializer& operator,(const DenseBase& other) - { - if(other.rows()==0) - { - m_col += other.cols(); - return *this; - } - if (m_col==m_xpr.cols()) - { - m_row+=m_currentBlockRows; - m_col = 0; - m_currentBlockRows = other.rows(); - imp_eigen_assert(m_row+m_currentBlockRows<=m_xpr.rows() - && "Too many rows passed to comma initializer (operator<<)"); - } - imp_eigen_assert((m_col - (m_row, m_col) = other; - else - m_xpr.block(m_row, m_col, other.rows(), other.cols()) = other; - m_col += other.cols(); - return *this; - } - - inline ~CommaInitializer() - { - imp_eigen_assert((m_row+m_currentBlockRows) == m_xpr.rows() - && m_col == m_xpr.cols() - && "Too few coefficients passed to comma initializer (operator<<)"); - } - - /** \returns the built matrix once all its coefficients have been set. - * Calling finished is 100% optional. Its purpose is to write expressions - * like this: - * \code - * quaternion.fromRotationMatrix((Matrix3f() << axis0, axis1, axis2).finished()); - * \endcode - */ - inline XprType& finished() { return m_xpr; } - - XprType& m_xpr; // target expression - Index m_row; // current row id - Index m_col; // current col id - Index m_currentBlockRows; // current block height -}; - -/** \anchor MatrixBaseCommaInitRef - * Convenient operator to set the coefficients of a matrix. - * - * The coefficients must be provided in a row major order and exactly match - * the size of the matrix. Otherwise an assertion is raised. - * - * Example: \include MatrixBase_set.cpp - * Output: \verbinclude MatrixBase_set.out - * - * \note According the c++ standard, the argument expressions of this comma initializer are evaluated in arbitrary order. - * - * \sa CommaInitializer::finished(), class CommaInitializer - */ -template -inline CommaInitializer DenseBase::operator<< (const Scalar& s) -{ - return CommaInitializer(*static_cast(this), s); -} - -/** \sa operator<<(const Scalar&) */ -template -template -inline CommaInitializer -DenseBase::operator<<(const DenseBase& other) -{ - return CommaInitializer(*static_cast(this), other); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_COMMAINITIALIZER_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/CoreIterators.h b/modules/algebra/include/eigen3/Eigen/src/Core/CoreIterators.h deleted file mode 100644 index f370acb337..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/CoreIterators.h +++ /dev/null @@ -1,61 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008-2010 Gael Guennebaud -// -// 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 IMP_EIGEN_COREITERATORS_H -#define IMP_EIGEN_COREITERATORS_H - -namespace IMP_Eigen { - -/* This file contains the respective InnerIterator definition of the expressions defined in Eigen/Core - */ - -/** \ingroup SparseCore_Module - * \class InnerIterator - * \brief An InnerIterator allows to loop over the element of a sparse (or dense) matrix or expression - * - * todo - */ - -// generic version for dense matrix and expressions -template class DenseBase::InnerIterator -{ - protected: - typedef typename Derived::Scalar Scalar; - typedef typename Derived::Index Index; - - enum { IsRowMajor = (Derived::Flags&RowMajorBit)==RowMajorBit }; - public: - IMP_EIGEN_STRONG_INLINE InnerIterator(const Derived& expr, Index outer) - : m_expression(expr), m_inner(0), m_outer(outer), m_end(expr.innerSize()) - {} - - IMP_EIGEN_STRONG_INLINE Scalar value() const - { - return (IsRowMajor) ? m_expression.coeff(m_outer, m_inner) - : m_expression.coeff(m_inner, m_outer); - } - - IMP_EIGEN_STRONG_INLINE InnerIterator& operator++() { m_inner++; return *this; } - - IMP_EIGEN_STRONG_INLINE Index index() const { return m_inner; } - inline Index row() const { return IsRowMajor ? m_outer : index(); } - inline Index col() const { return IsRowMajor ? index() : m_outer; } - - IMP_EIGEN_STRONG_INLINE operator bool() const { return m_inner < m_end && m_inner>=0; } - - protected: - const Derived& m_expression; - Index m_inner; - const Index m_outer; - const Index m_end; -}; - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_COREITERATORS_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h b/modules/algebra/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h deleted file mode 100644 index 28fabedddf..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h +++ /dev/null @@ -1,230 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008-2009 Gael Guennebaud -// Copyright (C) 2006-2008 Benoit Jacob -// -// 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 IMP_EIGEN_CWISE_BINARY_OP_H -#define IMP_EIGEN_CWISE_BINARY_OP_H - -namespace IMP_Eigen { - -/** \class CwiseBinaryOp - * \ingroup Core_Module - * - * \brief Generic expression where a coefficient-wise binary operator is applied to two expressions - * - * \param BinaryOp template functor implementing the operator - * \param Lhs the type of the left-hand side - * \param Rhs the type of the right-hand side - * - * This class represents an expression where a coefficient-wise binary operator is applied to two expressions. - * It is the return type of binary operators, by which we mean only those binary operators where - * both the left-hand side and the right-hand side are Eigen expressions. - * For example, the return type of matrix1+matrix2 is a CwiseBinaryOp. - * - * Most of the time, this is the only way that it is used, so you typically don't have to name - * CwiseBinaryOp types explicitly. - * - * \sa MatrixBase::binaryExpr(const MatrixBase &,const CustomBinaryOp &) const, class CwiseUnaryOp, class CwiseNullaryOp - */ - -namespace internal { -template -struct traits > -{ - // we must not inherit from traits since it has - // the potential to cause problems with MSVC - typedef typename remove_all::type Ancestor; - typedef typename traits::XprKind XprKind; - enum { - RowsAtCompileTime = traits::RowsAtCompileTime, - ColsAtCompileTime = traits::ColsAtCompileTime, - MaxRowsAtCompileTime = traits::MaxRowsAtCompileTime, - MaxColsAtCompileTime = traits::MaxColsAtCompileTime - }; - - // even though we require Lhs and Rhs to have the same scalar type (see CwiseBinaryOp constructor), - // we still want to handle the case when the result type is different. - typedef typename result_of< - BinaryOp( - typename Lhs::Scalar, - typename Rhs::Scalar - ) - >::type Scalar; - typedef typename promote_storage_type::StorageKind, - typename traits::StorageKind>::ret StorageKind; - typedef typename promote_index_type::Index, - typename traits::Index>::type Index; - typedef typename Lhs::Nested LhsNested; - typedef typename Rhs::Nested RhsNested; - typedef typename remove_reference::type _LhsNested; - typedef typename remove_reference::type _RhsNested; - enum { - LhsCoeffReadCost = _LhsNested::CoeffReadCost, - RhsCoeffReadCost = _RhsNested::CoeffReadCost, - LhsFlags = _LhsNested::Flags, - RhsFlags = _RhsNested::Flags, - SameType = is_same::value, - StorageOrdersAgree = (int(Lhs::Flags)&RowMajorBit)==(int(Rhs::Flags)&RowMajorBit), - Flags0 = (int(LhsFlags) | int(RhsFlags)) & ( - HereditaryBits - | (int(LhsFlags) & int(RhsFlags) & - ( AlignedBit - | (StorageOrdersAgree ? LinearAccessBit : 0) - | (functor_traits::PacketAccess && StorageOrdersAgree && SameType ? PacketAccessBit : 0) - ) - ) - ), - Flags = (Flags0 & ~RowMajorBit) | (LhsFlags & RowMajorBit), - Cost0 = IMP_EIGEN_ADD_COST(LhsCoeffReadCost,RhsCoeffReadCost), - CoeffReadCost = IMP_EIGEN_ADD_COST(Cost0,functor_traits::Cost) - }; -}; -} // end namespace internal - -// we require Lhs and Rhs to have the same scalar type. Currently there is no example of a binary functor -// that would take two operands of different types. If there were such an example, then this check should be -// moved to the BinaryOp functors, on a per-case basis. This would however require a change in the BinaryOp functors, as -// currently they take only one typename Scalar template parameter. -// It is tempting to always allow mixing different types but remember that this is often impossible in the vectorized paths. -// So allowing mixing different types gives very unexpected errors when enabling vectorization, when the user tries to -// add together a float matrix and a double matrix. -#define IMP_EIGEN_CHECK_BINARY_COMPATIBILIY(BINOP,LHS,RHS) \ - IMP_EIGEN_STATIC_ASSERT((internal::functor_is_product_like::ret \ - ? int(internal::scalar_product_traits::Defined) \ - : int(internal::is_same::value)), \ - YOU_MIXED_DIFFERENT_NUMERIC_TYPES__YOU_NEED_TO_USE_THE_CAST_METHOD_OF_MATRIXBASE_TO_CAST_NUMERIC_TYPES_EXPLICITLY) - -template -class CwiseBinaryOpImpl; - -template -class CwiseBinaryOp : internal::no_assignment_operator, - public CwiseBinaryOpImpl< - BinaryOp, Lhs, Rhs, - typename internal::promote_storage_type::StorageKind, - typename internal::traits::StorageKind>::ret> -{ - public: - - typedef typename CwiseBinaryOpImpl< - BinaryOp, Lhs, Rhs, - typename internal::promote_storage_type::StorageKind, - typename internal::traits::StorageKind>::ret>::Base Base; - IMP_EIGEN_GENERIC_PUBLIC_INTERFACE(CwiseBinaryOp) - - typedef typename internal::nested::type LhsNested; - typedef typename internal::nested::type RhsNested; - typedef typename internal::remove_reference::type _LhsNested; - typedef typename internal::remove_reference::type _RhsNested; - - IMP_EIGEN_STRONG_INLINE CwiseBinaryOp(const Lhs& aLhs, const Rhs& aRhs, const BinaryOp& func = BinaryOp()) - : m_lhs(aLhs), m_rhs(aRhs), m_functor(func) - { - IMP_EIGEN_CHECK_BINARY_COMPATIBILIY(BinaryOp,typename Lhs::Scalar,typename Rhs::Scalar); - // require the sizes to match - IMP_EIGEN_STATIC_ASSERT_SAME_MATRIX_SIZE(Lhs, Rhs) - imp_eigen_assert(aLhs.rows() == aRhs.rows() && aLhs.cols() == aRhs.cols()); - } - - IMP_EIGEN_STRONG_INLINE Index rows() const { - // return the fixed size type if available to enable compile time optimizations - if (internal::traits::type>::RowsAtCompileTime==Dynamic) - return m_rhs.rows(); - else - return m_lhs.rows(); - } - IMP_EIGEN_STRONG_INLINE Index cols() const { - // return the fixed size type if available to enable compile time optimizations - if (internal::traits::type>::ColsAtCompileTime==Dynamic) - return m_rhs.cols(); - else - return m_lhs.cols(); - } - - /** \returns the left hand side nested expression */ - const _LhsNested& lhs() const { return m_lhs; } - /** \returns the right hand side nested expression */ - const _RhsNested& rhs() const { return m_rhs; } - /** \returns the functor representing the binary operation */ - const BinaryOp& functor() const { return m_functor; } - - protected: - LhsNested m_lhs; - RhsNested m_rhs; - const BinaryOp m_functor; -}; - -template -class CwiseBinaryOpImpl - : public internal::dense_xpr_base >::type -{ - typedef CwiseBinaryOp Derived; - public: - - typedef typename internal::dense_xpr_base >::type Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE( Derived ) - - IMP_EIGEN_STRONG_INLINE const Scalar coeff(Index rowId, Index colId) const - { - return derived().functor()(derived().lhs().coeff(rowId, colId), - derived().rhs().coeff(rowId, colId)); - } - - template - IMP_EIGEN_STRONG_INLINE PacketScalar packet(Index rowId, Index colId) const - { - return derived().functor().packetOp(derived().lhs().template packet(rowId, colId), - derived().rhs().template packet(rowId, colId)); - } - - IMP_EIGEN_STRONG_INLINE const Scalar coeff(Index index) const - { - return derived().functor()(derived().lhs().coeff(index), - derived().rhs().coeff(index)); - } - - template - IMP_EIGEN_STRONG_INLINE PacketScalar packet(Index index) const - { - return derived().functor().packetOp(derived().lhs().template packet(index), - derived().rhs().template packet(index)); - } -}; - -/** replaces \c *this by \c *this - \a other. - * - * \returns a reference to \c *this - */ -template -template -IMP_EIGEN_STRONG_INLINE Derived & -MatrixBase::operator-=(const MatrixBase &other) -{ - SelfCwiseBinaryOp, Derived, OtherDerived> tmp(derived()); - tmp = other.derived(); - return derived(); -} - -/** replaces \c *this by \c *this + \a other. - * - * \returns a reference to \c *this - */ -template -template -IMP_EIGEN_STRONG_INLINE Derived & -MatrixBase::operator+=(const MatrixBase& other) -{ - SelfCwiseBinaryOp, Derived, OtherDerived> tmp(derived()); - tmp = other.derived(); - return derived(); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_CWISE_BINARY_OP_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h b/modules/algebra/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h deleted file mode 100644 index 152a08177e..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h +++ /dev/null @@ -1,864 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008-2010 Gael Guennebaud -// -// 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 IMP_EIGEN_CWISE_NULLARY_OP_H -#define IMP_EIGEN_CWISE_NULLARY_OP_H - -namespace IMP_Eigen { - -/** \class CwiseNullaryOp - * \ingroup Core_Module - * - * \brief Generic expression of a matrix where all coefficients are defined by a functor - * - * \param NullaryOp template functor implementing the operator - * \param PlainObjectType the underlying plain matrix/array type - * - * This class represents an expression of a generic nullary operator. - * It is the return type of the Ones(), Zero(), Constant(), Identity() and Random() methods, - * and most of the time this is the only way it is used. - * - * However, if you want to write a function returning such an expression, you - * will need to use this class. - * - * \sa class CwiseUnaryOp, class CwiseBinaryOp, DenseBase::NullaryExpr() - */ - -namespace internal { -template -struct traits > : traits -{ - enum { - Flags = (traits::Flags - & ( HereditaryBits - | (functor_has_linear_access::ret ? LinearAccessBit : 0) - | (functor_traits::PacketAccess ? PacketAccessBit : 0))) - | (functor_traits::IsRepeatable ? 0 : EvalBeforeNestingBit), - CoeffReadCost = functor_traits::Cost - }; -}; -} - -template -class CwiseNullaryOp : internal::no_assignment_operator, - public internal::dense_xpr_base< CwiseNullaryOp >::type -{ - public: - - typedef typename internal::dense_xpr_base::type Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(CwiseNullaryOp) - - CwiseNullaryOp(Index nbRows, Index nbCols, const NullaryOp& func = NullaryOp()) - : m_rows(nbRows), m_cols(nbCols), m_functor(func) - { - imp_eigen_assert(nbRows >= 0 - && (RowsAtCompileTime == Dynamic || RowsAtCompileTime == nbRows) - && nbCols >= 0 - && (ColsAtCompileTime == Dynamic || ColsAtCompileTime == nbCols)); - } - - IMP_EIGEN_STRONG_INLINE Index rows() const { return m_rows.value(); } - IMP_EIGEN_STRONG_INLINE Index cols() const { return m_cols.value(); } - - IMP_EIGEN_STRONG_INLINE const Scalar coeff(Index rowId, Index colId) const - { - return m_functor(rowId, colId); - } - - template - IMP_EIGEN_STRONG_INLINE PacketScalar packet(Index rowId, Index colId) const - { - return m_functor.packetOp(rowId, colId); - } - - IMP_EIGEN_STRONG_INLINE const Scalar coeff(Index index) const - { - return m_functor(index); - } - - template - IMP_EIGEN_STRONG_INLINE PacketScalar packet(Index index) const - { - return m_functor.packetOp(index); - } - - /** \returns the functor representing the nullary operation */ - const NullaryOp& functor() const { return m_functor; } - - protected: - const internal::variable_if_dynamic m_rows; - const internal::variable_if_dynamic m_cols; - const NullaryOp m_functor; -}; - - -/** \returns an expression of a matrix defined by a custom functor \a func - * - * The parameters \a rows and \a cols are the number of rows and of columns of - * the returned matrix. Must be compatible with this MatrixBase type. - * - * This variant is meant to be used for dynamic-size matrix types. For fixed-size types, - * it is redundant to pass \a rows and \a cols as arguments, so Zero() should be used - * instead. - * - * The template parameter \a CustomNullaryOp is the type of the functor. - * - * \sa class CwiseNullaryOp - */ -template -template -IMP_EIGEN_STRONG_INLINE const CwiseNullaryOp -DenseBase::NullaryExpr(Index rows, Index cols, const CustomNullaryOp& func) -{ - return CwiseNullaryOp(rows, cols, func); -} - -/** \returns an expression of a matrix defined by a custom functor \a func - * - * The parameter \a size is the size of the returned vector. - * Must be compatible with this MatrixBase type. - * - * \only_for_vectors - * - * This variant is meant to be used for dynamic-size vector types. For fixed-size types, - * it is redundant to pass \a size as argument, so Zero() should be used - * instead. - * - * The template parameter \a CustomNullaryOp is the type of the functor. - * - * \sa class CwiseNullaryOp - */ -template -template -IMP_EIGEN_STRONG_INLINE const CwiseNullaryOp -DenseBase::NullaryExpr(Index size, const CustomNullaryOp& func) -{ - IMP_EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived) - if(RowsAtCompileTime == 1) return CwiseNullaryOp(1, size, func); - else return CwiseNullaryOp(size, 1, func); -} - -/** \returns an expression of a matrix defined by a custom functor \a func - * - * This variant is only for fixed-size DenseBase types. For dynamic-size types, you - * need to use the variants taking size arguments. - * - * The template parameter \a CustomNullaryOp is the type of the functor. - * - * \sa class CwiseNullaryOp - */ -template -template -IMP_EIGEN_STRONG_INLINE const CwiseNullaryOp -DenseBase::NullaryExpr(const CustomNullaryOp& func) -{ - return CwiseNullaryOp(RowsAtCompileTime, ColsAtCompileTime, func); -} - -/** \returns an expression of a constant matrix of value \a value - * - * The parameters \a nbRows and \a nbCols are the number of rows and of columns of - * the returned matrix. Must be compatible with this DenseBase type. - * - * This variant is meant to be used for dynamic-size matrix types. For fixed-size types, - * it is redundant to pass \a nbRows and \a nbCols as arguments, so Zero() should be used - * instead. - * - * The template parameter \a CustomNullaryOp is the type of the functor. - * - * \sa class CwiseNullaryOp - */ -template -IMP_EIGEN_STRONG_INLINE const typename DenseBase::ConstantReturnType -DenseBase::Constant(Index nbRows, Index nbCols, const Scalar& value) -{ - return DenseBase::NullaryExpr(nbRows, nbCols, internal::scalar_constant_op(value)); -} - -/** \returns an expression of a constant matrix of value \a value - * - * The parameter \a size is the size of the returned vector. - * Must be compatible with this DenseBase type. - * - * \only_for_vectors - * - * This variant is meant to be used for dynamic-size vector types. For fixed-size types, - * it is redundant to pass \a size as argument, so Zero() should be used - * instead. - * - * The template parameter \a CustomNullaryOp is the type of the functor. - * - * \sa class CwiseNullaryOp - */ -template -IMP_EIGEN_STRONG_INLINE const typename DenseBase::ConstantReturnType -DenseBase::Constant(Index size, const Scalar& value) -{ - return DenseBase::NullaryExpr(size, internal::scalar_constant_op(value)); -} - -/** \returns an expression of a constant matrix of value \a value - * - * This variant is only for fixed-size DenseBase types. For dynamic-size types, you - * need to use the variants taking size arguments. - * - * The template parameter \a CustomNullaryOp is the type of the functor. - * - * \sa class CwiseNullaryOp - */ -template -IMP_EIGEN_STRONG_INLINE const typename DenseBase::ConstantReturnType -DenseBase::Constant(const Scalar& value) -{ - IMP_EIGEN_STATIC_ASSERT_FIXED_SIZE(Derived) - return DenseBase::NullaryExpr(RowsAtCompileTime, ColsAtCompileTime, internal::scalar_constant_op(value)); -} - -/** - * \brief Sets a linearly space vector. - * - * The function generates 'size' equally spaced values in the closed interval [low,high]. - * This particular version of LinSpaced() uses sequential access, i.e. vector access is - * assumed to be a(0), a(1), ..., a(size). This assumption allows for better vectorization - * and yields faster code than the random access version. - * - * When size is set to 1, a vector of length 1 containing 'high' is returned. - * - * \only_for_vectors - * - * Example: \include DenseBase_LinSpaced_seq.cpp - * Output: \verbinclude DenseBase_LinSpaced_seq.out - * - * \sa setLinSpaced(Index,const Scalar&,const Scalar&), LinSpaced(Index,Scalar,Scalar), CwiseNullaryOp - */ -template -IMP_EIGEN_STRONG_INLINE const typename DenseBase::SequentialLinSpacedReturnType -DenseBase::LinSpaced(Sequential_t, Index size, const Scalar& low, const Scalar& high) -{ - IMP_EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived) - return DenseBase::NullaryExpr(size, internal::linspaced_op(low,high,size)); -} - -/** - * \copydoc DenseBase::LinSpaced(Sequential_t, Index, const Scalar&, const Scalar&) - * Special version for fixed size types which does not require the size parameter. - */ -template -IMP_EIGEN_STRONG_INLINE const typename DenseBase::SequentialLinSpacedReturnType -DenseBase::LinSpaced(Sequential_t, const Scalar& low, const Scalar& high) -{ - IMP_EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived) - IMP_EIGEN_STATIC_ASSERT_FIXED_SIZE(Derived) - return DenseBase::NullaryExpr(Derived::SizeAtCompileTime, internal::linspaced_op(low,high,Derived::SizeAtCompileTime)); -} - -/** - * \brief Sets a linearly space vector. - * - * The function generates 'size' equally spaced values in the closed interval [low,high]. - * When size is set to 1, a vector of length 1 containing 'high' is returned. - * - * \only_for_vectors - * - * Example: \include DenseBase_LinSpaced.cpp - * Output: \verbinclude DenseBase_LinSpaced.out - * - * \sa setLinSpaced(Index,const Scalar&,const Scalar&), LinSpaced(Sequential_t,Index,const Scalar&,const Scalar&,Index), CwiseNullaryOp - */ -template -IMP_EIGEN_STRONG_INLINE const typename DenseBase::RandomAccessLinSpacedReturnType -DenseBase::LinSpaced(Index size, const Scalar& low, const Scalar& high) -{ - IMP_EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived) - return DenseBase::NullaryExpr(size, internal::linspaced_op(low,high,size)); -} - -/** - * \copydoc DenseBase::LinSpaced(Index, const Scalar&, const Scalar&) - * Special version for fixed size types which does not require the size parameter. - */ -template -IMP_EIGEN_STRONG_INLINE const typename DenseBase::RandomAccessLinSpacedReturnType -DenseBase::LinSpaced(const Scalar& low, const Scalar& high) -{ - IMP_EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived) - IMP_EIGEN_STATIC_ASSERT_FIXED_SIZE(Derived) - return DenseBase::NullaryExpr(Derived::SizeAtCompileTime, internal::linspaced_op(low,high,Derived::SizeAtCompileTime)); -} - -/** \returns true if all coefficients in this matrix are approximately equal to \a val, to within precision \a prec */ -template -bool DenseBase::isApproxToConstant -(const Scalar& val, const RealScalar& prec) const -{ - for(Index j = 0; j < cols(); ++j) - for(Index i = 0; i < rows(); ++i) - if(!internal::isApprox(this->coeff(i, j), val, prec)) - return false; - return true; -} - -/** This is just an alias for isApproxToConstant(). - * - * \returns true if all coefficients in this matrix are approximately equal to \a value, to within precision \a prec */ -template -bool DenseBase::isConstant -(const Scalar& val, const RealScalar& prec) const -{ - return isApproxToConstant(val, prec); -} - -/** Alias for setConstant(): sets all coefficients in this expression to \a val. - * - * \sa setConstant(), Constant(), class CwiseNullaryOp - */ -template -IMP_EIGEN_STRONG_INLINE void DenseBase::fill(const Scalar& val) -{ - setConstant(val); -} - -/** Sets all coefficients in this expression to \a value. - * - * \sa fill(), setConstant(Index,const Scalar&), setConstant(Index,Index,const Scalar&), setZero(), setOnes(), Constant(), class CwiseNullaryOp, setZero(), setOnes() - */ -template -IMP_EIGEN_STRONG_INLINE Derived& DenseBase::setConstant(const Scalar& val) -{ - return derived() = Constant(rows(), cols(), val); -} - -/** Resizes to the given \a size, and sets all coefficients in this expression to the given \a value. - * - * \only_for_vectors - * - * Example: \include Matrix_setConstant_int.cpp - * Output: \verbinclude Matrix_setConstant_int.out - * - * \sa MatrixBase::setConstant(const Scalar&), setConstant(Index,Index,const Scalar&), class CwiseNullaryOp, MatrixBase::Constant(const Scalar&) - */ -template -IMP_EIGEN_STRONG_INLINE Derived& -PlainObjectBase::setConstant(Index size, const Scalar& val) -{ - resize(size); - return setConstant(val); -} - -/** Resizes to the given size, and sets all coefficients in this expression to the given \a value. - * - * \param nbRows the new number of rows - * \param nbCols the new number of columns - * \param val the value to which all coefficients are set - * - * Example: \include Matrix_setConstant_int_int.cpp - * Output: \verbinclude Matrix_setConstant_int_int.out - * - * \sa MatrixBase::setConstant(const Scalar&), setConstant(Index,const Scalar&), class CwiseNullaryOp, MatrixBase::Constant(const Scalar&) - */ -template -IMP_EIGEN_STRONG_INLINE Derived& -PlainObjectBase::setConstant(Index nbRows, Index nbCols, const Scalar& val) -{ - resize(nbRows, nbCols); - return setConstant(val); -} - -/** - * \brief Sets a linearly space vector. - * - * The function generates 'size' equally spaced values in the closed interval [low,high]. - * When size is set to 1, a vector of length 1 containing 'high' is returned. - * - * \only_for_vectors - * - * Example: \include DenseBase_setLinSpaced.cpp - * Output: \verbinclude DenseBase_setLinSpaced.out - * - * \sa CwiseNullaryOp - */ -template -IMP_EIGEN_STRONG_INLINE Derived& DenseBase::setLinSpaced(Index newSize, const Scalar& low, const Scalar& high) -{ - IMP_EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived) - return derived() = Derived::NullaryExpr(newSize, internal::linspaced_op(low,high,newSize)); -} - -/** - * \brief Sets a linearly space vector. - * - * The function fill *this with equally spaced values in the closed interval [low,high]. - * When size is set to 1, a vector of length 1 containing 'high' is returned. - * - * \only_for_vectors - * - * \sa setLinSpaced(Index, const Scalar&, const Scalar&), CwiseNullaryOp - */ -template -IMP_EIGEN_STRONG_INLINE Derived& DenseBase::setLinSpaced(const Scalar& low, const Scalar& high) -{ - IMP_EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived) - return setLinSpaced(size(), low, high); -} - -// zero: - -/** \returns an expression of a zero matrix. - * - * The parameters \a rows and \a cols are the number of rows and of columns of - * the returned matrix. Must be compatible with this MatrixBase type. - * - * This variant is meant to be used for dynamic-size matrix types. For fixed-size types, - * it is redundant to pass \a rows and \a cols as arguments, so Zero() should be used - * instead. - * - * Example: \include MatrixBase_zero_int_int.cpp - * Output: \verbinclude MatrixBase_zero_int_int.out - * - * \sa Zero(), Zero(Index) - */ -template -IMP_EIGEN_STRONG_INLINE const typename DenseBase::ConstantReturnType -DenseBase::Zero(Index nbRows, Index nbCols) -{ - return Constant(nbRows, nbCols, Scalar(0)); -} - -/** \returns an expression of a zero vector. - * - * The parameter \a size is the size of the returned vector. - * Must be compatible with this MatrixBase type. - * - * \only_for_vectors - * - * This variant is meant to be used for dynamic-size vector types. For fixed-size types, - * it is redundant to pass \a size as argument, so Zero() should be used - * instead. - * - * Example: \include MatrixBase_zero_int.cpp - * Output: \verbinclude MatrixBase_zero_int.out - * - * \sa Zero(), Zero(Index,Index) - */ -template -IMP_EIGEN_STRONG_INLINE const typename DenseBase::ConstantReturnType -DenseBase::Zero(Index size) -{ - return Constant(size, Scalar(0)); -} - -/** \returns an expression of a fixed-size zero matrix or vector. - * - * This variant is only for fixed-size MatrixBase types. For dynamic-size types, you - * need to use the variants taking size arguments. - * - * Example: \include MatrixBase_zero.cpp - * Output: \verbinclude MatrixBase_zero.out - * - * \sa Zero(Index), Zero(Index,Index) - */ -template -IMP_EIGEN_STRONG_INLINE const typename DenseBase::ConstantReturnType -DenseBase::Zero() -{ - return Constant(Scalar(0)); -} - -/** \returns true if *this is approximately equal to the zero matrix, - * within the precision given by \a prec. - * - * Example: \include MatrixBase_isZero.cpp - * Output: \verbinclude MatrixBase_isZero.out - * - * \sa class CwiseNullaryOp, Zero() - */ -template -bool DenseBase::isZero(const RealScalar& prec) const -{ - for(Index j = 0; j < cols(); ++j) - for(Index i = 0; i < rows(); ++i) - if(!internal::isMuchSmallerThan(this->coeff(i, j), static_cast(1), prec)) - return false; - return true; -} - -/** Sets all coefficients in this expression to zero. - * - * Example: \include MatrixBase_setZero.cpp - * Output: \verbinclude MatrixBase_setZero.out - * - * \sa class CwiseNullaryOp, Zero() - */ -template -IMP_EIGEN_STRONG_INLINE Derived& DenseBase::setZero() -{ - return setConstant(Scalar(0)); -} - -/** Resizes to the given \a size, and sets all coefficients in this expression to zero. - * - * \only_for_vectors - * - * Example: \include Matrix_setZero_int.cpp - * Output: \verbinclude Matrix_setZero_int.out - * - * \sa DenseBase::setZero(), setZero(Index,Index), class CwiseNullaryOp, DenseBase::Zero() - */ -template -IMP_EIGEN_STRONG_INLINE Derived& -PlainObjectBase::setZero(Index newSize) -{ - resize(newSize); - return setConstant(Scalar(0)); -} - -/** Resizes to the given size, and sets all coefficients in this expression to zero. - * - * \param nbRows the new number of rows - * \param nbCols the new number of columns - * - * Example: \include Matrix_setZero_int_int.cpp - * Output: \verbinclude Matrix_setZero_int_int.out - * - * \sa DenseBase::setZero(), setZero(Index), class CwiseNullaryOp, DenseBase::Zero() - */ -template -IMP_EIGEN_STRONG_INLINE Derived& -PlainObjectBase::setZero(Index nbRows, Index nbCols) -{ - resize(nbRows, nbCols); - return setConstant(Scalar(0)); -} - -// ones: - -/** \returns an expression of a matrix where all coefficients equal one. - * - * The parameters \a nbRows and \a nbCols are the number of rows and of columns of - * the returned matrix. Must be compatible with this MatrixBase type. - * - * This variant is meant to be used for dynamic-size matrix types. For fixed-size types, - * it is redundant to pass \a rows and \a cols as arguments, so Ones() should be used - * instead. - * - * Example: \include MatrixBase_ones_int_int.cpp - * Output: \verbinclude MatrixBase_ones_int_int.out - * - * \sa Ones(), Ones(Index), isOnes(), class Ones - */ -template -IMP_EIGEN_STRONG_INLINE const typename DenseBase::ConstantReturnType -DenseBase::Ones(Index nbRows, Index nbCols) -{ - return Constant(nbRows, nbCols, Scalar(1)); -} - -/** \returns an expression of a vector where all coefficients equal one. - * - * The parameter \a newSize is the size of the returned vector. - * Must be compatible with this MatrixBase type. - * - * \only_for_vectors - * - * This variant is meant to be used for dynamic-size vector types. For fixed-size types, - * it is redundant to pass \a size as argument, so Ones() should be used - * instead. - * - * Example: \include MatrixBase_ones_int.cpp - * Output: \verbinclude MatrixBase_ones_int.out - * - * \sa Ones(), Ones(Index,Index), isOnes(), class Ones - */ -template -IMP_EIGEN_STRONG_INLINE const typename DenseBase::ConstantReturnType -DenseBase::Ones(Index newSize) -{ - return Constant(newSize, Scalar(1)); -} - -/** \returns an expression of a fixed-size matrix or vector where all coefficients equal one. - * - * This variant is only for fixed-size MatrixBase types. For dynamic-size types, you - * need to use the variants taking size arguments. - * - * Example: \include MatrixBase_ones.cpp - * Output: \verbinclude MatrixBase_ones.out - * - * \sa Ones(Index), Ones(Index,Index), isOnes(), class Ones - */ -template -IMP_EIGEN_STRONG_INLINE const typename DenseBase::ConstantReturnType -DenseBase::Ones() -{ - return Constant(Scalar(1)); -} - -/** \returns true if *this is approximately equal to the matrix where all coefficients - * are equal to 1, within the precision given by \a prec. - * - * Example: \include MatrixBase_isOnes.cpp - * Output: \verbinclude MatrixBase_isOnes.out - * - * \sa class CwiseNullaryOp, Ones() - */ -template -bool DenseBase::isOnes -(const RealScalar& prec) const -{ - return isApproxToConstant(Scalar(1), prec); -} - -/** Sets all coefficients in this expression to one. - * - * Example: \include MatrixBase_setOnes.cpp - * Output: \verbinclude MatrixBase_setOnes.out - * - * \sa class CwiseNullaryOp, Ones() - */ -template -IMP_EIGEN_STRONG_INLINE Derived& DenseBase::setOnes() -{ - return setConstant(Scalar(1)); -} - -/** Resizes to the given \a newSize, and sets all coefficients in this expression to one. - * - * \only_for_vectors - * - * Example: \include Matrix_setOnes_int.cpp - * Output: \verbinclude Matrix_setOnes_int.out - * - * \sa MatrixBase::setOnes(), setOnes(Index,Index), class CwiseNullaryOp, MatrixBase::Ones() - */ -template -IMP_EIGEN_STRONG_INLINE Derived& -PlainObjectBase::setOnes(Index newSize) -{ - resize(newSize); - return setConstant(Scalar(1)); -} - -/** Resizes to the given size, and sets all coefficients in this expression to one. - * - * \param nbRows the new number of rows - * \param nbCols the new number of columns - * - * Example: \include Matrix_setOnes_int_int.cpp - * Output: \verbinclude Matrix_setOnes_int_int.out - * - * \sa MatrixBase::setOnes(), setOnes(Index), class CwiseNullaryOp, MatrixBase::Ones() - */ -template -IMP_EIGEN_STRONG_INLINE Derived& -PlainObjectBase::setOnes(Index nbRows, Index nbCols) -{ - resize(nbRows, nbCols); - return setConstant(Scalar(1)); -} - -// Identity: - -/** \returns an expression of the identity matrix (not necessarily square). - * - * The parameters \a nbRows and \a nbCols are the number of rows and of columns of - * the returned matrix. Must be compatible with this MatrixBase type. - * - * This variant is meant to be used for dynamic-size matrix types. For fixed-size types, - * it is redundant to pass \a rows and \a cols as arguments, so Identity() should be used - * instead. - * - * Example: \include MatrixBase_identity_int_int.cpp - * Output: \verbinclude MatrixBase_identity_int_int.out - * - * \sa Identity(), setIdentity(), isIdentity() - */ -template -IMP_EIGEN_STRONG_INLINE const typename MatrixBase::IdentityReturnType -MatrixBase::Identity(Index nbRows, Index nbCols) -{ - return DenseBase::NullaryExpr(nbRows, nbCols, internal::scalar_identity_op()); -} - -/** \returns an expression of the identity matrix (not necessarily square). - * - * This variant is only for fixed-size MatrixBase types. For dynamic-size types, you - * need to use the variant taking size arguments. - * - * Example: \include MatrixBase_identity.cpp - * Output: \verbinclude MatrixBase_identity.out - * - * \sa Identity(Index,Index), setIdentity(), isIdentity() - */ -template -IMP_EIGEN_STRONG_INLINE const typename MatrixBase::IdentityReturnType -MatrixBase::Identity() -{ - IMP_EIGEN_STATIC_ASSERT_FIXED_SIZE(Derived) - return MatrixBase::NullaryExpr(RowsAtCompileTime, ColsAtCompileTime, internal::scalar_identity_op()); -} - -/** \returns true if *this is approximately equal to the identity matrix - * (not necessarily square), - * within the precision given by \a prec. - * - * Example: \include MatrixBase_isIdentity.cpp - * Output: \verbinclude MatrixBase_isIdentity.out - * - * \sa class CwiseNullaryOp, Identity(), Identity(Index,Index), setIdentity() - */ -template -bool MatrixBase::isIdentity -(const RealScalar& prec) const -{ - for(Index j = 0; j < cols(); ++j) - { - for(Index i = 0; i < rows(); ++i) - { - if(i == j) - { - if(!internal::isApprox(this->coeff(i, j), static_cast(1), prec)) - return false; - } - else - { - if(!internal::isMuchSmallerThan(this->coeff(i, j), static_cast(1), prec)) - return false; - } - } - } - return true; -} - -namespace internal { - -template=16)> -struct setIdentity_impl -{ - static IMP_EIGEN_STRONG_INLINE Derived& run(Derived& m) - { - return m = Derived::Identity(m.rows(), m.cols()); - } -}; - -template -struct setIdentity_impl -{ - typedef typename Derived::Index Index; - static IMP_EIGEN_STRONG_INLINE Derived& run(Derived& m) - { - m.setZero(); - const Index size = (std::min)(m.rows(), m.cols()); - for(Index i = 0; i < size; ++i) m.coeffRef(i,i) = typename Derived::Scalar(1); - return m; - } -}; - -} // end namespace internal - -/** Writes the identity expression (not necessarily square) into *this. - * - * Example: \include MatrixBase_setIdentity.cpp - * Output: \verbinclude MatrixBase_setIdentity.out - * - * \sa class CwiseNullaryOp, Identity(), Identity(Index,Index), isIdentity() - */ -template -IMP_EIGEN_STRONG_INLINE Derived& MatrixBase::setIdentity() -{ - return internal::setIdentity_impl::run(derived()); -} - -/** \brief Resizes to the given size, and writes the identity expression (not necessarily square) into *this. - * - * \param nbRows the new number of rows - * \param nbCols the new number of columns - * - * Example: \include Matrix_setIdentity_int_int.cpp - * Output: \verbinclude Matrix_setIdentity_int_int.out - * - * \sa MatrixBase::setIdentity(), class CwiseNullaryOp, MatrixBase::Identity() - */ -template -IMP_EIGEN_STRONG_INLINE Derived& MatrixBase::setIdentity(Index nbRows, Index nbCols) -{ - derived().resize(nbRows, nbCols); - return setIdentity(); -} - -/** \returns an expression of the i-th unit (basis) vector. - * - * \only_for_vectors - * - * \sa MatrixBase::Unit(Index), MatrixBase::UnitX(), MatrixBase::UnitY(), MatrixBase::UnitZ(), MatrixBase::UnitW() - */ -template -IMP_EIGEN_STRONG_INLINE const typename MatrixBase::BasisReturnType MatrixBase::Unit(Index newSize, Index i) -{ - IMP_EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived) - return BasisReturnType(SquareMatrixType::Identity(newSize,newSize), i); -} - -/** \returns an expression of the i-th unit (basis) vector. - * - * \only_for_vectors - * - * This variant is for fixed-size vector only. - * - * \sa MatrixBase::Unit(Index,Index), MatrixBase::UnitX(), MatrixBase::UnitY(), MatrixBase::UnitZ(), MatrixBase::UnitW() - */ -template -IMP_EIGEN_STRONG_INLINE const typename MatrixBase::BasisReturnType MatrixBase::Unit(Index i) -{ - IMP_EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived) - return BasisReturnType(SquareMatrixType::Identity(),i); -} - -/** \returns an expression of the X axis unit vector (1{,0}^*) - * - * \only_for_vectors - * - * \sa MatrixBase::Unit(Index,Index), MatrixBase::Unit(Index), MatrixBase::UnitY(), MatrixBase::UnitZ(), MatrixBase::UnitW() - */ -template -IMP_EIGEN_STRONG_INLINE const typename MatrixBase::BasisReturnType MatrixBase::UnitX() -{ return Derived::Unit(0); } - -/** \returns an expression of the Y axis unit vector (0,1{,0}^*) - * - * \only_for_vectors - * - * \sa MatrixBase::Unit(Index,Index), MatrixBase::Unit(Index), MatrixBase::UnitY(), MatrixBase::UnitZ(), MatrixBase::UnitW() - */ -template -IMP_EIGEN_STRONG_INLINE const typename MatrixBase::BasisReturnType MatrixBase::UnitY() -{ return Derived::Unit(1); } - -/** \returns an expression of the Z axis unit vector (0,0,1{,0}^*) - * - * \only_for_vectors - * - * \sa MatrixBase::Unit(Index,Index), MatrixBase::Unit(Index), MatrixBase::UnitY(), MatrixBase::UnitZ(), MatrixBase::UnitW() - */ -template -IMP_EIGEN_STRONG_INLINE const typename MatrixBase::BasisReturnType MatrixBase::UnitZ() -{ return Derived::Unit(2); } - -/** \returns an expression of the W axis unit vector (0,0,0,1) - * - * \only_for_vectors - * - * \sa MatrixBase::Unit(Index,Index), MatrixBase::Unit(Index), MatrixBase::UnitY(), MatrixBase::UnitZ(), MatrixBase::UnitW() - */ -template -IMP_EIGEN_STRONG_INLINE const typename MatrixBase::BasisReturnType MatrixBase::UnitW() -{ return Derived::Unit(3); } - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_CWISE_NULLARY_OP_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/CwiseUnaryOp.h b/modules/algebra/include/eigen3/Eigen/src/Core/CwiseUnaryOp.h deleted file mode 100644 index 4262e5bf1f..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/CwiseUnaryOp.h +++ /dev/null @@ -1,126 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008-2010 Gael Guennebaud -// Copyright (C) 2006-2008 Benoit Jacob -// -// 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 IMP_EIGEN_CWISE_UNARY_OP_H -#define IMP_EIGEN_CWISE_UNARY_OP_H - -namespace IMP_Eigen { - -/** \class CwiseUnaryOp - * \ingroup Core_Module - * - * \brief Generic expression where a coefficient-wise unary operator is applied to an expression - * - * \param UnaryOp template functor implementing the operator - * \param XprType the type of the expression to which we are applying the unary operator - * - * This class represents an expression where a unary operator is applied to an expression. - * It is the return type of all operations taking exactly 1 input expression, regardless of the - * presence of other inputs such as scalars. For example, the operator* in the expression 3*matrix - * is considered unary, because only the right-hand side is an expression, and its - * return type is a specialization of CwiseUnaryOp. - * - * Most of the time, this is the only way that it is used, so you typically don't have to name - * CwiseUnaryOp types explicitly. - * - * \sa MatrixBase::unaryExpr(const CustomUnaryOp &) const, class CwiseBinaryOp, class CwiseNullaryOp - */ - -namespace internal { -template -struct traits > - : traits -{ - typedef typename result_of< - UnaryOp(typename XprType::Scalar) - >::type Scalar; - typedef typename XprType::Nested XprTypeNested; - typedef typename remove_reference::type _XprTypeNested; - enum { - Flags = _XprTypeNested::Flags & ( - HereditaryBits | LinearAccessBit | AlignedBit - | (functor_traits::PacketAccess ? PacketAccessBit : 0)), - CoeffReadCost = IMP_EIGEN_ADD_COST(_XprTypeNested::CoeffReadCost, functor_traits::Cost) - }; -}; -} - -template -class CwiseUnaryOpImpl; - -template -class CwiseUnaryOp : internal::no_assignment_operator, - public CwiseUnaryOpImpl::StorageKind> -{ - public: - - typedef typename CwiseUnaryOpImpl::StorageKind>::Base Base; - IMP_EIGEN_GENERIC_PUBLIC_INTERFACE(CwiseUnaryOp) - - inline CwiseUnaryOp(const XprType& xpr, const UnaryOp& func = UnaryOp()) - : m_xpr(xpr), m_functor(func) {} - - IMP_EIGEN_STRONG_INLINE Index rows() const { return m_xpr.rows(); } - IMP_EIGEN_STRONG_INLINE Index cols() const { return m_xpr.cols(); } - - /** \returns the functor representing the unary operation */ - const UnaryOp& functor() const { return m_functor; } - - /** \returns the nested expression */ - const typename internal::remove_all::type& - nestedExpression() const { return m_xpr; } - - /** \returns the nested expression */ - typename internal::remove_all::type& - nestedExpression() { return m_xpr.const_cast_derived(); } - - protected: - typename XprType::Nested m_xpr; - const UnaryOp m_functor; -}; - -// This is the generic implementation for dense storage. -// It can be used for any expression types implementing the dense concept. -template -class CwiseUnaryOpImpl - : public internal::dense_xpr_base >::type -{ - public: - - typedef CwiseUnaryOp Derived; - typedef typename internal::dense_xpr_base >::type Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(Derived) - - IMP_EIGEN_STRONG_INLINE const Scalar coeff(Index rowId, Index colId) const - { - return derived().functor()(derived().nestedExpression().coeff(rowId, colId)); - } - - template - IMP_EIGEN_STRONG_INLINE PacketScalar packet(Index rowId, Index colId) const - { - return derived().functor().packetOp(derived().nestedExpression().template packet(rowId, colId)); - } - - IMP_EIGEN_STRONG_INLINE const Scalar coeff(Index index) const - { - return derived().functor()(derived().nestedExpression().coeff(index)); - } - - template - IMP_EIGEN_STRONG_INLINE PacketScalar packet(Index index) const - { - return derived().functor().packetOp(derived().nestedExpression().template packet(index)); - } -}; - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_CWISE_UNARY_OP_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/CwiseUnaryView.h b/modules/algebra/include/eigen3/Eigen/src/Core/CwiseUnaryView.h deleted file mode 100644 index 2b21f9557c..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/CwiseUnaryView.h +++ /dev/null @@ -1,139 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2009-2010 Gael Guennebaud -// -// 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 IMP_EIGEN_CWISE_UNARY_VIEW_H -#define IMP_EIGEN_CWISE_UNARY_VIEW_H - -namespace IMP_Eigen { - -/** \class CwiseUnaryView - * \ingroup Core_Module - * - * \brief Generic lvalue expression of a coefficient-wise unary operator of a matrix or a vector - * - * \param ViewOp template functor implementing the view - * \param MatrixType the type of the matrix we are applying the unary operator - * - * This class represents a lvalue expression of a generic unary view operator of a matrix or a vector. - * It is the return type of real() and imag(), and most of the time this is the only way it is used. - * - * \sa MatrixBase::unaryViewExpr(const CustomUnaryOp &) const, class CwiseUnaryOp - */ - -namespace internal { -template -struct traits > - : traits -{ - typedef typename result_of< - ViewOp(typename traits::Scalar) - >::type Scalar; - typedef typename MatrixType::Nested MatrixTypeNested; - typedef typename remove_all::type _MatrixTypeNested; - enum { - Flags = (traits<_MatrixTypeNested>::Flags & (HereditaryBits | LvalueBit | LinearAccessBit | DirectAccessBit)), - CoeffReadCost = IMP_EIGEN_ADD_COST(traits<_MatrixTypeNested>::CoeffReadCost, functor_traits::Cost), - MatrixTypeInnerStride = inner_stride_at_compile_time::ret, - // need to cast the sizeof's from size_t to int explicitly, otherwise: - // "error: no integral type can represent all of the enumerator values - InnerStrideAtCompileTime = MatrixTypeInnerStride == Dynamic - ? int(Dynamic) - : int(MatrixTypeInnerStride) * int(sizeof(typename traits::Scalar) / sizeof(Scalar)), - OuterStrideAtCompileTime = outer_stride_at_compile_time::ret == Dynamic - ? int(Dynamic) - : outer_stride_at_compile_time::ret * int(sizeof(typename traits::Scalar) / sizeof(Scalar)) - }; -}; -} - -template -class CwiseUnaryViewImpl; - -template -class CwiseUnaryView : public CwiseUnaryViewImpl::StorageKind> -{ - public: - - typedef typename CwiseUnaryViewImpl::StorageKind>::Base Base; - IMP_EIGEN_GENERIC_PUBLIC_INTERFACE(CwiseUnaryView) - - inline CwiseUnaryView(const MatrixType& mat, const ViewOp& func = ViewOp()) - : m_matrix(mat), m_functor(func) {} - - IMP_EIGEN_INHERIT_ASSIGNMENT_OPERATORS(CwiseUnaryView) - - IMP_EIGEN_STRONG_INLINE Index rows() const { return m_matrix.rows(); } - IMP_EIGEN_STRONG_INLINE Index cols() const { return m_matrix.cols(); } - - /** \returns the functor representing unary operation */ - const ViewOp& functor() const { return m_functor; } - - /** \returns the nested expression */ - const typename internal::remove_all::type& - nestedExpression() const { return m_matrix; } - - /** \returns the nested expression */ - typename internal::remove_all::type& - nestedExpression() { return m_matrix.const_cast_derived(); } - - protected: - // FIXME changed from MatrixType::Nested because of a weird compilation error with sun CC - typename internal::nested::type m_matrix; - ViewOp m_functor; -}; - -template -class CwiseUnaryViewImpl - : public internal::dense_xpr_base< CwiseUnaryView >::type -{ - public: - - typedef CwiseUnaryView Derived; - typedef typename internal::dense_xpr_base< CwiseUnaryView >::type Base; - - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(Derived) - IMP_EIGEN_INHERIT_ASSIGNMENT_OPERATORS(CwiseUnaryViewImpl) - - inline Scalar* data() { return &coeffRef(0); } - inline const Scalar* data() const { return &coeff(0); } - - inline Index innerStride() const - { - return derived().nestedExpression().innerStride() * sizeof(typename internal::traits::Scalar) / sizeof(Scalar); - } - - inline Index outerStride() const - { - return derived().nestedExpression().outerStride() * sizeof(typename internal::traits::Scalar) / sizeof(Scalar); - } - - IMP_EIGEN_STRONG_INLINE CoeffReturnType coeff(Index row, Index col) const - { - return derived().functor()(derived().nestedExpression().coeff(row, col)); - } - - IMP_EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const - { - return derived().functor()(derived().nestedExpression().coeff(index)); - } - - IMP_EIGEN_STRONG_INLINE Scalar& coeffRef(Index row, Index col) - { - return derived().functor()(const_cast_derived().nestedExpression().coeffRef(row, col)); - } - - IMP_EIGEN_STRONG_INLINE Scalar& coeffRef(Index index) - { - return derived().functor()(const_cast_derived().nestedExpression().coeffRef(index)); - } -}; - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_CWISE_UNARY_VIEW_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/DenseBase.h b/modules/algebra/include/eigen3/Eigen/src/Core/DenseBase.h deleted file mode 100644 index 9705d4c75a..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/DenseBase.h +++ /dev/null @@ -1,521 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2007-2010 Benoit Jacob -// Copyright (C) 2008-2010 Gael Guennebaud -// -// 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 IMP_EIGEN_DENSEBASE_H -#define IMP_EIGEN_DENSEBASE_H - -namespace IMP_Eigen { - -namespace internal { - -// The index type defined by IMP_EIGEN_DEFAULT_DENSE_INDEX_TYPE must be a signed type. -// This dummy function simply aims at checking that at compile time. -static inline void check_DenseIndex_is_signed() { - IMP_EIGEN_STATIC_ASSERT(NumTraits::IsSigned,THE_INDEX_TYPE_MUST_BE_A_SIGNED_TYPE); -} - -} // end namespace internal - -/** \class DenseBase - * \ingroup Core_Module - * - * \brief Base class for all dense matrices, vectors, and arrays - * - * This class is the base that is inherited by all dense objects (matrix, vector, arrays, - * and related expression types). The common Eigen API for dense objects is contained in this class. - * - * \tparam Derived is the derived type, e.g., a matrix type or an expression. - * - * This class can be extended with the help of the plugin mechanism described on the page - * \ref TopicCustomizingEigen by defining the preprocessor symbol \c IMP_EIGEN_DENSEBASE_PLUGIN. - * - * \sa \ref TopicClassHierarchy - */ -template class DenseBase -#ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - : public internal::special_scalar_op_base::Scalar, - typename NumTraits::Scalar>::Real, - DenseCoeffsBase > -#else - : public DenseCoeffsBase -#endif // not IMP_EIGEN_PARSED_BY_DOXYGEN -{ - public: - - class InnerIterator; - - typedef typename internal::traits::StorageKind StorageKind; - - /** \brief The type of indices - * \details To change this, \c \#define the preprocessor symbol \c IMP_EIGEN_DEFAULT_DENSE_INDEX_TYPE. - * \sa \ref TopicPreprocessorDirectives. - */ - typedef typename internal::traits::Index Index; - - typedef typename internal::traits::Scalar Scalar; - typedef typename internal::packet_traits::type PacketScalar; - typedef typename NumTraits::Real RealScalar; - typedef internal::special_scalar_op_base > Base; - - using Base::operator*; - using Base::derived; - using Base::const_cast_derived; - using Base::rows; - using Base::cols; - using Base::size; - using Base::rowIndexByOuterInner; - using Base::colIndexByOuterInner; - using Base::coeff; - using Base::coeffByOuterInner; - using Base::packet; - using Base::packetByOuterInner; - using Base::writePacket; - using Base::writePacketByOuterInner; - using Base::coeffRef; - using Base::coeffRefByOuterInner; - using Base::copyCoeff; - using Base::copyCoeffByOuterInner; - using Base::copyPacket; - using Base::copyPacketByOuterInner; - using Base::operator(); - using Base::operator[]; - using Base::x; - using Base::y; - using Base::z; - using Base::w; - using Base::stride; - using Base::innerStride; - using Base::outerStride; - using Base::rowStride; - using Base::colStride; - typedef typename Base::CoeffReturnType CoeffReturnType; - - enum { - - RowsAtCompileTime = internal::traits::RowsAtCompileTime, - /**< The number of rows at compile-time. This is just a copy of the value provided - * by the \a Derived type. If a value is not known at compile-time, - * it is set to the \a Dynamic constant. - * \sa MatrixBase::rows(), MatrixBase::cols(), ColsAtCompileTime, SizeAtCompileTime */ - - ColsAtCompileTime = internal::traits::ColsAtCompileTime, - /**< The number of columns at compile-time. This is just a copy of the value provided - * by the \a Derived type. If a value is not known at compile-time, - * it is set to the \a Dynamic constant. - * \sa MatrixBase::rows(), MatrixBase::cols(), RowsAtCompileTime, SizeAtCompileTime */ - - - SizeAtCompileTime = (internal::size_at_compile_time::RowsAtCompileTime, - internal::traits::ColsAtCompileTime>::ret), - /**< This is equal to the number of coefficients, i.e. the number of - * rows times the number of columns, or to \a Dynamic if this is not - * known at compile-time. \sa RowsAtCompileTime, ColsAtCompileTime */ - - MaxRowsAtCompileTime = internal::traits::MaxRowsAtCompileTime, - /**< This value is equal to the maximum possible number of rows that this expression - * might have. If this expression might have an arbitrarily high number of rows, - * this value is set to \a Dynamic. - * - * This value is useful to know when evaluating an expression, in order to determine - * whether it is possible to avoid doing a dynamic memory allocation. - * - * \sa RowsAtCompileTime, MaxColsAtCompileTime, MaxSizeAtCompileTime - */ - - MaxColsAtCompileTime = internal::traits::MaxColsAtCompileTime, - /**< This value is equal to the maximum possible number of columns that this expression - * might have. If this expression might have an arbitrarily high number of columns, - * this value is set to \a Dynamic. - * - * This value is useful to know when evaluating an expression, in order to determine - * whether it is possible to avoid doing a dynamic memory allocation. - * - * \sa ColsAtCompileTime, MaxRowsAtCompileTime, MaxSizeAtCompileTime - */ - - MaxSizeAtCompileTime = (internal::size_at_compile_time::MaxRowsAtCompileTime, - internal::traits::MaxColsAtCompileTime>::ret), - /**< This value is equal to the maximum possible number of coefficients that this expression - * might have. If this expression might have an arbitrarily high number of coefficients, - * this value is set to \a Dynamic. - * - * This value is useful to know when evaluating an expression, in order to determine - * whether it is possible to avoid doing a dynamic memory allocation. - * - * \sa SizeAtCompileTime, MaxRowsAtCompileTime, MaxColsAtCompileTime - */ - - IsVectorAtCompileTime = internal::traits::MaxRowsAtCompileTime == 1 - || internal::traits::MaxColsAtCompileTime == 1, - /**< This is set to true if either the number of rows or the number of - * columns is known at compile-time to be equal to 1. Indeed, in that case, - * we are dealing with a column-vector (if there is only one column) or with - * a row-vector (if there is only one row). */ - - Flags = internal::traits::Flags, - /**< This stores expression \ref flags flags which may or may not be inherited by new expressions - * constructed from this one. See the \ref flags "list of flags". - */ - - IsRowMajor = int(Flags) & RowMajorBit, /**< True if this expression has row-major storage order. */ - - InnerSizeAtCompileTime = int(IsVectorAtCompileTime) ? int(SizeAtCompileTime) - : int(IsRowMajor) ? int(ColsAtCompileTime) : int(RowsAtCompileTime), - - CoeffReadCost = internal::traits::CoeffReadCost, - /**< This is a rough measure of how expensive it is to read one coefficient from - * this expression. - */ - - InnerStrideAtCompileTime = internal::inner_stride_at_compile_time::ret, - OuterStrideAtCompileTime = internal::outer_stride_at_compile_time::ret - }; - - enum { ThisConstantIsPrivateInPlainObjectBase }; - - /** \returns the number of nonzero coefficients which is in practice the number - * of stored coefficients. */ - inline Index nonZeros() const { return size(); } - - /** \returns the outer size. - * - * \note For a vector, this returns just 1. For a matrix (non-vector), this is the major dimension - * with respect to the \ref TopicStorageOrders "storage order", i.e., the number of columns for a - * column-major matrix, and the number of rows for a row-major matrix. */ - Index outerSize() const - { - return IsVectorAtCompileTime ? 1 - : int(IsRowMajor) ? this->rows() : this->cols(); - } - - /** \returns the inner size. - * - * \note For a vector, this is just the size. For a matrix (non-vector), this is the minor dimension - * with respect to the \ref TopicStorageOrders "storage order", i.e., the number of rows for a - * column-major matrix, and the number of columns for a row-major matrix. */ - Index innerSize() const - { - return IsVectorAtCompileTime ? this->size() - : int(IsRowMajor) ? this->cols() : this->rows(); - } - - /** Only plain matrices/arrays, not expressions, may be resized; therefore the only useful resize methods are - * Matrix::resize() and Array::resize(). The present method only asserts that the new size equals the old size, and does - * nothing else. - */ - void resize(Index newSize) - { - IMP_EIGEN_ONLY_USED_FOR_DEBUG(newSize); - imp_eigen_assert(newSize == this->size() - && "DenseBase::resize() does not actually allow to resize."); - } - /** Only plain matrices/arrays, not expressions, may be resized; therefore the only useful resize methods are - * Matrix::resize() and Array::resize(). The present method only asserts that the new size equals the old size, and does - * nothing else. - */ - void resize(Index nbRows, Index nbCols) - { - IMP_EIGEN_ONLY_USED_FOR_DEBUG(nbRows); - IMP_EIGEN_ONLY_USED_FOR_DEBUG(nbCols); - imp_eigen_assert(nbRows == this->rows() && nbCols == this->cols() - && "DenseBase::resize() does not actually allow to resize."); - } - -#ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - - /** \internal Represents a matrix with all coefficients equal to one another*/ - typedef CwiseNullaryOp,Derived> ConstantReturnType; - /** \internal Represents a vector with linearly spaced coefficients that allows sequential access only. */ - typedef CwiseNullaryOp,Derived> SequentialLinSpacedReturnType; - /** \internal Represents a vector with linearly spaced coefficients that allows random access. */ - typedef CwiseNullaryOp,Derived> RandomAccessLinSpacedReturnType; - /** \internal the return type of MatrixBase::eigenvalues() */ - typedef Matrix::Scalar>::Real, internal::traits::ColsAtCompileTime, 1> EigenvaluesReturnType; - -#endif // not IMP_EIGEN_PARSED_BY_DOXYGEN - - /** Copies \a other into *this. \returns a reference to *this. */ - template - Derived& operator=(const DenseBase& other); - - /** Special case of the template operator=, in order to prevent the compiler - * from generating a default operator= (issue hit with g++ 4.1) - */ - Derived& operator=(const DenseBase& other); - - template - Derived& operator=(const EigenBase &other); - - template - Derived& operator+=(const EigenBase &other); - - template - Derived& operator-=(const EigenBase &other); - - template - Derived& operator=(const ReturnByValue& func); - - /** \internal Copies \a other into *this without evaluating other. \returns a reference to *this. */ - template - Derived& lazyAssign(const DenseBase& other); - - /** \internal Evaluates \a other into *this. \returns a reference to *this. */ - template - Derived& lazyAssign(const ReturnByValue& other); - - CommaInitializer operator<< (const Scalar& s); - - template - const Flagged flagged() const; - - template - CommaInitializer operator<< (const DenseBase& other); - - IMP_Eigen::Transpose transpose(); - typedef typename internal::add_const >::type ConstTransposeReturnType; - ConstTransposeReturnType transpose() const; - void transposeInPlace(); -#ifndef IMP_EIGEN_NO_DEBUG - protected: - template - void checkTransposeAliasing(const OtherDerived& other) const; - public: -#endif - - - static const ConstantReturnType - Constant(Index rows, Index cols, const Scalar& value); - static const ConstantReturnType - Constant(Index size, const Scalar& value); - static const ConstantReturnType - Constant(const Scalar& value); - - static const SequentialLinSpacedReturnType - LinSpaced(Sequential_t, Index size, const Scalar& low, const Scalar& high); - static const RandomAccessLinSpacedReturnType - LinSpaced(Index size, const Scalar& low, const Scalar& high); - static const SequentialLinSpacedReturnType - LinSpaced(Sequential_t, const Scalar& low, const Scalar& high); - static const RandomAccessLinSpacedReturnType - LinSpaced(const Scalar& low, const Scalar& high); - - template - static const CwiseNullaryOp - NullaryExpr(Index rows, Index cols, const CustomNullaryOp& func); - template - static const CwiseNullaryOp - NullaryExpr(Index size, const CustomNullaryOp& func); - template - static const CwiseNullaryOp - NullaryExpr(const CustomNullaryOp& func); - - static const ConstantReturnType Zero(Index rows, Index cols); - static const ConstantReturnType Zero(Index size); - static const ConstantReturnType Zero(); - static const ConstantReturnType Ones(Index rows, Index cols); - static const ConstantReturnType Ones(Index size); - static const ConstantReturnType Ones(); - - void fill(const Scalar& value); - Derived& setConstant(const Scalar& value); - Derived& setLinSpaced(Index size, const Scalar& low, const Scalar& high); - Derived& setLinSpaced(const Scalar& low, const Scalar& high); - Derived& setZero(); - Derived& setOnes(); - Derived& setRandom(); - - template - bool isApprox(const DenseBase& other, - const RealScalar& prec = NumTraits::dummy_precision()) const; - bool isMuchSmallerThan(const RealScalar& other, - const RealScalar& prec = NumTraits::dummy_precision()) const; - template - bool isMuchSmallerThan(const DenseBase& other, - const RealScalar& prec = NumTraits::dummy_precision()) const; - - bool isApproxToConstant(const Scalar& value, const RealScalar& prec = NumTraits::dummy_precision()) const; - bool isConstant(const Scalar& value, const RealScalar& prec = NumTraits::dummy_precision()) const; - bool isZero(const RealScalar& prec = NumTraits::dummy_precision()) const; - bool isOnes(const RealScalar& prec = NumTraits::dummy_precision()) const; - - inline bool hasNaN() const; - inline bool allFinite() const; - - inline Derived& operator*=(const Scalar& other); - inline Derived& operator/=(const Scalar& other); - - typedef typename internal::add_const_on_value_type::type>::type EvalReturnType; - /** \returns the matrix or vector obtained by evaluating this expression. - * - * Notice that in the case of a plain matrix or vector (not an expression) this function just returns - * a const reference, in order to avoid a useless copy. - */ - IMP_EIGEN_STRONG_INLINE EvalReturnType eval() const - { - // Even though MSVC does not honor strong inlining when the return type - // is a dynamic matrix, we desperately need strong inlining for fixed - // size types on MSVC. - return typename internal::eval::type(derived()); - } - - /** swaps *this with the expression \a other. - * - */ - template - void swap(const DenseBase& other, - int = OtherDerived::ThisConstantIsPrivateInPlainObjectBase) - { - SwapWrapper(derived()).lazyAssign(other.derived()); - } - - /** swaps *this with the matrix or array \a other. - * - */ - template - void swap(PlainObjectBase& other) - { - SwapWrapper(derived()).lazyAssign(other.derived()); - } - - - inline const NestByValue nestByValue() const; - inline const ForceAlignedAccess forceAlignedAccess() const; - inline ForceAlignedAccess forceAlignedAccess(); - template inline const typename internal::conditional,Derived&>::type forceAlignedAccessIf() const; - template inline typename internal::conditional,Derived&>::type forceAlignedAccessIf(); - - Scalar sum() const; - Scalar mean() const; - Scalar trace() const; - - Scalar prod() const; - - typename internal::traits::Scalar minCoeff() const; - typename internal::traits::Scalar maxCoeff() const; - - template - typename internal::traits::Scalar minCoeff(IndexType* row, IndexType* col) const; - template - typename internal::traits::Scalar maxCoeff(IndexType* row, IndexType* col) const; - template - typename internal::traits::Scalar minCoeff(IndexType* index) const; - template - typename internal::traits::Scalar maxCoeff(IndexType* index) const; - - template - typename internal::result_of::Scalar)>::type - redux(const BinaryOp& func) const; - - template - void visit(Visitor& func) const; - - inline const WithFormat format(const IOFormat& fmt) const; - - /** \returns the unique coefficient of a 1x1 expression */ - CoeffReturnType value() const - { - IMP_EIGEN_STATIC_ASSERT_SIZE_1x1(Derived) - imp_eigen_assert(this->rows() == 1 && this->cols() == 1); - return derived().coeff(0,0); - } - - bool all(void) const; - bool any(void) const; - Index count() const; - - typedef VectorwiseOp RowwiseReturnType; - typedef const VectorwiseOp ConstRowwiseReturnType; - typedef VectorwiseOp ColwiseReturnType; - typedef const VectorwiseOp ConstColwiseReturnType; - - ConstRowwiseReturnType rowwise() const; - RowwiseReturnType rowwise(); - ConstColwiseReturnType colwise() const; - ColwiseReturnType colwise(); - - static const CwiseNullaryOp,Derived> Random(Index rows, Index cols); - static const CwiseNullaryOp,Derived> Random(Index size); - static const CwiseNullaryOp,Derived> Random(); - - template - const Select - select(const DenseBase& thenMatrix, - const DenseBase& elseMatrix) const; - - template - inline const Select - select(const DenseBase& thenMatrix, const typename ThenDerived::Scalar& elseScalar) const; - - template - inline const Select - select(const typename ElseDerived::Scalar& thenScalar, const DenseBase& elseMatrix) const; - - template RealScalar lpNorm() const; - - template - inline const Replicate replicate() const; - - typedef Replicate ReplicateReturnType; - inline const ReplicateReturnType replicate(Index rowFacor,Index colFactor) const; - - typedef Reverse ReverseReturnType; - typedef const Reverse ConstReverseReturnType; - ReverseReturnType reverse(); - ConstReverseReturnType reverse() const; - void reverseInPlace(); - -#define IMP_EIGEN_CURRENT_STORAGE_BASE_CLASS IMP_Eigen::DenseBase -# include "../plugins/BlockMethods.h" -# ifdef IMP_EIGEN_DENSEBASE_PLUGIN -# include IMP_EIGEN_DENSEBASE_PLUGIN -# endif -#undef IMP_EIGEN_CURRENT_STORAGE_BASE_CLASS - -#ifdef IMP_EIGEN2_SUPPORT - - Block corner(CornerType type, Index cRows, Index cCols); - const Block corner(CornerType type, Index cRows, Index cCols) const; - template - Block corner(CornerType type); - template - const Block corner(CornerType type) const; - -#endif // IMP_EIGEN2_SUPPORT - - - // disable the use of evalTo for dense objects with a nice compilation error - template inline void evalTo(Dest& ) const - { - IMP_EIGEN_STATIC_ASSERT((internal::is_same::value),THE_EVAL_EVALTO_FUNCTION_SHOULD_NEVER_BE_CALLED_FOR_DENSE_OBJECTS); - } - - protected: - /** Default constructor. Do nothing. */ - DenseBase() - { - /* Just checks for self-consistency of the flags. - * Only do it when debugging Eigen, as this borders on paranoiac and could slow compilation down - */ -#ifdef IMP_EIGEN_INTERNAL_DEBUGGING - IMP_EIGEN_STATIC_ASSERT((IMP_EIGEN_IMPLIES(MaxRowsAtCompileTime==1 && MaxColsAtCompileTime!=1, int(IsRowMajor)) - && IMP_EIGEN_IMPLIES(MaxColsAtCompileTime==1 && MaxRowsAtCompileTime!=1, int(!IsRowMajor))), - INVALID_STORAGE_ORDER_FOR_THIS_VECTOR_EXPRESSION) -#endif - } - - private: - explicit DenseBase(int); - DenseBase(int,int); - template explicit DenseBase(const DenseBase&); -}; - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_DENSEBASE_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h b/modules/algebra/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h deleted file mode 100644 index 1c874ccea8..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h +++ /dev/null @@ -1,754 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2006-2010 Benoit Jacob -// -// 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 IMP_EIGEN_DENSECOEFFSBASE_H -#define IMP_EIGEN_DENSECOEFFSBASE_H - -namespace IMP_Eigen { - -namespace internal { -template struct add_const_on_value_type_if_arithmetic -{ - typedef typename conditional::value, T, typename add_const_on_value_type::type>::type type; -}; -} - -/** \brief Base class providing read-only coefficient access to matrices and arrays. - * \ingroup Core_Module - * \tparam Derived Type of the derived class - * \tparam #ReadOnlyAccessors Constant indicating read-only access - * - * This class defines the \c operator() \c const function and friends, which can be used to read specific - * entries of a matrix or array. - * - * \sa DenseCoeffsBase, DenseCoeffsBase, - * \ref TopicClassHierarchy - */ -template -class DenseCoeffsBase : public EigenBase -{ - public: - typedef typename internal::traits::StorageKind StorageKind; - typedef typename internal::traits::Index Index; - typedef typename internal::traits::Scalar Scalar; - typedef typename internal::packet_traits::type PacketScalar; - - // Explanation for this CoeffReturnType typedef. - // - This is the return type of the coeff() method. - // - The LvalueBit means exactly that we can offer a coeffRef() method, which means exactly that we can get references - // to coeffs, which means exactly that we can have coeff() return a const reference (as opposed to returning a value). - // - The is_artihmetic check is required since "const int", "const double", etc. will cause warnings on some systems - // while the declaration of "const T", where T is a non arithmetic type does not. Always returning "const Scalar&" is - // not possible, since the underlying expressions might not offer a valid address the reference could be referring to. - typedef typename internal::conditional::Flags&LvalueBit), - const Scalar&, - typename internal::conditional::value, Scalar, const Scalar>::type - >::type CoeffReturnType; - - typedef typename internal::add_const_on_value_type_if_arithmetic< - typename internal::packet_traits::type - >::type PacketReturnType; - - typedef EigenBase Base; - using Base::rows; - using Base::cols; - using Base::size; - using Base::derived; - - IMP_EIGEN_STRONG_INLINE Index rowIndexByOuterInner(Index outer, Index inner) const - { - return int(Derived::RowsAtCompileTime) == 1 ? 0 - : int(Derived::ColsAtCompileTime) == 1 ? inner - : int(Derived::Flags)&RowMajorBit ? outer - : inner; - } - - IMP_EIGEN_STRONG_INLINE Index colIndexByOuterInner(Index outer, Index inner) const - { - return int(Derived::ColsAtCompileTime) == 1 ? 0 - : int(Derived::RowsAtCompileTime) == 1 ? inner - : int(Derived::Flags)&RowMajorBit ? inner - : outer; - } - - /** Short version: don't use this function, use - * \link operator()(Index,Index) const \endlink instead. - * - * Long version: this function is similar to - * \link operator()(Index,Index) const \endlink, but without the assertion. - * Use this for limiting the performance cost of debugging code when doing - * repeated coefficient access. Only use this when it is guaranteed that the - * parameters \a row and \a col are in range. - * - * If IMP_EIGEN_INTERNAL_DEBUGGING is defined, an assertion will be made, making this - * function equivalent to \link operator()(Index,Index) const \endlink. - * - * \sa operator()(Index,Index) const, coeffRef(Index,Index), coeff(Index) const - */ - IMP_EIGEN_STRONG_INLINE CoeffReturnType coeff(Index row, Index col) const - { - imp_eigen_internal_assert(row >= 0 && row < rows() - && col >= 0 && col < cols()); - return derived().coeff(row, col); - } - - IMP_EIGEN_STRONG_INLINE CoeffReturnType coeffByOuterInner(Index outer, Index inner) const - { - return coeff(rowIndexByOuterInner(outer, inner), - colIndexByOuterInner(outer, inner)); - } - - /** \returns the coefficient at given the given row and column. - * - * \sa operator()(Index,Index), operator[](Index) - */ - IMP_EIGEN_STRONG_INLINE CoeffReturnType operator()(Index row, Index col) const - { - imp_eigen_assert(row >= 0 && row < rows() - && col >= 0 && col < cols()); - return derived().coeff(row, col); - } - - /** Short version: don't use this function, use - * \link operator[](Index) const \endlink instead. - * - * Long version: this function is similar to - * \link operator[](Index) const \endlink, but without the assertion. - * Use this for limiting the performance cost of debugging code when doing - * repeated coefficient access. Only use this when it is guaranteed that the - * parameter \a index is in range. - * - * If IMP_EIGEN_INTERNAL_DEBUGGING is defined, an assertion will be made, making this - * function equivalent to \link operator[](Index) const \endlink. - * - * \sa operator[](Index) const, coeffRef(Index), coeff(Index,Index) const - */ - - IMP_EIGEN_STRONG_INLINE CoeffReturnType - coeff(Index index) const - { - imp_eigen_internal_assert(index >= 0 && index < size()); - return derived().coeff(index); - } - - - /** \returns the coefficient at given index. - * - * This method is allowed only for vector expressions, and for matrix expressions having the LinearAccessBit. - * - * \sa operator[](Index), operator()(Index,Index) const, x() const, y() const, - * z() const, w() const - */ - - IMP_EIGEN_STRONG_INLINE CoeffReturnType - operator[](Index index) const - { - #ifndef IMP_EIGEN2_SUPPORT - IMP_EIGEN_STATIC_ASSERT(Derived::IsVectorAtCompileTime, - THE_BRACKET_OPERATOR_IS_ONLY_FOR_VECTORS__USE_THE_PARENTHESIS_OPERATOR_INSTEAD) - #endif - imp_eigen_assert(index >= 0 && index < size()); - return derived().coeff(index); - } - - /** \returns the coefficient at given index. - * - * This is synonymous to operator[](Index) const. - * - * This method is allowed only for vector expressions, and for matrix expressions having the LinearAccessBit. - * - * \sa operator[](Index), operator()(Index,Index) const, x() const, y() const, - * z() const, w() const - */ - - IMP_EIGEN_STRONG_INLINE CoeffReturnType - operator()(Index index) const - { - imp_eigen_assert(index >= 0 && index < size()); - return derived().coeff(index); - } - - /** equivalent to operator[](0). */ - - IMP_EIGEN_STRONG_INLINE CoeffReturnType - x() const { return (*this)[0]; } - - /** equivalent to operator[](1). */ - - IMP_EIGEN_STRONG_INLINE CoeffReturnType - y() const { return (*this)[1]; } - - /** equivalent to operator[](2). */ - - IMP_EIGEN_STRONG_INLINE CoeffReturnType - z() const { return (*this)[2]; } - - /** equivalent to operator[](3). */ - - IMP_EIGEN_STRONG_INLINE CoeffReturnType - w() const { return (*this)[3]; } - - /** \internal - * \returns the packet of coefficients starting at the given row and column. It is your responsibility - * to ensure that a packet really starts there. This method is only available on expressions having the - * PacketAccessBit. - * - * The \a LoadMode parameter may have the value \a #Aligned or \a #Unaligned. Its effect is to select - * the appropriate vectorization instruction. Aligned access is faster, but is only possible for packets - * starting at an address which is a multiple of the packet size. - */ - - template - IMP_EIGEN_STRONG_INLINE PacketReturnType packet(Index row, Index col) const - { - imp_eigen_internal_assert(row >= 0 && row < rows() - && col >= 0 && col < cols()); - return derived().template packet(row,col); - } - - - /** \internal */ - template - IMP_EIGEN_STRONG_INLINE PacketReturnType packetByOuterInner(Index outer, Index inner) const - { - return packet(rowIndexByOuterInner(outer, inner), - colIndexByOuterInner(outer, inner)); - } - - /** \internal - * \returns the packet of coefficients starting at the given index. It is your responsibility - * to ensure that a packet really starts there. This method is only available on expressions having the - * PacketAccessBit and the LinearAccessBit. - * - * The \a LoadMode parameter may have the value \a #Aligned or \a #Unaligned. Its effect is to select - * the appropriate vectorization instruction. Aligned access is faster, but is only possible for packets - * starting at an address which is a multiple of the packet size. - */ - - template - IMP_EIGEN_STRONG_INLINE PacketReturnType packet(Index index) const - { - imp_eigen_internal_assert(index >= 0 && index < size()); - return derived().template packet(index); - } - - protected: - // explanation: DenseBase is doing "using ..." on the methods from DenseCoeffsBase. - // But some methods are only available in the DirectAccess case. - // So we add dummy methods here with these names, so that "using... " doesn't fail. - // It's not private so that the child class DenseBase can access them, and it's not public - // either since it's an implementation detail, so has to be protected. - void coeffRef(); - void coeffRefByOuterInner(); - void writePacket(); - void writePacketByOuterInner(); - void copyCoeff(); - void copyCoeffByOuterInner(); - void copyPacket(); - void copyPacketByOuterInner(); - void stride(); - void innerStride(); - void outerStride(); - void rowStride(); - void colStride(); -}; - -/** \brief Base class providing read/write coefficient access to matrices and arrays. - * \ingroup Core_Module - * \tparam Derived Type of the derived class - * \tparam #WriteAccessors Constant indicating read/write access - * - * This class defines the non-const \c operator() function and friends, which can be used to write specific - * entries of a matrix or array. This class inherits DenseCoeffsBase which - * defines the const variant for reading specific entries. - * - * \sa DenseCoeffsBase, \ref TopicClassHierarchy - */ -template -class DenseCoeffsBase : public DenseCoeffsBase -{ - public: - - typedef DenseCoeffsBase Base; - - typedef typename internal::traits::StorageKind StorageKind; - typedef typename internal::traits::Index Index; - typedef typename internal::traits::Scalar Scalar; - typedef typename internal::packet_traits::type PacketScalar; - typedef typename NumTraits::Real RealScalar; - - using Base::coeff; - using Base::rows; - using Base::cols; - using Base::size; - using Base::derived; - using Base::rowIndexByOuterInner; - using Base::colIndexByOuterInner; - using Base::operator[]; - using Base::operator(); - using Base::x; - using Base::y; - using Base::z; - using Base::w; - - /** Short version: don't use this function, use - * \link operator()(Index,Index) \endlink instead. - * - * Long version: this function is similar to - * \link operator()(Index,Index) \endlink, but without the assertion. - * Use this for limiting the performance cost of debugging code when doing - * repeated coefficient access. Only use this when it is guaranteed that the - * parameters \a row and \a col are in range. - * - * If IMP_EIGEN_INTERNAL_DEBUGGING is defined, an assertion will be made, making this - * function equivalent to \link operator()(Index,Index) \endlink. - * - * \sa operator()(Index,Index), coeff(Index, Index) const, coeffRef(Index) - */ - IMP_EIGEN_STRONG_INLINE Scalar& coeffRef(Index row, Index col) - { - imp_eigen_internal_assert(row >= 0 && row < rows() - && col >= 0 && col < cols()); - return derived().coeffRef(row, col); - } - - IMP_EIGEN_STRONG_INLINE Scalar& - coeffRefByOuterInner(Index outer, Index inner) - { - return coeffRef(rowIndexByOuterInner(outer, inner), - colIndexByOuterInner(outer, inner)); - } - - /** \returns a reference to the coefficient at given the given row and column. - * - * \sa operator[](Index) - */ - - IMP_EIGEN_STRONG_INLINE Scalar& - operator()(Index row, Index col) - { - imp_eigen_assert(row >= 0 && row < rows() - && col >= 0 && col < cols()); - return derived().coeffRef(row, col); - } - - - /** Short version: don't use this function, use - * \link operator[](Index) \endlink instead. - * - * Long version: this function is similar to - * \link operator[](Index) \endlink, but without the assertion. - * Use this for limiting the performance cost of debugging code when doing - * repeated coefficient access. Only use this when it is guaranteed that the - * parameters \a row and \a col are in range. - * - * If IMP_EIGEN_INTERNAL_DEBUGGING is defined, an assertion will be made, making this - * function equivalent to \link operator[](Index) \endlink. - * - * \sa operator[](Index), coeff(Index) const, coeffRef(Index,Index) - */ - - IMP_EIGEN_STRONG_INLINE Scalar& - coeffRef(Index index) - { - imp_eigen_internal_assert(index >= 0 && index < size()); - return derived().coeffRef(index); - } - - /** \returns a reference to the coefficient at given index. - * - * This method is allowed only for vector expressions, and for matrix expressions having the LinearAccessBit. - * - * \sa operator[](Index) const, operator()(Index,Index), x(), y(), z(), w() - */ - - IMP_EIGEN_STRONG_INLINE Scalar& - operator[](Index index) - { - #ifndef IMP_EIGEN2_SUPPORT - IMP_EIGEN_STATIC_ASSERT(Derived::IsVectorAtCompileTime, - THE_BRACKET_OPERATOR_IS_ONLY_FOR_VECTORS__USE_THE_PARENTHESIS_OPERATOR_INSTEAD) - #endif - imp_eigen_assert(index >= 0 && index < size()); - return derived().coeffRef(index); - } - - /** \returns a reference to the coefficient at given index. - * - * This is synonymous to operator[](Index). - * - * This method is allowed only for vector expressions, and for matrix expressions having the LinearAccessBit. - * - * \sa operator[](Index) const, operator()(Index,Index), x(), y(), z(), w() - */ - - IMP_EIGEN_STRONG_INLINE Scalar& - operator()(Index index) - { - imp_eigen_assert(index >= 0 && index < size()); - return derived().coeffRef(index); - } - - /** equivalent to operator[](0). */ - - IMP_EIGEN_STRONG_INLINE Scalar& - x() { return (*this)[0]; } - - /** equivalent to operator[](1). */ - - IMP_EIGEN_STRONG_INLINE Scalar& - y() { return (*this)[1]; } - - /** equivalent to operator[](2). */ - - IMP_EIGEN_STRONG_INLINE Scalar& - z() { return (*this)[2]; } - - /** equivalent to operator[](3). */ - - IMP_EIGEN_STRONG_INLINE Scalar& - w() { return (*this)[3]; } - - /** \internal - * Stores the given packet of coefficients, at the given row and column of this expression. It is your responsibility - * to ensure that a packet really starts there. This method is only available on expressions having the - * PacketAccessBit. - * - * The \a LoadMode parameter may have the value \a #Aligned or \a #Unaligned. Its effect is to select - * the appropriate vectorization instruction. Aligned access is faster, but is only possible for packets - * starting at an address which is a multiple of the packet size. - */ - - template - IMP_EIGEN_STRONG_INLINE void writePacket - (Index row, Index col, const typename internal::packet_traits::type& val) - { - imp_eigen_internal_assert(row >= 0 && row < rows() - && col >= 0 && col < cols()); - derived().template writePacket(row,col,val); - } - - - /** \internal */ - template - IMP_EIGEN_STRONG_INLINE void writePacketByOuterInner - (Index outer, Index inner, const typename internal::packet_traits::type& val) - { - writePacket(rowIndexByOuterInner(outer, inner), - colIndexByOuterInner(outer, inner), - val); - } - - /** \internal - * Stores the given packet of coefficients, at the given index in this expression. It is your responsibility - * to ensure that a packet really starts there. This method is only available on expressions having the - * PacketAccessBit and the LinearAccessBit. - * - * The \a LoadMode parameter may have the value \a Aligned or \a Unaligned. Its effect is to select - * the appropriate vectorization instruction. Aligned access is faster, but is only possible for packets - * starting at an address which is a multiple of the packet size. - */ - template - IMP_EIGEN_STRONG_INLINE void writePacket - (Index index, const typename internal::packet_traits::type& val) - { - imp_eigen_internal_assert(index >= 0 && index < size()); - derived().template writePacket(index,val); - } - -#ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - - /** \internal Copies the coefficient at position (row,col) of other into *this. - * - * This method is overridden in SwapWrapper, allowing swap() assignments to share 99% of their code - * with usual assignments. - * - * Outside of this internal usage, this method has probably no usefulness. It is hidden in the public API dox. - */ - - template - IMP_EIGEN_STRONG_INLINE void copyCoeff(Index row, Index col, const DenseBase& other) - { - imp_eigen_internal_assert(row >= 0 && row < rows() - && col >= 0 && col < cols()); - derived().coeffRef(row, col) = other.derived().coeff(row, col); - } - - /** \internal Copies the coefficient at the given index of other into *this. - * - * This method is overridden in SwapWrapper, allowing swap() assignments to share 99% of their code - * with usual assignments. - * - * Outside of this internal usage, this method has probably no usefulness. It is hidden in the public API dox. - */ - - template - IMP_EIGEN_STRONG_INLINE void copyCoeff(Index index, const DenseBase& other) - { - imp_eigen_internal_assert(index >= 0 && index < size()); - derived().coeffRef(index) = other.derived().coeff(index); - } - - - template - IMP_EIGEN_STRONG_INLINE void copyCoeffByOuterInner(Index outer, Index inner, const DenseBase& other) - { - const Index row = rowIndexByOuterInner(outer,inner); - const Index col = colIndexByOuterInner(outer,inner); - // derived() is important here: copyCoeff() may be reimplemented in Derived! - derived().copyCoeff(row, col, other); - } - - /** \internal Copies the packet at position (row,col) of other into *this. - * - * This method is overridden in SwapWrapper, allowing swap() assignments to share 99% of their code - * with usual assignments. - * - * Outside of this internal usage, this method has probably no usefulness. It is hidden in the public API dox. - */ - - template - IMP_EIGEN_STRONG_INLINE void copyPacket(Index row, Index col, const DenseBase& other) - { - imp_eigen_internal_assert(row >= 0 && row < rows() - && col >= 0 && col < cols()); - derived().template writePacket(row, col, - other.derived().template packet(row, col)); - } - - /** \internal Copies the packet at the given index of other into *this. - * - * This method is overridden in SwapWrapper, allowing swap() assignments to share 99% of their code - * with usual assignments. - * - * Outside of this internal usage, this method has probably no usefulness. It is hidden in the public API dox. - */ - - template - IMP_EIGEN_STRONG_INLINE void copyPacket(Index index, const DenseBase& other) - { - imp_eigen_internal_assert(index >= 0 && index < size()); - derived().template writePacket(index, - other.derived().template packet(index)); - } - - /** \internal */ - template - IMP_EIGEN_STRONG_INLINE void copyPacketByOuterInner(Index outer, Index inner, const DenseBase& other) - { - const Index row = rowIndexByOuterInner(outer,inner); - const Index col = colIndexByOuterInner(outer,inner); - // derived() is important here: copyCoeff() may be reimplemented in Derived! - derived().template copyPacket< OtherDerived, StoreMode, LoadMode>(row, col, other); - } -#endif - -}; - -/** \brief Base class providing direct read-only coefficient access to matrices and arrays. - * \ingroup Core_Module - * \tparam Derived Type of the derived class - * \tparam #DirectAccessors Constant indicating direct access - * - * This class defines functions to work with strides which can be used to access entries directly. This class - * inherits DenseCoeffsBase which defines functions to access entries read-only using - * \c operator() . - * - * \sa \ref TopicClassHierarchy - */ -template -class DenseCoeffsBase : public DenseCoeffsBase -{ - public: - - typedef DenseCoeffsBase Base; - typedef typename internal::traits::Index Index; - typedef typename internal::traits::Scalar Scalar; - typedef typename NumTraits::Real RealScalar; - - using Base::rows; - using Base::cols; - using Base::size; - using Base::derived; - - /** \returns the pointer increment between two consecutive elements within a slice in the inner direction. - * - * \sa outerStride(), rowStride(), colStride() - */ - inline Index innerStride() const - { - return derived().innerStride(); - } - - /** \returns the pointer increment between two consecutive inner slices (for example, between two consecutive columns - * in a column-major matrix). - * - * \sa innerStride(), rowStride(), colStride() - */ - inline Index outerStride() const - { - return derived().outerStride(); - } - - // FIXME shall we remove it ? - inline Index stride() const - { - return Derived::IsVectorAtCompileTime ? innerStride() : outerStride(); - } - - /** \returns the pointer increment between two consecutive rows. - * - * \sa innerStride(), outerStride(), colStride() - */ - inline Index rowStride() const - { - return Derived::IsRowMajor ? outerStride() : innerStride(); - } - - /** \returns the pointer increment between two consecutive columns. - * - * \sa innerStride(), outerStride(), rowStride() - */ - inline Index colStride() const - { - return Derived::IsRowMajor ? innerStride() : outerStride(); - } -}; - -/** \brief Base class providing direct read/write coefficient access to matrices and arrays. - * \ingroup Core_Module - * \tparam Derived Type of the derived class - * \tparam #DirectWriteAccessors Constant indicating direct access - * - * This class defines functions to work with strides which can be used to access entries directly. This class - * inherits DenseCoeffsBase which defines functions to access entries read/write using - * \c operator(). - * - * \sa \ref TopicClassHierarchy - */ -template -class DenseCoeffsBase - : public DenseCoeffsBase -{ - public: - - typedef DenseCoeffsBase Base; - typedef typename internal::traits::Index Index; - typedef typename internal::traits::Scalar Scalar; - typedef typename NumTraits::Real RealScalar; - - using Base::rows; - using Base::cols; - using Base::size; - using Base::derived; - - /** \returns the pointer increment between two consecutive elements within a slice in the inner direction. - * - * \sa outerStride(), rowStride(), colStride() - */ - inline Index innerStride() const - { - return derived().innerStride(); - } - - /** \returns the pointer increment between two consecutive inner slices (for example, between two consecutive columns - * in a column-major matrix). - * - * \sa innerStride(), rowStride(), colStride() - */ - inline Index outerStride() const - { - return derived().outerStride(); - } - - // FIXME shall we remove it ? - inline Index stride() const - { - return Derived::IsVectorAtCompileTime ? innerStride() : outerStride(); - } - - /** \returns the pointer increment between two consecutive rows. - * - * \sa innerStride(), outerStride(), colStride() - */ - inline Index rowStride() const - { - return Derived::IsRowMajor ? outerStride() : innerStride(); - } - - /** \returns the pointer increment between two consecutive columns. - * - * \sa innerStride(), outerStride(), rowStride() - */ - inline Index colStride() const - { - return Derived::IsRowMajor ? innerStride() : outerStride(); - } -}; - -namespace internal { - -template -struct first_aligned_impl -{ - static inline typename Derived::Index run(const Derived&) - { return 0; } -}; - -template -struct first_aligned_impl -{ - static inline typename Derived::Index run(const Derived& m) - { - return internal::first_aligned(&m.const_cast_derived().coeffRef(0,0), m.size()); - } -}; - -/** \internal \returns the index of the first element of the array that is well aligned for vectorization. - * - * There is also the variant first_aligned(const Scalar*, Integer) defined in Memory.h. See it for more - * documentation. - */ -template -static inline typename Derived::Index first_aligned(const Derived& m) -{ - return first_aligned_impl - - ::run(m); -} - -template::ret> -struct inner_stride_at_compile_time -{ - enum { ret = traits::InnerStrideAtCompileTime }; -}; - -template -struct inner_stride_at_compile_time -{ - enum { ret = 0 }; -}; - -template::ret> -struct outer_stride_at_compile_time -{ - enum { ret = traits::OuterStrideAtCompileTime }; -}; - -template -struct outer_stride_at_compile_time -{ - enum { ret = 0 }; -}; - -} // end namespace internal - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_DENSECOEFFSBASE_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/DenseStorage.h b/modules/algebra/include/eigen3/Eigen/src/Core/DenseStorage.h deleted file mode 100644 index 99fcb09f66..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/DenseStorage.h +++ /dev/null @@ -1,434 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008 Gael Guennebaud -// Copyright (C) 2006-2009 Benoit Jacob -// Copyright (C) 2010 Hauke Heibel -// -// 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 IMP_EIGEN_MATRIXSTORAGE_H -#define IMP_EIGEN_MATRIXSTORAGE_H - -#ifdef IMP_EIGEN_DENSE_STORAGE_CTOR_PLUGIN - #define IMP_EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN IMP_EIGEN_DENSE_STORAGE_CTOR_PLUGIN; -#else - #define IMP_EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN -#endif - -namespace IMP_Eigen { - -namespace internal { - -struct constructor_without_unaligned_array_assert {}; - -template void check_static_allocation_size() -{ - // if IMP_EIGEN_STACK_ALLOCATION_LIMIT is defined to 0, then no limit - #if IMP_EIGEN_STACK_ALLOCATION_LIMIT - IMP_EIGEN_STATIC_ASSERT(Size * sizeof(T) <= IMP_EIGEN_STACK_ALLOCATION_LIMIT, OBJECT_ALLOCATED_ON_STACK_IS_TOO_BIG); - #endif -} - -/** \internal - * Static array. If the MatrixOrArrayOptions require auto-alignment, the array will be automatically aligned: - * to 16 bytes boundary if the total size is a multiple of 16 bytes. - */ -template -struct plain_array -{ - T array[Size]; - - plain_array() - { - check_static_allocation_size(); - } - - plain_array(constructor_without_unaligned_array_assert) - { - check_static_allocation_size(); - } -}; - -#if defined(IMP_EIGEN_DISABLE_UNALIGNED_ARRAY_ASSERT) - #define IMP_EIGEN_MAKE_UNALIGNED_ARRAY_ASSERT(sizemask) -#elif IMP_EIGEN_GNUC_AT_LEAST(4,7) - // GCC 4.7 is too aggressive in its optimizations and remove the alignement test based on the fact the array is declared to be aligned. - // See this bug report: http://gcc.gnu.org/bugzilla/show_bug.cgi?id=53900 - // Hiding the origin of the array pointer behind a function argument seems to do the trick even if the function is inlined: - template - IMP_EIGEN_ALWAYS_INLINE PtrType eigen_unaligned_array_assert_workaround_gcc47(PtrType array) { return array; } - #define IMP_EIGEN_MAKE_UNALIGNED_ARRAY_ASSERT(sizemask) \ - imp_eigen_assert((reinterpret_cast(eigen_unaligned_array_assert_workaround_gcc47(array)) & sizemask) == 0 \ - && "this assertion is explained here: " \ - "http://eigen.tuxfamily.org/dox-devel/group__TopicUnalignedArrayAssert.html" \ - " **** READ THIS WEB PAGE !!! ****"); -#else - #define IMP_EIGEN_MAKE_UNALIGNED_ARRAY_ASSERT(sizemask) \ - imp_eigen_assert((reinterpret_cast(array) & sizemask) == 0 \ - && "this assertion is explained here: " \ - "http://eigen.tuxfamily.org/dox-devel/group__TopicUnalignedArrayAssert.html" \ - " **** READ THIS WEB PAGE !!! ****"); -#endif - -template -struct plain_array -{ - IMP_EIGEN_USER_ALIGN16 T array[Size]; - - plain_array() - { - IMP_EIGEN_MAKE_UNALIGNED_ARRAY_ASSERT(0xf); - check_static_allocation_size(); - } - - plain_array(constructor_without_unaligned_array_assert) - { - check_static_allocation_size(); - } -}; - -template -struct plain_array -{ - IMP_EIGEN_USER_ALIGN16 T array[1]; - plain_array() {} - plain_array(constructor_without_unaligned_array_assert) {} -}; - -} // end namespace internal - -/** \internal - * - * \class DenseStorage - * \ingroup Core_Module - * - * \brief Stores the data of a matrix - * - * This class stores the data of fixed-size, dynamic-size or mixed matrices - * in a way as compact as possible. - * - * \sa Matrix - */ -template class DenseStorage; - -// purely fixed-size matrix -template class DenseStorage -{ - internal::plain_array m_data; - public: - DenseStorage() {} - DenseStorage(internal::constructor_without_unaligned_array_assert) - : m_data(internal::constructor_without_unaligned_array_assert()) {} - DenseStorage(const DenseStorage& other) : m_data(other.m_data) {} - DenseStorage& operator=(const DenseStorage& other) - { - if (this != &other) m_data = other.m_data; - return *this; - } - DenseStorage(DenseIndex,DenseIndex,DenseIndex) {} - void swap(DenseStorage& other) { std::swap(m_data,other.m_data); } - static DenseIndex rows(void) {return _Rows;} - static DenseIndex cols(void) {return _Cols;} - void conservativeResize(DenseIndex,DenseIndex,DenseIndex) {} - void resize(DenseIndex,DenseIndex,DenseIndex) {} - const T *data() const { return m_data.array; } - T *data() { return m_data.array; } -}; - -// null matrix -template class DenseStorage -{ - public: - DenseStorage() {} - DenseStorage(internal::constructor_without_unaligned_array_assert) {} - DenseStorage(const DenseStorage&) {} - DenseStorage& operator=(const DenseStorage&) { return *this; } - DenseStorage(DenseIndex,DenseIndex,DenseIndex) {} - void swap(DenseStorage& ) {} - static DenseIndex rows(void) {return _Rows;} - static DenseIndex cols(void) {return _Cols;} - void conservativeResize(DenseIndex,DenseIndex,DenseIndex) {} - void resize(DenseIndex,DenseIndex,DenseIndex) {} - const T *data() const { return 0; } - T *data() { return 0; } -}; - -// more specializations for null matrices; these are necessary to resolve ambiguities -template class DenseStorage -: public DenseStorage { }; - -template class DenseStorage -: public DenseStorage { }; - -template class DenseStorage -: public DenseStorage { }; - -// dynamic-size matrix with fixed-size storage -template class DenseStorage -{ - internal::plain_array m_data; - DenseIndex m_rows; - DenseIndex m_cols; - public: - DenseStorage() : m_rows(0), m_cols(0) {} - DenseStorage(internal::constructor_without_unaligned_array_assert) - : m_data(internal::constructor_without_unaligned_array_assert()), m_rows(0), m_cols(0) {} - DenseStorage(const DenseStorage& other) : m_data(other.m_data), m_rows(other.m_rows), m_cols(other.m_cols) {} - DenseStorage& operator=(const DenseStorage& other) - { - if (this != &other) - { - m_data = other.m_data; - m_rows = other.m_rows; - m_cols = other.m_cols; - } - return *this; - } - DenseStorage(DenseIndex, DenseIndex nbRows, DenseIndex nbCols) : m_rows(nbRows), m_cols(nbCols) {} - void swap(DenseStorage& other) - { std::swap(m_data,other.m_data); std::swap(m_rows,other.m_rows); std::swap(m_cols,other.m_cols); } - DenseIndex rows() const {return m_rows;} - DenseIndex cols() const {return m_cols;} - void conservativeResize(DenseIndex, DenseIndex nbRows, DenseIndex nbCols) { m_rows = nbRows; m_cols = nbCols; } - void resize(DenseIndex, DenseIndex nbRows, DenseIndex nbCols) { m_rows = nbRows; m_cols = nbCols; } - const T *data() const { return m_data.array; } - T *data() { return m_data.array; } -}; - -// dynamic-size matrix with fixed-size storage and fixed width -template class DenseStorage -{ - internal::plain_array m_data; - DenseIndex m_rows; - public: - DenseStorage() : m_rows(0) {} - DenseStorage(internal::constructor_without_unaligned_array_assert) - : m_data(internal::constructor_without_unaligned_array_assert()), m_rows(0) {} - DenseStorage(const DenseStorage& other) : m_data(other.m_data), m_rows(other.m_rows) {} - DenseStorage& operator=(const DenseStorage& other) - { - if (this != &other) - { - m_data = other.m_data; - m_rows = other.m_rows; - } - return *this; - } - DenseStorage(DenseIndex, DenseIndex nbRows, DenseIndex) : m_rows(nbRows) {} - void swap(DenseStorage& other) { std::swap(m_data,other.m_data); std::swap(m_rows,other.m_rows); } - DenseIndex rows(void) const {return m_rows;} - DenseIndex cols(void) const {return _Cols;} - void conservativeResize(DenseIndex, DenseIndex nbRows, DenseIndex) { m_rows = nbRows; } - void resize(DenseIndex, DenseIndex nbRows, DenseIndex) { m_rows = nbRows; } - const T *data() const { return m_data.array; } - T *data() { return m_data.array; } -}; - -// dynamic-size matrix with fixed-size storage and fixed height -template class DenseStorage -{ - internal::plain_array m_data; - DenseIndex m_cols; - public: - DenseStorage() : m_cols(0) {} - DenseStorage(internal::constructor_without_unaligned_array_assert) - : m_data(internal::constructor_without_unaligned_array_assert()), m_cols(0) {} - DenseStorage(const DenseStorage& other) : m_data(other.m_data), m_cols(other.m_cols) {} - DenseStorage& operator=(const DenseStorage& other) - { - if (this != &other) - { - m_data = other.m_data; - m_cols = other.m_cols; - } - return *this; - } - DenseStorage(DenseIndex, DenseIndex, DenseIndex nbCols) : m_cols(nbCols) {} - void swap(DenseStorage& other) { std::swap(m_data,other.m_data); std::swap(m_cols,other.m_cols); } - DenseIndex rows(void) const {return _Rows;} - DenseIndex cols(void) const {return m_cols;} - void conservativeResize(DenseIndex, DenseIndex, DenseIndex nbCols) { m_cols = nbCols; } - void resize(DenseIndex, DenseIndex, DenseIndex nbCols) { m_cols = nbCols; } - const T *data() const { return m_data.array; } - T *data() { return m_data.array; } -}; - -// purely dynamic matrix. -template class DenseStorage -{ - T *m_data; - DenseIndex m_rows; - DenseIndex m_cols; - public: - DenseStorage() : m_data(0), m_rows(0), m_cols(0) {} - DenseStorage(internal::constructor_without_unaligned_array_assert) - : m_data(0), m_rows(0), m_cols(0) {} - DenseStorage(DenseIndex size, DenseIndex nbRows, DenseIndex nbCols) - : m_data(internal::conditional_aligned_new_auto(size)), m_rows(nbRows), m_cols(nbCols) - { IMP_EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN } -#ifdef IMP_EIGEN_HAVE_RVALUE_REFERENCES - DenseStorage(DenseStorage&& other) - : m_data(std::move(other.m_data)) - , m_rows(std::move(other.m_rows)) - , m_cols(std::move(other.m_cols)) - { - other.m_data = nullptr; - } - DenseStorage& operator=(DenseStorage&& other) - { - using std::swap; - swap(m_data, other.m_data); - swap(m_rows, other.m_rows); - swap(m_cols, other.m_cols); - return *this; - } -#endif - ~DenseStorage() { internal::conditional_aligned_delete_auto(m_data, m_rows*m_cols); } - void swap(DenseStorage& other) - { std::swap(m_data,other.m_data); std::swap(m_rows,other.m_rows); std::swap(m_cols,other.m_cols); } - DenseIndex rows(void) const {return m_rows;} - DenseIndex cols(void) const {return m_cols;} - void conservativeResize(DenseIndex size, DenseIndex nbRows, DenseIndex nbCols) - { - m_data = internal::conditional_aligned_realloc_new_auto(m_data, size, m_rows*m_cols); - m_rows = nbRows; - m_cols = nbCols; - } - void resize(DenseIndex size, DenseIndex nbRows, DenseIndex nbCols) - { - if(size != m_rows*m_cols) - { - internal::conditional_aligned_delete_auto(m_data, m_rows*m_cols); - if (size) - m_data = internal::conditional_aligned_new_auto(size); - else - m_data = 0; - IMP_EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN - } - m_rows = nbRows; - m_cols = nbCols; - } - const T *data() const { return m_data; } - T *data() { return m_data; } - private: - DenseStorage(const DenseStorage&); - DenseStorage& operator=(const DenseStorage&); -}; - -// matrix with dynamic width and fixed height (so that matrix has dynamic size). -template class DenseStorage -{ - T *m_data; - DenseIndex m_cols; - public: - DenseStorage() : m_data(0), m_cols(0) {} - DenseStorage(internal::constructor_without_unaligned_array_assert) : m_data(0), m_cols(0) {} - DenseStorage(DenseIndex size, DenseIndex, DenseIndex nbCols) : m_data(internal::conditional_aligned_new_auto(size)), m_cols(nbCols) - { IMP_EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN } -#ifdef IMP_EIGEN_HAVE_RVALUE_REFERENCES - DenseStorage(DenseStorage&& other) - : m_data(std::move(other.m_data)) - , m_cols(std::move(other.m_cols)) - { - other.m_data = nullptr; - } - DenseStorage& operator=(DenseStorage&& other) - { - using std::swap; - swap(m_data, other.m_data); - swap(m_cols, other.m_cols); - return *this; - } -#endif - ~DenseStorage() { internal::conditional_aligned_delete_auto(m_data, _Rows*m_cols); } - void swap(DenseStorage& other) { std::swap(m_data,other.m_data); std::swap(m_cols,other.m_cols); } - static DenseIndex rows(void) {return _Rows;} - DenseIndex cols(void) const {return m_cols;} - void conservativeResize(DenseIndex size, DenseIndex, DenseIndex nbCols) - { - m_data = internal::conditional_aligned_realloc_new_auto(m_data, size, _Rows*m_cols); - m_cols = nbCols; - } - IMP_EIGEN_STRONG_INLINE void resize(DenseIndex size, DenseIndex, DenseIndex nbCols) - { - if(size != _Rows*m_cols) - { - internal::conditional_aligned_delete_auto(m_data, _Rows*m_cols); - if (size) - m_data = internal::conditional_aligned_new_auto(size); - else - m_data = 0; - IMP_EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN - } - m_cols = nbCols; - } - const T *data() const { return m_data; } - T *data() { return m_data; } - private: - DenseStorage(const DenseStorage&); - DenseStorage& operator=(const DenseStorage&); -}; - -// matrix with dynamic height and fixed width (so that matrix has dynamic size). -template class DenseStorage -{ - T *m_data; - DenseIndex m_rows; - public: - DenseStorage() : m_data(0), m_rows(0) {} - DenseStorage(internal::constructor_without_unaligned_array_assert) : m_data(0), m_rows(0) {} - DenseStorage(DenseIndex size, DenseIndex nbRows, DenseIndex) : m_data(internal::conditional_aligned_new_auto(size)), m_rows(nbRows) - { IMP_EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN } -#ifdef IMP_EIGEN_HAVE_RVALUE_REFERENCES - DenseStorage(DenseStorage&& other) - : m_data(std::move(other.m_data)) - , m_rows(std::move(other.m_rows)) - { - other.m_data = nullptr; - } - DenseStorage& operator=(DenseStorage&& other) - { - using std::swap; - swap(m_data, other.m_data); - swap(m_rows, other.m_rows); - return *this; - } -#endif - ~DenseStorage() { internal::conditional_aligned_delete_auto(m_data, _Cols*m_rows); } - void swap(DenseStorage& other) { std::swap(m_data,other.m_data); std::swap(m_rows,other.m_rows); } - DenseIndex rows(void) const {return m_rows;} - static DenseIndex cols(void) {return _Cols;} - void conservativeResize(DenseIndex size, DenseIndex nbRows, DenseIndex) - { - m_data = internal::conditional_aligned_realloc_new_auto(m_data, size, m_rows*_Cols); - m_rows = nbRows; - } - IMP_EIGEN_STRONG_INLINE void resize(DenseIndex size, DenseIndex nbRows, DenseIndex) - { - if(size != m_rows*_Cols) - { - internal::conditional_aligned_delete_auto(m_data, _Cols*m_rows); - if (size) - m_data = internal::conditional_aligned_new_auto(size); - else - m_data = 0; - IMP_EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN - } - m_rows = nbRows; - } - const T *data() const { return m_data; } - T *data() { return m_data; } - private: - DenseStorage(const DenseStorage&); - DenseStorage& operator=(const DenseStorage&); -}; - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_MATRIX_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/Diagonal.h b/modules/algebra/include/eigen3/Eigen/src/Core/Diagonal.h deleted file mode 100644 index 7102525faf..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/Diagonal.h +++ /dev/null @@ -1,237 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2007-2009 Benoit Jacob -// Copyright (C) 2009-2010 Gael Guennebaud -// -// 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 IMP_EIGEN_DIAGONAL_H -#define IMP_EIGEN_DIAGONAL_H - -namespace IMP_Eigen { - -/** \class Diagonal - * \ingroup Core_Module - * - * \brief Expression of a diagonal/subdiagonal/superdiagonal in a matrix - * - * \param MatrixType the type of the object in which we are taking a sub/main/super diagonal - * \param DiagIndex the index of the sub/super diagonal. The default is 0 and it means the main diagonal. - * A positive value means a superdiagonal, a negative value means a subdiagonal. - * You can also use Dynamic so the index can be set at runtime. - * - * The matrix is not required to be square. - * - * This class represents an expression of the main diagonal, or any sub/super diagonal - * of a square matrix. It is the return type of MatrixBase::diagonal() and MatrixBase::diagonal(Index) and most of the - * time this is the only way it is used. - * - * \sa MatrixBase::diagonal(), MatrixBase::diagonal(Index) - */ - -namespace internal { -template -struct traits > - : traits -{ - typedef typename nested::type MatrixTypeNested; - typedef typename remove_reference::type _MatrixTypeNested; - typedef typename MatrixType::StorageKind StorageKind; - enum { - RowsAtCompileTime = (int(DiagIndex) == DynamicIndex || int(MatrixType::SizeAtCompileTime) == Dynamic) ? Dynamic - : (IMP_EIGEN_PLAIN_ENUM_MIN(MatrixType::RowsAtCompileTime - IMP_EIGEN_PLAIN_ENUM_MAX(-DiagIndex, 0), - MatrixType::ColsAtCompileTime - IMP_EIGEN_PLAIN_ENUM_MAX( DiagIndex, 0))), - ColsAtCompileTime = 1, - MaxRowsAtCompileTime = int(MatrixType::MaxSizeAtCompileTime) == Dynamic ? Dynamic - : DiagIndex == DynamicIndex ? IMP_EIGEN_SIZE_MIN_PREFER_FIXED(MatrixType::MaxRowsAtCompileTime, - MatrixType::MaxColsAtCompileTime) - : (IMP_EIGEN_PLAIN_ENUM_MIN(MatrixType::MaxRowsAtCompileTime - IMP_EIGEN_PLAIN_ENUM_MAX(-DiagIndex, 0), - MatrixType::MaxColsAtCompileTime - IMP_EIGEN_PLAIN_ENUM_MAX( DiagIndex, 0))), - MaxColsAtCompileTime = 1, - MaskLvalueBit = is_lvalue::value ? LvalueBit : 0, - Flags = (unsigned int)_MatrixTypeNested::Flags & (HereditaryBits | LinearAccessBit | MaskLvalueBit | DirectAccessBit) & ~RowMajorBit, - CoeffReadCost = _MatrixTypeNested::CoeffReadCost, - MatrixTypeOuterStride = outer_stride_at_compile_time::ret, - InnerStrideAtCompileTime = MatrixTypeOuterStride == Dynamic ? Dynamic : MatrixTypeOuterStride+1, - OuterStrideAtCompileTime = 0 - }; -}; -} - -template class Diagonal - : public internal::dense_xpr_base< Diagonal >::type -{ - public: - - enum { DiagIndex = _DiagIndex }; - typedef typename internal::dense_xpr_base::type Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(Diagonal) - - inline Diagonal(MatrixType& matrix, Index a_index = DiagIndex) : m_matrix(matrix), m_index(a_index) {} - - IMP_EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Diagonal) - - inline Index rows() const - { return m_index.value()<0 ? (std::min)(m_matrix.cols(),m_matrix.rows()+m_index.value()) : (std::min)(m_matrix.rows(),m_matrix.cols()-m_index.value()); } - - inline Index cols() const { return 1; } - - inline Index innerStride() const - { - return m_matrix.outerStride() + 1; - } - - inline Index outerStride() const - { - return 0; - } - - typedef typename internal::conditional< - internal::is_lvalue::value, - Scalar, - const Scalar - >::type ScalarWithConstIfNotLvalue; - - inline ScalarWithConstIfNotLvalue* data() { return &(m_matrix.const_cast_derived().coeffRef(rowOffset(), colOffset())); } - inline const Scalar* data() const { return &(m_matrix.const_cast_derived().coeffRef(rowOffset(), colOffset())); } - - inline Scalar& coeffRef(Index row, Index) - { - IMP_EIGEN_STATIC_ASSERT_LVALUE(MatrixType) - return m_matrix.const_cast_derived().coeffRef(row+rowOffset(), row+colOffset()); - } - - inline const Scalar& coeffRef(Index row, Index) const - { - return m_matrix.const_cast_derived().coeffRef(row+rowOffset(), row+colOffset()); - } - - inline CoeffReturnType coeff(Index row, Index) const - { - return m_matrix.coeff(row+rowOffset(), row+colOffset()); - } - - inline Scalar& coeffRef(Index idx) - { - IMP_EIGEN_STATIC_ASSERT_LVALUE(MatrixType) - return m_matrix.const_cast_derived().coeffRef(idx+rowOffset(), idx+colOffset()); - } - - inline const Scalar& coeffRef(Index idx) const - { - return m_matrix.const_cast_derived().coeffRef(idx+rowOffset(), idx+colOffset()); - } - - inline CoeffReturnType coeff(Index idx) const - { - return m_matrix.coeff(idx+rowOffset(), idx+colOffset()); - } - - const typename internal::remove_all::type& - nestedExpression() const - { - return m_matrix; - } - - int index() const - { - return m_index.value(); - } - - protected: - typename MatrixType::Nested m_matrix; - const internal::variable_if_dynamicindex m_index; - - private: - // some compilers may fail to optimize std::max etc in case of compile-time constants... - IMP_EIGEN_STRONG_INLINE Index absDiagIndex() const { return m_index.value()>0 ? m_index.value() : -m_index.value(); } - IMP_EIGEN_STRONG_INLINE Index rowOffset() const { return m_index.value()>0 ? 0 : -m_index.value(); } - IMP_EIGEN_STRONG_INLINE Index colOffset() const { return m_index.value()>0 ? m_index.value() : 0; } - // triger a compile time error is someone try to call packet - template typename MatrixType::PacketReturnType packet(Index) const; - template typename MatrixType::PacketReturnType packet(Index,Index) const; -}; - -/** \returns an expression of the main diagonal of the matrix \c *this - * - * \c *this is not required to be square. - * - * Example: \include MatrixBase_diagonal.cpp - * Output: \verbinclude MatrixBase_diagonal.out - * - * \sa class Diagonal */ -template -inline typename MatrixBase::DiagonalReturnType -MatrixBase::diagonal() -{ - return derived(); -} - -/** This is the const version of diagonal(). */ -template -inline typename MatrixBase::ConstDiagonalReturnType -MatrixBase::diagonal() const -{ - return ConstDiagonalReturnType(derived()); -} - -/** \returns an expression of the \a DiagIndex-th sub or super diagonal of the matrix \c *this - * - * \c *this is not required to be square. - * - * The template parameter \a DiagIndex represent a super diagonal if \a DiagIndex > 0 - * and a sub diagonal otherwise. \a DiagIndex == 0 is equivalent to the main diagonal. - * - * Example: \include MatrixBase_diagonal_int.cpp - * Output: \verbinclude MatrixBase_diagonal_int.out - * - * \sa MatrixBase::diagonal(), class Diagonal */ -template -inline typename MatrixBase::DiagonalDynamicIndexReturnType -MatrixBase::diagonal(Index index) -{ - return DiagonalDynamicIndexReturnType(derived(), index); -} - -/** This is the const version of diagonal(Index). */ -template -inline typename MatrixBase::ConstDiagonalDynamicIndexReturnType -MatrixBase::diagonal(Index index) const -{ - return ConstDiagonalDynamicIndexReturnType(derived(), index); -} - -/** \returns an expression of the \a DiagIndex-th sub or super diagonal of the matrix \c *this - * - * \c *this is not required to be square. - * - * The template parameter \a DiagIndex represent a super diagonal if \a DiagIndex > 0 - * and a sub diagonal otherwise. \a DiagIndex == 0 is equivalent to the main diagonal. - * - * Example: \include MatrixBase_diagonal_template_int.cpp - * Output: \verbinclude MatrixBase_diagonal_template_int.out - * - * \sa MatrixBase::diagonal(), class Diagonal */ -template -template -inline typename MatrixBase::template DiagonalIndexReturnType::Type -MatrixBase::diagonal() -{ - return derived(); -} - -/** This is the const version of diagonal(). */ -template -template -inline typename MatrixBase::template ConstDiagonalIndexReturnType::Type -MatrixBase::diagonal() const -{ - return derived(); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_DIAGONAL_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/DiagonalMatrix.h b/modules/algebra/include/eigen3/Eigen/src/Core/DiagonalMatrix.h deleted file mode 100644 index b857b00916..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/DiagonalMatrix.h +++ /dev/null @@ -1,313 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2009 Gael Guennebaud -// Copyright (C) 2007-2009 Benoit Jacob -// -// 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 IMP_EIGEN_DIAGONALMATRIX_H -#define IMP_EIGEN_DIAGONALMATRIX_H - -namespace IMP_Eigen { - -#ifndef IMP_EIGEN_PARSED_BY_DOXYGEN -template -class DiagonalBase : public EigenBase -{ - public: - typedef typename internal::traits::DiagonalVectorType DiagonalVectorType; - typedef typename DiagonalVectorType::Scalar Scalar; - typedef typename DiagonalVectorType::RealScalar RealScalar; - typedef typename internal::traits::StorageKind StorageKind; - typedef typename internal::traits::Index Index; - - enum { - RowsAtCompileTime = DiagonalVectorType::SizeAtCompileTime, - ColsAtCompileTime = DiagonalVectorType::SizeAtCompileTime, - MaxRowsAtCompileTime = DiagonalVectorType::MaxSizeAtCompileTime, - MaxColsAtCompileTime = DiagonalVectorType::MaxSizeAtCompileTime, - IsVectorAtCompileTime = 0, - Flags = 0 - }; - - typedef Matrix DenseMatrixType; - typedef DenseMatrixType DenseType; - typedef DiagonalMatrix PlainObject; - - inline const Derived& derived() const { return *static_cast(this); } - inline Derived& derived() { return *static_cast(this); } - - DenseMatrixType toDenseMatrix() const { return derived(); } - template - void evalTo(MatrixBase &other) const; - template - inline void addTo(MatrixBase &other) const - { other.diagonal() += diagonal(); } - template - inline void subTo(MatrixBase &other) const - { other.diagonal() -= diagonal(); } - - inline const DiagonalVectorType& diagonal() const { return derived().diagonal(); } - inline DiagonalVectorType& diagonal() { return derived().diagonal(); } - - inline Index rows() const { return diagonal().size(); } - inline Index cols() const { return diagonal().size(); } - - /** \returns the diagonal matrix product of \c *this by the matrix \a matrix. - */ - template - const DiagonalProduct - operator*(const MatrixBase &matrix) const - { - return DiagonalProduct(matrix.derived(), derived()); - } - - inline const DiagonalWrapper, const DiagonalVectorType> > - inverse() const - { - return diagonal().cwiseInverse(); - } - - inline const DiagonalWrapper, const DiagonalVectorType> > - operator*(const Scalar& scalar) const - { - return diagonal() * scalar; - } - friend inline const DiagonalWrapper, const DiagonalVectorType> > - operator*(const Scalar& scalar, const DiagonalBase& other) - { - return other.diagonal() * scalar; - } - - #ifdef IMP_EIGEN2_SUPPORT - template - bool isApprox(const DiagonalBase& other, typename NumTraits::Real precision = NumTraits::dummy_precision()) const - { - return diagonal().isApprox(other.diagonal(), precision); - } - template - bool isApprox(const MatrixBase& other, typename NumTraits::Real precision = NumTraits::dummy_precision()) const - { - return toDenseMatrix().isApprox(other, precision); - } - #endif -}; - -template -template -inline void DiagonalBase::evalTo(MatrixBase &other) const -{ - other.setZero(); - other.diagonal() = diagonal(); -} -#endif - -/** \class DiagonalMatrix - * \ingroup Core_Module - * - * \brief Represents a diagonal matrix with its storage - * - * \param _Scalar the type of coefficients - * \param SizeAtCompileTime the dimension of the matrix, or Dynamic - * \param MaxSizeAtCompileTime the dimension of the matrix, or Dynamic. This parameter is optional and defaults - * to SizeAtCompileTime. Most of the time, you do not need to specify it. - * - * \sa class DiagonalWrapper - */ - -namespace internal { -template -struct traits > - : traits > -{ - typedef Matrix<_Scalar,SizeAtCompileTime,1,0,MaxSizeAtCompileTime,1> DiagonalVectorType; - typedef Dense StorageKind; - typedef DenseIndex Index; - enum { - Flags = LvalueBit - }; -}; -} -template -class DiagonalMatrix - : public DiagonalBase > -{ - public: - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - typedef typename internal::traits::DiagonalVectorType DiagonalVectorType; - typedef const DiagonalMatrix& Nested; - typedef _Scalar Scalar; - typedef typename internal::traits::StorageKind StorageKind; - typedef typename internal::traits::Index Index; - #endif - - protected: - - DiagonalVectorType m_diagonal; - - public: - - /** const version of diagonal(). */ - inline const DiagonalVectorType& diagonal() const { return m_diagonal; } - /** \returns a reference to the stored vector of diagonal coefficients. */ - inline DiagonalVectorType& diagonal() { return m_diagonal; } - - /** Default constructor without initialization */ - inline DiagonalMatrix() {} - - /** Constructs a diagonal matrix with given dimension */ - inline DiagonalMatrix(Index dim) : m_diagonal(dim) {} - - /** 2D constructor. */ - inline DiagonalMatrix(const Scalar& x, const Scalar& y) : m_diagonal(x,y) {} - - /** 3D constructor. */ - inline DiagonalMatrix(const Scalar& x, const Scalar& y, const Scalar& z) : m_diagonal(x,y,z) {} - - /** Copy constructor. */ - template - inline DiagonalMatrix(const DiagonalBase& other) : m_diagonal(other.diagonal()) {} - - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - /** copy constructor. prevent a default copy constructor from hiding the other templated constructor */ - inline DiagonalMatrix(const DiagonalMatrix& other) : m_diagonal(other.diagonal()) {} - #endif - - /** generic constructor from expression of the diagonal coefficients */ - template - explicit inline DiagonalMatrix(const MatrixBase& other) : m_diagonal(other) - {} - - /** Copy operator. */ - template - DiagonalMatrix& operator=(const DiagonalBase& other) - { - m_diagonal = other.diagonal(); - return *this; - } - - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - /** This is a special case of the templated operator=. Its purpose is to - * prevent a default operator= from hiding the templated operator=. - */ - DiagonalMatrix& operator=(const DiagonalMatrix& other) - { - m_diagonal = other.diagonal(); - return *this; - } - #endif - - /** Resizes to given size. */ - inline void resize(Index size) { m_diagonal.resize(size); } - /** Sets all coefficients to zero. */ - inline void setZero() { m_diagonal.setZero(); } - /** Resizes and sets all coefficients to zero. */ - inline void setZero(Index size) { m_diagonal.setZero(size); } - /** Sets this matrix to be the identity matrix of the current size. */ - inline void setIdentity() { m_diagonal.setOnes(); } - /** Sets this matrix to be the identity matrix of the given size. */ - inline void setIdentity(Index size) { m_diagonal.setOnes(size); } -}; - -/** \class DiagonalWrapper - * \ingroup Core_Module - * - * \brief Expression of a diagonal matrix - * - * \param _DiagonalVectorType the type of the vector of diagonal coefficients - * - * This class is an expression of a diagonal matrix, but not storing its own vector of diagonal coefficients, - * instead wrapping an existing vector expression. It is the return type of MatrixBase::asDiagonal() - * and most of the time this is the only way that it is used. - * - * \sa class DiagonalMatrix, class DiagonalBase, MatrixBase::asDiagonal() - */ - -namespace internal { -template -struct traits > -{ - typedef _DiagonalVectorType DiagonalVectorType; - typedef typename DiagonalVectorType::Scalar Scalar; - typedef typename DiagonalVectorType::Index Index; - typedef typename DiagonalVectorType::StorageKind StorageKind; - enum { - RowsAtCompileTime = DiagonalVectorType::SizeAtCompileTime, - ColsAtCompileTime = DiagonalVectorType::SizeAtCompileTime, - MaxRowsAtCompileTime = DiagonalVectorType::SizeAtCompileTime, - MaxColsAtCompileTime = DiagonalVectorType::SizeAtCompileTime, - Flags = traits::Flags & LvalueBit - }; -}; -} - -template -class DiagonalWrapper - : public DiagonalBase >, internal::no_assignment_operator -{ - public: - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - typedef _DiagonalVectorType DiagonalVectorType; - typedef DiagonalWrapper Nested; - #endif - - /** Constructor from expression of diagonal coefficients to wrap. */ - inline DiagonalWrapper(DiagonalVectorType& a_diagonal) : m_diagonal(a_diagonal) {} - - /** \returns a const reference to the wrapped expression of diagonal coefficients. */ - const DiagonalVectorType& diagonal() const { return m_diagonal; } - - protected: - typename DiagonalVectorType::Nested m_diagonal; -}; - -/** \returns a pseudo-expression of a diagonal matrix with *this as vector of diagonal coefficients - * - * \only_for_vectors - * - * Example: \include MatrixBase_asDiagonal.cpp - * Output: \verbinclude MatrixBase_asDiagonal.out - * - * \sa class DiagonalWrapper, class DiagonalMatrix, diagonal(), isDiagonal() - **/ -template -inline const DiagonalWrapper -MatrixBase::asDiagonal() const -{ - return derived(); -} - -/** \returns true if *this is approximately equal to a diagonal matrix, - * within the precision given by \a prec. - * - * Example: \include MatrixBase_isDiagonal.cpp - * Output: \verbinclude MatrixBase_isDiagonal.out - * - * \sa asDiagonal() - */ -template -bool MatrixBase::isDiagonal(const RealScalar& prec) const -{ - using std::abs; - if(cols() != rows()) return false; - RealScalar maxAbsOnDiagonal = static_cast(-1); - for(Index j = 0; j < cols(); ++j) - { - RealScalar absOnDiagonal = abs(coeff(j,j)); - if(absOnDiagonal > maxAbsOnDiagonal) maxAbsOnDiagonal = absOnDiagonal; - } - for(Index j = 0; j < cols(); ++j) - for(Index i = 0; i < j; ++i) - { - if(!internal::isMuchSmallerThan(coeff(i, j), maxAbsOnDiagonal, prec)) return false; - if(!internal::isMuchSmallerThan(coeff(j, i), maxAbsOnDiagonal, prec)) return false; - } - return true; -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_DIAGONALMATRIX_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/DiagonalProduct.h b/modules/algebra/include/eigen3/Eigen/src/Core/DiagonalProduct.h deleted file mode 100644 index 5d928e01c6..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/DiagonalProduct.h +++ /dev/null @@ -1,131 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008 Gael Guennebaud -// Copyright (C) 2007-2009 Benoit Jacob -// -// 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 IMP_EIGEN_DIAGONALPRODUCT_H -#define IMP_EIGEN_DIAGONALPRODUCT_H - -namespace IMP_Eigen { - -namespace internal { -template -struct traits > - : traits -{ - typedef typename scalar_product_traits::ReturnType Scalar; - enum { - RowsAtCompileTime = MatrixType::RowsAtCompileTime, - ColsAtCompileTime = MatrixType::ColsAtCompileTime, - MaxRowsAtCompileTime = MatrixType::MaxRowsAtCompileTime, - MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime, - - _StorageOrder = MatrixType::Flags & RowMajorBit ? RowMajor : ColMajor, - _ScalarAccessOnDiag = !((int(_StorageOrder) == ColMajor && int(ProductOrder) == OnTheLeft) - ||(int(_StorageOrder) == RowMajor && int(ProductOrder) == OnTheRight)), - _SameTypes = is_same::value, - // FIXME currently we need same types, but in the future the next rule should be the one - //_Vectorizable = bool(int(MatrixType::Flags)&PacketAccessBit) && ((!_PacketOnDiag) || (_SameTypes && bool(int(DiagonalType::DiagonalVectorType::Flags)&PacketAccessBit))), - _Vectorizable = bool(int(MatrixType::Flags)&PacketAccessBit) && _SameTypes && (_ScalarAccessOnDiag || (bool(int(DiagonalType::DiagonalVectorType::Flags)&PacketAccessBit))), - _LinearAccessMask = (RowsAtCompileTime==1 || ColsAtCompileTime==1) ? LinearAccessBit : 0, - - Flags = ((HereditaryBits|_LinearAccessMask|AlignedBit) & (unsigned int)(MatrixType::Flags)) | (_Vectorizable ? PacketAccessBit : 0),//(int(MatrixType::Flags)&int(DiagonalType::DiagonalVectorType::Flags)&AlignedBit), - Cost0 = IMP_EIGEN_ADD_COST(NumTraits::MulCost, MatrixType::CoeffReadCost), - CoeffReadCost = IMP_EIGEN_ADD_COST(Cost0,DiagonalType::DiagonalVectorType::CoeffReadCost) - }; -}; -} - -template -class DiagonalProduct : internal::no_assignment_operator, - public MatrixBase > -{ - public: - - typedef MatrixBase Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(DiagonalProduct) - - inline DiagonalProduct(const MatrixType& matrix, const DiagonalType& diagonal) - : m_matrix(matrix), m_diagonal(diagonal) - { - imp_eigen_assert(diagonal.diagonal().size() == (ProductOrder == OnTheLeft ? matrix.rows() : matrix.cols())); - } - - IMP_EIGEN_STRONG_INLINE Index rows() const { return m_matrix.rows(); } - IMP_EIGEN_STRONG_INLINE Index cols() const { return m_matrix.cols(); } - - IMP_EIGEN_STRONG_INLINE const Scalar coeff(Index row, Index col) const - { - return m_diagonal.diagonal().coeff(ProductOrder == OnTheLeft ? row : col) * m_matrix.coeff(row, col); - } - - IMP_EIGEN_STRONG_INLINE const Scalar coeff(Index idx) const - { - enum { - StorageOrder = int(MatrixType::Flags) & RowMajorBit ? RowMajor : ColMajor - }; - return coeff(int(StorageOrder)==ColMajor?idx:0,int(StorageOrder)==ColMajor?0:idx); - } - - template - IMP_EIGEN_STRONG_INLINE PacketScalar packet(Index row, Index col) const - { - enum { - StorageOrder = Flags & RowMajorBit ? RowMajor : ColMajor - }; - const Index indexInDiagonalVector = ProductOrder == OnTheLeft ? row : col; - return packet_impl(row,col,indexInDiagonalVector,typename internal::conditional< - ((int(StorageOrder) == RowMajor && int(ProductOrder) == OnTheLeft) - ||(int(StorageOrder) == ColMajor && int(ProductOrder) == OnTheRight)), internal::true_type, internal::false_type>::type()); - } - - template - IMP_EIGEN_STRONG_INLINE PacketScalar packet(Index idx) const - { - enum { - StorageOrder = int(MatrixType::Flags) & RowMajorBit ? RowMajor : ColMajor - }; - return packet(int(StorageOrder)==ColMajor?idx:0,int(StorageOrder)==ColMajor?0:idx); - } - - protected: - template - IMP_EIGEN_STRONG_INLINE PacketScalar packet_impl(Index row, Index col, Index id, internal::true_type) const - { - return internal::pmul(m_matrix.template packet(row, col), - internal::pset1(m_diagonal.diagonal().coeff(id))); - } - - template - IMP_EIGEN_STRONG_INLINE PacketScalar packet_impl(Index row, Index col, Index id, internal::false_type) const - { - enum { - InnerSize = (MatrixType::Flags & RowMajorBit) ? MatrixType::ColsAtCompileTime : MatrixType::RowsAtCompileTime, - DiagonalVectorPacketLoadMode = (LoadMode == Aligned && (((InnerSize%16) == 0) || (int(DiagonalType::DiagonalVectorType::Flags)&AlignedBit)==AlignedBit) ? Aligned : Unaligned) - }; - return internal::pmul(m_matrix.template packet(row, col), - m_diagonal.diagonal().template packet(id)); - } - - typename MatrixType::Nested m_matrix; - typename DiagonalType::Nested m_diagonal; -}; - -/** \returns the diagonal matrix product of \c *this by the diagonal matrix \a diagonal. - */ -template -template -inline const DiagonalProduct -MatrixBase::operator*(const DiagonalBase &a_diagonal) const -{ - return DiagonalProduct(derived(), a_diagonal.derived()); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_DIAGONALPRODUCT_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/Dot.h b/modules/algebra/include/eigen3/Eigen/src/Core/Dot.h deleted file mode 100644 index 08361be5ff..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/Dot.h +++ /dev/null @@ -1,263 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2006-2008, 2010 Benoit Jacob -// -// 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 IMP_EIGEN_DOT_H -#define IMP_EIGEN_DOT_H - -namespace IMP_Eigen { - -namespace internal { - -// helper function for dot(). The problem is that if we put that in the body of dot(), then upon calling dot -// with mismatched types, the compiler emits errors about failing to instantiate cwiseProduct BEFORE -// looking at the static assertions. Thus this is a trick to get better compile errors. -template -struct dot_nocheck -{ - typedef typename scalar_product_traits::Scalar,typename traits::Scalar>::ReturnType ResScalar; - static inline ResScalar run(const MatrixBase& a, const MatrixBase& b) - { - return a.template binaryExpr::Scalar,typename traits::Scalar> >(b).sum(); - } -}; - -template -struct dot_nocheck -{ - typedef typename scalar_product_traits::Scalar,typename traits::Scalar>::ReturnType ResScalar; - static inline ResScalar run(const MatrixBase& a, const MatrixBase& b) - { - return a.transpose().template binaryExpr::Scalar,typename traits::Scalar> >(b).sum(); - } -}; - -} // end namespace internal - -/** \returns the dot product of *this with other. - * - * \only_for_vectors - * - * \note If the scalar type is complex numbers, then this function returns the hermitian - * (sesquilinear) dot product, conjugate-linear in the first variable and linear in the - * second variable. - * - * \sa squaredNorm(), norm() - */ -template -template -inline typename internal::scalar_product_traits::Scalar,typename internal::traits::Scalar>::ReturnType -MatrixBase::dot(const MatrixBase& other) const -{ - IMP_EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived) - IMP_EIGEN_STATIC_ASSERT_VECTOR_ONLY(OtherDerived) - IMP_EIGEN_STATIC_ASSERT_SAME_VECTOR_SIZE(Derived,OtherDerived) - typedef internal::scalar_conj_product_op func; - IMP_EIGEN_CHECK_BINARY_COMPATIBILIY(func,Scalar,typename OtherDerived::Scalar); - - imp_eigen_assert(size() == other.size()); - - return internal::dot_nocheck::run(*this, other); -} - -#ifdef IMP_EIGEN2_SUPPORT -/** \returns the dot product of *this with other, with the Eigen2 convention that the dot product is linear in the first variable - * (conjugating the second variable). Of course this only makes a difference in the complex case. - * - * This method is only available in IMP_EIGEN2_SUPPORT mode. - * - * \only_for_vectors - * - * \sa dot() - */ -template -template -typename internal::traits::Scalar -MatrixBase::eigen2_dot(const MatrixBase& other) const -{ - IMP_EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived) - IMP_EIGEN_STATIC_ASSERT_VECTOR_ONLY(OtherDerived) - IMP_EIGEN_STATIC_ASSERT_SAME_VECTOR_SIZE(Derived,OtherDerived) - IMP_EIGEN_STATIC_ASSERT((internal::is_same::value), - YOU_MIXED_DIFFERENT_NUMERIC_TYPES__YOU_NEED_TO_USE_THE_CAST_METHOD_OF_MATRIXBASE_TO_CAST_NUMERIC_TYPES_EXPLICITLY) - - imp_eigen_assert(size() == other.size()); - - return internal::dot_nocheck::run(other,*this); -} -#endif - - -//---------- implementation of L2 norm and related functions ---------- - -/** \returns, for vectors, the squared \em l2 norm of \c *this, and for matrices the Frobenius norm. - * In both cases, it consists in the sum of the square of all the matrix entries. - * For vectors, this is also equals to the dot product of \c *this with itself. - * - * \sa dot(), norm() - */ -template -IMP_EIGEN_STRONG_INLINE typename NumTraits::Scalar>::Real MatrixBase::squaredNorm() const -{ - return numext::real((*this).cwiseAbs2().sum()); -} - -/** \returns, for vectors, the \em l2 norm of \c *this, and for matrices the Frobenius norm. - * In both cases, it consists in the square root of the sum of the square of all the matrix entries. - * For vectors, this is also equals to the square root of the dot product of \c *this with itself. - * - * \sa dot(), squaredNorm() - */ -template -inline typename NumTraits::Scalar>::Real MatrixBase::norm() const -{ - using std::sqrt; - return sqrt(squaredNorm()); -} - -/** \returns an expression of the quotient of *this by its own norm. - * - * \only_for_vectors - * - * \sa norm(), normalize() - */ -template -inline const typename MatrixBase::PlainObject -MatrixBase::normalized() const -{ - typedef typename internal::nested::type Nested; - typedef typename internal::remove_reference::type _Nested; - _Nested n(derived()); - return n / n.norm(); -} - -/** Normalizes the vector, i.e. divides it by its own norm. - * - * \only_for_vectors - * - * \sa norm(), normalized() - */ -template -inline void MatrixBase::normalize() -{ - *this /= norm(); -} - -//---------- implementation of other norms ---------- - -namespace internal { - -template -struct lpNorm_selector -{ - typedef typename NumTraits::Scalar>::Real RealScalar; - static inline RealScalar run(const MatrixBase& m) - { - using std::pow; - return pow(m.cwiseAbs().array().pow(p).sum(), RealScalar(1)/p); - } -}; - -template -struct lpNorm_selector -{ - static inline typename NumTraits::Scalar>::Real run(const MatrixBase& m) - { - return m.cwiseAbs().sum(); - } -}; - -template -struct lpNorm_selector -{ - static inline typename NumTraits::Scalar>::Real run(const MatrixBase& m) - { - return m.norm(); - } -}; - -template -struct lpNorm_selector -{ - static inline typename NumTraits::Scalar>::Real run(const MatrixBase& m) - { - return m.cwiseAbs().maxCoeff(); - } -}; - -} // end namespace internal - -/** \returns the \f$ \ell^p \f$ norm of *this, that is, returns the p-th root of the sum of the p-th powers of the absolute values - * of the coefficients of *this. If \a p is the special value \a IMP_Eigen::Infinity, this function returns the \f$ \ell^\infty \f$ - * norm, that is the maximum of the absolute values of the coefficients of *this. - * - * \sa norm() - */ -template -template -inline typename NumTraits::Scalar>::Real -MatrixBase::lpNorm() const -{ - return internal::lpNorm_selector::run(*this); -} - -//---------- implementation of isOrthogonal / isUnitary ---------- - -/** \returns true if *this is approximately orthogonal to \a other, - * within the precision given by \a prec. - * - * Example: \include MatrixBase_isOrthogonal.cpp - * Output: \verbinclude MatrixBase_isOrthogonal.out - */ -template -template -bool MatrixBase::isOrthogonal -(const MatrixBase& other, const RealScalar& prec) const -{ - typename internal::nested::type nested(derived()); - typename internal::nested::type otherNested(other.derived()); - return numext::abs2(nested.dot(otherNested)) <= prec * prec * nested.squaredNorm() * otherNested.squaredNorm(); -} - -/** \returns true if *this is approximately an unitary matrix, - * within the precision given by \a prec. In the case where the \a Scalar - * type is real numbers, a unitary matrix is an orthogonal matrix, whence the name. - * - * \note This can be used to check whether a family of vectors forms an orthonormal basis. - * Indeed, \c m.isUnitary() returns true if and only if the columns (equivalently, the rows) of m form an - * orthonormal basis. - * - * Example: \include MatrixBase_isUnitary.cpp - * Output: \verbinclude MatrixBase_isUnitary.out - */ -template -bool MatrixBase::isUnitary(const RealScalar& prec) const -{ - typename Derived::Nested nested(derived()); - for(Index i = 0; i < cols(); ++i) - { - if(!internal::isApprox(nested.col(i).squaredNorm(), static_cast(1), prec)) - return false; - for(Index j = 0; j < i; ++j) - if(!internal::isMuchSmallerThan(nested.col(i).dot(nested.col(j)), static_cast(1), prec)) - return false; - } - return true; -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_DOT_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/EigenBase.h b/modules/algebra/include/eigen3/Eigen/src/Core/EigenBase.h deleted file mode 100644 index ae98dd20af..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/EigenBase.h +++ /dev/null @@ -1,131 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2009 Benoit Jacob -// Copyright (C) 2009 Gael Guennebaud -// -// 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 IMP_EIGEN_EIGENBASE_H -#define IMP_EIGEN_EIGENBASE_H - -namespace IMP_Eigen { - -/** Common base class for all classes T such that MatrixBase has an operator=(T) and a constructor MatrixBase(T). - * - * In other words, an EigenBase object is an object that can be copied into a MatrixBase. - * - * Besides MatrixBase-derived classes, this also includes special matrix classes such as diagonal matrices, etc. - * - * Notice that this class is trivial, it is only used to disambiguate overloaded functions. - * - * \sa \ref TopicClassHierarchy - */ -template struct EigenBase -{ -// typedef typename internal::plain_matrix_type::type PlainObject; - - typedef typename internal::traits::StorageKind StorageKind; - typedef typename internal::traits::Index Index; - - /** \returns a reference to the derived object */ - Derived& derived() { return *static_cast(this); } - /** \returns a const reference to the derived object */ - const Derived& derived() const { return *static_cast(this); } - - inline Derived& const_cast_derived() const - { return *static_cast(const_cast(this)); } - inline const Derived& const_derived() const - { return *static_cast(this); } - - /** \returns the number of rows. \sa cols(), RowsAtCompileTime */ - inline Index rows() const { return derived().rows(); } - /** \returns the number of columns. \sa rows(), ColsAtCompileTime*/ - inline Index cols() const { return derived().cols(); } - /** \returns the number of coefficients, which is rows()*cols(). - * \sa rows(), cols(), SizeAtCompileTime. */ - inline Index size() const { return rows() * cols(); } - - /** \internal Don't use it, but do the equivalent: \code dst = *this; \endcode */ - template inline void evalTo(Dest& dst) const - { derived().evalTo(dst); } - - /** \internal Don't use it, but do the equivalent: \code dst += *this; \endcode */ - template inline void addTo(Dest& dst) const - { - // This is the default implementation, - // derived class can reimplement it in a more optimized way. - typename Dest::PlainObject res(rows(),cols()); - evalTo(res); - dst += res; - } - - /** \internal Don't use it, but do the equivalent: \code dst -= *this; \endcode */ - template inline void subTo(Dest& dst) const - { - // This is the default implementation, - // derived class can reimplement it in a more optimized way. - typename Dest::PlainObject res(rows(),cols()); - evalTo(res); - dst -= res; - } - - /** \internal Don't use it, but do the equivalent: \code dst.applyOnTheRight(*this); \endcode */ - template inline void applyThisOnTheRight(Dest& dst) const - { - // This is the default implementation, - // derived class can reimplement it in a more optimized way. - dst = dst * this->derived(); - } - - /** \internal Don't use it, but do the equivalent: \code dst.applyOnTheLeft(*this); \endcode */ - template inline void applyThisOnTheLeft(Dest& dst) const - { - // This is the default implementation, - // derived class can reimplement it in a more optimized way. - dst = this->derived() * dst; - } - -}; - -/*************************************************************************** -* Implementation of matrix base methods -***************************************************************************/ - -/** \brief Copies the generic expression \a other into *this. - * - * \details The expression must provide a (templated) evalTo(Derived& dst) const - * function which does the actual job. In practice, this allows any user to write - * its own special matrix without having to modify MatrixBase - * - * \returns a reference to *this. - */ -template -template -Derived& DenseBase::operator=(const EigenBase &other) -{ - other.derived().evalTo(derived()); - return derived(); -} - -template -template -Derived& DenseBase::operator+=(const EigenBase &other) -{ - other.derived().addTo(derived()); - return derived(); -} - -template -template -Derived& DenseBase::operator-=(const EigenBase &other) -{ - other.derived().subTo(derived()); - return derived(); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_EIGENBASE_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/Flagged.h b/modules/algebra/include/eigen3/Eigen/src/Core/Flagged.h deleted file mode 100644 index 2df0d2bd22..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/Flagged.h +++ /dev/null @@ -1,140 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008 Benoit Jacob -// -// 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 IMP_EIGEN_FLAGGED_H -#define IMP_EIGEN_FLAGGED_H - -namespace IMP_Eigen { - -/** \class Flagged - * \ingroup Core_Module - * - * \brief Expression with modified flags - * - * \param ExpressionType the type of the object of which we are modifying the flags - * \param Added the flags added to the expression - * \param Removed the flags removed from the expression (has priority over Added). - * - * This class represents an expression whose flags have been modified. - * It is the return type of MatrixBase::flagged() - * and most of the time this is the only way it is used. - * - * \sa MatrixBase::flagged() - */ - -namespace internal { -template -struct traits > : traits -{ - enum { Flags = (ExpressionType::Flags | Added) & ~Removed }; -}; -} - -template class Flagged - : public MatrixBase > -{ - public: - - typedef MatrixBase Base; - - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(Flagged) - typedef typename internal::conditional::ret, - ExpressionType, const ExpressionType&>::type ExpressionTypeNested; - typedef typename ExpressionType::InnerIterator InnerIterator; - - inline Flagged(const ExpressionType& matrix) : m_matrix(matrix) {} - - inline Index rows() const { return m_matrix.rows(); } - inline Index cols() const { return m_matrix.cols(); } - inline Index outerStride() const { return m_matrix.outerStride(); } - inline Index innerStride() const { return m_matrix.innerStride(); } - - inline CoeffReturnType coeff(Index row, Index col) const - { - return m_matrix.coeff(row, col); - } - - inline CoeffReturnType coeff(Index index) const - { - return m_matrix.coeff(index); - } - - inline const Scalar& coeffRef(Index row, Index col) const - { - return m_matrix.const_cast_derived().coeffRef(row, col); - } - - inline const Scalar& coeffRef(Index index) const - { - return m_matrix.const_cast_derived().coeffRef(index); - } - - inline Scalar& coeffRef(Index row, Index col) - { - return m_matrix.const_cast_derived().coeffRef(row, col); - } - - inline Scalar& coeffRef(Index index) - { - return m_matrix.const_cast_derived().coeffRef(index); - } - - template - inline const PacketScalar packet(Index row, Index col) const - { - return m_matrix.template packet(row, col); - } - - template - inline void writePacket(Index row, Index col, const PacketScalar& x) - { - m_matrix.const_cast_derived().template writePacket(row, col, x); - } - - template - inline const PacketScalar packet(Index index) const - { - return m_matrix.template packet(index); - } - - template - inline void writePacket(Index index, const PacketScalar& x) - { - m_matrix.const_cast_derived().template writePacket(index, x); - } - - const ExpressionType& _expression() const { return m_matrix; } - - template - typename ExpressionType::PlainObject solveTriangular(const MatrixBase& other) const; - - template - void solveTriangularInPlace(const MatrixBase& other) const; - - protected: - ExpressionTypeNested m_matrix; -}; - -/** \returns an expression of *this with added and removed flags - * - * This is mostly for internal use. - * - * \sa class Flagged - */ -template -template -inline const Flagged -DenseBase::flagged() const -{ - return derived(); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_FLAGGED_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/ForceAlignedAccess.h b/modules/algebra/include/eigen3/Eigen/src/Core/ForceAlignedAccess.h deleted file mode 100644 index 7efdb263d2..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/ForceAlignedAccess.h +++ /dev/null @@ -1,146 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2009-2010 Gael Guennebaud -// -// 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 IMP_EIGEN_FORCEALIGNEDACCESS_H -#define IMP_EIGEN_FORCEALIGNEDACCESS_H - -namespace IMP_Eigen { - -/** \class ForceAlignedAccess - * \ingroup Core_Module - * - * \brief Enforce aligned packet loads and stores regardless of what is requested - * - * \param ExpressionType the type of the object of which we are forcing aligned packet access - * - * This class is the return type of MatrixBase::forceAlignedAccess() - * and most of the time this is the only way it is used. - * - * \sa MatrixBase::forceAlignedAccess() - */ - -namespace internal { -template -struct traits > : public traits -{}; -} - -template class ForceAlignedAccess - : public internal::dense_xpr_base< ForceAlignedAccess >::type -{ - public: - - typedef typename internal::dense_xpr_base::type Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(ForceAlignedAccess) - - inline ForceAlignedAccess(const ExpressionType& matrix) : m_expression(matrix) {} - - inline Index rows() const { return m_expression.rows(); } - inline Index cols() const { return m_expression.cols(); } - inline Index outerStride() const { return m_expression.outerStride(); } - inline Index innerStride() const { return m_expression.innerStride(); } - - inline const CoeffReturnType coeff(Index row, Index col) const - { - return m_expression.coeff(row, col); - } - - inline Scalar& coeffRef(Index row, Index col) - { - return m_expression.const_cast_derived().coeffRef(row, col); - } - - inline const CoeffReturnType coeff(Index index) const - { - return m_expression.coeff(index); - } - - inline Scalar& coeffRef(Index index) - { - return m_expression.const_cast_derived().coeffRef(index); - } - - template - inline const PacketScalar packet(Index row, Index col) const - { - return m_expression.template packet(row, col); - } - - template - inline void writePacket(Index row, Index col, const PacketScalar& x) - { - m_expression.const_cast_derived().template writePacket(row, col, x); - } - - template - inline const PacketScalar packet(Index index) const - { - return m_expression.template packet(index); - } - - template - inline void writePacket(Index index, const PacketScalar& x) - { - m_expression.const_cast_derived().template writePacket(index, x); - } - - operator const ExpressionType&() const { return m_expression; } - - protected: - const ExpressionType& m_expression; - - private: - ForceAlignedAccess& operator=(const ForceAlignedAccess&); -}; - -/** \returns an expression of *this with forced aligned access - * \sa forceAlignedAccessIf(),class ForceAlignedAccess - */ -template -inline const ForceAlignedAccess -MatrixBase::forceAlignedAccess() const -{ - return ForceAlignedAccess(derived()); -} - -/** \returns an expression of *this with forced aligned access - * \sa forceAlignedAccessIf(), class ForceAlignedAccess - */ -template -inline ForceAlignedAccess -MatrixBase::forceAlignedAccess() -{ - return ForceAlignedAccess(derived()); -} - -/** \returns an expression of *this with forced aligned access if \a Enable is true. - * \sa forceAlignedAccess(), class ForceAlignedAccess - */ -template -template -inline typename internal::add_const_on_value_type,Derived&>::type>::type -MatrixBase::forceAlignedAccessIf() const -{ - return derived(); -} - -/** \returns an expression of *this with forced aligned access if \a Enable is true. - * \sa forceAlignedAccess(), class ForceAlignedAccess - */ -template -template -inline typename internal::conditional,Derived&>::type -MatrixBase::forceAlignedAccessIf() -{ - return derived(); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_FORCEALIGNEDACCESS_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/Functors.h b/modules/algebra/include/eigen3/Eigen/src/Core/Functors.h deleted file mode 100644 index b415e63a62..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/Functors.h +++ /dev/null @@ -1,1029 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008-2010 Gael Guennebaud -// -// 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 IMP_EIGEN_FUNCTORS_H -#define IMP_EIGEN_FUNCTORS_H - -namespace IMP_Eigen { - -namespace internal { - -// associative functors: - -/** \internal - * \brief Template functor to compute the sum of two scalars - * - * \sa class CwiseBinaryOp, MatrixBase::operator+, class VectorwiseOp, MatrixBase::sum() - */ -template struct scalar_sum_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_sum_op) - IMP_EIGEN_STRONG_INLINE const Scalar operator() (const Scalar& a, const Scalar& b) const { return a + b; } - template - IMP_EIGEN_STRONG_INLINE const Packet packetOp(const Packet& a, const Packet& b) const - { return internal::padd(a,b); } - template - IMP_EIGEN_STRONG_INLINE const Scalar predux(const Packet& a) const - { return internal::predux(a); } -}; -template -struct functor_traits > { - enum { - Cost = NumTraits::AddCost, - PacketAccess = packet_traits::HasAdd - }; -}; - -/** \internal - * \brief Template functor to compute the product of two scalars - * - * \sa class CwiseBinaryOp, Cwise::operator*(), class VectorwiseOp, MatrixBase::redux() - */ -template struct scalar_product_op { - enum { - // TODO vectorize mixed product - Vectorizable = is_same::value && packet_traits::HasMul && packet_traits::HasMul - }; - typedef typename scalar_product_traits::ReturnType result_type; - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_product_op) - IMP_EIGEN_STRONG_INLINE const result_type operator() (const LhsScalar& a, const RhsScalar& b) const { return a * b; } - template - IMP_EIGEN_STRONG_INLINE const Packet packetOp(const Packet& a, const Packet& b) const - { return internal::pmul(a,b); } - template - IMP_EIGEN_STRONG_INLINE const result_type predux(const Packet& a) const - { return internal::predux_mul(a); } -}; -template -struct functor_traits > { - enum { - Cost = (NumTraits::MulCost + NumTraits::MulCost)/2, // rough estimate! - PacketAccess = scalar_product_op::Vectorizable - }; -}; - -/** \internal - * \brief Template functor to compute the conjugate product of two scalars - * - * This is a short cut for conj(x) * y which is needed for optimization purpose; in Eigen2 support mode, this becomes x * conj(y) - */ -template struct scalar_conj_product_op { - - enum { - Conj = NumTraits::IsComplex - }; - - typedef typename scalar_product_traits::ReturnType result_type; - - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_conj_product_op) - IMP_EIGEN_STRONG_INLINE const result_type operator() (const LhsScalar& a, const RhsScalar& b) const - { return conj_helper().pmul(a,b); } - - template - IMP_EIGEN_STRONG_INLINE const Packet packetOp(const Packet& a, const Packet& b) const - { return conj_helper().pmul(a,b); } -}; -template -struct functor_traits > { - enum { - Cost = NumTraits::MulCost, - PacketAccess = internal::is_same::value && packet_traits::HasMul - }; -}; - -/** \internal - * \brief Template functor to compute the min of two scalars - * - * \sa class CwiseBinaryOp, MatrixBase::cwiseMin, class VectorwiseOp, MatrixBase::minCoeff() - */ -template struct scalar_min_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_min_op) - IMP_EIGEN_STRONG_INLINE const Scalar operator() (const Scalar& a, const Scalar& b) const { using std::min; return (min)(a, b); } - template - IMP_EIGEN_STRONG_INLINE const Packet packetOp(const Packet& a, const Packet& b) const - { return internal::pmin(a,b); } - template - IMP_EIGEN_STRONG_INLINE const Scalar predux(const Packet& a) const - { return internal::predux_min(a); } -}; -template -struct functor_traits > { - enum { - Cost = NumTraits::AddCost, - PacketAccess = packet_traits::HasMin - }; -}; - -/** \internal - * \brief Template functor to compute the max of two scalars - * - * \sa class CwiseBinaryOp, MatrixBase::cwiseMax, class VectorwiseOp, MatrixBase::maxCoeff() - */ -template struct scalar_max_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_max_op) - IMP_EIGEN_STRONG_INLINE const Scalar operator() (const Scalar& a, const Scalar& b) const { using std::max; return (max)(a, b); } - template - IMP_EIGEN_STRONG_INLINE const Packet packetOp(const Packet& a, const Packet& b) const - { return internal::pmax(a,b); } - template - IMP_EIGEN_STRONG_INLINE const Scalar predux(const Packet& a) const - { return internal::predux_max(a); } -}; -template -struct functor_traits > { - enum { - Cost = NumTraits::AddCost, - PacketAccess = packet_traits::HasMax - }; -}; - -/** \internal - * \brief Template functor to compute the hypot of two scalars - * - * \sa MatrixBase::stableNorm(), class Redux - */ -template struct scalar_hypot_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_hypot_op) -// typedef typename NumTraits::Real result_type; - IMP_EIGEN_STRONG_INLINE const Scalar operator() (const Scalar& _x, const Scalar& _y) const - { - using std::max; - using std::min; - using std::sqrt; - Scalar p = (max)(_x, _y); - Scalar q = (min)(_x, _y); - Scalar qp = q/p; - return p * sqrt(Scalar(1) + qp*qp); - } -}; -template -struct functor_traits > { - enum { Cost = 5 * NumTraits::MulCost, PacketAccess=0 }; -}; - -/** \internal - * \brief Template functor to compute the pow of two scalars - */ -template struct scalar_binary_pow_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_binary_pow_op) - inline Scalar operator() (const Scalar& a, const OtherScalar& b) const { return numext::pow(a, b); } -}; -template -struct functor_traits > { - enum { Cost = 5 * NumTraits::MulCost, PacketAccess = false }; -}; - -// other binary functors: - -/** \internal - * \brief Template functor to compute the difference of two scalars - * - * \sa class CwiseBinaryOp, MatrixBase::operator- - */ -template struct scalar_difference_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_difference_op) - IMP_EIGEN_STRONG_INLINE const Scalar operator() (const Scalar& a, const Scalar& b) const { return a - b; } - template - IMP_EIGEN_STRONG_INLINE const Packet packetOp(const Packet& a, const Packet& b) const - { return internal::psub(a,b); } -}; -template -struct functor_traits > { - enum { - Cost = NumTraits::AddCost, - PacketAccess = packet_traits::HasSub - }; -}; - -/** \internal - * \brief Template functor to compute the quotient of two scalars - * - * \sa class CwiseBinaryOp, Cwise::operator/() - */ -template struct scalar_quotient_op { - enum { - // TODO vectorize mixed product - Vectorizable = is_same::value && packet_traits::HasDiv && packet_traits::HasDiv - }; - typedef typename scalar_product_traits::ReturnType result_type; - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_quotient_op) - IMP_EIGEN_STRONG_INLINE const result_type operator() (const LhsScalar& a, const RhsScalar& b) const { return a / b; } - template - IMP_EIGEN_STRONG_INLINE const Packet packetOp(const Packet& a, const Packet& b) const - { return internal::pdiv(a,b); } -}; -template -struct functor_traits > { - enum { - Cost = (NumTraits::MulCost + NumTraits::MulCost), // rough estimate! - PacketAccess = scalar_quotient_op::Vectorizable - }; -}; - - - -/** \internal - * \brief Template functor to compute the and of two booleans - * - * \sa class CwiseBinaryOp, ArrayBase::operator&& - */ -struct scalar_boolean_and_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_boolean_and_op) - IMP_EIGEN_STRONG_INLINE bool operator() (const bool& a, const bool& b) const { return a && b; } -}; -template<> struct functor_traits { - enum { - Cost = NumTraits::AddCost, - PacketAccess = false - }; -}; - -/** \internal - * \brief Template functor to compute the or of two booleans - * - * \sa class CwiseBinaryOp, ArrayBase::operator|| - */ -struct scalar_boolean_or_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_boolean_or_op) - IMP_EIGEN_STRONG_INLINE bool operator() (const bool& a, const bool& b) const { return a || b; } -}; -template<> struct functor_traits { - enum { - Cost = NumTraits::AddCost, - PacketAccess = false - }; -}; - -/** \internal - * \brief Template functors for comparison of two scalars - * \todo Implement packet-comparisons - */ -template struct scalar_cmp_op; - -template -struct functor_traits > { - enum { - Cost = NumTraits::AddCost, - PacketAccess = false - }; -}; - -template -struct result_of(Scalar,Scalar)> { - typedef bool type; -}; - - -template struct scalar_cmp_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_cmp_op) - IMP_EIGEN_STRONG_INLINE bool operator()(const Scalar& a, const Scalar& b) const {return a==b;} -}; -template struct scalar_cmp_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_cmp_op) - IMP_EIGEN_STRONG_INLINE bool operator()(const Scalar& a, const Scalar& b) const {return a struct scalar_cmp_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_cmp_op) - IMP_EIGEN_STRONG_INLINE bool operator()(const Scalar& a, const Scalar& b) const {return a<=b;} -}; -template struct scalar_cmp_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_cmp_op) - IMP_EIGEN_STRONG_INLINE bool operator()(const Scalar& a, const Scalar& b) const {return !(a<=b || b<=a);} -}; -template struct scalar_cmp_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_cmp_op) - IMP_EIGEN_STRONG_INLINE bool operator()(const Scalar& a, const Scalar& b) const {return a!=b;} -}; - -// unary functors: - -/** \internal - * \brief Template functor to compute the opposite of a scalar - * - * \sa class CwiseUnaryOp, MatrixBase::operator- - */ -template struct scalar_opposite_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_opposite_op) - IMP_EIGEN_STRONG_INLINE const Scalar operator() (const Scalar& a) const { return -a; } - template - IMP_EIGEN_STRONG_INLINE const Packet packetOp(const Packet& a) const - { return internal::pnegate(a); } -}; -template -struct functor_traits > -{ enum { - Cost = NumTraits::AddCost, - PacketAccess = packet_traits::HasNegate }; -}; - -/** \internal - * \brief Template functor to compute the absolute value of a scalar - * - * \sa class CwiseUnaryOp, Cwise::abs - */ -template struct scalar_abs_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_abs_op) - typedef typename NumTraits::Real result_type; - IMP_EIGEN_STRONG_INLINE const result_type operator() (const Scalar& a) const { using std::abs; return abs(a); } - template - IMP_EIGEN_STRONG_INLINE const Packet packetOp(const Packet& a) const - { return internal::pabs(a); } -}; -template -struct functor_traits > -{ - enum { - Cost = NumTraits::AddCost, - PacketAccess = packet_traits::HasAbs - }; -}; - -/** \internal - * \brief Template functor to compute the squared absolute value of a scalar - * - * \sa class CwiseUnaryOp, Cwise::abs2 - */ -template struct scalar_abs2_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_abs2_op) - typedef typename NumTraits::Real result_type; - IMP_EIGEN_STRONG_INLINE const result_type operator() (const Scalar& a) const { return numext::abs2(a); } - template - IMP_EIGEN_STRONG_INLINE const Packet packetOp(const Packet& a) const - { return internal::pmul(a,a); } -}; -template -struct functor_traits > -{ enum { Cost = NumTraits::MulCost, PacketAccess = packet_traits::HasAbs2 }; }; - -/** \internal - * \brief Template functor to compute the conjugate of a complex value - * - * \sa class CwiseUnaryOp, MatrixBase::conjugate() - */ -template struct scalar_conjugate_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_conjugate_op) - IMP_EIGEN_STRONG_INLINE const Scalar operator() (const Scalar& a) const { using numext::conj; return conj(a); } - template - IMP_EIGEN_STRONG_INLINE const Packet packetOp(const Packet& a) const { return internal::pconj(a); } -}; -template -struct functor_traits > -{ - enum { - Cost = NumTraits::IsComplex ? NumTraits::AddCost : 0, - PacketAccess = packet_traits::HasConj - }; -}; - -/** \internal - * \brief Template functor to cast a scalar to another type - * - * \sa class CwiseUnaryOp, MatrixBase::cast() - */ -template -struct scalar_cast_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_cast_op) - typedef NewType result_type; - IMP_EIGEN_STRONG_INLINE const NewType operator() (const Scalar& a) const { return cast(a); } -}; -template -struct functor_traits > -{ enum { Cost = is_same::value ? 0 : NumTraits::AddCost, PacketAccess = false }; }; - -/** \internal - * \brief Template functor to extract the real part of a complex - * - * \sa class CwiseUnaryOp, MatrixBase::real() - */ -template -struct scalar_real_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_real_op) - typedef typename NumTraits::Real result_type; - IMP_EIGEN_STRONG_INLINE result_type operator() (const Scalar& a) const { return numext::real(a); } -}; -template -struct functor_traits > -{ enum { Cost = 0, PacketAccess = false }; }; - -/** \internal - * \brief Template functor to extract the imaginary part of a complex - * - * \sa class CwiseUnaryOp, MatrixBase::imag() - */ -template -struct scalar_imag_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_imag_op) - typedef typename NumTraits::Real result_type; - IMP_EIGEN_STRONG_INLINE result_type operator() (const Scalar& a) const { return numext::imag(a); } -}; -template -struct functor_traits > -{ enum { Cost = 0, PacketAccess = false }; }; - -/** \internal - * \brief Template functor to extract the real part of a complex as a reference - * - * \sa class CwiseUnaryOp, MatrixBase::real() - */ -template -struct scalar_real_ref_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_real_ref_op) - typedef typename NumTraits::Real result_type; - IMP_EIGEN_STRONG_INLINE result_type& operator() (const Scalar& a) const { return numext::real_ref(*const_cast(&a)); } -}; -template -struct functor_traits > -{ enum { Cost = 0, PacketAccess = false }; }; - -/** \internal - * \brief Template functor to extract the imaginary part of a complex as a reference - * - * \sa class CwiseUnaryOp, MatrixBase::imag() - */ -template -struct scalar_imag_ref_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_imag_ref_op) - typedef typename NumTraits::Real result_type; - IMP_EIGEN_STRONG_INLINE result_type& operator() (const Scalar& a) const { return numext::imag_ref(*const_cast(&a)); } -}; -template -struct functor_traits > -{ enum { Cost = 0, PacketAccess = false }; }; - -/** \internal - * - * \brief Template functor to compute the exponential of a scalar - * - * \sa class CwiseUnaryOp, Cwise::exp() - */ -template struct scalar_exp_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_exp_op) - inline const Scalar operator() (const Scalar& a) const { using std::exp; return exp(a); } - typedef typename packet_traits::type Packet; - inline Packet packetOp(const Packet& a) const { return internal::pexp(a); } -}; -template -struct functor_traits > -{ enum { Cost = 5 * NumTraits::MulCost, PacketAccess = packet_traits::HasExp }; }; - -/** \internal - * - * \brief Template functor to compute the logarithm of a scalar - * - * \sa class CwiseUnaryOp, Cwise::log() - */ -template struct scalar_log_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_log_op) - inline const Scalar operator() (const Scalar& a) const { using std::log; return log(a); } - typedef typename packet_traits::type Packet; - inline Packet packetOp(const Packet& a) const { return internal::plog(a); } -}; -template -struct functor_traits > -{ enum { Cost = 5 * NumTraits::MulCost, PacketAccess = packet_traits::HasLog }; }; - -/** \internal - * \brief Template functor to multiply a scalar by a fixed other one - * - * \sa class CwiseUnaryOp, MatrixBase::operator*, MatrixBase::operator/ - */ -/* NOTE why doing the pset1() in packetOp *is* an optimization ? - * indeed it seems better to declare m_other as a Packet and do the pset1() once - * in the constructor. However, in practice: - * - GCC does not like m_other as a Packet and generate a load every time it needs it - * - on the other hand GCC is able to moves the pset1() outside the loop :) - * - simpler code ;) - * (ICC and gcc 4.4 seems to perform well in both cases, the issue is visible with y = a*x + b*y) - */ -template -struct scalar_multiple_op { - typedef typename packet_traits::type Packet; - // FIXME default copy constructors seems bugged with std::complex<> - IMP_EIGEN_STRONG_INLINE scalar_multiple_op(const scalar_multiple_op& other) : m_other(other.m_other) { } - IMP_EIGEN_STRONG_INLINE scalar_multiple_op(const Scalar& other) : m_other(other) { } - IMP_EIGEN_STRONG_INLINE Scalar operator() (const Scalar& a) const { return a * m_other; } - IMP_EIGEN_STRONG_INLINE const Packet packetOp(const Packet& a) const - { return internal::pmul(a, pset1(m_other)); } - typename add_const_on_value_type::Nested>::type m_other; -}; -template -struct functor_traits > -{ enum { Cost = NumTraits::MulCost, PacketAccess = packet_traits::HasMul }; }; - -template -struct scalar_multiple2_op { - typedef typename scalar_product_traits::ReturnType result_type; - IMP_EIGEN_STRONG_INLINE scalar_multiple2_op(const scalar_multiple2_op& other) : m_other(other.m_other) { } - IMP_EIGEN_STRONG_INLINE scalar_multiple2_op(const Scalar2& other) : m_other(other) { } - IMP_EIGEN_STRONG_INLINE result_type operator() (const Scalar1& a) const { return a * m_other; } - typename add_const_on_value_type::Nested>::type m_other; -}; -template -struct functor_traits > -{ enum { Cost = NumTraits::MulCost, PacketAccess = false }; }; - -/** \internal - * \brief Template functor to divide a scalar by a fixed other one - * - * This functor is used to implement the quotient of a matrix by - * a scalar where the scalar type is not necessarily a floating point type. - * - * \sa class CwiseUnaryOp, MatrixBase::operator/ - */ -template -struct scalar_quotient1_op { - typedef typename packet_traits::type Packet; - // FIXME default copy constructors seems bugged with std::complex<> - IMP_EIGEN_STRONG_INLINE scalar_quotient1_op(const scalar_quotient1_op& other) : m_other(other.m_other) { } - IMP_EIGEN_STRONG_INLINE scalar_quotient1_op(const Scalar& other) : m_other(other) {} - IMP_EIGEN_STRONG_INLINE Scalar operator() (const Scalar& a) const { return a / m_other; } - IMP_EIGEN_STRONG_INLINE const Packet packetOp(const Packet& a) const - { return internal::pdiv(a, pset1(m_other)); } - typename add_const_on_value_type::Nested>::type m_other; -}; -template -struct functor_traits > -{ enum { Cost = 2 * NumTraits::MulCost, PacketAccess = packet_traits::HasDiv }; }; - -// nullary functors - -template -struct scalar_constant_op { - typedef typename packet_traits::type Packet; - IMP_EIGEN_STRONG_INLINE scalar_constant_op(const scalar_constant_op& other) : m_other(other.m_other) { } - IMP_EIGEN_STRONG_INLINE scalar_constant_op(const Scalar& other) : m_other(other) { } - template - IMP_EIGEN_STRONG_INLINE const Scalar operator() (Index, Index = 0) const { return m_other; } - template - IMP_EIGEN_STRONG_INLINE const Packet packetOp(Index, Index = 0) const { return internal::pset1(m_other); } - const Scalar m_other; -}; -template -struct functor_traits > -// FIXME replace this packet test by a safe one -{ enum { Cost = 1, PacketAccess = packet_traits::Vectorizable, IsRepeatable = true }; }; - -template struct scalar_identity_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_identity_op) - template - IMP_EIGEN_STRONG_INLINE const Scalar operator() (Index row, Index col) const { return row==col ? Scalar(1) : Scalar(0); } -}; -template -struct functor_traits > -{ enum { Cost = NumTraits::AddCost, PacketAccess = false, IsRepeatable = true }; }; - -template struct linspaced_op_impl; - -// linear access for packet ops: -// 1) initialization -// base = [low, ..., low] + ([step, ..., step] * [-size, ..., 0]) -// 2) each step (where size is 1 for coeff access or PacketSize for packet access) -// base += [size*step, ..., size*step] -// -// TODO: Perhaps it's better to initialize lazily (so not in the constructor but in packetOp) -// in order to avoid the padd() in operator() ? -template -struct linspaced_op_impl -{ - typedef typename packet_traits::type Packet; - - linspaced_op_impl(const Scalar& low, const Scalar& step) : - m_low(low), m_step(step), - m_packetStep(pset1(packet_traits::size*step)), - m_base(padd(pset1(low), pmul(pset1(step),plset(-packet_traits::size)))) {} - - template - IMP_EIGEN_STRONG_INLINE const Scalar operator() (Index i) const - { - m_base = padd(m_base, pset1(m_step)); - return m_low+Scalar(i)*m_step; - } - - template - IMP_EIGEN_STRONG_INLINE const Packet packetOp(Index) const { return m_base = padd(m_base,m_packetStep); } - - const Scalar m_low; - const Scalar m_step; - const Packet m_packetStep; - mutable Packet m_base; -}; - -// random access for packet ops: -// 1) each step -// [low, ..., low] + ( [step, ..., step] * ( [i, ..., i] + [0, ..., size] ) ) -template -struct linspaced_op_impl -{ - typedef typename packet_traits::type Packet; - - linspaced_op_impl(const Scalar& low, const Scalar& step) : - m_low(low), m_step(step), - m_lowPacket(pset1(m_low)), m_stepPacket(pset1(m_step)), m_interPacket(plset(0)) {} - - template - IMP_EIGEN_STRONG_INLINE const Scalar operator() (Index i) const { return m_low+i*m_step; } - - template - IMP_EIGEN_STRONG_INLINE const Packet packetOp(Index i) const - { return internal::padd(m_lowPacket, pmul(m_stepPacket, padd(pset1(Scalar(i)),m_interPacket))); } - - const Scalar m_low; - const Scalar m_step; - const Packet m_lowPacket; - const Packet m_stepPacket; - const Packet m_interPacket; -}; - -// ----- Linspace functor ---------------------------------------------------------------- - -// Forward declaration (we default to random access which does not really give -// us a speed gain when using packet access but it allows to use the functor in -// nested expressions). -template struct linspaced_op; -template struct functor_traits< linspaced_op > -{ enum { Cost = 1, PacketAccess = packet_traits::HasSetLinear, IsRepeatable = true }; }; -template struct linspaced_op -{ - typedef typename packet_traits::type Packet; - linspaced_op(const Scalar& low, const Scalar& high, DenseIndex num_steps) : impl((num_steps==1 ? high : low), (num_steps==1 ? Scalar() : (high-low)/Scalar(num_steps-1))) {} - - template - IMP_EIGEN_STRONG_INLINE const Scalar operator() (Index i) const { return impl(i); } - - // We need this function when assigning e.g. a RowVectorXd to a MatrixXd since - // there row==0 and col is used for the actual iteration. - template - IMP_EIGEN_STRONG_INLINE const Scalar operator() (Index row, Index col) const - { - imp_eigen_assert(col==0 || row==0); - return impl(col + row); - } - - template - IMP_EIGEN_STRONG_INLINE const Packet packetOp(Index i) const { return impl.packetOp(i); } - - // We need this function when assigning e.g. a RowVectorXd to a MatrixXd since - // there row==0 and col is used for the actual iteration. - template - IMP_EIGEN_STRONG_INLINE const Packet packetOp(Index row, Index col) const - { - imp_eigen_assert(col==0 || row==0); - return impl.packetOp(col + row); - } - - // This proxy object handles the actual required temporaries, the different - // implementations (random vs. sequential access) as well as the - // correct piping to size 2/4 packet operations. - const linspaced_op_impl impl; -}; - -// all functors allow linear access, except scalar_identity_op. So we fix here a quick meta -// to indicate whether a functor allows linear access, just always answering 'yes' except for -// scalar_identity_op. -// FIXME move this to functor_traits adding a functor_default -template struct functor_has_linear_access { enum { ret = 1 }; }; -template struct functor_has_linear_access > { enum { ret = 0 }; }; - -// In Eigen, any binary op (Product, CwiseBinaryOp) require the Lhs and Rhs to have the same scalar type, except for multiplication -// where the mixing of different types is handled by scalar_product_traits -// In particular, real * complex is allowed. -// FIXME move this to functor_traits adding a functor_default -template struct functor_is_product_like { enum { ret = 0 }; }; -template struct functor_is_product_like > { enum { ret = 1 }; }; -template struct functor_is_product_like > { enum { ret = 1 }; }; -template struct functor_is_product_like > { enum { ret = 1 }; }; - - -/** \internal - * \brief Template functor to add a scalar to a fixed other one - * \sa class CwiseUnaryOp, Array::operator+ - */ -/* If you wonder why doing the pset1() in packetOp() is an optimization check scalar_multiple_op */ -template -struct scalar_add_op { - typedef typename packet_traits::type Packet; - // FIXME default copy constructors seems bugged with std::complex<> - inline scalar_add_op(const scalar_add_op& other) : m_other(other.m_other) { } - inline scalar_add_op(const Scalar& other) : m_other(other) { } - inline Scalar operator() (const Scalar& a) const { return a + m_other; } - inline const Packet packetOp(const Packet& a) const - { return internal::padd(a, pset1(m_other)); } - const Scalar m_other; -}; -template -struct functor_traits > -{ enum { Cost = NumTraits::AddCost, PacketAccess = packet_traits::HasAdd }; }; - -/** \internal - * \brief Template functor to compute the square root of a scalar - * \sa class CwiseUnaryOp, Cwise::sqrt() - */ -template struct scalar_sqrt_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_sqrt_op) - inline const Scalar operator() (const Scalar& a) const { using std::sqrt; return sqrt(a); } - typedef typename packet_traits::type Packet; - inline Packet packetOp(const Packet& a) const { return internal::psqrt(a); } -}; -template -struct functor_traits > -{ enum { - Cost = 5 * NumTraits::MulCost, - PacketAccess = packet_traits::HasSqrt - }; -}; - -/** \internal - * \brief Template functor to compute the cosine of a scalar - * \sa class CwiseUnaryOp, ArrayBase::cos() - */ -template struct scalar_cos_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_cos_op) - inline Scalar operator() (const Scalar& a) const { using std::cos; return cos(a); } - typedef typename packet_traits::type Packet; - inline Packet packetOp(const Packet& a) const { return internal::pcos(a); } -}; -template -struct functor_traits > -{ - enum { - Cost = 5 * NumTraits::MulCost, - PacketAccess = packet_traits::HasCos - }; -}; - -/** \internal - * \brief Template functor to compute the sine of a scalar - * \sa class CwiseUnaryOp, ArrayBase::sin() - */ -template struct scalar_sin_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_sin_op) - inline const Scalar operator() (const Scalar& a) const { using std::sin; return sin(a); } - typedef typename packet_traits::type Packet; - inline Packet packetOp(const Packet& a) const { return internal::psin(a); } -}; -template -struct functor_traits > -{ - enum { - Cost = 5 * NumTraits::MulCost, - PacketAccess = packet_traits::HasSin - }; -}; - - -/** \internal - * \brief Template functor to compute the tan of a scalar - * \sa class CwiseUnaryOp, ArrayBase::tan() - */ -template struct scalar_tan_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_tan_op) - inline const Scalar operator() (const Scalar& a) const { using std::tan; return tan(a); } - typedef typename packet_traits::type Packet; - inline Packet packetOp(const Packet& a) const { return internal::ptan(a); } -}; -template -struct functor_traits > -{ - enum { - Cost = 5 * NumTraits::MulCost, - PacketAccess = packet_traits::HasTan - }; -}; - -/** \internal - * \brief Template functor to compute the arc cosine of a scalar - * \sa class CwiseUnaryOp, ArrayBase::acos() - */ -template struct scalar_acos_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_acos_op) - inline const Scalar operator() (const Scalar& a) const { using std::acos; return acos(a); } - typedef typename packet_traits::type Packet; - inline Packet packetOp(const Packet& a) const { return internal::pacos(a); } -}; -template -struct functor_traits > -{ - enum { - Cost = 5 * NumTraits::MulCost, - PacketAccess = packet_traits::HasACos - }; -}; - -/** \internal - * \brief Template functor to compute the arc sine of a scalar - * \sa class CwiseUnaryOp, ArrayBase::asin() - */ -template struct scalar_asin_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_asin_op) - inline const Scalar operator() (const Scalar& a) const { using std::asin; return asin(a); } - typedef typename packet_traits::type Packet; - inline Packet packetOp(const Packet& a) const { return internal::pasin(a); } -}; -template -struct functor_traits > -{ - enum { - Cost = 5 * NumTraits::MulCost, - PacketAccess = packet_traits::HasASin - }; -}; - -/** \internal - * \brief Template functor to raise a scalar to a power - * \sa class CwiseUnaryOp, Cwise::pow - */ -template -struct scalar_pow_op { - // FIXME default copy constructors seems bugged with std::complex<> - inline scalar_pow_op(const scalar_pow_op& other) : m_exponent(other.m_exponent) { } - inline scalar_pow_op(const Scalar& exponent) : m_exponent(exponent) {} - inline Scalar operator() (const Scalar& a) const { return numext::pow(a, m_exponent); } - const Scalar m_exponent; -}; -template -struct functor_traits > -{ enum { Cost = 5 * NumTraits::MulCost, PacketAccess = false }; }; - -/** \internal - * \brief Template functor to compute the quotient between a scalar and array entries. - * \sa class CwiseUnaryOp, Cwise::inverse() - */ -template -struct scalar_inverse_mult_op { - scalar_inverse_mult_op(const Scalar& other) : m_other(other) {} - inline Scalar operator() (const Scalar& a) const { return m_other / a; } - template - inline const Packet packetOp(const Packet& a) const - { return internal::pdiv(pset1(m_other),a); } - Scalar m_other; -}; - -/** \internal - * \brief Template functor to compute the inverse of a scalar - * \sa class CwiseUnaryOp, Cwise::inverse() - */ -template -struct scalar_inverse_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_inverse_op) - inline Scalar operator() (const Scalar& a) const { return Scalar(1)/a; } - template - inline const Packet packetOp(const Packet& a) const - { return internal::pdiv(pset1(Scalar(1)),a); } -}; -template -struct functor_traits > -{ enum { Cost = NumTraits::MulCost, PacketAccess = packet_traits::HasDiv }; }; - -/** \internal - * \brief Template functor to compute the square of a scalar - * \sa class CwiseUnaryOp, Cwise::square() - */ -template -struct scalar_square_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_square_op) - inline Scalar operator() (const Scalar& a) const { return a*a; } - template - inline const Packet packetOp(const Packet& a) const - { return internal::pmul(a,a); } -}; -template -struct functor_traits > -{ enum { Cost = NumTraits::MulCost, PacketAccess = packet_traits::HasMul }; }; - -/** \internal - * \brief Template functor to compute the cube of a scalar - * \sa class CwiseUnaryOp, Cwise::cube() - */ -template -struct scalar_cube_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_cube_op) - inline Scalar operator() (const Scalar& a) const { return a*a*a; } - template - inline const Packet packetOp(const Packet& a) const - { return internal::pmul(a,pmul(a,a)); } -}; -template -struct functor_traits > -{ enum { Cost = 2*NumTraits::MulCost, PacketAccess = packet_traits::HasMul }; }; - -// default functor traits for STL functors: - -template -struct functor_traits > -{ enum { Cost = NumTraits::MulCost, PacketAccess = false }; }; - -template -struct functor_traits > -{ enum { Cost = NumTraits::MulCost, PacketAccess = false }; }; - -template -struct functor_traits > -{ enum { Cost = NumTraits::AddCost, PacketAccess = false }; }; - -template -struct functor_traits > -{ enum { Cost = NumTraits::AddCost, PacketAccess = false }; }; - -template -struct functor_traits > -{ enum { Cost = NumTraits::AddCost, PacketAccess = false }; }; - -template -struct functor_traits > -{ enum { Cost = 1, PacketAccess = false }; }; - -template -struct functor_traits > -{ enum { Cost = 1, PacketAccess = false }; }; - -template -struct functor_traits > -{ enum { Cost = 1, PacketAccess = false }; }; - -template -struct functor_traits > -{ enum { Cost = 1, PacketAccess = false }; }; - -template -struct functor_traits > -{ enum { Cost = 1, PacketAccess = false }; }; - -template -struct functor_traits > -{ enum { Cost = 1, PacketAccess = false }; }; - -template -struct functor_traits > -{ enum { Cost = 1, PacketAccess = false }; }; - -template -struct functor_traits > -{ enum { Cost = 1, PacketAccess = false }; }; - -template -struct functor_traits > -{ enum { Cost = 1, PacketAccess = false }; }; - -#if(__cplusplus < 201103L) -// std::binder* are deprecated since c++11 and will be removed in c++17 -template -struct functor_traits > -{ enum { Cost = functor_traits::Cost, PacketAccess = false }; }; - -template -struct functor_traits > -{ enum { Cost = functor_traits::Cost, PacketAccess = false }; }; -#endif - -template -struct functor_traits > -{ enum { Cost = 1 + functor_traits::Cost, PacketAccess = false }; }; - -template -struct functor_traits > -{ enum { Cost = 1 + functor_traits::Cost, PacketAccess = false }; }; - -#ifdef IMP_EIGEN_STDEXT_SUPPORT - -template -struct functor_traits > -{ enum { Cost = 0, PacketAccess = false }; }; - -template -struct functor_traits > -{ enum { Cost = 0, PacketAccess = false }; }; - -template -struct functor_traits > > -{ enum { Cost = 0, PacketAccess = false }; }; - -template -struct functor_traits > > -{ enum { Cost = 0, PacketAccess = false }; }; - -template -struct functor_traits > -{ enum { Cost = functor_traits::Cost + functor_traits::Cost, PacketAccess = false }; }; - -template -struct functor_traits > -{ enum { Cost = functor_traits::Cost + functor_traits::Cost + functor_traits::Cost, PacketAccess = false }; }; - -#endif // IMP_EIGEN_STDEXT_SUPPORT - -// allow to add new functors and specializations of functor_traits from outside Eigen. -// this macro is really needed because functor_traits must be specialized after it is declared but before it is used... -#ifdef IMP_EIGEN_FUNCTORS_PLUGIN -#include IMP_EIGEN_FUNCTORS_PLUGIN -#endif - -} // end namespace internal - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_FUNCTORS_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/Fuzzy.h b/modules/algebra/include/eigen3/Eigen/src/Core/Fuzzy.h deleted file mode 100644 index 1842ad7e38..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/Fuzzy.h +++ /dev/null @@ -1,150 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2006-2008 Benoit Jacob -// Copyright (C) 2008 Gael Guennebaud -// -// 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 IMP_EIGEN_FUZZY_H -#define IMP_EIGEN_FUZZY_H - -namespace IMP_Eigen { - -namespace internal -{ - -template::IsInteger> -struct isApprox_selector -{ - static bool run(const Derived& x, const OtherDerived& y, const typename Derived::RealScalar& prec) - { - using std::min; - typename internal::nested::type nested(x); - typename internal::nested::type otherNested(y); - return (nested - otherNested).cwiseAbs2().sum() <= prec * prec * (min)(nested.cwiseAbs2().sum(), otherNested.cwiseAbs2().sum()); - } -}; - -template -struct isApprox_selector -{ - static bool run(const Derived& x, const OtherDerived& y, const typename Derived::RealScalar&) - { - return x.matrix() == y.matrix(); - } -}; - -template::IsInteger> -struct isMuchSmallerThan_object_selector -{ - static bool run(const Derived& x, const OtherDerived& y, const typename Derived::RealScalar& prec) - { - return x.cwiseAbs2().sum() <= numext::abs2(prec) * y.cwiseAbs2().sum(); - } -}; - -template -struct isMuchSmallerThan_object_selector -{ - static bool run(const Derived& x, const OtherDerived&, const typename Derived::RealScalar&) - { - return x.matrix() == Derived::Zero(x.rows(), x.cols()).matrix(); - } -}; - -template::IsInteger> -struct isMuchSmallerThan_scalar_selector -{ - static bool run(const Derived& x, const typename Derived::RealScalar& y, const typename Derived::RealScalar& prec) - { - return x.cwiseAbs2().sum() <= numext::abs2(prec * y); - } -}; - -template -struct isMuchSmallerThan_scalar_selector -{ - static bool run(const Derived& x, const typename Derived::RealScalar&, const typename Derived::RealScalar&) - { - return x.matrix() == Derived::Zero(x.rows(), x.cols()).matrix(); - } -}; - -} // end namespace internal - - -/** \returns \c true if \c *this is approximately equal to \a other, within the precision - * determined by \a prec. - * - * \note The fuzzy compares are done multiplicatively. Two vectors \f$ v \f$ and \f$ w \f$ - * are considered to be approximately equal within precision \f$ p \f$ if - * \f[ \Vert v - w \Vert \leqslant p\,\min(\Vert v\Vert, \Vert w\Vert). \f] - * For matrices, the comparison is done using the Hilbert-Schmidt norm (aka Frobenius norm - * L2 norm). - * - * \note Because of the multiplicativeness of this comparison, one can't use this function - * to check whether \c *this is approximately equal to the zero matrix or vector. - * Indeed, \c isApprox(zero) returns false unless \c *this itself is exactly the zero matrix - * or vector. If you want to test whether \c *this is zero, use internal::isMuchSmallerThan(const - * RealScalar&, RealScalar) instead. - * - * \sa internal::isMuchSmallerThan(const RealScalar&, RealScalar) const - */ -template -template -bool DenseBase::isApprox( - const DenseBase& other, - const RealScalar& prec -) const -{ - return internal::isApprox_selector::run(derived(), other.derived(), prec); -} - -/** \returns \c true if the norm of \c *this is much smaller than \a other, - * within the precision determined by \a prec. - * - * \note The fuzzy compares are done multiplicatively. A vector \f$ v \f$ is - * considered to be much smaller than \f$ x \f$ within precision \f$ p \f$ if - * \f[ \Vert v \Vert \leqslant p\,\vert x\vert. \f] - * - * For matrices, the comparison is done using the Hilbert-Schmidt norm. For this reason, - * the value of the reference scalar \a other should come from the Hilbert-Schmidt norm - * of a reference matrix of same dimensions. - * - * \sa isApprox(), isMuchSmallerThan(const DenseBase&, RealScalar) const - */ -template -bool DenseBase::isMuchSmallerThan( - const typename NumTraits::Real& other, - const RealScalar& prec -) const -{ - return internal::isMuchSmallerThan_scalar_selector::run(derived(), other, prec); -} - -/** \returns \c true if the norm of \c *this is much smaller than the norm of \a other, - * within the precision determined by \a prec. - * - * \note The fuzzy compares are done multiplicatively. A vector \f$ v \f$ is - * considered to be much smaller than a vector \f$ w \f$ within precision \f$ p \f$ if - * \f[ \Vert v \Vert \leqslant p\,\Vert w\Vert. \f] - * For matrices, the comparison is done using the Hilbert-Schmidt norm. - * - * \sa isApprox(), isMuchSmallerThan(const RealScalar&, RealScalar) const - */ -template -template -bool DenseBase::isMuchSmallerThan( - const DenseBase& other, - const RealScalar& prec -) const -{ - return internal::isMuchSmallerThan_object_selector::run(derived(), other.derived(), prec); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_FUZZY_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/GeneralProduct.h b/modules/algebra/include/eigen3/Eigen/src/Core/GeneralProduct.h deleted file mode 100644 index f1fe729931..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/GeneralProduct.h +++ /dev/null @@ -1,633 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2006-2008 Benoit Jacob -// Copyright (C) 2008-2011 Gael Guennebaud -// -// 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 IMP_EIGEN_GENERAL_PRODUCT_H -#define IMP_EIGEN_GENERAL_PRODUCT_H - -namespace IMP_Eigen { - -/** \class GeneralProduct - * \ingroup Core_Module - * - * \brief Expression of the product of two general matrices or vectors - * - * \param LhsNested the type used to store the left-hand side - * \param RhsNested the type used to store the right-hand side - * \param ProductMode the type of the product - * - * This class represents an expression of the product of two general matrices. - * We call a general matrix, a dense matrix with full storage. For instance, - * This excludes triangular, selfadjoint, and sparse matrices. - * It is the return type of the operator* between general matrices. Its template - * arguments are determined automatically by ProductReturnType. Therefore, - * GeneralProduct should never be used direclty. To determine the result type of a - * function which involves a matrix product, use ProductReturnType::Type. - * - * \sa ProductReturnType, MatrixBase::operator*(const MatrixBase&) - */ -template::value> -class GeneralProduct; - -enum { - Large = 2, - Small = 3 -}; - -namespace internal { - -template struct product_type_selector; - -template struct product_size_category -{ - enum { is_large = MaxSize == Dynamic || - Size >= IMP_EIGEN_CACHEFRIENDLY_PRODUCT_THRESHOLD, - value = is_large ? Large - : Size == 1 ? 1 - : Small - }; -}; - -template struct product_type -{ - typedef typename remove_all::type _Lhs; - typedef typename remove_all::type _Rhs; - enum { - MaxRows = _Lhs::MaxRowsAtCompileTime, - Rows = _Lhs::RowsAtCompileTime, - MaxCols = _Rhs::MaxColsAtCompileTime, - Cols = _Rhs::ColsAtCompileTime, - MaxDepth = IMP_EIGEN_SIZE_MIN_PREFER_FIXED(_Lhs::MaxColsAtCompileTime, - _Rhs::MaxRowsAtCompileTime), - Depth = IMP_EIGEN_SIZE_MIN_PREFER_FIXED(_Lhs::ColsAtCompileTime, - _Rhs::RowsAtCompileTime), - LargeThreshold = IMP_EIGEN_CACHEFRIENDLY_PRODUCT_THRESHOLD - }; - - // the splitting into different lines of code here, introducing the _select enums and the typedef below, - // is to work around an internal compiler error with gcc 4.1 and 4.2. -private: - enum { - rows_select = product_size_category::value, - cols_select = product_size_category::value, - depth_select = product_size_category::value - }; - typedef product_type_selector selector; - -public: - enum { - value = selector::ret - }; -#ifdef IMP_EIGEN_DEBUG_PRODUCT - static void debug() - { - IMP_EIGEN_DEBUG_VAR(Rows); - IMP_EIGEN_DEBUG_VAR(Cols); - IMP_EIGEN_DEBUG_VAR(Depth); - IMP_EIGEN_DEBUG_VAR(rows_select); - IMP_EIGEN_DEBUG_VAR(cols_select); - IMP_EIGEN_DEBUG_VAR(depth_select); - IMP_EIGEN_DEBUG_VAR(value); - } -#endif -}; - - -/* The following allows to select the kind of product at compile time - * based on the three dimensions of the product. - * This is a compile time mapping from {1,Small,Large}^3 -> {product types} */ -// FIXME I'm not sure the current mapping is the ideal one. -template struct product_type_selector { enum { ret = OuterProduct }; }; -template struct product_type_selector<1, 1, Depth> { enum { ret = InnerProduct }; }; -template<> struct product_type_selector<1, 1, 1> { enum { ret = InnerProduct }; }; -template<> struct product_type_selector { enum { ret = CoeffBasedProductMode }; }; -template<> struct product_type_selector<1, Small,Small> { enum { ret = CoeffBasedProductMode }; }; -template<> struct product_type_selector { enum { ret = CoeffBasedProductMode }; }; -template<> struct product_type_selector { enum { ret = LazyCoeffBasedProductMode }; }; -template<> struct product_type_selector { enum { ret = LazyCoeffBasedProductMode }; }; -template<> struct product_type_selector { enum { ret = LazyCoeffBasedProductMode }; }; -template<> struct product_type_selector<1, Large,Small> { enum { ret = CoeffBasedProductMode }; }; -template<> struct product_type_selector<1, Large,Large> { enum { ret = GemvProduct }; }; -template<> struct product_type_selector<1, Small,Large> { enum { ret = CoeffBasedProductMode }; }; -template<> struct product_type_selector { enum { ret = CoeffBasedProductMode }; }; -template<> struct product_type_selector { enum { ret = GemvProduct }; }; -template<> struct product_type_selector { enum { ret = CoeffBasedProductMode }; }; -template<> struct product_type_selector { enum { ret = GemmProduct }; }; -template<> struct product_type_selector { enum { ret = GemmProduct }; }; -template<> struct product_type_selector { enum { ret = GemmProduct }; }; -template<> struct product_type_selector { enum { ret = GemmProduct }; }; -template<> struct product_type_selector { enum { ret = GemmProduct }; }; -template<> struct product_type_selector { enum { ret = GemmProduct }; }; -template<> struct product_type_selector { enum { ret = GemmProduct }; }; - -} // end namespace internal - -/** \class ProductReturnType - * \ingroup Core_Module - * - * \brief Helper class to get the correct and optimized returned type of operator* - * - * \param Lhs the type of the left-hand side - * \param Rhs the type of the right-hand side - * \param ProductMode the type of the product (determined automatically by internal::product_mode) - * - * This class defines the typename Type representing the optimized product expression - * between two matrix expressions. In practice, using ProductReturnType::Type - * is the recommended way to define the result type of a function returning an expression - * which involve a matrix product. The class Product should never be - * used directly. - * - * \sa class Product, MatrixBase::operator*(const MatrixBase&) - */ -template -struct ProductReturnType -{ - // TODO use the nested type to reduce instanciations ???? -// typedef typename internal::nested::type LhsNested; -// typedef typename internal::nested::type RhsNested; - - typedef GeneralProduct Type; -}; - -template -struct ProductReturnType -{ - typedef typename internal::nested::type >::type LhsNested; - typedef typename internal::nested::type >::type RhsNested; - typedef CoeffBasedProduct Type; -}; - -template -struct ProductReturnType -{ - typedef typename internal::nested::type >::type LhsNested; - typedef typename internal::nested::type >::type RhsNested; - typedef CoeffBasedProduct Type; -}; - -// this is a workaround for sun CC -template -struct LazyProductReturnType : public ProductReturnType -{}; - -/*********************************************************************** -* Implementation of Inner Vector Vector Product -***********************************************************************/ - -// FIXME : maybe the "inner product" could return a Scalar -// instead of a 1x1 matrix ?? -// Pro: more natural for the user -// Cons: this could be a problem if in a meta unrolled algorithm a matrix-matrix -// product ends up to a row-vector times col-vector product... To tackle this use -// case, we could have a specialization for Block with: operator=(Scalar x); - -namespace internal { - -template -struct traits > - : traits::ReturnType,1,1> > -{}; - -} - -template -class GeneralProduct - : internal::no_assignment_operator, - public Matrix::ReturnType,1,1> -{ - typedef Matrix::ReturnType,1,1> Base; - public: - GeneralProduct(const Lhs& lhs, const Rhs& rhs) - { - Base::coeffRef(0,0) = (lhs.transpose().cwiseProduct(rhs)).sum(); - } - - /** Convertion to scalar */ - operator const typename Base::Scalar() const { - return Base::coeff(0,0); - } -}; - -/*********************************************************************** -* Implementation of Outer Vector Vector Product -***********************************************************************/ - -namespace internal { - -// Column major -template -IMP_EIGEN_DONT_INLINE void outer_product_selector_run(const ProductType& prod, Dest& dest, const Func& func, const false_type&) -{ - typedef typename Dest::Index Index; - // FIXME make sure lhs is sequentially stored - // FIXME not very good if rhs is real and lhs complex while alpha is real too - const Index cols = dest.cols(); - for (Index j=0; j -IMP_EIGEN_DONT_INLINE void outer_product_selector_run(const ProductType& prod, Dest& dest, const Func& func, const true_type&) { - typedef typename Dest::Index Index; - // FIXME make sure rhs is sequentially stored - // FIXME not very good if lhs is real and rhs complex while alpha is real too - const Index rows = dest.rows(); - for (Index i=0; i -struct traits > - : traits, Lhs, Rhs> > -{}; - -} - -template -class GeneralProduct - : public ProductBase, Lhs, Rhs> -{ - template struct is_row_major : internal::conditional<(int(T::Flags)&RowMajorBit), internal::true_type, internal::false_type>::type {}; - - public: - IMP_EIGEN_PRODUCT_PUBLIC_INTERFACE(GeneralProduct) - - GeneralProduct(const Lhs& lhs, const Rhs& rhs) : Base(lhs,rhs) - { - } - - struct set { template void operator()(const Dst& dst, const Src& src) const { dst.const_cast_derived() = src; } }; - struct add { template void operator()(const Dst& dst, const Src& src) const { dst.const_cast_derived() += src; } }; - struct sub { template void operator()(const Dst& dst, const Src& src) const { dst.const_cast_derived() -= src; } }; - struct adds { - Scalar m_scale; - adds(const Scalar& s) : m_scale(s) {} - template void operator()(const Dst& dst, const Src& src) const { - dst.const_cast_derived() += m_scale * src; - } - }; - - template - inline void evalTo(Dest& dest) const { - internal::outer_product_selector_run(*this, dest, set(), is_row_major()); - } - - template - inline void addTo(Dest& dest) const { - internal::outer_product_selector_run(*this, dest, add(), is_row_major()); - } - - template - inline void subTo(Dest& dest) const { - internal::outer_product_selector_run(*this, dest, sub(), is_row_major()); - } - - template void scaleAndAddTo(Dest& dest, const Scalar& alpha) const - { - internal::outer_product_selector_run(*this, dest, adds(alpha), is_row_major()); - } -}; - -/*********************************************************************** -* Implementation of General Matrix Vector Product -***********************************************************************/ - -/* According to the shape/flags of the matrix we have to distinghish 3 different cases: - * 1 - the matrix is col-major, BLAS compatible and M is large => call fast BLAS-like colmajor routine - * 2 - the matrix is row-major, BLAS compatible and N is large => call fast BLAS-like rowmajor routine - * 3 - all other cases are handled using a simple loop along the outer-storage direction. - * Therefore we need a lower level meta selector. - * Furthermore, if the matrix is the rhs, then the product has to be transposed. - */ -namespace internal { - -template -struct traits > - : traits, Lhs, Rhs> > -{}; - -template -struct gemv_selector; - -} // end namespace internal - -template -class GeneralProduct - : public ProductBase, Lhs, Rhs> -{ - public: - IMP_EIGEN_PRODUCT_PUBLIC_INTERFACE(GeneralProduct) - - typedef typename Lhs::Scalar LhsScalar; - typedef typename Rhs::Scalar RhsScalar; - - GeneralProduct(const Lhs& a_lhs, const Rhs& a_rhs) : Base(a_lhs,a_rhs) - { -// IMP_EIGEN_STATIC_ASSERT((internal::is_same::value), -// YOU_MIXED_DIFFERENT_NUMERIC_TYPES__YOU_NEED_TO_USE_THE_CAST_METHOD_OF_MATRIXBASE_TO_CAST_NUMERIC_TYPES_EXPLICITLY) - } - - enum { Side = Lhs::IsVectorAtCompileTime ? OnTheLeft : OnTheRight }; - typedef typename internal::conditional::type MatrixType; - - template void scaleAndAddTo(Dest& dst, const Scalar& alpha) const - { - imp_eigen_assert(m_lhs.rows() == dst.rows() && m_rhs.cols() == dst.cols()); - internal::gemv_selector::HasUsableDirectAccess)>::run(*this, dst, alpha); - } -}; - -namespace internal { - -// The vector is on the left => transposition -template -struct gemv_selector -{ - template - static void run(const ProductType& prod, Dest& dest, const typename ProductType::Scalar& alpha) - { - Transpose destT(dest); - enum { OtherStorageOrder = StorageOrder == RowMajor ? ColMajor : RowMajor }; - gemv_selector - ::run(GeneralProduct,Transpose, GemvProduct> - (prod.rhs().transpose(), prod.lhs().transpose()), destT, alpha); - } -}; - -template struct gemv_static_vector_if; - -template -struct gemv_static_vector_if -{ - IMP_EIGEN_STRONG_INLINE Scalar* data() { imp_eigen_internal_assert(false && "should never be called"); return 0; } -}; - -template -struct gemv_static_vector_if -{ - IMP_EIGEN_STRONG_INLINE Scalar* data() { return 0; } -}; - -template -struct gemv_static_vector_if -{ - #if IMP_EIGEN_ALIGN_STATICALLY - internal::plain_array m_data; - IMP_EIGEN_STRONG_INLINE Scalar* data() { return m_data.array; } - #else - // Some architectures cannot align on the stack, - // => let's manually enforce alignment by allocating more data and return the address of the first aligned element. - enum { - ForceAlignment = internal::packet_traits::Vectorizable, - PacketSize = internal::packet_traits::size - }; - internal::plain_array m_data; - IMP_EIGEN_STRONG_INLINE Scalar* data() { - return ForceAlignment - ? reinterpret_cast((reinterpret_cast(m_data.array) & ~(size_t(15))) + 16) - : m_data.array; - } - #endif -}; - -template<> struct gemv_selector -{ - template - static inline void run(const ProductType& prod, Dest& dest, const typename ProductType::Scalar& alpha) - { - typedef typename ProductType::Index Index; - typedef typename ProductType::LhsScalar LhsScalar; - typedef typename ProductType::RhsScalar RhsScalar; - typedef typename ProductType::Scalar ResScalar; - typedef typename ProductType::RealScalar RealScalar; - typedef typename ProductType::ActualLhsType ActualLhsType; - typedef typename ProductType::ActualRhsType ActualRhsType; - typedef typename ProductType::LhsBlasTraits LhsBlasTraits; - typedef typename ProductType::RhsBlasTraits RhsBlasTraits; - typedef Map, Aligned> MappedDest; - - ActualLhsType actualLhs = LhsBlasTraits::extract(prod.lhs()); - ActualRhsType actualRhs = RhsBlasTraits::extract(prod.rhs()); - - ResScalar actualAlpha = alpha * LhsBlasTraits::extractScalarFactor(prod.lhs()) - * RhsBlasTraits::extractScalarFactor(prod.rhs()); - - // make sure Dest is a compile-time vector type (bug 1166) - typedef typename conditional::type ActualDest; - - enum { - // FIXME find a way to allow an inner stride on the result if packet_traits::size==1 - // on, the other hand it is good for the cache to pack the vector anyways... - EvalToDestAtCompileTime = (ActualDest::InnerStrideAtCompileTime==1), - ComplexByReal = (NumTraits::IsComplex) && (!NumTraits::IsComplex), - MightCannotUseDest = (ActualDest::InnerStrideAtCompileTime!=1) || ComplexByReal - }; - - gemv_static_vector_if static_dest; - - bool alphaIsCompatible = (!ComplexByReal) || (numext::imag(actualAlpha)==RealScalar(0)); - bool evalToDest = EvalToDestAtCompileTime && alphaIsCompatible; - - RhsScalar compatibleAlpha = get_factor::run(actualAlpha); - - imp_ei_declare_aligned_stack_constructed_variable(ResScalar,actualDestPtr,dest.size(), - evalToDest ? dest.data() : static_dest.data()); - - if(!evalToDest) - { - #ifdef IMP_EIGEN_DENSE_STORAGE_CTOR_PLUGIN - int size = dest.size(); - IMP_EIGEN_DENSE_STORAGE_CTOR_PLUGIN - #endif - if(!alphaIsCompatible) - { - MappedDest(actualDestPtr, dest.size()).setZero(); - compatibleAlpha = RhsScalar(1); - } - else - MappedDest(actualDestPtr, dest.size()) = dest; - } - - general_matrix_vector_product - ::run( - actualLhs.rows(), actualLhs.cols(), - actualLhs.data(), actualLhs.outerStride(), - actualRhs.data(), actualRhs.innerStride(), - actualDestPtr, 1, - compatibleAlpha); - - if (!evalToDest) - { - if(!alphaIsCompatible) - dest += actualAlpha * MappedDest(actualDestPtr, dest.size()); - else - dest = MappedDest(actualDestPtr, dest.size()); - } - } -}; - -template<> struct gemv_selector -{ - template - static void run(const ProductType& prod, Dest& dest, const typename ProductType::Scalar& alpha) - { - typedef typename ProductType::LhsScalar LhsScalar; - typedef typename ProductType::RhsScalar RhsScalar; - typedef typename ProductType::Scalar ResScalar; - typedef typename ProductType::Index Index; - typedef typename ProductType::ActualLhsType ActualLhsType; - typedef typename ProductType::ActualRhsType ActualRhsType; - typedef typename ProductType::_ActualRhsType _ActualRhsType; - typedef typename ProductType::LhsBlasTraits LhsBlasTraits; - typedef typename ProductType::RhsBlasTraits RhsBlasTraits; - - typename add_const::type actualLhs = LhsBlasTraits::extract(prod.lhs()); - typename add_const::type actualRhs = RhsBlasTraits::extract(prod.rhs()); - - ResScalar actualAlpha = alpha * LhsBlasTraits::extractScalarFactor(prod.lhs()) - * RhsBlasTraits::extractScalarFactor(prod.rhs()); - - enum { - // FIXME find a way to allow an inner stride on the result if packet_traits::size==1 - // on, the other hand it is good for the cache to pack the vector anyways... - DirectlyUseRhs = _ActualRhsType::InnerStrideAtCompileTime==1 - }; - - gemv_static_vector_if static_rhs; - - imp_ei_declare_aligned_stack_constructed_variable(RhsScalar,actualRhsPtr,actualRhs.size(), - DirectlyUseRhs ? const_cast(actualRhs.data()) : static_rhs.data()); - - if(!DirectlyUseRhs) - { - #ifdef IMP_EIGEN_DENSE_STORAGE_CTOR_PLUGIN - int size = actualRhs.size(); - IMP_EIGEN_DENSE_STORAGE_CTOR_PLUGIN - #endif - Map(actualRhsPtr, actualRhs.size()) = actualRhs; - } - - general_matrix_vector_product - ::run( - actualLhs.rows(), actualLhs.cols(), - actualLhs.data(), actualLhs.outerStride(), - actualRhsPtr, 1, - dest.data(), dest.col(0).innerStride(), //NOTE if dest is not a vector at compile-time, then dest.innerStride() might be wrong. (bug 1166) - actualAlpha); - } -}; - -template<> struct gemv_selector -{ - template - static void run(const ProductType& prod, Dest& dest, const typename ProductType::Scalar& alpha) - { - typedef typename Dest::Index Index; - // TODO makes sure dest is sequentially stored in memory, otherwise use a temp - const Index size = prod.rhs().rows(); - for(Index k=0; k struct gemv_selector -{ - template - static void run(const ProductType& prod, Dest& dest, const typename ProductType::Scalar& alpha) - { - typedef typename Dest::Index Index; - // TODO makes sure rhs is sequentially stored in memory, otherwise use a temp - const Index rows = prod.rows(); - for(Index i=0; i -template -inline const typename ProductReturnType::Type -MatrixBase::operator*(const MatrixBase &other) const -{ - // A note regarding the function declaration: In MSVC, this function will sometimes - // not be inlined since DenseStorage is an unwindable object for dynamic - // matrices and product types are holding a member to store the result. - // Thus it does not help tagging this function with IMP_EIGEN_STRONG_INLINE. - enum { - ProductIsValid = Derived::ColsAtCompileTime==Dynamic - || OtherDerived::RowsAtCompileTime==Dynamic - || int(Derived::ColsAtCompileTime)==int(OtherDerived::RowsAtCompileTime), - AreVectors = Derived::IsVectorAtCompileTime && OtherDerived::IsVectorAtCompileTime, - SameSizes = IMP_EIGEN_PREDICATE_SAME_MATRIX_SIZE(Derived,OtherDerived) - }; - // note to the lost user: - // * for a dot product use: v1.dot(v2) - // * for a coeff-wise product use: v1.cwiseProduct(v2) - IMP_EIGEN_STATIC_ASSERT(ProductIsValid || !(AreVectors && SameSizes), - INVALID_VECTOR_VECTOR_PRODUCT__IF_YOU_WANTED_A_DOT_OR_COEFF_WISE_PRODUCT_YOU_MUST_USE_THE_EXPLICIT_FUNCTIONS) - IMP_EIGEN_STATIC_ASSERT(ProductIsValid || !(SameSizes && !AreVectors), - INVALID_MATRIX_PRODUCT__IF_YOU_WANTED_A_COEFF_WISE_PRODUCT_YOU_MUST_USE_THE_EXPLICIT_FUNCTION) - IMP_EIGEN_STATIC_ASSERT(ProductIsValid || SameSizes, INVALID_MATRIX_PRODUCT) -#ifdef IMP_EIGEN_DEBUG_PRODUCT - internal::product_type::debug(); -#endif - return typename ProductReturnType::Type(derived(), other.derived()); -} - -/** \returns an expression of the matrix product of \c *this and \a other without implicit evaluation. - * - * The returned product will behave like any other expressions: the coefficients of the product will be - * computed once at a time as requested. This might be useful in some extremely rare cases when only - * a small and no coherent fraction of the result's coefficients have to be computed. - * - * \warning This version of the matrix product can be much much slower. So use it only if you know - * what you are doing and that you measured a true speed improvement. - * - * \sa operator*(const MatrixBase&) - */ -template -template -const typename LazyProductReturnType::Type -MatrixBase::lazyProduct(const MatrixBase &other) const -{ - enum { - ProductIsValid = Derived::ColsAtCompileTime==Dynamic - || OtherDerived::RowsAtCompileTime==Dynamic - || int(Derived::ColsAtCompileTime)==int(OtherDerived::RowsAtCompileTime), - AreVectors = Derived::IsVectorAtCompileTime && OtherDerived::IsVectorAtCompileTime, - SameSizes = IMP_EIGEN_PREDICATE_SAME_MATRIX_SIZE(Derived,OtherDerived) - }; - // note to the lost user: - // * for a dot product use: v1.dot(v2) - // * for a coeff-wise product use: v1.cwiseProduct(v2) - IMP_EIGEN_STATIC_ASSERT(ProductIsValid || !(AreVectors && SameSizes), - INVALID_VECTOR_VECTOR_PRODUCT__IF_YOU_WANTED_A_DOT_OR_COEFF_WISE_PRODUCT_YOU_MUST_USE_THE_EXPLICIT_FUNCTIONS) - IMP_EIGEN_STATIC_ASSERT(ProductIsValid || !(SameSizes && !AreVectors), - INVALID_MATRIX_PRODUCT__IF_YOU_WANTED_A_COEFF_WISE_PRODUCT_YOU_MUST_USE_THE_EXPLICIT_FUNCTION) - IMP_EIGEN_STATIC_ASSERT(ProductIsValid || SameSizes, INVALID_MATRIX_PRODUCT) - - return typename LazyProductReturnType::Type(derived(), other.derived()); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_PRODUCT_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/GenericPacketMath.h b/modules/algebra/include/eigen3/Eigen/src/Core/GenericPacketMath.h deleted file mode 100644 index 1c7ac7ceb8..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/GenericPacketMath.h +++ /dev/null @@ -1,350 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008 Gael Guennebaud -// Copyright (C) 2006-2008 Benoit Jacob -// -// 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 IMP_EIGEN_GENERIC_PACKET_MATH_H -#define IMP_EIGEN_GENERIC_PACKET_MATH_H - -namespace IMP_Eigen { - -namespace internal { - -/** \internal - * \file GenericPacketMath.h - * - * Default implementation for types not supported by the vectorization. - * In practice these functions are provided to make easier the writing - * of generic vectorized code. - */ - -#ifndef IMP_EIGEN_DEBUG_ALIGNED_LOAD -#define IMP_EIGEN_DEBUG_ALIGNED_LOAD -#endif - -#ifndef IMP_EIGEN_DEBUG_UNALIGNED_LOAD -#define IMP_EIGEN_DEBUG_UNALIGNED_LOAD -#endif - -#ifndef IMP_EIGEN_DEBUG_ALIGNED_STORE -#define IMP_EIGEN_DEBUG_ALIGNED_STORE -#endif - -#ifndef IMP_EIGEN_DEBUG_UNALIGNED_STORE -#define IMP_EIGEN_DEBUG_UNALIGNED_STORE -#endif - -struct default_packet_traits -{ - enum { - HasAdd = 1, - HasSub = 1, - HasMul = 1, - HasNegate = 1, - HasAbs = 1, - HasAbs2 = 1, - HasMin = 1, - HasMax = 1, - HasConj = 1, - HasSetLinear = 1, - - HasDiv = 0, - HasSqrt = 0, - HasExp = 0, - HasLog = 0, - HasPow = 0, - - HasSin = 0, - HasCos = 0, - HasTan = 0, - HasASin = 0, - HasACos = 0, - HasATan = 0 - }; -}; - -template struct packet_traits : default_packet_traits -{ - typedef T type; - enum { - Vectorizable = 0, - size = 1, - AlignedOnScalar = 0 - }; - enum { - HasAdd = 0, - HasSub = 0, - HasMul = 0, - HasNegate = 0, - HasAbs = 0, - HasAbs2 = 0, - HasMin = 0, - HasMax = 0, - HasConj = 0, - HasSetLinear = 0 - }; -}; - -/** \internal \returns a + b (coeff-wise) */ -template inline Packet -padd(const Packet& a, - const Packet& b) { return a+b; } - -/** \internal \returns a - b (coeff-wise) */ -template inline Packet -psub(const Packet& a, - const Packet& b) { return a-b; } - -/** \internal \returns -a (coeff-wise) */ -template inline Packet -pnegate(const Packet& a) { return -a; } - -/** \internal \returns conj(a) (coeff-wise) */ -template inline Packet -pconj(const Packet& a) { return numext::conj(a); } - -/** \internal \returns a * b (coeff-wise) */ -template inline Packet -pmul(const Packet& a, - const Packet& b) { return a*b; } - -/** \internal \returns a / b (coeff-wise) */ -template inline Packet -pdiv(const Packet& a, - const Packet& b) { return a/b; } - -/** \internal \returns the min of \a a and \a b (coeff-wise) */ -template inline Packet -pmin(const Packet& a, - const Packet& b) { using std::min; return (min)(a, b); } - -/** \internal \returns the max of \a a and \a b (coeff-wise) */ -template inline Packet -pmax(const Packet& a, - const Packet& b) { using std::max; return (max)(a, b); } - -/** \internal \returns the absolute value of \a a */ -template inline Packet -pabs(const Packet& a) { using std::abs; return abs(a); } - -/** \internal \returns the bitwise and of \a a and \a b */ -template inline Packet -pand(const Packet& a, const Packet& b) { return a & b; } - -/** \internal \returns the bitwise or of \a a and \a b */ -template inline Packet -por(const Packet& a, const Packet& b) { return a | b; } - -/** \internal \returns the bitwise xor of \a a and \a b */ -template inline Packet -pxor(const Packet& a, const Packet& b) { return a ^ b; } - -/** \internal \returns the bitwise andnot of \a a and \a b */ -template inline Packet -pandnot(const Packet& a, const Packet& b) { return a & (!b); } - -/** \internal \returns a packet version of \a *from, from must be 16 bytes aligned */ -template inline Packet -pload(const typename unpacket_traits::type* from) { return *from; } - -/** \internal \returns a packet version of \a *from, (un-aligned load) */ -template inline Packet -ploadu(const typename unpacket_traits::type* from) { return *from; } - -/** \internal \returns a packet with elements of \a *from duplicated. - * For instance, for a packet of 8 elements, 4 scalar will be read from \a *from and - * duplicated to form: {from[0],from[0],from[1],from[1],,from[2],from[2],,from[3],from[3]} - * Currently, this function is only used for scalar * complex products. - */ -template inline Packet -ploaddup(const typename unpacket_traits::type* from) { return *from; } - -/** \internal \returns a packet with constant coefficients \a a, e.g.: (a,a,a,a) */ -template inline Packet -pset1(const typename unpacket_traits::type& a) { return a; } - -/** \internal \brief Returns a packet with coefficients (a,a+1,...,a+packet_size-1). */ -template inline typename packet_traits::type -plset(const Scalar& a) { return a; } - -/** \internal copy the packet \a from to \a *to, \a to must be 16 bytes aligned */ -template inline void pstore(Scalar* to, const Packet& from) -{ (*to) = from; } - -/** \internal copy the packet \a from to \a *to, (un-aligned store) */ -template inline void pstoreu(Scalar* to, const Packet& from) -{ (*to) = from; } - -/** \internal tries to do cache prefetching of \a addr */ -template inline void prefetch(const Scalar* addr) -{ -#if !defined(_MSC_VER) -__builtin_prefetch(addr); -#endif -} - -/** \internal \returns the first element of a packet */ -template inline typename unpacket_traits::type pfirst(const Packet& a) -{ return a; } - -/** \internal \returns a packet where the element i contains the sum of the packet of \a vec[i] */ -template inline Packet -preduxp(const Packet* vecs) { return vecs[0]; } - -/** \internal \returns the sum of the elements of \a a*/ -template inline typename unpacket_traits::type predux(const Packet& a) -{ return a; } - -/** \internal \returns the product of the elements of \a a*/ -template inline typename unpacket_traits::type predux_mul(const Packet& a) -{ return a; } - -/** \internal \returns the min of the elements of \a a*/ -template inline typename unpacket_traits::type predux_min(const Packet& a) -{ return a; } - -/** \internal \returns the max of the elements of \a a*/ -template inline typename unpacket_traits::type predux_max(const Packet& a) -{ return a; } - -/** \internal \returns the reversed elements of \a a*/ -template inline Packet preverse(const Packet& a) -{ return a; } - - -/** \internal \returns \a a with real and imaginary part flipped (for complex type only) */ -template inline Packet pcplxflip(const Packet& a) -{ - // FIXME: uncomment the following in case we drop the internal imag and real functions. -// using std::imag; -// using std::real; - return Packet(imag(a),real(a)); -} - -/************************** -* Special math functions -***************************/ - -/** \internal \returns the sine of \a a (coeff-wise) */ -template IMP_EIGEN_DECLARE_FUNCTION_ALLOWING_MULTIPLE_DEFINITIONS -Packet psin(const Packet& a) { using std::sin; return sin(a); } - -/** \internal \returns the cosine of \a a (coeff-wise) */ -template IMP_EIGEN_DECLARE_FUNCTION_ALLOWING_MULTIPLE_DEFINITIONS -Packet pcos(const Packet& a) { using std::cos; return cos(a); } - -/** \internal \returns the tan of \a a (coeff-wise) */ -template IMP_EIGEN_DECLARE_FUNCTION_ALLOWING_MULTIPLE_DEFINITIONS -Packet ptan(const Packet& a) { using std::tan; return tan(a); } - -/** \internal \returns the arc sine of \a a (coeff-wise) */ -template IMP_EIGEN_DECLARE_FUNCTION_ALLOWING_MULTIPLE_DEFINITIONS -Packet pasin(const Packet& a) { using std::asin; return asin(a); } - -/** \internal \returns the arc cosine of \a a (coeff-wise) */ -template IMP_EIGEN_DECLARE_FUNCTION_ALLOWING_MULTIPLE_DEFINITIONS -Packet pacos(const Packet& a) { using std::acos; return acos(a); } - -/** \internal \returns the exp of \a a (coeff-wise) */ -template IMP_EIGEN_DECLARE_FUNCTION_ALLOWING_MULTIPLE_DEFINITIONS -Packet pexp(const Packet& a) { using std::exp; return exp(a); } - -/** \internal \returns the log of \a a (coeff-wise) */ -template IMP_EIGEN_DECLARE_FUNCTION_ALLOWING_MULTIPLE_DEFINITIONS -Packet plog(const Packet& a) { using std::log; return log(a); } - -/** \internal \returns the square-root of \a a (coeff-wise) */ -template IMP_EIGEN_DECLARE_FUNCTION_ALLOWING_MULTIPLE_DEFINITIONS -Packet psqrt(const Packet& a) { using std::sqrt; return sqrt(a); } - -/*************************************************************************** -* The following functions might not have to be overwritten for vectorized types -***************************************************************************/ - -/** \internal copy a packet with constant coeficient \a a (e.g., [a,a,a,a]) to \a *to. \a to must be 16 bytes aligned */ -// NOTE: this function must really be templated on the packet type (think about different packet types for the same scalar type) -template -inline void pstore1(typename unpacket_traits::type* to, const typename unpacket_traits::type& a) -{ - pstore(to, pset1(a)); -} - -/** \internal \returns a * b + c (coeff-wise) */ -template inline Packet -pmadd(const Packet& a, - const Packet& b, - const Packet& c) -{ return padd(pmul(a, b),c); } - -/** \internal \returns a packet version of \a *from. - * If LoadMode equals #Aligned, \a from must be 16 bytes aligned */ -template -inline Packet ploadt(const typename unpacket_traits::type* from) -{ - if(LoadMode == Aligned) - return pload(from); - else - return ploadu(from); -} - -/** \internal copy the packet \a from to \a *to. - * If StoreMode equals #Aligned, \a to must be 16 bytes aligned */ -template -inline void pstoret(Scalar* to, const Packet& from) -{ - if(LoadMode == Aligned) - pstore(to, from); - else - pstoreu(to, from); -} - -/** \internal default implementation of palign() allowing partial specialization */ -template -struct palign_impl -{ - // by default data are aligned, so there is nothing to be done :) - static inline void run(PacketType&, const PacketType&) {} -}; - -/** \internal update \a first using the concatenation of the packet_size minus \a Offset last elements - * of \a first and \a Offset first elements of \a second. - * - * This function is currently only used to optimize matrix-vector products on unligned matrices. - * It takes 2 packets that represent a contiguous memory array, and returns a packet starting - * at the position \a Offset. For instance, for packets of 4 elements, we have: - * Input: - * - first = {f0,f1,f2,f3} - * - second = {s0,s1,s2,s3} - * Output: - * - if Offset==0 then {f0,f1,f2,f3} - * - if Offset==1 then {f1,f2,f3,s0} - * - if Offset==2 then {f2,f3,s0,s1} - * - if Offset==3 then {f3,s0,s1,s3} - */ -template -inline void palign(PacketType& first, const PacketType& second) -{ - palign_impl::run(first,second); -} - -/*************************************************************************** -* Fast complex products (GCC generates a function call which is very slow) -***************************************************************************/ - -template<> inline std::complex pmul(const std::complex& a, const std::complex& b) -{ return std::complex(real(a)*real(b) - imag(a)*imag(b), imag(a)*real(b) + real(a)*imag(b)); } - -template<> inline std::complex pmul(const std::complex& a, const std::complex& b) -{ return std::complex(real(a)*real(b) - imag(a)*imag(b), imag(a)*real(b) + real(a)*imag(b)); } - -} // end namespace internal - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_GENERIC_PACKET_MATH_H - diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/GlobalFunctions.h b/modules/algebra/include/eigen3/Eigen/src/Core/GlobalFunctions.h deleted file mode 100644 index 68f24029e9..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/GlobalFunctions.h +++ /dev/null @@ -1,92 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2010-2012 Gael Guennebaud -// Copyright (C) 2010 Benoit Jacob -// -// 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 IMP_EIGEN_GLOBAL_FUNCTIONS_H -#define IMP_EIGEN_GLOBAL_FUNCTIONS_H - -#define IMP_EIGEN_ARRAY_DECLARE_GLOBAL_UNARY(NAME,FUNCTOR) \ - template \ - inline const IMP_Eigen::CwiseUnaryOp, const Derived> \ - NAME(const IMP_Eigen::ArrayBase& x) { \ - return x.derived(); \ - } - -#define IMP_EIGEN_ARRAY_DECLARE_GLOBAL_EIGEN_UNARY(NAME,FUNCTOR) \ - \ - template \ - struct NAME##_retval > \ - { \ - typedef const IMP_Eigen::CwiseUnaryOp, const Derived> type; \ - }; \ - template \ - struct NAME##_impl > \ - { \ - static inline typename NAME##_retval >::type run(const IMP_Eigen::ArrayBase& x) \ - { \ - return x.derived(); \ - } \ - }; - - -namespace IMP_Eigen -{ - IMP_EIGEN_ARRAY_DECLARE_GLOBAL_UNARY(real,scalar_real_op) - IMP_EIGEN_ARRAY_DECLARE_GLOBAL_UNARY(imag,scalar_imag_op) - IMP_EIGEN_ARRAY_DECLARE_GLOBAL_UNARY(conj,scalar_conjugate_op) - IMP_EIGEN_ARRAY_DECLARE_GLOBAL_UNARY(sin,scalar_sin_op) - IMP_EIGEN_ARRAY_DECLARE_GLOBAL_UNARY(cos,scalar_cos_op) - IMP_EIGEN_ARRAY_DECLARE_GLOBAL_UNARY(asin,scalar_asin_op) - IMP_EIGEN_ARRAY_DECLARE_GLOBAL_UNARY(acos,scalar_acos_op) - IMP_EIGEN_ARRAY_DECLARE_GLOBAL_UNARY(tan,scalar_tan_op) - IMP_EIGEN_ARRAY_DECLARE_GLOBAL_UNARY(exp,scalar_exp_op) - IMP_EIGEN_ARRAY_DECLARE_GLOBAL_UNARY(log,scalar_log_op) - IMP_EIGEN_ARRAY_DECLARE_GLOBAL_UNARY(abs,scalar_abs_op) - IMP_EIGEN_ARRAY_DECLARE_GLOBAL_UNARY(sqrt,scalar_sqrt_op) - - template - inline const IMP_Eigen::CwiseUnaryOp, const Derived> - pow(const IMP_Eigen::ArrayBase& x, const typename Derived::Scalar& exponent) { - return x.derived().pow(exponent); - } - - template - inline const IMP_Eigen::CwiseBinaryOp, const Derived, const Derived> - pow(const IMP_Eigen::ArrayBase& x, const IMP_Eigen::ArrayBase& exponents) - { - return IMP_Eigen::CwiseBinaryOp, const Derived, const Derived>( - x.derived(), - exponents.derived() - ); - } - - /** - * \brief Component-wise division of a scalar by array elements. - **/ - template - inline const IMP_Eigen::CwiseUnaryOp, const Derived> - operator/(const typename Derived::Scalar& s, const IMP_Eigen::ArrayBase& a) - { - return IMP_Eigen::CwiseUnaryOp, const Derived>( - a.derived(), - IMP_Eigen::internal::scalar_inverse_mult_op(s) - ); - } - - namespace internal - { - IMP_EIGEN_ARRAY_DECLARE_GLOBAL_EIGEN_UNARY(real,scalar_real_op) - IMP_EIGEN_ARRAY_DECLARE_GLOBAL_EIGEN_UNARY(imag,scalar_imag_op) - IMP_EIGEN_ARRAY_DECLARE_GLOBAL_EIGEN_UNARY(abs2,scalar_abs2_op) - } -} - -// TODO: cleanly disable those functions that are not supported on Array (numext::real_ref, internal::random, internal::isApprox...) - -#endif // IMP_EIGEN_GLOBAL_FUNCTIONS_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/IO.h b/modules/algebra/include/eigen3/Eigen/src/Core/IO.h deleted file mode 100644 index e68995dbbd..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/IO.h +++ /dev/null @@ -1,250 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2006-2008 Benoit Jacob -// Copyright (C) 2008 Gael Guennebaud -// -// 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 IMP_EIGEN_IO_H -#define IMP_EIGEN_IO_H - -namespace IMP_Eigen { - -enum { DontAlignCols = 1 }; -enum { StreamPrecision = -1, - FullPrecision = -2 }; - -namespace internal { -template -std::ostream & print_matrix(std::ostream & s, const Derived& _m, const IOFormat& fmt); -} - -/** \class IOFormat - * \ingroup Core_Module - * - * \brief Stores a set of parameters controlling the way matrices are printed - * - * List of available parameters: - * - \b precision number of digits for floating point values, or one of the special constants \c StreamPrecision and \c FullPrecision. - * The default is the special value \c StreamPrecision which means to use the - * stream's own precision setting, as set for instance using \c cout.precision(3). The other special value - * \c FullPrecision means that the number of digits will be computed to match the full precision of each floating-point - * type. - * - \b flags an OR-ed combination of flags, the default value is 0, the only currently available flag is \c DontAlignCols which - * allows to disable the alignment of columns, resulting in faster code. - * - \b coeffSeparator string printed between two coefficients of the same row - * - \b rowSeparator string printed between two rows - * - \b rowPrefix string printed at the beginning of each row - * - \b rowSuffix string printed at the end of each row - * - \b matPrefix string printed at the beginning of the matrix - * - \b matSuffix string printed at the end of the matrix - * - * Example: \include IOFormat.cpp - * Output: \verbinclude IOFormat.out - * - * \sa DenseBase::format(), class WithFormat - */ -struct IOFormat -{ - /** Default contructor, see class IOFormat for the meaning of the parameters */ - IOFormat(int _precision = StreamPrecision, int _flags = 0, - const std::string& _coeffSeparator = " ", - const std::string& _rowSeparator = "\n", const std::string& _rowPrefix="", const std::string& _rowSuffix="", - const std::string& _matPrefix="", const std::string& _matSuffix="") - : matPrefix(_matPrefix), matSuffix(_matSuffix), rowPrefix(_rowPrefix), rowSuffix(_rowSuffix), rowSeparator(_rowSeparator), - rowSpacer(""), coeffSeparator(_coeffSeparator), precision(_precision), flags(_flags) - { - int i = int(matSuffix.length())-1; - while (i>=0 && matSuffix[i]!='\n') - { - rowSpacer += ' '; - i--; - } - } - std::string matPrefix, matSuffix; - std::string rowPrefix, rowSuffix, rowSeparator, rowSpacer; - std::string coeffSeparator; - int precision; - int flags; -}; - -/** \class WithFormat - * \ingroup Core_Module - * - * \brief Pseudo expression providing matrix output with given format - * - * \param ExpressionType the type of the object on which IO stream operations are performed - * - * This class represents an expression with stream operators controlled by a given IOFormat. - * It is the return type of DenseBase::format() - * and most of the time this is the only way it is used. - * - * See class IOFormat for some examples. - * - * \sa DenseBase::format(), class IOFormat - */ -template -class WithFormat -{ - public: - - WithFormat(const ExpressionType& matrix, const IOFormat& format) - : m_matrix(matrix), m_format(format) - {} - - friend std::ostream & operator << (std::ostream & s, const WithFormat& wf) - { - return internal::print_matrix(s, wf.m_matrix.eval(), wf.m_format); - } - - protected: - const typename ExpressionType::Nested m_matrix; - IOFormat m_format; -}; - -/** \returns a WithFormat proxy object allowing to print a matrix the with given - * format \a fmt. - * - * See class IOFormat for some examples. - * - * \sa class IOFormat, class WithFormat - */ -template -inline const WithFormat -DenseBase::format(const IOFormat& fmt) const -{ - return WithFormat(derived(), fmt); -} - -namespace internal { - -template -struct significant_decimals_default_impl -{ - typedef typename NumTraits::Real RealScalar; - static inline int run() - { - using std::ceil; - using std::log; - return cast(ceil(-log(NumTraits::epsilon())/log(RealScalar(10)))); - } -}; - -template -struct significant_decimals_default_impl -{ - static inline int run() - { - return 0; - } -}; - -template -struct significant_decimals_impl - : significant_decimals_default_impl::IsInteger> -{}; - -/** \internal - * print the matrix \a _m to the output stream \a s using the output format \a fmt */ -template -std::ostream & print_matrix(std::ostream & s, const Derived& _m, const IOFormat& fmt) -{ - if(_m.size() == 0) - { - s << fmt.matPrefix << fmt.matSuffix; - return s; - } - - typename Derived::Nested m = _m; - typedef typename Derived::Scalar Scalar; - typedef typename Derived::Index Index; - - Index width = 0; - - std::streamsize explicit_precision; - if(fmt.precision == StreamPrecision) - { - explicit_precision = 0; - } - else if(fmt.precision == FullPrecision) - { - if (NumTraits::IsInteger) - { - explicit_precision = 0; - } - else - { - explicit_precision = significant_decimals_impl::run(); - } - } - else - { - explicit_precision = fmt.precision; - } - - std::streamsize old_precision = 0; - if(explicit_precision) old_precision = s.precision(explicit_precision); - - bool align_cols = !(fmt.flags & DontAlignCols); - if(align_cols) - { - // compute the largest width - for(Index j = 0; j < m.cols(); ++j) - for(Index i = 0; i < m.rows(); ++i) - { - std::stringstream sstr; - sstr.copyfmt(s); - sstr << m.coeff(i,j); - width = std::max(width, Index(sstr.str().length())); - } - } - s << fmt.matPrefix; - for(Index i = 0; i < m.rows(); ++i) - { - if (i) - s << fmt.rowSpacer; - s << fmt.rowPrefix; - if(width) s.width(width); - s << m.coeff(i, 0); - for(Index j = 1; j < m.cols(); ++j) - { - s << fmt.coeffSeparator; - if (width) s.width(width); - s << m.coeff(i, j); - } - s << fmt.rowSuffix; - if( i < m.rows() - 1) - s << fmt.rowSeparator; - } - s << fmt.matSuffix; - if(explicit_precision) s.precision(old_precision); - return s; -} - -} // end namespace internal - -/** \relates DenseBase - * - * Outputs the matrix, to the given stream. - * - * If you wish to print the matrix with a format different than the default, use DenseBase::format(). - * - * It is also possible to change the default format by defining IMP_EIGEN_DEFAULT_IO_FORMAT before including Eigen headers. - * If not defined, this will automatically be defined to IMP_Eigen::IOFormat(), that is the IMP_Eigen::IOFormat with default parameters. - * - * \sa DenseBase::format() - */ -template -std::ostream & operator << -(std::ostream & s, - const DenseBase & m) -{ - return internal::print_matrix(s, m.eval(), IMP_EIGEN_DEFAULT_IO_FORMAT); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_IO_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/Map.h b/modules/algebra/include/eigen3/Eigen/src/Core/Map.h deleted file mode 100644 index 08db9634ab..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/Map.h +++ /dev/null @@ -1,192 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2007-2010 Benoit Jacob -// Copyright (C) 2008 Gael Guennebaud -// -// 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 IMP_EIGEN_MAP_H -#define IMP_EIGEN_MAP_H - -namespace IMP_Eigen { - -/** \class Map - * \ingroup Core_Module - * - * \brief A matrix or vector expression mapping an existing array of data. - * - * \tparam PlainObjectType the equivalent matrix type of the mapped data - * \tparam MapOptions specifies whether the pointer is \c #Aligned, or \c #Unaligned. - * The default is \c #Unaligned. - * \tparam StrideType optionally specifies strides. By default, Map assumes the memory layout - * of an ordinary, contiguous array. This can be overridden by specifying strides. - * The type passed here must be a specialization of the Stride template, see examples below. - * - * This class represents a matrix or vector expression mapping an existing array of data. - * It can be used to let Eigen interface without any overhead with non-Eigen data structures, - * such as plain C arrays or structures from other libraries. By default, it assumes that the - * data is laid out contiguously in memory. You can however override this by explicitly specifying - * inner and outer strides. - * - * Here's an example of simply mapping a contiguous array as a \ref TopicStorageOrders "column-major" matrix: - * \include Map_simple.cpp - * Output: \verbinclude Map_simple.out - * - * If you need to map non-contiguous arrays, you can do so by specifying strides: - * - * Here's an example of mapping an array as a vector, specifying an inner stride, that is, the pointer - * increment between two consecutive coefficients. Here, we're specifying the inner stride as a compile-time - * fixed value. - * \include Map_inner_stride.cpp - * Output: \verbinclude Map_inner_stride.out - * - * Here's an example of mapping an array while specifying an outer stride. Here, since we're mapping - * as a column-major matrix, 'outer stride' means the pointer increment between two consecutive columns. - * Here, we're specifying the outer stride as a runtime parameter. Note that here \c OuterStride<> is - * a short version of \c OuterStride because the default template parameter of OuterStride - * is \c Dynamic - * \include Map_outer_stride.cpp - * Output: \verbinclude Map_outer_stride.out - * - * For more details and for an example of specifying both an inner and an outer stride, see class Stride. - * - * \b Tip: to change the array of data mapped by a Map object, you can use the C++ - * placement new syntax: - * - * Example: \include Map_placement_new.cpp - * Output: \verbinclude Map_placement_new.out - * - * This class is the return type of PlainObjectBase::Map() but can also be used directly. - * - * \sa PlainObjectBase::Map(), \ref TopicStorageOrders - */ - -namespace internal { -template -struct traits > - : public traits -{ - typedef traits TraitsBase; - typedef typename PlainObjectType::Index Index; - typedef typename PlainObjectType::Scalar Scalar; - enum { - InnerStrideAtCompileTime = StrideType::InnerStrideAtCompileTime == 0 - ? int(PlainObjectType::InnerStrideAtCompileTime) - : int(StrideType::InnerStrideAtCompileTime), - OuterStrideAtCompileTime = StrideType::OuterStrideAtCompileTime == 0 - ? int(PlainObjectType::OuterStrideAtCompileTime) - : int(StrideType::OuterStrideAtCompileTime), - HasNoInnerStride = InnerStrideAtCompileTime == 1, - HasNoOuterStride = StrideType::OuterStrideAtCompileTime == 0, - HasNoStride = HasNoInnerStride && HasNoOuterStride, - IsAligned = bool(IMP_EIGEN_ALIGN) && ((int(MapOptions)&Aligned)==Aligned), - IsDynamicSize = PlainObjectType::SizeAtCompileTime==Dynamic, - KeepsPacketAccess = bool(HasNoInnerStride) - && ( bool(IsDynamicSize) - || HasNoOuterStride - || ( OuterStrideAtCompileTime!=Dynamic - && ((static_cast(sizeof(Scalar))*OuterStrideAtCompileTime)%16)==0 ) ), - Flags0 = TraitsBase::Flags & (~NestByRefBit), - Flags1 = IsAligned ? (int(Flags0) | AlignedBit) : (int(Flags0) & ~AlignedBit), - Flags2 = (bool(HasNoStride) || bool(PlainObjectType::IsVectorAtCompileTime)) - ? int(Flags1) : int(Flags1 & ~LinearAccessBit), - Flags3 = is_lvalue::value ? int(Flags2) : (int(Flags2) & ~LvalueBit), - Flags = KeepsPacketAccess ? int(Flags3) : (int(Flags3) & ~PacketAccessBit) - }; -private: - enum { Options }; // Expressions don't have Options -}; -} - -template class Map - : public MapBase > -{ - public: - - typedef MapBase Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(Map) - - typedef typename Base::PointerType PointerType; -#if IMP_EIGEN2_SUPPORT_STAGE <= STAGE30_FULL_EIGEN3_API - typedef const Scalar* PointerArgType; - inline PointerType cast_to_pointer_type(PointerArgType ptr) { return const_cast(ptr); } -#else - typedef PointerType PointerArgType; - inline PointerType cast_to_pointer_type(PointerArgType ptr) { return ptr; } -#endif - - inline Index innerStride() const - { - return StrideType::InnerStrideAtCompileTime != 0 ? m_stride.inner() : 1; - } - - inline Index outerStride() const - { - return StrideType::OuterStrideAtCompileTime != 0 ? m_stride.outer() - : IsVectorAtCompileTime ? this->size() - : int(Flags)&RowMajorBit ? this->cols() - : this->rows(); - } - - /** Constructor in the fixed-size case. - * - * \param dataPtr pointer to the array to map - * \param a_stride optional Stride object, passing the strides. - */ - inline Map(PointerArgType dataPtr, const StrideType& a_stride = StrideType()) - : Base(cast_to_pointer_type(dataPtr)), m_stride(a_stride) - { - PlainObjectType::Base::_check_template_params(); - } - - /** Constructor in the dynamic-size vector case. - * - * \param dataPtr pointer to the array to map - * \param a_size the size of the vector expression - * \param a_stride optional Stride object, passing the strides. - */ - inline Map(PointerArgType dataPtr, Index a_size, const StrideType& a_stride = StrideType()) - : Base(cast_to_pointer_type(dataPtr), a_size), m_stride(a_stride) - { - PlainObjectType::Base::_check_template_params(); - } - - /** Constructor in the dynamic-size matrix case. - * - * \param dataPtr pointer to the array to map - * \param nbRows the number of rows of the matrix expression - * \param nbCols the number of columns of the matrix expression - * \param a_stride optional Stride object, passing the strides. - */ - inline Map(PointerArgType dataPtr, Index nbRows, Index nbCols, const StrideType& a_stride = StrideType()) - : Base(cast_to_pointer_type(dataPtr), nbRows, nbCols), m_stride(a_stride) - { - PlainObjectType::Base::_check_template_params(); - } - - IMP_EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Map) - - protected: - StrideType m_stride; -}; - -template -inline Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols> - ::Array(const Scalar *data) -{ - this->_set_noalias(IMP_Eigen::Map(data)); -} - -template -inline Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols> - ::Matrix(const Scalar *data) -{ - this->_set_noalias(IMP_Eigen::Map(data)); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_MAP_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/MapBase.h b/modules/algebra/include/eigen3/Eigen/src/Core/MapBase.h deleted file mode 100644 index a685700e69..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/MapBase.h +++ /dev/null @@ -1,251 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2007-2010 Benoit Jacob -// Copyright (C) 2008 Gael Guennebaud -// -// 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 IMP_EIGEN_MAPBASE_H -#define IMP_EIGEN_MAPBASE_H - -#define IMP_EIGEN_STATIC_ASSERT_INDEX_BASED_ACCESS(Derived) \ - IMP_EIGEN_STATIC_ASSERT((int(internal::traits::Flags) & LinearAccessBit) || Derived::IsVectorAtCompileTime, \ - YOU_ARE_TRYING_TO_USE_AN_INDEX_BASED_ACCESSOR_ON_AN_EXPRESSION_THAT_DOES_NOT_SUPPORT_THAT) - -namespace IMP_Eigen { - -/** \class MapBase - * \ingroup Core_Module - * - * \brief Base class for Map and Block expression with direct access - * - * \sa class Map, class Block - */ -template class MapBase - : public internal::dense_xpr_base::type -{ - public: - - typedef typename internal::dense_xpr_base::type Base; - enum { - RowsAtCompileTime = internal::traits::RowsAtCompileTime, - ColsAtCompileTime = internal::traits::ColsAtCompileTime, - SizeAtCompileTime = Base::SizeAtCompileTime - }; - - typedef typename internal::traits::StorageKind StorageKind; - typedef typename internal::traits::Index Index; - typedef typename internal::traits::Scalar Scalar; - typedef typename internal::packet_traits::type PacketScalar; - typedef typename NumTraits::Real RealScalar; - typedef typename internal::conditional< - bool(internal::is_lvalue::value), - Scalar *, - const Scalar *>::type - PointerType; - - using Base::derived; -// using Base::RowsAtCompileTime; -// using Base::ColsAtCompileTime; -// using Base::SizeAtCompileTime; - using Base::MaxRowsAtCompileTime; - using Base::MaxColsAtCompileTime; - using Base::MaxSizeAtCompileTime; - using Base::IsVectorAtCompileTime; - using Base::Flags; - using Base::IsRowMajor; - - using Base::rows; - using Base::cols; - using Base::size; - using Base::coeff; - using Base::coeffRef; - using Base::lazyAssign; - using Base::eval; - - using Base::innerStride; - using Base::outerStride; - using Base::rowStride; - using Base::colStride; - - // bug 217 - compile error on ICC 11.1 - using Base::operator=; - - typedef typename Base::CoeffReturnType CoeffReturnType; - - inline Index rows() const { return m_rows.value(); } - inline Index cols() const { return m_cols.value(); } - - /** Returns a pointer to the first coefficient of the matrix or vector. - * - * \note When addressing this data, make sure to honor the strides returned by innerStride() and outerStride(). - * - * \sa innerStride(), outerStride() - */ - inline const Scalar* data() const { return m_data; } - - inline const Scalar& coeff(Index rowId, Index colId) const - { - return m_data[colId * colStride() + rowId * rowStride()]; - } - - inline const Scalar& coeff(Index index) const - { - IMP_EIGEN_STATIC_ASSERT_INDEX_BASED_ACCESS(Derived) - return m_data[index * innerStride()]; - } - - inline const Scalar& coeffRef(Index rowId, Index colId) const - { - return this->m_data[colId * colStride() + rowId * rowStride()]; - } - - inline const Scalar& coeffRef(Index index) const - { - IMP_EIGEN_STATIC_ASSERT_INDEX_BASED_ACCESS(Derived) - return this->m_data[index * innerStride()]; - } - - template - inline PacketScalar packet(Index rowId, Index colId) const - { - return internal::ploadt - (m_data + (colId * colStride() + rowId * rowStride())); - } - - template - inline PacketScalar packet(Index index) const - { - IMP_EIGEN_STATIC_ASSERT_INDEX_BASED_ACCESS(Derived) - return internal::ploadt(m_data + index * innerStride()); - } - - explicit inline MapBase(PointerType dataPtr) : m_data(dataPtr), m_rows(RowsAtCompileTime), m_cols(ColsAtCompileTime) - { - IMP_EIGEN_STATIC_ASSERT_FIXED_SIZE(Derived) - checkSanity(); - } - - inline MapBase(PointerType dataPtr, Index vecSize) - : m_data(dataPtr), - m_rows(RowsAtCompileTime == Dynamic ? vecSize : Index(RowsAtCompileTime)), - m_cols(ColsAtCompileTime == Dynamic ? vecSize : Index(ColsAtCompileTime)) - { - IMP_EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived) - imp_eigen_assert(vecSize >= 0); - imp_eigen_assert(dataPtr == 0 || SizeAtCompileTime == Dynamic || SizeAtCompileTime == vecSize); - checkSanity(); - } - - inline MapBase(PointerType dataPtr, Index nbRows, Index nbCols) - : m_data(dataPtr), m_rows(nbRows), m_cols(nbCols) - { - imp_eigen_assert( (dataPtr == 0) - || ( nbRows >= 0 && (RowsAtCompileTime == Dynamic || RowsAtCompileTime == nbRows) - && nbCols >= 0 && (ColsAtCompileTime == Dynamic || ColsAtCompileTime == nbCols))); - checkSanity(); - } - - #ifdef IMP_EIGEN_MAPBASE_PLUGIN - #include IMP_EIGEN_MAPBASE_PLUGIN - #endif - - protected: - - void checkSanity() const - { - IMP_EIGEN_STATIC_ASSERT(IMP_EIGEN_IMPLIES(internal::traits::Flags&PacketAccessBit, - internal::inner_stride_at_compile_time::ret==1), - PACKET_ACCESS_REQUIRES_TO_HAVE_INNER_STRIDE_FIXED_TO_1); - imp_eigen_assert(IMP_EIGEN_IMPLIES(internal::traits::Flags&AlignedBit, (size_t(m_data) % 16) == 0) - && "input pointer is not aligned on a 16 byte boundary"); - } - - PointerType m_data; - const internal::variable_if_dynamic m_rows; - const internal::variable_if_dynamic m_cols; -}; - -template class MapBase - : public MapBase -{ - typedef MapBase ReadOnlyMapBase; - public: - - typedef MapBase Base; - - typedef typename Base::Scalar Scalar; - typedef typename Base::PacketScalar PacketScalar; - typedef typename Base::Index Index; - typedef typename Base::PointerType PointerType; - - using Base::derived; - using Base::rows; - using Base::cols; - using Base::size; - using Base::coeff; - using Base::coeffRef; - - using Base::innerStride; - using Base::outerStride; - using Base::rowStride; - using Base::colStride; - - typedef typename internal::conditional< - internal::is_lvalue::value, - Scalar, - const Scalar - >::type ScalarWithConstIfNotLvalue; - - inline const Scalar* data() const { return this->m_data; } - inline ScalarWithConstIfNotLvalue* data() { return this->m_data; } // no const-cast here so non-const-correct code will give a compile error - - inline ScalarWithConstIfNotLvalue& coeffRef(Index row, Index col) - { - return this->m_data[col * colStride() + row * rowStride()]; - } - - inline ScalarWithConstIfNotLvalue& coeffRef(Index index) - { - IMP_EIGEN_STATIC_ASSERT_INDEX_BASED_ACCESS(Derived) - return this->m_data[index * innerStride()]; - } - - template - inline void writePacket(Index row, Index col, const PacketScalar& val) - { - internal::pstoret - (this->m_data + (col * colStride() + row * rowStride()), val); - } - - template - inline void writePacket(Index index, const PacketScalar& val) - { - IMP_EIGEN_STATIC_ASSERT_INDEX_BASED_ACCESS(Derived) - internal::pstoret - (this->m_data + index * innerStride(), val); - } - - explicit inline MapBase(PointerType dataPtr) : Base(dataPtr) {} - inline MapBase(PointerType dataPtr, Index vecSize) : Base(dataPtr, vecSize) {} - inline MapBase(PointerType dataPtr, Index nbRows, Index nbCols) : Base(dataPtr, nbRows, nbCols) {} - - Derived& operator=(const MapBase& other) - { - ReadOnlyMapBase::Base::operator=(other); - return derived(); - } - - // In theory we could simply refer to Base:Base::operator=, but MSVC does not like Base::Base, - // see bugs 821 and 920. - using ReadOnlyMapBase::Base::operator=; -}; - -#undef IMP_EIGEN_STATIC_ASSERT_INDEX_BASED_ACCESS - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_MAPBASE_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/MathFunctions.h b/modules/algebra/include/eigen3/Eigen/src/Core/MathFunctions.h deleted file mode 100644 index e8aaf689fa..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/MathFunctions.h +++ /dev/null @@ -1,779 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2006-2010 Benoit Jacob -// -// 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 IMP_EIGEN_MATHFUNCTIONS_H -#define IMP_EIGEN_MATHFUNCTIONS_H - -namespace IMP_Eigen { - -namespace internal { - -/** \internal \struct global_math_functions_filtering_base - * - * What it does: - * Defines a typedef 'type' as follows: - * - if type T has a member typedef Eigen_BaseClassForSpecializationOfGlobalMathFuncImpl, then - * global_math_functions_filtering_base::type is a typedef for it. - * - otherwise, global_math_functions_filtering_base::type is a typedef for T. - * - * How it's used: - * To allow to defined the global math functions (like sin...) in certain cases, like the Array expressions. - * When you do sin(array1+array2), the object array1+array2 has a complicated expression type, all what you want to know - * is that it inherits ArrayBase. So we implement a partial specialization of sin_impl for ArrayBase. - * So we must make sure to use sin_impl > and not sin_impl, otherwise our partial specialization - * won't be used. How does sin know that? That's exactly what global_math_functions_filtering_base tells it. - * - * How it's implemented: - * SFINAE in the style of enable_if. Highly susceptible of breaking compilers. With GCC, it sure does work, but if you replace - * the typename dummy by an integer template parameter, it doesn't work anymore! - */ - -template -struct global_math_functions_filtering_base -{ - typedef T type; -}; - -template struct always_void { typedef void type; }; - -template -struct global_math_functions_filtering_base - ::type - > -{ - typedef typename T::Eigen_BaseClassForSpecializationOfGlobalMathFuncImpl type; -}; - -#define IMP_EIGEN_MATHFUNC_IMPL(func, scalar) IMP_Eigen::internal::func##_impl::type> -#define IMP_EIGEN_MATHFUNC_RETVAL(func, scalar) typename IMP_Eigen::internal::func##_retval::type>::type - -/**************************************************************************** -* Implementation of real * -****************************************************************************/ - -template::IsComplex> -struct real_default_impl -{ - typedef typename NumTraits::Real RealScalar; - static inline RealScalar run(const Scalar& x) - { - return x; - } -}; - -template -struct real_default_impl -{ - typedef typename NumTraits::Real RealScalar; - static inline RealScalar run(const Scalar& x) - { - using std::real; - return real(x); - } -}; - -template struct real_impl : real_default_impl {}; - -template -struct real_retval -{ - typedef typename NumTraits::Real type; -}; - - -/**************************************************************************** -* Implementation of imag * -****************************************************************************/ - -template::IsComplex> -struct imag_default_impl -{ - typedef typename NumTraits::Real RealScalar; - static inline RealScalar run(const Scalar&) - { - return RealScalar(0); - } -}; - -template -struct imag_default_impl -{ - typedef typename NumTraits::Real RealScalar; - static inline RealScalar run(const Scalar& x) - { - using std::imag; - return imag(x); - } -}; - -template struct imag_impl : imag_default_impl {}; - -template -struct imag_retval -{ - typedef typename NumTraits::Real type; -}; - -/**************************************************************************** -* Implementation of real_ref * -****************************************************************************/ - -template -struct real_ref_impl -{ - typedef typename NumTraits::Real RealScalar; - static inline RealScalar& run(Scalar& x) - { - return reinterpret_cast(&x)[0]; - } - static inline const RealScalar& run(const Scalar& x) - { - return reinterpret_cast(&x)[0]; - } -}; - -template -struct real_ref_retval -{ - typedef typename NumTraits::Real & type; -}; - -/**************************************************************************** -* Implementation of imag_ref * -****************************************************************************/ - -template -struct imag_ref_default_impl -{ - typedef typename NumTraits::Real RealScalar; - static inline RealScalar& run(Scalar& x) - { - return reinterpret_cast(&x)[1]; - } - static inline const RealScalar& run(const Scalar& x) - { - return reinterpret_cast(&x)[1]; - } -}; - -template -struct imag_ref_default_impl -{ - static inline Scalar run(Scalar&) - { - return Scalar(0); - } - static inline const Scalar run(const Scalar&) - { - return Scalar(0); - } -}; - -template -struct imag_ref_impl : imag_ref_default_impl::IsComplex> {}; - -template -struct imag_ref_retval -{ - typedef typename NumTraits::Real & type; -}; - -/**************************************************************************** -* Implementation of conj * -****************************************************************************/ - -template::IsComplex> -struct conj_impl -{ - static inline Scalar run(const Scalar& x) - { - return x; - } -}; - -template -struct conj_impl -{ - static inline Scalar run(const Scalar& x) - { - using std::conj; - return conj(x); - } -}; - -template -struct conj_retval -{ - typedef Scalar type; -}; - -/**************************************************************************** -* Implementation of abs2 * -****************************************************************************/ - -template -struct abs2_impl_default -{ - typedef typename NumTraits::Real RealScalar; - static inline RealScalar run(const Scalar& x) - { - return x*x; - } -}; - -template -struct abs2_impl_default // IsComplex -{ - typedef typename NumTraits::Real RealScalar; - static inline RealScalar run(const Scalar& x) - { - return real(x)*real(x) + imag(x)*imag(x); - } -}; - -template -struct abs2_impl -{ - typedef typename NumTraits::Real RealScalar; - static inline RealScalar run(const Scalar& x) - { - return abs2_impl_default::IsComplex>::run(x); - } -}; - -template -struct abs2_retval -{ - typedef typename NumTraits::Real type; -}; - -/**************************************************************************** -* Implementation of norm1 * -****************************************************************************/ - -template -struct norm1_default_impl -{ - typedef typename NumTraits::Real RealScalar; - static inline RealScalar run(const Scalar& x) - { - using std::abs; - return abs(real(x)) + abs(imag(x)); - } -}; - -template -struct norm1_default_impl -{ - static inline Scalar run(const Scalar& x) - { - using std::abs; - return abs(x); - } -}; - -template -struct norm1_impl : norm1_default_impl::IsComplex> {}; - -template -struct norm1_retval -{ - typedef typename NumTraits::Real type; -}; - -/**************************************************************************** -* Implementation of hypot * -****************************************************************************/ - -template -struct hypot_impl -{ - typedef typename NumTraits::Real RealScalar; - static inline RealScalar run(const Scalar& x, const Scalar& y) - { - using std::max; - using std::min; - using std::abs; - using std::sqrt; - RealScalar _x = abs(x); - RealScalar _y = abs(y); - RealScalar p = (max)(_x, _y); - if(p==RealScalar(0)) return RealScalar(0); - RealScalar q = (min)(_x, _y); - RealScalar qp = q/p; - return p * sqrt(RealScalar(1) + qp*qp); - } -}; - -template -struct hypot_retval -{ - typedef typename NumTraits::Real type; -}; - -/**************************************************************************** -* Implementation of cast * -****************************************************************************/ - -template -struct cast_impl -{ - static inline NewType run(const OldType& x) - { - return static_cast(x); - } -}; - -// here, for once, we're plainly returning NewType: we don't want cast to do weird things. - -template -inline NewType cast(const OldType& x) -{ - return cast_impl::run(x); -} - -/**************************************************************************** -* Implementation of atanh2 * -****************************************************************************/ - -template -struct atanh2_default_impl -{ - typedef Scalar retval; - typedef typename NumTraits::Real RealScalar; - static inline Scalar run(const Scalar& x, const Scalar& y) - { - using std::abs; - using std::log; - using std::sqrt; - Scalar z = x / y; - if (y == Scalar(0) || abs(z) > sqrt(NumTraits::epsilon())) - return RealScalar(0.5) * log((y + x) / (y - x)); - else - return z + z*z*z / RealScalar(3); - } -}; - -template -struct atanh2_default_impl -{ - static inline Scalar run(const Scalar&, const Scalar&) - { - IMP_EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar) - return Scalar(0); - } -}; - -template -struct atanh2_impl : atanh2_default_impl::IsInteger> {}; - -template -struct atanh2_retval -{ - typedef Scalar type; -}; - -/**************************************************************************** -* Implementation of pow * -****************************************************************************/ - -template -struct pow_default_impl -{ - typedef Scalar retval; - static inline Scalar run(const Scalar& x, const Scalar& y) - { - using std::pow; - return pow(x, y); - } -}; - -template -struct pow_default_impl -{ - static inline Scalar run(Scalar x, Scalar y) - { - Scalar res(1); - imp_eigen_assert(!NumTraits::IsSigned || y >= 0); - if(y & 1) res *= x; - y >>= 1; - while(y) - { - x *= x; - if(y&1) res *= x; - y >>= 1; - } - return res; - } -}; - -template -struct pow_impl : pow_default_impl::IsInteger> {}; - -template -struct pow_retval -{ - typedef Scalar type; -}; - -/**************************************************************************** -* Implementation of random * -****************************************************************************/ - -template -struct random_default_impl {}; - -template -struct random_impl : random_default_impl::IsComplex, NumTraits::IsInteger> {}; - -template -struct random_retval -{ - typedef Scalar type; -}; - -template inline IMP_EIGEN_MATHFUNC_RETVAL(random, Scalar) random(const Scalar& x, const Scalar& y); -template inline IMP_EIGEN_MATHFUNC_RETVAL(random, Scalar) random(); - -template -struct random_default_impl -{ - static inline Scalar run(const Scalar& x, const Scalar& y) - { - return x + (y-x) * Scalar(std::rand()) / Scalar(RAND_MAX); - } - static inline Scalar run() - { - return run(Scalar(NumTraits::IsSigned ? -1 : 0), Scalar(1)); - } -}; - -enum { - floor_log2_terminate, - floor_log2_move_up, - floor_log2_move_down, - floor_log2_bogus -}; - -template struct floor_log2_selector -{ - enum { middle = (lower + upper) / 2, - value = (upper <= lower + 1) ? int(floor_log2_terminate) - : (n < (1 << middle)) ? int(floor_log2_move_down) - : (n==0) ? int(floor_log2_bogus) - : int(floor_log2_move_up) - }; -}; - -template::value> -struct floor_log2 {}; - -template -struct floor_log2 -{ - enum { value = floor_log2::middle>::value }; -}; - -template -struct floor_log2 -{ - enum { value = floor_log2::middle, upper>::value }; -}; - -template -struct floor_log2 -{ - enum { value = (n >= ((unsigned int)(1) << (lower+1))) ? lower+1 : lower }; -}; - -template -struct floor_log2 -{ - // no value, error at compile time -}; - -template -struct random_default_impl -{ - typedef typename NumTraits::NonInteger NonInteger; - - static inline Scalar run(const Scalar& x, const Scalar& y) - { - return x + Scalar((NonInteger(y)-x+1) * std::rand() / (RAND_MAX + NonInteger(1))); - } - - static inline Scalar run() - { -#ifdef IMP_EIGEN_MAKING_DOCS - return run(Scalar(NumTraits::IsSigned ? -10 : 0), Scalar(10)); -#else - enum { rand_bits = floor_log2<(unsigned int)(RAND_MAX)+1>::value, - scalar_bits = sizeof(Scalar) * CHAR_BIT, - shift = IMP_EIGEN_PLAIN_ENUM_MAX(0, int(rand_bits) - int(scalar_bits)), - offset = NumTraits::IsSigned ? (1 << (IMP_EIGEN_PLAIN_ENUM_MIN(rand_bits,scalar_bits)-1)) : 0 - }; - return Scalar((std::rand() >> shift) - offset); -#endif - } -}; - -template -struct random_default_impl -{ - static inline Scalar run(const Scalar& x, const Scalar& y) - { - return Scalar(random(real(x), real(y)), - random(imag(x), imag(y))); - } - static inline Scalar run() - { - typedef typename NumTraits::Real RealScalar; - return Scalar(random(), random()); - } -}; - -template -inline IMP_EIGEN_MATHFUNC_RETVAL(random, Scalar) random(const Scalar& x, const Scalar& y) -{ - return IMP_EIGEN_MATHFUNC_IMPL(random, Scalar)::run(x, y); -} - -template -inline IMP_EIGEN_MATHFUNC_RETVAL(random, Scalar) random() -{ - return IMP_EIGEN_MATHFUNC_IMPL(random, Scalar)::run(); -} - -} // end namespace internal - -/**************************************************************************** -* Generic math function * -****************************************************************************/ - -namespace numext { - -template -inline IMP_EIGEN_MATHFUNC_RETVAL(real, Scalar) real(const Scalar& x) -{ - return IMP_EIGEN_MATHFUNC_IMPL(real, Scalar)::run(x); -} - -template -inline typename internal::add_const_on_value_type< IMP_EIGEN_MATHFUNC_RETVAL(real_ref, Scalar) >::type real_ref(const Scalar& x) -{ - return internal::real_ref_impl::run(x); -} - -template -inline IMP_EIGEN_MATHFUNC_RETVAL(real_ref, Scalar) real_ref(Scalar& x) -{ - return IMP_EIGEN_MATHFUNC_IMPL(real_ref, Scalar)::run(x); -} - -template -inline IMP_EIGEN_MATHFUNC_RETVAL(imag, Scalar) imag(const Scalar& x) -{ - return IMP_EIGEN_MATHFUNC_IMPL(imag, Scalar)::run(x); -} - -template -inline typename internal::add_const_on_value_type< IMP_EIGEN_MATHFUNC_RETVAL(imag_ref, Scalar) >::type imag_ref(const Scalar& x) -{ - return internal::imag_ref_impl::run(x); -} - -template -inline IMP_EIGEN_MATHFUNC_RETVAL(imag_ref, Scalar) imag_ref(Scalar& x) -{ - return IMP_EIGEN_MATHFUNC_IMPL(imag_ref, Scalar)::run(x); -} - -template -inline IMP_EIGEN_MATHFUNC_RETVAL(conj, Scalar) conj(const Scalar& x) -{ - return IMP_EIGEN_MATHFUNC_IMPL(conj, Scalar)::run(x); -} - -template -inline IMP_EIGEN_MATHFUNC_RETVAL(abs2, Scalar) abs2(const Scalar& x) -{ - return IMP_EIGEN_MATHFUNC_IMPL(abs2, Scalar)::run(x); -} - -template -inline IMP_EIGEN_MATHFUNC_RETVAL(norm1, Scalar) norm1(const Scalar& x) -{ - return IMP_EIGEN_MATHFUNC_IMPL(norm1, Scalar)::run(x); -} - -template -inline IMP_EIGEN_MATHFUNC_RETVAL(hypot, Scalar) hypot(const Scalar& x, const Scalar& y) -{ - return IMP_EIGEN_MATHFUNC_IMPL(hypot, Scalar)::run(x, y); -} - -template -inline IMP_EIGEN_MATHFUNC_RETVAL(atanh2, Scalar) atanh2(const Scalar& x, const Scalar& y) -{ - return IMP_EIGEN_MATHFUNC_IMPL(atanh2, Scalar)::run(x, y); -} - -template -inline IMP_EIGEN_MATHFUNC_RETVAL(pow, Scalar) pow(const Scalar& x, const Scalar& y) -{ - return IMP_EIGEN_MATHFUNC_IMPL(pow, Scalar)::run(x, y); -} - -// std::isfinite is non standard, so let's define our own version, -// even though it is not very efficient. -template bool (isfinite)(const T& x) -{ - return x::highest() && x>NumTraits::lowest(); -} - -} // end namespace numext - -namespace internal { - -/**************************************************************************** -* Implementation of fuzzy comparisons * -****************************************************************************/ - -template -struct scalar_fuzzy_default_impl {}; - -template -struct scalar_fuzzy_default_impl -{ - typedef typename NumTraits::Real RealScalar; - template - static inline bool isMuchSmallerThan(const Scalar& x, const OtherScalar& y, const RealScalar& prec) - { - using std::abs; - return abs(x) <= abs(y) * prec; - } - static inline bool isApprox(const Scalar& x, const Scalar& y, const RealScalar& prec) - { - using std::min; - using std::abs; - return abs(x - y) <= (min)(abs(x), abs(y)) * prec; - } - static inline bool isApproxOrLessThan(const Scalar& x, const Scalar& y, const RealScalar& prec) - { - return x <= y || isApprox(x, y, prec); - } -}; - -template -struct scalar_fuzzy_default_impl -{ - typedef typename NumTraits::Real RealScalar; - template - static inline bool isMuchSmallerThan(const Scalar& x, const Scalar&, const RealScalar&) - { - return x == Scalar(0); - } - static inline bool isApprox(const Scalar& x, const Scalar& y, const RealScalar&) - { - return x == y; - } - static inline bool isApproxOrLessThan(const Scalar& x, const Scalar& y, const RealScalar&) - { - return x <= y; - } -}; - -template -struct scalar_fuzzy_default_impl -{ - typedef typename NumTraits::Real RealScalar; - template - static inline bool isMuchSmallerThan(const Scalar& x, const OtherScalar& y, const RealScalar& prec) - { - return numext::abs2(x) <= numext::abs2(y) * prec * prec; - } - static inline bool isApprox(const Scalar& x, const Scalar& y, const RealScalar& prec) - { - using std::min; - return numext::abs2(x - y) <= (min)(numext::abs2(x), numext::abs2(y)) * prec * prec; - } -}; - -template -struct scalar_fuzzy_impl : scalar_fuzzy_default_impl::IsComplex, NumTraits::IsInteger> {}; - -template -inline bool isMuchSmallerThan(const Scalar& x, const OtherScalar& y, - const typename NumTraits::Real &precision = NumTraits::dummy_precision()) -{ - return scalar_fuzzy_impl::template isMuchSmallerThan(x, y, precision); -} - -template -inline bool isApprox(const Scalar& x, const Scalar& y, - const typename NumTraits::Real &precision = NumTraits::dummy_precision()) -{ - return scalar_fuzzy_impl::isApprox(x, y, precision); -} - -template -inline bool isApproxOrLessThan(const Scalar& x, const Scalar& y, - const typename NumTraits::Real &precision = NumTraits::dummy_precision()) -{ - return scalar_fuzzy_impl::isApproxOrLessThan(x, y, precision); -} - -/****************************************** -*** The special case of the bool type *** -******************************************/ - -template<> struct random_impl -{ - static inline bool run() - { - return random(0,1)==0 ? false : true; - } -}; - -template<> struct scalar_fuzzy_impl -{ - typedef bool RealScalar; - - template - static inline bool isMuchSmallerThan(const bool& x, const bool&, const bool&) - { - return !x; - } - - static inline bool isApprox(bool x, bool y, bool) - { - return x == y; - } - - static inline bool isApproxOrLessThan(const bool& x, const bool& y, const bool&) - { - return (!x) || y; - } - -}; - - -} // end namespace internal - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_MATHFUNCTIONS_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/Matrix.h b/modules/algebra/include/eigen3/Eigen/src/Core/Matrix.h deleted file mode 100644 index bd5bc4fc6d..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/Matrix.h +++ /dev/null @@ -1,420 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2006-2010 Benoit Jacob -// Copyright (C) 2008-2009 Gael Guennebaud -// -// 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 IMP_EIGEN_MATRIX_H -#define IMP_EIGEN_MATRIX_H - -namespace IMP_Eigen { - -/** \class Matrix - * \ingroup Core_Module - * - * \brief The matrix class, also used for vectors and row-vectors - * - * The %Matrix class is the work-horse for all \em dense (\ref dense "note") matrices and vectors within Eigen. - * Vectors are matrices with one column, and row-vectors are matrices with one row. - * - * The %Matrix class encompasses \em both fixed-size and dynamic-size objects (\ref fixedsize "note"). - * - * The first three template parameters are required: - * \tparam _Scalar \anchor matrix_tparam_scalar Numeric type, e.g. float, double, int or std::complex. - * User defined sclar types are supported as well (see \ref user_defined_scalars "here"). - * \tparam _Rows Number of rows, or \b Dynamic - * \tparam _Cols Number of columns, or \b Dynamic - * - * The remaining template parameters are optional -- in most cases you don't have to worry about them. - * \tparam _Options \anchor matrix_tparam_options A combination of either \b #RowMajor or \b #ColMajor, and of either - * \b #AutoAlign or \b #DontAlign. - * The former controls \ref TopicStorageOrders "storage order", and defaults to column-major. The latter controls alignment, which is required - * for vectorization. It defaults to aligning matrices except for fixed sizes that aren't a multiple of the packet size. - * \tparam _MaxRows Maximum number of rows. Defaults to \a _Rows (\ref maxrows "note"). - * \tparam _MaxCols Maximum number of columns. Defaults to \a _Cols (\ref maxrows "note"). - * - * Eigen provides a number of typedefs covering the usual cases. Here are some examples: - * - * \li \c Matrix2d is a 2x2 square matrix of doubles (\c Matrix) - * \li \c Vector4f is a vector of 4 floats (\c Matrix) - * \li \c RowVector3i is a row-vector of 3 ints (\c Matrix) - * - * \li \c MatrixXf is a dynamic-size matrix of floats (\c Matrix) - * \li \c VectorXf is a dynamic-size vector of floats (\c Matrix) - * - * \li \c Matrix2Xf is a partially fixed-size (dynamic-size) matrix of floats (\c Matrix) - * \li \c MatrixX3d is a partially dynamic-size (fixed-size) matrix of double (\c Matrix) - * - * See \link matrixtypedefs this page \endlink for a complete list of predefined \em %Matrix and \em Vector typedefs. - * - * You can access elements of vectors and matrices using normal subscripting: - * - * \code - * IMP_Eigen::VectorXd v(10); - * v[0] = 0.1; - * v[1] = 0.2; - * v(0) = 0.3; - * v(1) = 0.4; - * - * IMP_Eigen::MatrixXi m(10, 10); - * m(0, 1) = 1; - * m(0, 2) = 2; - * m(0, 3) = 3; - * \endcode - * - * This class can be extended with the help of the plugin mechanism described on the page - * \ref TopicCustomizingEigen by defining the preprocessor symbol \c IMP_EIGEN_MATRIX_PLUGIN. - * - * Some notes: - * - *
- *
\anchor dense Dense versus sparse:
- *
This %Matrix class handles dense, not sparse matrices and vectors. For sparse matrices and vectors, see the Sparse module. - * - * Dense matrices and vectors are plain usual arrays of coefficients. All the coefficients are stored, in an ordinary contiguous array. - * This is unlike Sparse matrices and vectors where the coefficients are stored as a list of nonzero coefficients.
- * - *
\anchor fixedsize Fixed-size versus dynamic-size:
- *
Fixed-size means that the numbers of rows and columns are known are compile-time. In this case, Eigen allocates the array - * of coefficients as a fixed-size array, as a class member. This makes sense for very small matrices, typically up to 4x4, sometimes up - * to 16x16. Larger matrices should be declared as dynamic-size even if one happens to know their size at compile-time. - * - * Dynamic-size means that the numbers of rows or columns are not necessarily known at compile-time. In this case they are runtime - * variables, and the array of coefficients is allocated dynamically on the heap. - * - * Note that \em dense matrices, be they Fixed-size or Dynamic-size, do not expand dynamically in the sense of a std::map. - * If you want this behavior, see the Sparse module.
- * - *
\anchor maxrows _MaxRows and _MaxCols:
- *
In most cases, one just leaves these parameters to the default values. - * These parameters mean the maximum size of rows and columns that the matrix may have. They are useful in cases - * when the exact numbers of rows and columns are not known are compile-time, but it is known at compile-time that they cannot - * exceed a certain value. This happens when taking dynamic-size blocks inside fixed-size matrices: in this case _MaxRows and _MaxCols - * are the dimensions of the original matrix, while _Rows and _Cols are Dynamic.
- *
- * - * \see MatrixBase for the majority of the API methods for matrices, \ref TopicClassHierarchy, - * \ref TopicStorageOrders - */ - -namespace internal { -template -struct traits > -{ - typedef _Scalar Scalar; - typedef Dense StorageKind; - typedef DenseIndex Index; - typedef MatrixXpr XprKind; - enum { - RowsAtCompileTime = _Rows, - ColsAtCompileTime = _Cols, - MaxRowsAtCompileTime = _MaxRows, - MaxColsAtCompileTime = _MaxCols, - Flags = compute_matrix_flags<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::ret, - CoeffReadCost = NumTraits::ReadCost, - Options = _Options, - InnerStrideAtCompileTime = 1, - OuterStrideAtCompileTime = (Options&RowMajor) ? ColsAtCompileTime : RowsAtCompileTime - }; -}; -} - -template -class Matrix - : public PlainObjectBase > -{ - public: - - /** \brief Base class typedef. - * \sa PlainObjectBase - */ - typedef PlainObjectBase Base; - - enum { Options = _Options }; - - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(Matrix) - - typedef typename Base::PlainObject PlainObject; - - using Base::base; - using Base::coeffRef; - - /** - * \brief Assigns matrices to each other. - * - * \note This is a special case of the templated operator=. Its purpose is - * to prevent a default operator= from hiding the templated operator=. - * - * \callgraph - */ - IMP_EIGEN_STRONG_INLINE Matrix& operator=(const Matrix& other) - { - return Base::_set(other); - } - - /** \internal - * \brief Copies the value of the expression \a other into \c *this with automatic resizing. - * - * *this might be resized to match the dimensions of \a other. If *this was a null matrix (not already initialized), - * it will be initialized. - * - * Note that copying a row-vector into a vector (and conversely) is allowed. - * The resizing, if any, is then done in the appropriate way so that row-vectors - * remain row-vectors and vectors remain vectors. - */ - template - IMP_EIGEN_STRONG_INLINE Matrix& operator=(const MatrixBase& other) - { - return Base::_set(other); - } - - /* Here, doxygen failed to copy the brief information when using \copydoc */ - - /** - * \brief Copies the generic expression \a other into *this. - * \copydetails DenseBase::operator=(const EigenBase &other) - */ - template - IMP_EIGEN_STRONG_INLINE Matrix& operator=(const EigenBase &other) - { - return Base::operator=(other); - } - - template - IMP_EIGEN_STRONG_INLINE Matrix& operator=(const ReturnByValue& func) - { - return Base::operator=(func); - } - - /** \brief Default constructor. - * - * For fixed-size matrices, does nothing. - * - * For dynamic-size matrices, creates an empty matrix of size 0. Does not allocate any array. Such a matrix - * is called a null matrix. This constructor is the unique way to create null matrices: resizing - * a matrix to 0 is not supported. - * - * \sa resize(Index,Index) - */ - IMP_EIGEN_STRONG_INLINE Matrix() : Base() - { - Base::_check_template_params(); - IMP_EIGEN_INITIALIZE_COEFFS_IF_THAT_OPTION_IS_ENABLED - } - - // FIXME is it still needed - Matrix(internal::constructor_without_unaligned_array_assert) - : Base(internal::constructor_without_unaligned_array_assert()) - { Base::_check_template_params(); IMP_EIGEN_INITIALIZE_COEFFS_IF_THAT_OPTION_IS_ENABLED } - -#ifdef IMP_EIGEN_HAVE_RVALUE_REFERENCES - Matrix(Matrix&& other) - : Base(std::move(other)) - { - Base::_check_template_params(); - if (RowsAtCompileTime!=Dynamic && ColsAtCompileTime!=Dynamic) - Base::_set_noalias(other); - } - Matrix& operator=(Matrix&& other) - { - other.swap(*this); - return *this; - } -#endif - - /** \brief Constructs a vector or row-vector with given dimension. \only_for_vectors - * - * Note that this is only useful for dynamic-size vectors. For fixed-size vectors, - * it is redundant to pass the dimension here, so it makes more sense to use the default - * constructor Matrix() instead. - */ - IMP_EIGEN_STRONG_INLINE explicit Matrix(Index dim) - : Base(dim, RowsAtCompileTime == 1 ? 1 : dim, ColsAtCompileTime == 1 ? 1 : dim) - { - Base::_check_template_params(); - IMP_EIGEN_STATIC_ASSERT_VECTOR_ONLY(Matrix) - imp_eigen_assert(dim >= 0); - imp_eigen_assert(SizeAtCompileTime == Dynamic || SizeAtCompileTime == dim); - IMP_EIGEN_INITIALIZE_COEFFS_IF_THAT_OPTION_IS_ENABLED - } - - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - template - IMP_EIGEN_STRONG_INLINE Matrix(const T0& x, const T1& y) - { - Base::_check_template_params(); - Base::template _init2(x, y); - } - #else - /** \brief Constructs an uninitialized matrix with \a rows rows and \a cols columns. - * - * This is useful for dynamic-size matrices. For fixed-size matrices, - * it is redundant to pass these parameters, so one should use the default constructor - * Matrix() instead. */ - Matrix(Index rows, Index cols); - /** \brief Constructs an initialized 2D vector with given coefficients */ - Matrix(const Scalar& x, const Scalar& y); - #endif - - /** \brief Constructs an initialized 3D vector with given coefficients */ - IMP_EIGEN_STRONG_INLINE Matrix(const Scalar& x, const Scalar& y, const Scalar& z) - { - Base::_check_template_params(); - IMP_EIGEN_STATIC_ASSERT_VECTOR_SPECIFIC_SIZE(Matrix, 3) - m_storage.data()[0] = x; - m_storage.data()[1] = y; - m_storage.data()[2] = z; - } - /** \brief Constructs an initialized 4D vector with given coefficients */ - IMP_EIGEN_STRONG_INLINE Matrix(const Scalar& x, const Scalar& y, const Scalar& z, const Scalar& w) - { - Base::_check_template_params(); - IMP_EIGEN_STATIC_ASSERT_VECTOR_SPECIFIC_SIZE(Matrix, 4) - m_storage.data()[0] = x; - m_storage.data()[1] = y; - m_storage.data()[2] = z; - m_storage.data()[3] = w; - } - - explicit Matrix(const Scalar *data); - - /** \brief Constructor copying the value of the expression \a other */ - template - IMP_EIGEN_STRONG_INLINE Matrix(const MatrixBase& other) - : Base(other.rows() * other.cols(), other.rows(), other.cols()) - { - // This test resides here, to bring the error messages closer to the user. Normally, these checks - // are performed deeply within the library, thus causing long and scary error traces. - IMP_EIGEN_STATIC_ASSERT((internal::is_same::value), - YOU_MIXED_DIFFERENT_NUMERIC_TYPES__YOU_NEED_TO_USE_THE_CAST_METHOD_OF_MATRIXBASE_TO_CAST_NUMERIC_TYPES_EXPLICITLY) - - Base::_check_template_params(); - Base::_set_noalias(other); - } - /** \brief Copy constructor */ - IMP_EIGEN_STRONG_INLINE Matrix(const Matrix& other) - : Base(other.rows() * other.cols(), other.rows(), other.cols()) - { - Base::_check_template_params(); - Base::_set_noalias(other); - } - /** \brief Copy constructor with in-place evaluation */ - template - IMP_EIGEN_STRONG_INLINE Matrix(const ReturnByValue& other) - { - Base::_check_template_params(); - Base::resize(other.rows(), other.cols()); - other.evalTo(*this); - } - - /** \brief Copy constructor for generic expressions. - * \sa MatrixBase::operator=(const EigenBase&) - */ - template - IMP_EIGEN_STRONG_INLINE Matrix(const EigenBase &other) - : Base(other.derived().rows() * other.derived().cols(), other.derived().rows(), other.derived().cols()) - { - Base::_check_template_params(); - Base::_resize_to_match(other); - // FIXME/CHECK: isn't *this = other.derived() more efficient. it allows to - // go for pure _set() implementations, right? - *this = other; - } - - /** \internal - * \brief Override MatrixBase::swap() since for dynamic-sized matrices - * of same type it is enough to swap the data pointers. - */ - template - void swap(MatrixBase const & other) - { this->_swap(other.derived()); } - - inline Index innerStride() const { return 1; } - inline Index outerStride() const { return this->innerSize(); } - - /////////// Geometry module /////////// - - template - explicit Matrix(const RotationBase& r); - template - Matrix& operator=(const RotationBase& r); - - #ifdef IMP_EIGEN2_SUPPORT - template - explicit Matrix(const eigen2_RotationBase& r); - template - Matrix& operator=(const eigen2_RotationBase& r); - #endif - - // allow to extend Matrix outside Eigen - #ifdef IMP_EIGEN_MATRIX_PLUGIN - #include IMP_EIGEN_MATRIX_PLUGIN - #endif - - protected: - template - friend struct internal::conservative_resize_like_impl; - - using Base::m_storage; -}; - -/** \defgroup matrixtypedefs Global matrix typedefs - * - * \ingroup Core_Module - * - * Eigen defines several typedef shortcuts for most common matrix and vector types. - * - * The general patterns are the following: - * - * \c MatrixSizeType where \c Size can be \c 2,\c 3,\c 4 for fixed size square matrices or \c X for dynamic size, - * and where \c Type can be \c i for integer, \c f for float, \c d for double, \c cf for complex float, \c cd - * for complex double. - * - * For example, \c Matrix3d is a fixed-size 3x3 matrix type of doubles, and \c MatrixXf is a dynamic-size matrix of floats. - * - * There are also \c VectorSizeType and \c RowVectorSizeType which are self-explanatory. For example, \c Vector4cf is - * a fixed-size vector of 4 complex floats. - * - * \sa class Matrix - */ - -#define IMP_EIGEN_MAKE_TYPEDEFS(Type, TypeSuffix, Size, SizeSuffix) \ -/** \ingroup matrixtypedefs */ \ -typedef Matrix Matrix##SizeSuffix##TypeSuffix; \ -/** \ingroup matrixtypedefs */ \ -typedef Matrix Vector##SizeSuffix##TypeSuffix; \ -/** \ingroup matrixtypedefs */ \ -typedef Matrix RowVector##SizeSuffix##TypeSuffix; - -#define IMP_EIGEN_MAKE_FIXED_TYPEDEFS(Type, TypeSuffix, Size) \ -/** \ingroup matrixtypedefs */ \ -typedef Matrix Matrix##Size##X##TypeSuffix; \ -/** \ingroup matrixtypedefs */ \ -typedef Matrix Matrix##X##Size##TypeSuffix; - -#define IMP_EIGEN_MAKE_TYPEDEFS_ALL_SIZES(Type, TypeSuffix) \ -IMP_EIGEN_MAKE_TYPEDEFS(Type, TypeSuffix, 2, 2) \ -IMP_EIGEN_MAKE_TYPEDEFS(Type, TypeSuffix, 3, 3) \ -IMP_EIGEN_MAKE_TYPEDEFS(Type, TypeSuffix, 4, 4) \ -IMP_EIGEN_MAKE_TYPEDEFS(Type, TypeSuffix, Dynamic, X) \ -IMP_EIGEN_MAKE_FIXED_TYPEDEFS(Type, TypeSuffix, 2) \ -IMP_EIGEN_MAKE_FIXED_TYPEDEFS(Type, TypeSuffix, 3) \ -IMP_EIGEN_MAKE_FIXED_TYPEDEFS(Type, TypeSuffix, 4) - -IMP_EIGEN_MAKE_TYPEDEFS_ALL_SIZES(int, i) -IMP_EIGEN_MAKE_TYPEDEFS_ALL_SIZES(float, f) -IMP_EIGEN_MAKE_TYPEDEFS_ALL_SIZES(double, d) -IMP_EIGEN_MAKE_TYPEDEFS_ALL_SIZES(std::complex, cf) -IMP_EIGEN_MAKE_TYPEDEFS_ALL_SIZES(std::complex, cd) - -#undef IMP_EIGEN_MAKE_TYPEDEFS_ALL_SIZES -#undef IMP_EIGEN_MAKE_TYPEDEFS -#undef IMP_EIGEN_MAKE_FIXED_TYPEDEFS - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_MATRIX_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/MatrixBase.h b/modules/algebra/include/eigen3/Eigen/src/Core/MatrixBase.h deleted file mode 100644 index aa5e7203e1..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/MatrixBase.h +++ /dev/null @@ -1,563 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2006-2009 Benoit Jacob -// Copyright (C) 2008 Gael Guennebaud -// -// 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 IMP_EIGEN_MATRIXBASE_H -#define IMP_EIGEN_MATRIXBASE_H - -namespace IMP_Eigen { - -/** \class MatrixBase - * \ingroup Core_Module - * - * \brief Base class for all dense matrices, vectors, and expressions - * - * This class is the base that is inherited by all matrix, vector, and related expression - * types. Most of the Eigen API is contained in this class, and its base classes. Other important - * classes for the Eigen API are Matrix, and VectorwiseOp. - * - * Note that some methods are defined in other modules such as the \ref LU_Module LU module - * for all functions related to matrix inversions. - * - * \tparam Derived is the derived type, e.g. a matrix type, or an expression, etc. - * - * When writing a function taking Eigen objects as argument, if you want your function - * to take as argument any matrix, vector, or expression, just let it take a - * MatrixBase argument. As an example, here is a function printFirstRow which, given - * a matrix, vector, or expression \a x, prints the first row of \a x. - * - * \code - template - void printFirstRow(const IMP_Eigen::MatrixBase& x) - { - cout << x.row(0) << endl; - } - * \endcode - * - * This class can be extended with the help of the plugin mechanism described on the page - * \ref TopicCustomizingEigen by defining the preprocessor symbol \c IMP_EIGEN_MATRIXBASE_PLUGIN. - * - * \sa \ref TopicClassHierarchy - */ -template class MatrixBase - : public DenseBase -{ - public: -#ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - typedef MatrixBase StorageBaseType; - typedef typename internal::traits::StorageKind StorageKind; - typedef typename internal::traits::Index Index; - typedef typename internal::traits::Scalar Scalar; - typedef typename internal::packet_traits::type PacketScalar; - typedef typename NumTraits::Real RealScalar; - - typedef DenseBase Base; - using Base::RowsAtCompileTime; - using Base::ColsAtCompileTime; - using Base::SizeAtCompileTime; - using Base::MaxRowsAtCompileTime; - using Base::MaxColsAtCompileTime; - using Base::MaxSizeAtCompileTime; - using Base::IsVectorAtCompileTime; - using Base::Flags; - using Base::CoeffReadCost; - - using Base::derived; - using Base::const_cast_derived; - using Base::rows; - using Base::cols; - using Base::size; - using Base::coeff; - using Base::coeffRef; - using Base::lazyAssign; - using Base::eval; - using Base::operator+=; - using Base::operator-=; - using Base::operator*=; - using Base::operator/=; - - typedef typename Base::CoeffReturnType CoeffReturnType; - typedef typename Base::ConstTransposeReturnType ConstTransposeReturnType; - typedef typename Base::RowXpr RowXpr; - typedef typename Base::ColXpr ColXpr; -#endif // not IMP_EIGEN_PARSED_BY_DOXYGEN - - - -#ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - /** type of the equivalent square matrix */ - typedef Matrix SquareMatrixType; -#endif // not IMP_EIGEN_PARSED_BY_DOXYGEN - - /** \returns the size of the main diagonal, which is min(rows(),cols()). - * \sa rows(), cols(), SizeAtCompileTime. */ - inline Index diagonalSize() const { return (std::min)(rows(),cols()); } - - /** \brief The plain matrix type corresponding to this expression. - * - * This is not necessarily exactly the return type of eval(). In the case of plain matrices, - * the return type of eval() is a const reference to a matrix, not a matrix! It is however guaranteed - * that the return type of eval() is either PlainObject or const PlainObject&. - */ - typedef Matrix::Scalar, - internal::traits::RowsAtCompileTime, - internal::traits::ColsAtCompileTime, - AutoAlign | (internal::traits::Flags&RowMajorBit ? RowMajor : ColMajor), - internal::traits::MaxRowsAtCompileTime, - internal::traits::MaxColsAtCompileTime - > PlainObject; - -#ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - /** \internal Represents a matrix with all coefficients equal to one another*/ - typedef CwiseNullaryOp,Derived> ConstantReturnType; - /** \internal the return type of MatrixBase::adjoint() */ - typedef typename internal::conditional::IsComplex, - CwiseUnaryOp, ConstTransposeReturnType>, - ConstTransposeReturnType - >::type AdjointReturnType; - /** \internal Return type of eigenvalues() */ - typedef Matrix, internal::traits::ColsAtCompileTime, 1, ColMajor> EigenvaluesReturnType; - /** \internal the return type of identity */ - typedef CwiseNullaryOp,Derived> IdentityReturnType; - /** \internal the return type of unit vectors */ - typedef Block, SquareMatrixType>, - internal::traits::RowsAtCompileTime, - internal::traits::ColsAtCompileTime> BasisReturnType; -#endif // not IMP_EIGEN_PARSED_BY_DOXYGEN - -#define IMP_EIGEN_CURRENT_STORAGE_BASE_CLASS IMP_Eigen::MatrixBase -# include "../plugins/CommonCwiseUnaryOps.h" -# include "../plugins/CommonCwiseBinaryOps.h" -# include "../plugins/MatrixCwiseUnaryOps.h" -# include "../plugins/MatrixCwiseBinaryOps.h" -# ifdef IMP_EIGEN_MATRIXBASE_PLUGIN -# include IMP_EIGEN_MATRIXBASE_PLUGIN -# endif -#undef IMP_EIGEN_CURRENT_STORAGE_BASE_CLASS - - /** Special case of the template operator=, in order to prevent the compiler - * from generating a default operator= (issue hit with g++ 4.1) - */ - Derived& operator=(const MatrixBase& other); - - // We cannot inherit here via Base::operator= since it is causing - // trouble with MSVC. - - template - Derived& operator=(const DenseBase& other); - - template - Derived& operator=(const EigenBase& other); - - template - Derived& operator=(const ReturnByValue& other); - - template - Derived& lazyAssign(const ProductBase& other); - - template - Derived& lazyAssign(const MatrixPowerProduct& other); - - template - Derived& operator+=(const MatrixBase& other); - template - Derived& operator-=(const MatrixBase& other); - - template - const typename ProductReturnType::Type - operator*(const MatrixBase &other) const; - - template - const typename LazyProductReturnType::Type - lazyProduct(const MatrixBase &other) const; - - template - Derived& operator*=(const EigenBase& other); - - template - void applyOnTheLeft(const EigenBase& other); - - template - void applyOnTheRight(const EigenBase& other); - - template - const DiagonalProduct - operator*(const DiagonalBase &diagonal) const; - - template - typename internal::scalar_product_traits::Scalar,typename internal::traits::Scalar>::ReturnType - dot(const MatrixBase& other) const; - - #ifdef IMP_EIGEN2_SUPPORT - template - Scalar eigen2_dot(const MatrixBase& other) const; - #endif - - RealScalar squaredNorm() const; - RealScalar norm() const; - RealScalar stableNorm() const; - RealScalar blueNorm() const; - RealScalar hypotNorm() const; - const PlainObject normalized() const; - void normalize(); - - const AdjointReturnType adjoint() const; - void adjointInPlace(); - - typedef Diagonal DiagonalReturnType; - DiagonalReturnType diagonal(); - typedef typename internal::add_const >::type ConstDiagonalReturnType; - ConstDiagonalReturnType diagonal() const; - - template struct DiagonalIndexReturnType { typedef Diagonal Type; }; - template struct ConstDiagonalIndexReturnType { typedef const Diagonal Type; }; - - template typename DiagonalIndexReturnType::Type diagonal(); - template typename ConstDiagonalIndexReturnType::Type diagonal() const; - - typedef Diagonal DiagonalDynamicIndexReturnType; - typedef typename internal::add_const >::type ConstDiagonalDynamicIndexReturnType; - - DiagonalDynamicIndexReturnType diagonal(Index index); - ConstDiagonalDynamicIndexReturnType diagonal(Index index) const; - - #ifdef IMP_EIGEN2_SUPPORT - template typename internal::eigen2_part_return_type::type part(); - template const typename internal::eigen2_part_return_type::type part() const; - - // huuuge hack. make Eigen2's matrix.part() work in eigen3. Problem: Diagonal is now a class template instead - // of an integer constant. Solution: overload the part() method template wrt template parameters list. - template class U> - const DiagonalWrapper part() const - { return diagonal().asDiagonal(); } - #endif // IMP_EIGEN2_SUPPORT - - template struct TriangularViewReturnType { typedef TriangularView Type; }; - template struct ConstTriangularViewReturnType { typedef const TriangularView Type; }; - - template typename TriangularViewReturnType::Type triangularView(); - template typename ConstTriangularViewReturnType::Type triangularView() const; - - template struct SelfAdjointViewReturnType { typedef SelfAdjointView Type; }; - template struct ConstSelfAdjointViewReturnType { typedef const SelfAdjointView Type; }; - - template typename SelfAdjointViewReturnType::Type selfadjointView(); - template typename ConstSelfAdjointViewReturnType::Type selfadjointView() const; - - const SparseView sparseView(const Scalar& m_reference = Scalar(0), - const typename NumTraits::Real& m_epsilon = NumTraits::dummy_precision()) const; - static const IdentityReturnType Identity(); - static const IdentityReturnType Identity(Index rows, Index cols); - static const BasisReturnType Unit(Index size, Index i); - static const BasisReturnType Unit(Index i); - static const BasisReturnType UnitX(); - static const BasisReturnType UnitY(); - static const BasisReturnType UnitZ(); - static const BasisReturnType UnitW(); - - const DiagonalWrapper asDiagonal() const; - const PermutationWrapper asPermutation() const; - - Derived& setIdentity(); - Derived& setIdentity(Index rows, Index cols); - - bool isIdentity(const RealScalar& prec = NumTraits::dummy_precision()) const; - bool isDiagonal(const RealScalar& prec = NumTraits::dummy_precision()) const; - - bool isUpperTriangular(const RealScalar& prec = NumTraits::dummy_precision()) const; - bool isLowerTriangular(const RealScalar& prec = NumTraits::dummy_precision()) const; - - template - bool isOrthogonal(const MatrixBase& other, - const RealScalar& prec = NumTraits::dummy_precision()) const; - bool isUnitary(const RealScalar& prec = NumTraits::dummy_precision()) const; - - /** \returns true if each coefficients of \c *this and \a other are all exactly equal. - * \warning When using floating point scalar values you probably should rather use a - * fuzzy comparison such as isApprox() - * \sa isApprox(), operator!= */ - template - inline bool operator==(const MatrixBase& other) const - { return cwiseEqual(other).all(); } - - /** \returns true if at least one pair of coefficients of \c *this and \a other are not exactly equal to each other. - * \warning When using floating point scalar values you probably should rather use a - * fuzzy comparison such as isApprox() - * \sa isApprox(), operator== */ - template - inline bool operator!=(const MatrixBase& other) const - { return cwiseNotEqual(other).any(); } - - NoAlias noalias(); - - inline const ForceAlignedAccess forceAlignedAccess() const; - inline ForceAlignedAccess forceAlignedAccess(); - template inline typename internal::add_const_on_value_type,Derived&>::type>::type forceAlignedAccessIf() const; - template inline typename internal::conditional,Derived&>::type forceAlignedAccessIf(); - - Scalar trace() const; - -/////////// Array module /////////// - - template RealScalar lpNorm() const; - - MatrixBase& matrix() { return *this; } - const MatrixBase& matrix() const { return *this; } - - /** \returns an \link IMP_Eigen::ArrayBase Array \endlink expression of this matrix - * \sa ArrayBase::matrix() */ - ArrayWrapper array() { return derived(); } - const ArrayWrapper array() const { return derived(); } - -/////////// LU module /////////// - - const FullPivLU fullPivLu() const; - const PartialPivLU partialPivLu() const; - - #if IMP_EIGEN2_SUPPORT_STAGE < STAGE20_RESOLVE_API_CONFLICTS - const LU lu() const; - #endif - - #ifdef IMP_EIGEN2_SUPPORT - const LU eigen2_lu() const; - #endif - - #if IMP_EIGEN2_SUPPORT_STAGE > STAGE20_RESOLVE_API_CONFLICTS - const PartialPivLU lu() const; - #endif - - #ifdef IMP_EIGEN2_SUPPORT - template - void computeInverse(MatrixBase *result) const { - *result = this->inverse(); - } - #endif - - const internal::inverse_impl inverse() const; - template - void computeInverseAndDetWithCheck( - ResultType& inverse, - typename ResultType::Scalar& determinant, - bool& invertible, - const RealScalar& absDeterminantThreshold = NumTraits::dummy_precision() - ) const; - template - void computeInverseWithCheck( - ResultType& inverse, - bool& invertible, - const RealScalar& absDeterminantThreshold = NumTraits::dummy_precision() - ) const; - Scalar determinant() const; - -/////////// Cholesky module /////////// - - const LLT llt() const; - const LDLT ldlt() const; - -/////////// QR module /////////// - - const HouseholderQR householderQr() const; - const ColPivHouseholderQR colPivHouseholderQr() const; - const FullPivHouseholderQR fullPivHouseholderQr() const; - - #ifdef IMP_EIGEN2_SUPPORT - const QR qr() const; - #endif - - EigenvaluesReturnType eigenvalues() const; - RealScalar operatorNorm() const; - -/////////// SVD module /////////// - - JacobiSVD jacobiSvd(unsigned int computationOptions = 0) const; - - #ifdef IMP_EIGEN2_SUPPORT - SVD svd() const; - #endif - -/////////// Geometry module /////////// - - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - /// \internal helper struct to form the return type of the cross product - template struct cross_product_return_type { - typedef typename internal::scalar_product_traits::Scalar,typename internal::traits::Scalar>::ReturnType Scalar; - typedef Matrix type; - }; - #endif // IMP_EIGEN_PARSED_BY_DOXYGEN - template - typename cross_product_return_type::type - cross(const MatrixBase& other) const; - template - PlainObject cross3(const MatrixBase& other) const; - PlainObject unitOrthogonal(void) const; - Matrix eulerAngles(Index a0, Index a1, Index a2) const; - - #if IMP_EIGEN2_SUPPORT_STAGE > STAGE20_RESOLVE_API_CONFLICTS - ScalarMultipleReturnType operator*(const UniformScaling& s) const; - // put this as separate enum value to work around possible GCC 4.3 bug (?) - enum { HomogeneousReturnTypeDirection = ColsAtCompileTime==1?Vertical:Horizontal }; - typedef Homogeneous HomogeneousReturnType; - HomogeneousReturnType homogeneous() const; - #endif - - enum { - SizeMinusOne = SizeAtCompileTime==Dynamic ? Dynamic : SizeAtCompileTime-1 - }; - typedef Block::ColsAtCompileTime==1 ? SizeMinusOne : 1, - internal::traits::ColsAtCompileTime==1 ? 1 : SizeMinusOne> ConstStartMinusOne; - typedef CwiseUnaryOp::Scalar>, - const ConstStartMinusOne > HNormalizedReturnType; - - const HNormalizedReturnType hnormalized() const; - -////////// Householder module /////////// - - void makeHouseholderInPlace(Scalar& tau, RealScalar& beta); - template - void makeHouseholder(EssentialPart& essential, - Scalar& tau, RealScalar& beta) const; - template - void applyHouseholderOnTheLeft(const EssentialPart& essential, - const Scalar& tau, - Scalar* workspace); - template - void applyHouseholderOnTheRight(const EssentialPart& essential, - const Scalar& tau, - Scalar* workspace); - -///////// Jacobi module ///////// - - template - void applyOnTheLeft(Index p, Index q, const JacobiRotation& j); - template - void applyOnTheRight(Index p, Index q, const JacobiRotation& j); - -///////// SparseCore module ///////// - - template - IMP_EIGEN_STRONG_INLINE const typename SparseMatrixBase::template CwiseProductDenseReturnType::Type - cwiseProduct(const SparseMatrixBase &other) const - { - return other.cwiseProduct(derived()); - } - -///////// MatrixFunctions module ///////// - - typedef typename internal::stem_function::type StemFunction; - const MatrixExponentialReturnValue exp() const; - const MatrixFunctionReturnValue matrixFunction(StemFunction f) const; - const MatrixFunctionReturnValue cosh() const; - const MatrixFunctionReturnValue sinh() const; - const MatrixFunctionReturnValue cos() const; - const MatrixFunctionReturnValue sin() const; - const MatrixSquareRootReturnValue sqrt() const; - const MatrixLogarithmReturnValue log() const; - const MatrixPowerReturnValue pow(const RealScalar& p) const; - -#ifdef IMP_EIGEN2_SUPPORT - template - Derived& operator+=(const Flagged, 0, - EvalBeforeAssigningBit>& other); - - template - Derived& operator-=(const Flagged, 0, - EvalBeforeAssigningBit>& other); - - /** \deprecated because .lazy() is deprecated - * Overloaded for cache friendly product evaluation */ - template - Derived& lazyAssign(const Flagged& other) - { return lazyAssign(other._expression()); } - - template - const Flagged marked() const; - const Flagged lazy() const; - - inline const Cwise cwise() const; - inline Cwise cwise(); - - VectorBlock start(Index size); - const VectorBlock start(Index size) const; - VectorBlock end(Index size); - const VectorBlock end(Index size) const; - template VectorBlock start(); - template const VectorBlock start() const; - template VectorBlock end(); - template const VectorBlock end() const; - - Minor minor(Index row, Index col); - const Minor minor(Index row, Index col) const; -#endif - - protected: - MatrixBase() : Base() {} - - private: - explicit MatrixBase(int); - MatrixBase(int,int); - template explicit MatrixBase(const MatrixBase&); - protected: - // mixing arrays and matrices is not legal - template Derived& operator+=(const ArrayBase& ) - {IMP_EIGEN_STATIC_ASSERT(std::ptrdiff_t(sizeof(typename OtherDerived::Scalar))==-1,YOU_CANNOT_MIX_ARRAYS_AND_MATRICES); return *this;} - // mixing arrays and matrices is not legal - template Derived& operator-=(const ArrayBase& ) - {IMP_EIGEN_STATIC_ASSERT(std::ptrdiff_t(sizeof(typename OtherDerived::Scalar))==-1,YOU_CANNOT_MIX_ARRAYS_AND_MATRICES); return *this;} -}; - - -/*************************************************************************** -* Implementation of matrix base methods -***************************************************************************/ - -/** replaces \c *this by \c *this * \a other. - * - * \returns a reference to \c *this - * - * Example: \include MatrixBase_applyOnTheRight.cpp - * Output: \verbinclude MatrixBase_applyOnTheRight.out - */ -template -template -inline Derived& -MatrixBase::operator*=(const EigenBase &other) -{ - other.derived().applyThisOnTheRight(derived()); - return derived(); -} - -/** replaces \c *this by \c *this * \a other. It is equivalent to MatrixBase::operator*=(). - * - * Example: \include MatrixBase_applyOnTheRight.cpp - * Output: \verbinclude MatrixBase_applyOnTheRight.out - */ -template -template -inline void MatrixBase::applyOnTheRight(const EigenBase &other) -{ - other.derived().applyThisOnTheRight(derived()); -} - -/** replaces \c *this by \a other * \c *this. - * - * Example: \include MatrixBase_applyOnTheLeft.cpp - * Output: \verbinclude MatrixBase_applyOnTheLeft.out - */ -template -template -inline void MatrixBase::applyOnTheLeft(const EigenBase &other) -{ - other.derived().applyThisOnTheLeft(derived()); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_MATRIXBASE_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/NestByValue.h b/modules/algebra/include/eigen3/Eigen/src/Core/NestByValue.h deleted file mode 100644 index ff8b154d0f..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/NestByValue.h +++ /dev/null @@ -1,111 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008 Gael Guennebaud -// Copyright (C) 2006-2008 Benoit Jacob -// -// 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 IMP_EIGEN_NESTBYVALUE_H -#define IMP_EIGEN_NESTBYVALUE_H - -namespace IMP_Eigen { - -/** \class NestByValue - * \ingroup Core_Module - * - * \brief Expression which must be nested by value - * - * \param ExpressionType the type of the object of which we are requiring nesting-by-value - * - * This class is the return type of MatrixBase::nestByValue() - * and most of the time this is the only way it is used. - * - * \sa MatrixBase::nestByValue() - */ - -namespace internal { -template -struct traits > : public traits -{}; -} - -template class NestByValue - : public internal::dense_xpr_base< NestByValue >::type -{ - public: - - typedef typename internal::dense_xpr_base::type Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(NestByValue) - - inline NestByValue(const ExpressionType& matrix) : m_expression(matrix) {} - - inline Index rows() const { return m_expression.rows(); } - inline Index cols() const { return m_expression.cols(); } - inline Index outerStride() const { return m_expression.outerStride(); } - inline Index innerStride() const { return m_expression.innerStride(); } - - inline const CoeffReturnType coeff(Index row, Index col) const - { - return m_expression.coeff(row, col); - } - - inline Scalar& coeffRef(Index row, Index col) - { - return m_expression.const_cast_derived().coeffRef(row, col); - } - - inline const CoeffReturnType coeff(Index index) const - { - return m_expression.coeff(index); - } - - inline Scalar& coeffRef(Index index) - { - return m_expression.const_cast_derived().coeffRef(index); - } - - template - inline const PacketScalar packet(Index row, Index col) const - { - return m_expression.template packet(row, col); - } - - template - inline void writePacket(Index row, Index col, const PacketScalar& x) - { - m_expression.const_cast_derived().template writePacket(row, col, x); - } - - template - inline const PacketScalar packet(Index index) const - { - return m_expression.template packet(index); - } - - template - inline void writePacket(Index index, const PacketScalar& x) - { - m_expression.const_cast_derived().template writePacket(index, x); - } - - operator const ExpressionType&() const { return m_expression; } - - protected: - const ExpressionType m_expression; -}; - -/** \returns an expression of the temporary version of *this. - */ -template -inline const NestByValue -DenseBase::nestByValue() const -{ - return NestByValue(derived()); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_NESTBYVALUE_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/NoAlias.h b/modules/algebra/include/eigen3/Eigen/src/Core/NoAlias.h deleted file mode 100644 index 0ed9e3a4a5..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/NoAlias.h +++ /dev/null @@ -1,134 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2009 Gael Guennebaud -// -// 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 IMP_EIGEN_NOALIAS_H -#define IMP_EIGEN_NOALIAS_H - -namespace IMP_Eigen { - -/** \class NoAlias - * \ingroup Core_Module - * - * \brief Pseudo expression providing an operator = assuming no aliasing - * - * \param ExpressionType the type of the object on which to do the lazy assignment - * - * This class represents an expression with special assignment operators - * assuming no aliasing between the target expression and the source expression. - * More precisely it alloas to bypass the EvalBeforeAssignBit flag of the source expression. - * It is the return type of MatrixBase::noalias() - * and most of the time this is the only way it is used. - * - * \sa MatrixBase::noalias() - */ -template class StorageBase> -class NoAlias -{ - typedef typename ExpressionType::Scalar Scalar; - public: - NoAlias(ExpressionType& expression) : m_expression(expression) {} - - /** Behaves like MatrixBase::lazyAssign(other) - * \sa MatrixBase::lazyAssign() */ - template - IMP_EIGEN_STRONG_INLINE ExpressionType& operator=(const StorageBase& other) - { return internal::assign_selector::run(m_expression,other.derived()); } - - /** \sa MatrixBase::operator+= */ - template - IMP_EIGEN_STRONG_INLINE ExpressionType& operator+=(const StorageBase& other) - { - typedef SelfCwiseBinaryOp, ExpressionType, OtherDerived> SelfAdder; - SelfAdder tmp(m_expression); - typedef typename internal::nested::type OtherDerivedNested; - typedef typename internal::remove_all::type _OtherDerivedNested; - internal::assign_selector::run(tmp,OtherDerivedNested(other.derived())); - return m_expression; - } - - /** \sa MatrixBase::operator-= */ - template - IMP_EIGEN_STRONG_INLINE ExpressionType& operator-=(const StorageBase& other) - { - typedef SelfCwiseBinaryOp, ExpressionType, OtherDerived> SelfAdder; - SelfAdder tmp(m_expression); - typedef typename internal::nested::type OtherDerivedNested; - typedef typename internal::remove_all::type _OtherDerivedNested; - internal::assign_selector::run(tmp,OtherDerivedNested(other.derived())); - return m_expression; - } - -#ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - template - IMP_EIGEN_STRONG_INLINE ExpressionType& operator+=(const ProductBase& other) - { other.derived().addTo(m_expression); return m_expression; } - - template - IMP_EIGEN_STRONG_INLINE ExpressionType& operator-=(const ProductBase& other) - { other.derived().subTo(m_expression); return m_expression; } - - template - IMP_EIGEN_STRONG_INLINE ExpressionType& operator+=(const CoeffBasedProduct& other) - { return m_expression.derived() += CoeffBasedProduct(other.lhs(), other.rhs()); } - - template - IMP_EIGEN_STRONG_INLINE ExpressionType& operator-=(const CoeffBasedProduct& other) - { return m_expression.derived() -= CoeffBasedProduct(other.lhs(), other.rhs()); } - - template - ExpressionType& operator=(const ReturnByValue& func) - { return m_expression = func; } -#endif - - ExpressionType& expression() const - { - return m_expression; - } - - protected: - ExpressionType& m_expression; -}; - -/** \returns a pseudo expression of \c *this with an operator= assuming - * no aliasing between \c *this and the source expression. - * - * More precisely, noalias() allows to bypass the EvalBeforeAssignBit flag. - * Currently, even though several expressions may alias, only product - * expressions have this flag. Therefore, noalias() is only usefull when - * the source expression contains a matrix product. - * - * Here are some examples where noalias is usefull: - * \code - * D.noalias() = A * B; - * D.noalias() += A.transpose() * B; - * D.noalias() -= 2 * A * B.adjoint(); - * \endcode - * - * On the other hand the following example will lead to a \b wrong result: - * \code - * A.noalias() = A * B; - * \endcode - * because the result matrix A is also an operand of the matrix product. Therefore, - * there is no alternative than evaluating A * B in a temporary, that is the default - * behavior when you write: - * \code - * A = A * B; - * \endcode - * - * \sa class NoAlias - */ -template -NoAlias MatrixBase::noalias() -{ - return derived(); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_NOALIAS_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/NumTraits.h b/modules/algebra/include/eigen3/Eigen/src/Core/NumTraits.h deleted file mode 100644 index bd4ed6ab42..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/NumTraits.h +++ /dev/null @@ -1,150 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2006-2010 Benoit Jacob -// -// 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 IMP_EIGEN_NUMTRAITS_H -#define IMP_EIGEN_NUMTRAITS_H - -namespace IMP_Eigen { - -/** \class NumTraits - * \ingroup Core_Module - * - * \brief Holds information about the various numeric (i.e. scalar) types allowed by Eigen. - * - * \param T the numeric type at hand - * - * This class stores enums, typedefs and static methods giving information about a numeric type. - * - * The provided data consists of: - * \li A typedef \a Real, giving the "real part" type of \a T. If \a T is already real, - * then \a Real is just a typedef to \a T. If \a T is \c std::complex then \a Real - * is a typedef to \a U. - * \li A typedef \a NonInteger, giving the type that should be used for operations producing non-integral values, - * such as quotients, square roots, etc. If \a T is a floating-point type, then this typedef just gives - * \a T again. Note however that many Eigen functions such as internal::sqrt simply refuse to - * take integers. Outside of a few cases, Eigen doesn't do automatic type promotion. Thus, this typedef is - * only intended as a helper for code that needs to explicitly promote types. - * \li A typedef \a Nested giving the type to use to nest a value inside of the expression tree. If you don't know what - * this means, just use \a T here. - * \li An enum value \a IsComplex. It is equal to 1 if \a T is a \c std::complex - * type, and to 0 otherwise. - * \li An enum value \a IsInteger. It is equal to \c 1 if \a T is an integer type such as \c int, - * and to \c 0 otherwise. - * \li Enum values ReadCost, AddCost and MulCost representing a rough estimate of the number of CPU cycles needed - * to by move / add / mul instructions respectively, assuming the data is already stored in CPU registers. - * Stay vague here. No need to do architecture-specific stuff. - * \li An enum value \a IsSigned. It is equal to \c 1 if \a T is a signed type and to 0 if \a T is unsigned. - * \li An enum value \a RequireInitialization. It is equal to \c 1 if the constructor of the numeric type \a T must - * be called, and to 0 if it is safe not to call it. Default is 0 if \a T is an arithmetic type, and 1 otherwise. - * \li An epsilon() function which, unlike std::numeric_limits::epsilon(), returns a \a Real instead of a \a T. - * \li A dummy_precision() function returning a weak epsilon value. It is mainly used as a default - * value by the fuzzy comparison operators. - * \li highest() and lowest() functions returning the highest and lowest possible values respectively. - */ - -template struct GenericNumTraits -{ - enum { - IsInteger = std::numeric_limits::is_integer, - IsSigned = std::numeric_limits::is_signed, - IsComplex = 0, - RequireInitialization = internal::is_arithmetic::value ? 0 : 1, - ReadCost = 1, - AddCost = 1, - MulCost = 1 - }; - - typedef T Real; - typedef typename internal::conditional< - IsInteger, - typename internal::conditional::type, - T - >::type NonInteger; - typedef T Nested; - - static inline Real epsilon() { return std::numeric_limits::epsilon(); } - static inline Real dummy_precision() - { - // make sure to override this for floating-point types - return Real(0); - } - static inline T highest() { return (std::numeric_limits::max)(); } - static inline T lowest() { return IsInteger ? (std::numeric_limits::min)() : (-(std::numeric_limits::max)()); } - -#ifdef IMP_EIGEN2_SUPPORT - enum { - HasFloatingPoint = !IsInteger - }; - typedef NonInteger FloatingPoint; -#endif -}; - -template struct NumTraits : GenericNumTraits -{}; - -template<> struct NumTraits - : GenericNumTraits -{ - static inline float dummy_precision() { return 1e-5f; } -}; - -template<> struct NumTraits : GenericNumTraits -{ - static inline double dummy_precision() { return 1e-12; } -}; - -template<> struct NumTraits - : GenericNumTraits -{ - static inline long double dummy_precision() { return 1e-15l; } -}; - -template struct NumTraits > - : GenericNumTraits > -{ - typedef _Real Real; - enum { - IsComplex = 1, - RequireInitialization = NumTraits<_Real>::RequireInitialization, - ReadCost = 2 * NumTraits<_Real>::ReadCost, - AddCost = 2 * NumTraits::AddCost, - MulCost = 4 * NumTraits::MulCost + 2 * NumTraits::AddCost - }; - - static inline Real epsilon() { return NumTraits::epsilon(); } - static inline Real dummy_precision() { return NumTraits::dummy_precision(); } -}; - -template -struct NumTraits > -{ - typedef Array ArrayType; - typedef typename NumTraits::Real RealScalar; - typedef Array Real; - typedef typename NumTraits::NonInteger NonIntegerScalar; - typedef Array NonInteger; - typedef ArrayType & Nested; - - enum { - IsComplex = NumTraits::IsComplex, - IsInteger = NumTraits::IsInteger, - IsSigned = NumTraits::IsSigned, - RequireInitialization = 1, - ReadCost = ArrayType::SizeAtCompileTime==Dynamic ? Dynamic : ArrayType::SizeAtCompileTime * NumTraits::ReadCost, - AddCost = ArrayType::SizeAtCompileTime==Dynamic ? Dynamic : ArrayType::SizeAtCompileTime * NumTraits::AddCost, - MulCost = ArrayType::SizeAtCompileTime==Dynamic ? Dynamic : ArrayType::SizeAtCompileTime * NumTraits::MulCost - }; - - static inline RealScalar epsilon() { return NumTraits::epsilon(); } - static inline RealScalar dummy_precision() { return NumTraits::dummy_precision(); } -}; - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_NUMTRAITS_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/PermutationMatrix.h b/modules/algebra/include/eigen3/Eigen/src/Core/PermutationMatrix.h deleted file mode 100644 index 1b1ed4ab78..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/PermutationMatrix.h +++ /dev/null @@ -1,722 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2009 Benoit Jacob -// Copyright (C) 2009-2011 Gael Guennebaud -// -// 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 IMP_EIGEN_PERMUTATIONMATRIX_H -#define IMP_EIGEN_PERMUTATIONMATRIX_H - -namespace IMP_Eigen { - -template class PermutedImpl; - -/** \class PermutationBase - * \ingroup Core_Module - * - * \brief Base class for permutations - * - * \param Derived the derived class - * - * This class is the base class for all expressions representing a permutation matrix, - * internally stored as a vector of integers. - * The convention followed here is that if \f$ \sigma \f$ is a permutation, the corresponding permutation matrix - * \f$ P_\sigma \f$ is such that if \f$ (e_1,\ldots,e_p) \f$ is the canonical basis, we have: - * \f[ P_\sigma(e_i) = e_{\sigma(i)}. \f] - * This convention ensures that for any two permutations \f$ \sigma, \tau \f$, we have: - * \f[ P_{\sigma\circ\tau} = P_\sigma P_\tau. \f] - * - * Permutation matrices are square and invertible. - * - * Notice that in addition to the member functions and operators listed here, there also are non-member - * operator* to multiply any kind of permutation object with any kind of matrix expression (MatrixBase) - * on either side. - * - * \sa class PermutationMatrix, class PermutationWrapper - */ - -namespace internal { - -template -struct permut_matrix_product_retval; -template -struct permut_sparsematrix_product_retval; -enum PermPermProduct_t {PermPermProduct}; - -} // end namespace internal - -template -class PermutationBase : public EigenBase -{ - typedef internal::traits Traits; - typedef EigenBase Base; - public: - - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - typedef typename Traits::IndicesType IndicesType; - enum { - Flags = Traits::Flags, - CoeffReadCost = Traits::CoeffReadCost, - RowsAtCompileTime = Traits::RowsAtCompileTime, - ColsAtCompileTime = Traits::ColsAtCompileTime, - MaxRowsAtCompileTime = Traits::MaxRowsAtCompileTime, - MaxColsAtCompileTime = Traits::MaxColsAtCompileTime - }; - typedef typename Traits::Scalar Scalar; - typedef typename Traits::Index Index; - typedef Matrix - DenseMatrixType; - typedef PermutationMatrix - PlainPermutationType; - using Base::derived; - #endif - - /** Copies the other permutation into *this */ - template - Derived& operator=(const PermutationBase& other) - { - indices() = other.indices(); - return derived(); - } - - /** Assignment from the Transpositions \a tr */ - template - Derived& operator=(const TranspositionsBase& tr) - { - setIdentity(tr.size()); - for(Index k=size()-1; k>=0; --k) - applyTranspositionOnTheRight(k,tr.coeff(k)); - return derived(); - } - - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - /** This is a special case of the templated operator=. Its purpose is to - * prevent a default operator= from hiding the templated operator=. - */ - Derived& operator=(const PermutationBase& other) - { - indices() = other.indices(); - return derived(); - } - #endif - - /** \returns the number of rows */ - inline Index rows() const { return Index(indices().size()); } - - /** \returns the number of columns */ - inline Index cols() const { return Index(indices().size()); } - - /** \returns the size of a side of the respective square matrix, i.e., the number of indices */ - inline Index size() const { return Index(indices().size()); } - - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - template - void evalTo(MatrixBase& other) const - { - other.setZero(); - for (int i=0; i=0 && j>=0 && i=0 && j>=0 && i inverse() const - { return derived(); } - /** \returns the tranpose permutation matrix. - * - * \note \note_try_to_help_rvo - */ - inline Transpose transpose() const - { return derived(); } - - /**** multiplication helpers to hopefully get RVO ****/ - - -#ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - protected: - template - void assignTranspose(const PermutationBase& other) - { - for (int i=0; i - void assignProduct(const Lhs& lhs, const Rhs& rhs) - { - imp_eigen_assert(lhs.cols() == rhs.rows()); - for (int i=0; i - inline PlainPermutationType operator*(const PermutationBase& other) const - { return PlainPermutationType(internal::PermPermProduct, derived(), other.derived()); } - - /** \returns the product of a permutation with another inverse permutation. - * - * \note \note_try_to_help_rvo - */ - template - inline PlainPermutationType operator*(const Transpose >& other) const - { return PlainPermutationType(internal::PermPermProduct, *this, other.eval()); } - - /** \returns the product of an inverse permutation with another permutation. - * - * \note \note_try_to_help_rvo - */ - template friend - inline PlainPermutationType operator*(const Transpose >& other, const PermutationBase& perm) - { return PlainPermutationType(internal::PermPermProduct, other.eval(), perm); } - - /** \returns the determinant of the permutation matrix, which is either 1 or -1 depending on the parity of the permutation. - * - * This function is O(\c n) procedure allocating a buffer of \c n booleans. - */ - Index determinant() const - { - Index res = 1; - Index n = size(); - Matrix mask(n); - mask.fill(false); - Index r = 0; - while(r < n) - { - // search for the next seed - while(r=n) - break; - // we got one, let's follow it until we are back to the seed - Index k0 = r++; - mask.coeffRef(k0) = true; - for(Index k=indices().coeff(k0); k!=k0; k=indices().coeff(k)) - { - mask.coeffRef(k) = true; - res = -res; - } - } - return res; - } - - protected: - -}; - -/** \class PermutationMatrix - * \ingroup Core_Module - * - * \brief Permutation matrix - * - * \param SizeAtCompileTime the number of rows/cols, or Dynamic - * \param MaxSizeAtCompileTime the maximum number of rows/cols, or Dynamic. This optional parameter defaults to SizeAtCompileTime. Most of the time, you should not have to specify it. - * \param IndexType the interger type of the indices - * - * This class represents a permutation matrix, internally stored as a vector of integers. - * - * \sa class PermutationBase, class PermutationWrapper, class DiagonalMatrix - */ - -namespace internal { -template -struct traits > - : traits > -{ - typedef IndexType Index; - typedef Matrix IndicesType; -}; -} - -template -class PermutationMatrix : public PermutationBase > -{ - typedef PermutationBase Base; - typedef internal::traits Traits; - public: - - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - typedef typename Traits::IndicesType IndicesType; - #endif - - inline PermutationMatrix() - {} - - /** Constructs an uninitialized permutation matrix of given size. - */ - inline PermutationMatrix(int size) : m_indices(size) - {} - - /** Copy constructor. */ - template - inline PermutationMatrix(const PermutationBase& other) - : m_indices(other.indices()) {} - - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - /** Standard copy constructor. Defined only to prevent a default copy constructor - * from hiding the other templated constructor */ - inline PermutationMatrix(const PermutationMatrix& other) : m_indices(other.indices()) {} - #endif - - /** Generic constructor from expression of the indices. The indices - * array has the meaning that the permutations sends each integer i to indices[i]. - * - * \warning It is your responsibility to check that the indices array that you passes actually - * describes a permutation, i.e., each value between 0 and n-1 occurs exactly once, where n is the - * array's size. - */ - template - explicit inline PermutationMatrix(const MatrixBase& a_indices) : m_indices(a_indices) - {} - - /** Convert the Transpositions \a tr to a permutation matrix */ - template - explicit PermutationMatrix(const TranspositionsBase& tr) - : m_indices(tr.size()) - { - *this = tr; - } - - /** Copies the other permutation into *this */ - template - PermutationMatrix& operator=(const PermutationBase& other) - { - m_indices = other.indices(); - return *this; - } - - /** Assignment from the Transpositions \a tr */ - template - PermutationMatrix& operator=(const TranspositionsBase& tr) - { - return Base::operator=(tr.derived()); - } - - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - /** This is a special case of the templated operator=. Its purpose is to - * prevent a default operator= from hiding the templated operator=. - */ - PermutationMatrix& operator=(const PermutationMatrix& other) - { - m_indices = other.m_indices; - return *this; - } - #endif - - /** const version of indices(). */ - const IndicesType& indices() const { return m_indices; } - /** \returns a reference to the stored array representing the permutation. */ - IndicesType& indices() { return m_indices; } - - - /**** multiplication helpers to hopefully get RVO ****/ - -#ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - template - PermutationMatrix(const Transpose >& other) - : m_indices(other.nestedPermutation().size()) - { - for (int i=0; i - PermutationMatrix(internal::PermPermProduct_t, const Lhs& lhs, const Rhs& rhs) - : m_indices(lhs.indices().size()) - { - Base::assignProduct(lhs,rhs); - } -#endif - - protected: - - IndicesType m_indices; -}; - - -namespace internal { -template -struct traits,_PacketAccess> > - : traits > -{ - typedef IndexType Index; - typedef Map, _PacketAccess> IndicesType; -}; -} - -template -class Map,_PacketAccess> - : public PermutationBase,_PacketAccess> > -{ - typedef PermutationBase Base; - typedef internal::traits Traits; - public: - - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - typedef typename Traits::IndicesType IndicesType; - typedef typename IndicesType::Scalar Index; - #endif - - inline Map(const Index* indicesPtr) - : m_indices(indicesPtr) - {} - - inline Map(const Index* indicesPtr, Index size) - : m_indices(indicesPtr,size) - {} - - /** Copies the other permutation into *this */ - template - Map& operator=(const PermutationBase& other) - { return Base::operator=(other.derived()); } - - /** Assignment from the Transpositions \a tr */ - template - Map& operator=(const TranspositionsBase& tr) - { return Base::operator=(tr.derived()); } - - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - /** This is a special case of the templated operator=. Its purpose is to - * prevent a default operator= from hiding the templated operator=. - */ - Map& operator=(const Map& other) - { - m_indices = other.m_indices; - return *this; - } - #endif - - /** const version of indices(). */ - const IndicesType& indices() const { return m_indices; } - /** \returns a reference to the stored array representing the permutation. */ - IndicesType& indices() { return m_indices; } - - protected: - - IndicesType m_indices; -}; - -/** \class PermutationWrapper - * \ingroup Core_Module - * - * \brief Class to view a vector of integers as a permutation matrix - * - * \param _IndicesType the type of the vector of integer (can be any compatible expression) - * - * This class allows to view any vector expression of integers as a permutation matrix. - * - * \sa class PermutationBase, class PermutationMatrix - */ - -struct PermutationStorage {}; - -template class TranspositionsWrapper; -namespace internal { -template -struct traits > -{ - typedef PermutationStorage StorageKind; - typedef typename _IndicesType::Scalar Scalar; - typedef typename _IndicesType::Scalar Index; - typedef _IndicesType IndicesType; - enum { - RowsAtCompileTime = _IndicesType::SizeAtCompileTime, - ColsAtCompileTime = _IndicesType::SizeAtCompileTime, - MaxRowsAtCompileTime = IndicesType::MaxRowsAtCompileTime, - MaxColsAtCompileTime = IndicesType::MaxColsAtCompileTime, - Flags = 0, - CoeffReadCost = _IndicesType::CoeffReadCost - }; -}; -} - -template -class PermutationWrapper : public PermutationBase > -{ - typedef PermutationBase Base; - typedef internal::traits Traits; - public: - - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - typedef typename Traits::IndicesType IndicesType; - #endif - - inline PermutationWrapper(const IndicesType& a_indices) - : m_indices(a_indices) - {} - - /** const version of indices(). */ - const typename internal::remove_all::type& - indices() const { return m_indices; } - - protected: - - typename IndicesType::Nested m_indices; -}; - -/** \returns the matrix with the permutation applied to the columns. - */ -template -inline const internal::permut_matrix_product_retval -operator*(const MatrixBase& matrix, - const PermutationBase &permutation) -{ - return internal::permut_matrix_product_retval - - (permutation.derived(), matrix.derived()); -} - -/** \returns the matrix with the permutation applied to the rows. - */ -template -inline const internal::permut_matrix_product_retval - -operator*(const PermutationBase &permutation, - const MatrixBase& matrix) -{ - return internal::permut_matrix_product_retval - - (permutation.derived(), matrix.derived()); -} - -namespace internal { - -template -struct traits > -{ - typedef typename MatrixType::PlainObject ReturnType; -}; - -template -struct permut_matrix_product_retval - : public ReturnByValue > -{ - typedef typename remove_all::type MatrixTypeNestedCleaned; - typedef typename MatrixType::Index Index; - - permut_matrix_product_retval(const PermutationType& perm, const MatrixType& matrix) - : m_permutation(perm), m_matrix(matrix) - {} - - inline Index rows() const { return m_matrix.rows(); } - inline Index cols() const { return m_matrix.cols(); } - - template inline void evalTo(Dest& dst) const - { - const Index n = Side==OnTheLeft ? rows() : cols(); - // FIXME we need an is_same for expression that is not sensitive to constness. For instance - // is_same_xpr, Block >::value should be true. - const typename Dest::Scalar *dst_data = internal::extract_data(dst); - if( is_same::value - && blas_traits::HasUsableDirectAccess - && blas_traits::HasUsableDirectAccess - && dst_data!=0 && dst_data == extract_data(m_matrix)) - { - // apply the permutation inplace - Matrix mask(m_permutation.size()); - mask.fill(false); - Index r = 0; - while(r < m_permutation.size()) - { - // search for the next seed - while(r=m_permutation.size()) - break; - // we got one, let's follow it until we are back to the seed - Index k0 = r++; - Index kPrev = k0; - mask.coeffRef(k0) = true; - for(Index k=m_permutation.indices().coeff(k0); k!=k0; k=m_permutation.indices().coeff(k)) - { - Block(dst, k) - .swap(Block - (dst,((Side==OnTheLeft) ^ Transposed) ? k0 : kPrev)); - - mask.coeffRef(k) = true; - kPrev = k; - } - } - } - else - { - for(int i = 0; i < n; ++i) - { - Block - (dst, ((Side==OnTheLeft) ^ Transposed) ? m_permutation.indices().coeff(i) : i) - - = - - Block - (m_matrix, ((Side==OnTheRight) ^ Transposed) ? m_permutation.indices().coeff(i) : i); - } - } - } - - protected: - const PermutationType& m_permutation; - typename MatrixType::Nested m_matrix; -}; - -/* Template partial specialization for transposed/inverse permutations */ - -template -struct traits > > - : traits -{}; - -} // end namespace internal - -template -class Transpose > - : public EigenBase > > -{ - typedef Derived PermutationType; - typedef typename PermutationType::IndicesType IndicesType; - typedef typename PermutationType::PlainPermutationType PlainPermutationType; - public: - - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - typedef internal::traits Traits; - typedef typename Derived::DenseMatrixType DenseMatrixType; - enum { - Flags = Traits::Flags, - CoeffReadCost = Traits::CoeffReadCost, - RowsAtCompileTime = Traits::RowsAtCompileTime, - ColsAtCompileTime = Traits::ColsAtCompileTime, - MaxRowsAtCompileTime = Traits::MaxRowsAtCompileTime, - MaxColsAtCompileTime = Traits::MaxColsAtCompileTime - }; - typedef typename Traits::Scalar Scalar; - #endif - - Transpose(const PermutationType& p) : m_permutation(p) {} - - inline int rows() const { return m_permutation.rows(); } - inline int cols() const { return m_permutation.cols(); } - - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - template - void evalTo(MatrixBase& other) const - { - other.setZero(); - for (int i=0; i friend - inline const internal::permut_matrix_product_retval - operator*(const MatrixBase& matrix, const Transpose& trPerm) - { - return internal::permut_matrix_product_retval(trPerm.m_permutation, matrix.derived()); - } - - /** \returns the matrix with the inverse permutation applied to the rows. - */ - template - inline const internal::permut_matrix_product_retval - operator*(const MatrixBase& matrix) const - { - return internal::permut_matrix_product_retval(m_permutation, matrix.derived()); - } - - const PermutationType& nestedPermutation() const { return m_permutation; } - - protected: - const PermutationType& m_permutation; -}; - -template -const PermutationWrapper MatrixBase::asPermutation() const -{ - return derived(); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_PERMUTATIONMATRIX_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/PlainObjectBase.h b/modules/algebra/include/eigen3/Eigen/src/Core/PlainObjectBase.h deleted file mode 100644 index 4e91bd6b39..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/PlainObjectBase.h +++ /dev/null @@ -1,822 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008-2009 Gael Guennebaud -// Copyright (C) 2006-2008 Benoit Jacob -// -// 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 IMP_EIGEN_DENSESTORAGEBASE_H -#define IMP_EIGEN_DENSESTORAGEBASE_H - -#if defined(IMP_EIGEN_INITIALIZE_MATRICES_BY_ZERO) -# define IMP_EIGEN_INITIALIZE_COEFFS -# define IMP_EIGEN_INITIALIZE_COEFFS_IF_THAT_OPTION_IS_ENABLED for(int i=0;i::quiet_NaN(); -#else -# undef IMP_EIGEN_INITIALIZE_COEFFS -# define IMP_EIGEN_INITIALIZE_COEFFS_IF_THAT_OPTION_IS_ENABLED -#endif - -namespace IMP_Eigen { - -namespace internal { - -template struct check_rows_cols_for_overflow { - template - static IMP_EIGEN_ALWAYS_INLINE void run(Index, Index) - { - } -}; - -template<> struct check_rows_cols_for_overflow { - template - static IMP_EIGEN_ALWAYS_INLINE void run(Index rows, Index cols) - { - // http://hg.mozilla.org/mozilla-central/file/6c8a909977d3/xpcom/ds/CheckedInt.h#l242 - // we assume Index is signed - Index max_index = (size_t(1) << (8 * sizeof(Index) - 1)) - 1; // assume Index is signed - bool error = (rows == 0 || cols == 0) ? false - : (rows > max_index / cols); - if (error) - throw_std_bad_alloc(); - } -}; - -template -struct conservative_resize_like_impl; - -template struct matrix_swap_impl; - -} // end namespace internal - -/** \class PlainObjectBase - * \brief %Dense storage base class for matrices and arrays. - * - * This class can be extended with the help of the plugin mechanism described on the page - * \ref TopicCustomizingEigen by defining the preprocessor symbol \c IMP_EIGEN_PLAINOBJECTBASE_PLUGIN. - * - * \sa \ref TopicClassHierarchy - */ -#ifdef IMP_EIGEN_PARSED_BY_DOXYGEN -namespace internal { - -// this is a warkaround to doxygen not being able to understand the inheritence logic -// when it is hidden by the dense_xpr_base helper struct. -template struct dense_xpr_base_dispatcher_for_doxygen;// : public MatrixBase {}; -/** This class is just a workaround for Doxygen and it does not not actually exist. */ -template -struct dense_xpr_base_dispatcher_for_doxygen > - : public MatrixBase > {}; -/** This class is just a workaround for Doxygen and it does not not actually exist. */ -template -struct dense_xpr_base_dispatcher_for_doxygen > - : public ArrayBase > {}; - -} // namespace internal - -template -class PlainObjectBase : public internal::dense_xpr_base_dispatcher_for_doxygen -#else -template -class PlainObjectBase : public internal::dense_xpr_base::type -#endif -{ - public: - enum { Options = internal::traits::Options }; - typedef typename internal::dense_xpr_base::type Base; - - typedef typename internal::traits::StorageKind StorageKind; - typedef typename internal::traits::Index Index; - typedef typename internal::traits::Scalar Scalar; - typedef typename internal::packet_traits::type PacketScalar; - typedef typename NumTraits::Real RealScalar; - typedef Derived DenseType; - - using Base::RowsAtCompileTime; - using Base::ColsAtCompileTime; - using Base::SizeAtCompileTime; - using Base::MaxRowsAtCompileTime; - using Base::MaxColsAtCompileTime; - using Base::MaxSizeAtCompileTime; - using Base::IsVectorAtCompileTime; - using Base::Flags; - - template friend class IMP_Eigen::Map; - friend class IMP_Eigen::Map; - typedef IMP_Eigen::Map MapType; - friend class IMP_Eigen::Map; - typedef const IMP_Eigen::Map ConstMapType; - friend class IMP_Eigen::Map; - typedef IMP_Eigen::Map AlignedMapType; - friend class IMP_Eigen::Map; - typedef const IMP_Eigen::Map ConstAlignedMapType; - template struct StridedMapType { typedef IMP_Eigen::Map type; }; - template struct StridedConstMapType { typedef IMP_Eigen::Map type; }; - template struct StridedAlignedMapType { typedef IMP_Eigen::Map type; }; - template struct StridedConstAlignedMapType { typedef IMP_Eigen::Map type; }; - - protected: - DenseStorage m_storage; - - public: - enum { NeedsToAlign = SizeAtCompileTime != Dynamic && (internal::traits::Flags & AlignedBit) != 0 }; - IMP_EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF(NeedsToAlign) - - Base& base() { return *static_cast(this); } - const Base& base() const { return *static_cast(this); } - - IMP_EIGEN_STRONG_INLINE Index rows() const { return m_storage.rows(); } - IMP_EIGEN_STRONG_INLINE Index cols() const { return m_storage.cols(); } - - IMP_EIGEN_STRONG_INLINE const Scalar& coeff(Index rowId, Index colId) const - { - if(Flags & RowMajorBit) - return m_storage.data()[colId + rowId * m_storage.cols()]; - else // column-major - return m_storage.data()[rowId + colId * m_storage.rows()]; - } - - IMP_EIGEN_STRONG_INLINE const Scalar& coeff(Index index) const - { - return m_storage.data()[index]; - } - - IMP_EIGEN_STRONG_INLINE Scalar& coeffRef(Index rowId, Index colId) - { - if(Flags & RowMajorBit) - return m_storage.data()[colId + rowId * m_storage.cols()]; - else // column-major - return m_storage.data()[rowId + colId * m_storage.rows()]; - } - - IMP_EIGEN_STRONG_INLINE Scalar& coeffRef(Index index) - { - return m_storage.data()[index]; - } - - IMP_EIGEN_STRONG_INLINE const Scalar& coeffRef(Index rowId, Index colId) const - { - if(Flags & RowMajorBit) - return m_storage.data()[colId + rowId * m_storage.cols()]; - else // column-major - return m_storage.data()[rowId + colId * m_storage.rows()]; - } - - IMP_EIGEN_STRONG_INLINE const Scalar& coeffRef(Index index) const - { - return m_storage.data()[index]; - } - - /** \internal */ - template - IMP_EIGEN_STRONG_INLINE PacketScalar packet(Index rowId, Index colId) const - { - return internal::ploadt - (m_storage.data() + (Flags & RowMajorBit - ? colId + rowId * m_storage.cols() - : rowId + colId * m_storage.rows())); - } - - /** \internal */ - template - IMP_EIGEN_STRONG_INLINE PacketScalar packet(Index index) const - { - return internal::ploadt(m_storage.data() + index); - } - - /** \internal */ - template - IMP_EIGEN_STRONG_INLINE void writePacket(Index rowId, Index colId, const PacketScalar& val) - { - internal::pstoret - (m_storage.data() + (Flags & RowMajorBit - ? colId + rowId * m_storage.cols() - : rowId + colId * m_storage.rows()), val); - } - - /** \internal */ - template - IMP_EIGEN_STRONG_INLINE void writePacket(Index index, const PacketScalar& val) - { - internal::pstoret(m_storage.data() + index, val); - } - - /** \returns a const pointer to the data array of this matrix */ - IMP_EIGEN_STRONG_INLINE const Scalar *data() const - { return m_storage.data(); } - - /** \returns a pointer to the data array of this matrix */ - IMP_EIGEN_STRONG_INLINE Scalar *data() - { return m_storage.data(); } - - /** Resizes \c *this to a \a rows x \a cols matrix. - * - * This method is intended for dynamic-size matrices, although it is legal to call it on any - * matrix as long as fixed dimensions are left unchanged. If you only want to change the number - * of rows and/or of columns, you can use resize(NoChange_t, Index), resize(Index, NoChange_t). - * - * If the current number of coefficients of \c *this exactly matches the - * product \a rows * \a cols, then no memory allocation is performed and - * the current values are left unchanged. In all other cases, including - * shrinking, the data is reallocated and all previous values are lost. - * - * Example: \include Matrix_resize_int_int.cpp - * Output: \verbinclude Matrix_resize_int_int.out - * - * \sa resize(Index) for vectors, resize(NoChange_t, Index), resize(Index, NoChange_t) - */ - IMP_EIGEN_STRONG_INLINE void resize(Index nbRows, Index nbCols) - { - imp_eigen_assert( IMP_EIGEN_IMPLIES(RowsAtCompileTime!=Dynamic,nbRows==RowsAtCompileTime) - && IMP_EIGEN_IMPLIES(ColsAtCompileTime!=Dynamic,nbCols==ColsAtCompileTime) - && IMP_EIGEN_IMPLIES(RowsAtCompileTime==Dynamic && MaxRowsAtCompileTime!=Dynamic,nbRows<=MaxRowsAtCompileTime) - && IMP_EIGEN_IMPLIES(ColsAtCompileTime==Dynamic && MaxColsAtCompileTime!=Dynamic,nbCols<=MaxColsAtCompileTime) - && nbRows>=0 && nbCols>=0 && "Invalid sizes when resizing a matrix or array."); - internal::check_rows_cols_for_overflow::run(nbRows, nbCols); - #ifdef IMP_EIGEN_INITIALIZE_COEFFS - Index size = nbRows*nbCols; - bool size_changed = size != this->size(); - m_storage.resize(size, nbRows, nbCols); - if(size_changed) IMP_EIGEN_INITIALIZE_COEFFS_IF_THAT_OPTION_IS_ENABLED - #else - internal::check_rows_cols_for_overflow::run(nbRows, nbCols); - m_storage.resize(nbRows*nbCols, nbRows, nbCols); - #endif - } - - /** Resizes \c *this to a vector of length \a size - * - * \only_for_vectors. This method does not work for - * partially dynamic matrices when the static dimension is anything other - * than 1. For example it will not work with Matrix. - * - * Example: \include Matrix_resize_int.cpp - * Output: \verbinclude Matrix_resize_int.out - * - * \sa resize(Index,Index), resize(NoChange_t, Index), resize(Index, NoChange_t) - */ - inline void resize(Index size) - { - IMP_EIGEN_STATIC_ASSERT_VECTOR_ONLY(PlainObjectBase) - imp_eigen_assert(((SizeAtCompileTime == Dynamic && (MaxSizeAtCompileTime==Dynamic || size<=MaxSizeAtCompileTime)) || SizeAtCompileTime == size) && size>=0); - #ifdef IMP_EIGEN_INITIALIZE_COEFFS - bool size_changed = size != this->size(); - #endif - if(RowsAtCompileTime == 1) - m_storage.resize(size, 1, size); - else - m_storage.resize(size, size, 1); - #ifdef IMP_EIGEN_INITIALIZE_COEFFS - if(size_changed) IMP_EIGEN_INITIALIZE_COEFFS_IF_THAT_OPTION_IS_ENABLED - #endif - } - - /** Resizes the matrix, changing only the number of columns. For the parameter of type NoChange_t, just pass the special value \c NoChange - * as in the example below. - * - * Example: \include Matrix_resize_NoChange_int.cpp - * Output: \verbinclude Matrix_resize_NoChange_int.out - * - * \sa resize(Index,Index) - */ - inline void resize(NoChange_t, Index nbCols) - { - resize(rows(), nbCols); - } - - /** Resizes the matrix, changing only the number of rows. For the parameter of type NoChange_t, just pass the special value \c NoChange - * as in the example below. - * - * Example: \include Matrix_resize_int_NoChange.cpp - * Output: \verbinclude Matrix_resize_int_NoChange.out - * - * \sa resize(Index,Index) - */ - inline void resize(Index nbRows, NoChange_t) - { - resize(nbRows, cols()); - } - - /** Resizes \c *this to have the same dimensions as \a other. - * Takes care of doing all the checking that's needed. - * - * Note that copying a row-vector into a vector (and conversely) is allowed. - * The resizing, if any, is then done in the appropriate way so that row-vectors - * remain row-vectors and vectors remain vectors. - */ - template - IMP_EIGEN_STRONG_INLINE void resizeLike(const EigenBase& _other) - { - const OtherDerived& other = _other.derived(); - internal::check_rows_cols_for_overflow::run(Index(other.rows()), Index(other.cols())); - const Index othersize = Index(other.rows())*Index(other.cols()); - if(RowsAtCompileTime == 1) - { - imp_eigen_assert(other.rows() == 1 || other.cols() == 1); - resize(1, othersize); - } - else if(ColsAtCompileTime == 1) - { - imp_eigen_assert(other.rows() == 1 || other.cols() == 1); - resize(othersize, 1); - } - else resize(other.rows(), other.cols()); - } - - /** Resizes the matrix to \a rows x \a cols while leaving old values untouched. - * - * The method is intended for matrices of dynamic size. If you only want to change the number - * of rows and/or of columns, you can use conservativeResize(NoChange_t, Index) or - * conservativeResize(Index, NoChange_t). - * - * Matrices are resized relative to the top-left element. In case values need to be - * appended to the matrix they will be uninitialized. - */ - IMP_EIGEN_STRONG_INLINE void conservativeResize(Index nbRows, Index nbCols) - { - internal::conservative_resize_like_impl::run(*this, nbRows, nbCols); - } - - /** Resizes the matrix to \a rows x \a cols while leaving old values untouched. - * - * As opposed to conservativeResize(Index rows, Index cols), this version leaves - * the number of columns unchanged. - * - * In case the matrix is growing, new rows will be uninitialized. - */ - IMP_EIGEN_STRONG_INLINE void conservativeResize(Index nbRows, NoChange_t) - { - // Note: see the comment in conservativeResize(Index,Index) - conservativeResize(nbRows, cols()); - } - - /** Resizes the matrix to \a rows x \a cols while leaving old values untouched. - * - * As opposed to conservativeResize(Index rows, Index cols), this version leaves - * the number of rows unchanged. - * - * In case the matrix is growing, new columns will be uninitialized. - */ - IMP_EIGEN_STRONG_INLINE void conservativeResize(NoChange_t, Index nbCols) - { - // Note: see the comment in conservativeResize(Index,Index) - conservativeResize(rows(), nbCols); - } - - /** Resizes the vector to \a size while retaining old values. - * - * \only_for_vectors. This method does not work for - * partially dynamic matrices when the static dimension is anything other - * than 1. For example it will not work with Matrix. - * - * When values are appended, they will be uninitialized. - */ - IMP_EIGEN_STRONG_INLINE void conservativeResize(Index size) - { - internal::conservative_resize_like_impl::run(*this, size); - } - - /** Resizes the matrix to \a rows x \a cols of \c other, while leaving old values untouched. - * - * The method is intended for matrices of dynamic size. If you only want to change the number - * of rows and/or of columns, you can use conservativeResize(NoChange_t, Index) or - * conservativeResize(Index, NoChange_t). - * - * Matrices are resized relative to the top-left element. In case values need to be - * appended to the matrix they will copied from \c other. - */ - template - IMP_EIGEN_STRONG_INLINE void conservativeResizeLike(const DenseBase& other) - { - internal::conservative_resize_like_impl::run(*this, other); - } - - /** This is a special case of the templated operator=. Its purpose is to - * prevent a default operator= from hiding the templated operator=. - */ - IMP_EIGEN_STRONG_INLINE Derived& operator=(const PlainObjectBase& other) - { - return _set(other); - } - - /** \sa MatrixBase::lazyAssign() */ - template - IMP_EIGEN_STRONG_INLINE Derived& lazyAssign(const DenseBase& other) - { - _resize_to_match(other); - return Base::lazyAssign(other.derived()); - } - - template - IMP_EIGEN_STRONG_INLINE Derived& operator=(const ReturnByValue& func) - { - resize(func.rows(), func.cols()); - return Base::operator=(func); - } - - IMP_EIGEN_STRONG_INLINE PlainObjectBase() : m_storage() - { -// _check_template_params(); -// IMP_EIGEN_INITIALIZE_COEFFS_IF_THAT_OPTION_IS_ENABLED - } - -#ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - // FIXME is it still needed ? - /** \internal */ - PlainObjectBase(internal::constructor_without_unaligned_array_assert) - : m_storage(internal::constructor_without_unaligned_array_assert()) - { -// _check_template_params(); IMP_EIGEN_INITIALIZE_COEFFS_IF_THAT_OPTION_IS_ENABLED - } -#endif - -#ifdef IMP_EIGEN_HAVE_RVALUE_REFERENCES - PlainObjectBase(PlainObjectBase&& other) - : m_storage( std::move(other.m_storage) ) - { - } - - PlainObjectBase& operator=(PlainObjectBase&& other) - { - using std::swap; - swap(m_storage, other.m_storage); - return *this; - } -#endif - - /** Copy constructor */ - IMP_EIGEN_STRONG_INLINE PlainObjectBase(const PlainObjectBase& other) - : m_storage() - { - _check_template_params(); - lazyAssign(other); - } - - template - IMP_EIGEN_STRONG_INLINE PlainObjectBase(const DenseBase &other) - : m_storage() - { - _check_template_params(); - lazyAssign(other); - } - - IMP_EIGEN_STRONG_INLINE PlainObjectBase(Index a_size, Index nbRows, Index nbCols) - : m_storage(a_size, nbRows, nbCols) - { -// _check_template_params(); -// IMP_EIGEN_INITIALIZE_COEFFS_IF_THAT_OPTION_IS_ENABLED - } - - /** \copydoc MatrixBase::operator=(const EigenBase&) - */ - template - IMP_EIGEN_STRONG_INLINE Derived& operator=(const EigenBase &other) - { - _resize_to_match(other); - Base::operator=(other.derived()); - return this->derived(); - } - - /** \sa MatrixBase::operator=(const EigenBase&) */ - template - IMP_EIGEN_STRONG_INLINE PlainObjectBase(const EigenBase &other) - : m_storage(Index(other.derived().rows()) * Index(other.derived().cols()), other.derived().rows(), other.derived().cols()) - { - _check_template_params(); - internal::check_rows_cols_for_overflow::run(other.derived().rows(), other.derived().cols()); - Base::operator=(other.derived()); - } - - /** \name Map - * These are convenience functions returning Map objects. The Map() static functions return unaligned Map objects, - * while the AlignedMap() functions return aligned Map objects and thus should be called only with 16-byte-aligned - * \a data pointers. - * - * \see class Map - */ - //@{ - static inline ConstMapType Map(const Scalar* data) - { return ConstMapType(data); } - static inline MapType Map(Scalar* data) - { return MapType(data); } - static inline ConstMapType Map(const Scalar* data, Index size) - { return ConstMapType(data, size); } - static inline MapType Map(Scalar* data, Index size) - { return MapType(data, size); } - static inline ConstMapType Map(const Scalar* data, Index rows, Index cols) - { return ConstMapType(data, rows, cols); } - static inline MapType Map(Scalar* data, Index rows, Index cols) - { return MapType(data, rows, cols); } - - static inline ConstAlignedMapType MapAligned(const Scalar* data) - { return ConstAlignedMapType(data); } - static inline AlignedMapType MapAligned(Scalar* data) - { return AlignedMapType(data); } - static inline ConstAlignedMapType MapAligned(const Scalar* data, Index size) - { return ConstAlignedMapType(data, size); } - static inline AlignedMapType MapAligned(Scalar* data, Index size) - { return AlignedMapType(data, size); } - static inline ConstAlignedMapType MapAligned(const Scalar* data, Index rows, Index cols) - { return ConstAlignedMapType(data, rows, cols); } - static inline AlignedMapType MapAligned(Scalar* data, Index rows, Index cols) - { return AlignedMapType(data, rows, cols); } - - template - static inline typename StridedConstMapType >::type Map(const Scalar* data, const Stride& stride) - { return typename StridedConstMapType >::type(data, stride); } - template - static inline typename StridedMapType >::type Map(Scalar* data, const Stride& stride) - { return typename StridedMapType >::type(data, stride); } - template - static inline typename StridedConstMapType >::type Map(const Scalar* data, Index size, const Stride& stride) - { return typename StridedConstMapType >::type(data, size, stride); } - template - static inline typename StridedMapType >::type Map(Scalar* data, Index size, const Stride& stride) - { return typename StridedMapType >::type(data, size, stride); } - template - static inline typename StridedConstMapType >::type Map(const Scalar* data, Index rows, Index cols, const Stride& stride) - { return typename StridedConstMapType >::type(data, rows, cols, stride); } - template - static inline typename StridedMapType >::type Map(Scalar* data, Index rows, Index cols, const Stride& stride) - { return typename StridedMapType >::type(data, rows, cols, stride); } - - template - static inline typename StridedConstAlignedMapType >::type MapAligned(const Scalar* data, const Stride& stride) - { return typename StridedConstAlignedMapType >::type(data, stride); } - template - static inline typename StridedAlignedMapType >::type MapAligned(Scalar* data, const Stride& stride) - { return typename StridedAlignedMapType >::type(data, stride); } - template - static inline typename StridedConstAlignedMapType >::type MapAligned(const Scalar* data, Index size, const Stride& stride) - { return typename StridedConstAlignedMapType >::type(data, size, stride); } - template - static inline typename StridedAlignedMapType >::type MapAligned(Scalar* data, Index size, const Stride& stride) - { return typename StridedAlignedMapType >::type(data, size, stride); } - template - static inline typename StridedConstAlignedMapType >::type MapAligned(const Scalar* data, Index rows, Index cols, const Stride& stride) - { return typename StridedConstAlignedMapType >::type(data, rows, cols, stride); } - template - static inline typename StridedAlignedMapType >::type MapAligned(Scalar* data, Index rows, Index cols, const Stride& stride) - { return typename StridedAlignedMapType >::type(data, rows, cols, stride); } - //@} - - using Base::setConstant; - Derived& setConstant(Index size, const Scalar& value); - Derived& setConstant(Index rows, Index cols, const Scalar& value); - - using Base::setZero; - Derived& setZero(Index size); - Derived& setZero(Index rows, Index cols); - - using Base::setOnes; - Derived& setOnes(Index size); - Derived& setOnes(Index rows, Index cols); - - using Base::setRandom; - Derived& setRandom(Index size); - Derived& setRandom(Index rows, Index cols); - - #ifdef IMP_EIGEN_PLAINOBJECTBASE_PLUGIN - #include IMP_EIGEN_PLAINOBJECTBASE_PLUGIN - #endif - - protected: - /** \internal Resizes *this in preparation for assigning \a other to it. - * Takes care of doing all the checking that's needed. - * - * Note that copying a row-vector into a vector (and conversely) is allowed. - * The resizing, if any, is then done in the appropriate way so that row-vectors - * remain row-vectors and vectors remain vectors. - */ - template - IMP_EIGEN_STRONG_INLINE void _resize_to_match(const EigenBase& other) - { - #ifdef IMP_EIGEN_NO_AUTOMATIC_RESIZING - imp_eigen_assert((this->size()==0 || (IsVectorAtCompileTime ? (this->size() == other.size()) - : (rows() == other.rows() && cols() == other.cols()))) - && "Size mismatch. Automatic resizing is disabled because IMP_EIGEN_NO_AUTOMATIC_RESIZING is defined"); - IMP_EIGEN_ONLY_USED_FOR_DEBUG(other); - if(this->size()==0) - resizeLike(other); - #else - resizeLike(other); - #endif - } - - /** - * \brief Copies the value of the expression \a other into \c *this with automatic resizing. - * - * *this might be resized to match the dimensions of \a other. If *this was a null matrix (not already initialized), - * it will be initialized. - * - * Note that copying a row-vector into a vector (and conversely) is allowed. - * The resizing, if any, is then done in the appropriate way so that row-vectors - * remain row-vectors and vectors remain vectors. - * - * \sa operator=(const MatrixBase&), _set_noalias() - * - * \internal - */ - template - IMP_EIGEN_STRONG_INLINE Derived& _set(const DenseBase& other) - { - _set_selector(other.derived(), typename internal::conditional(int(OtherDerived::Flags) & EvalBeforeAssigningBit), internal::true_type, internal::false_type>::type()); - return this->derived(); - } - - template - IMP_EIGEN_STRONG_INLINE void _set_selector(const OtherDerived& other, const internal::true_type&) { _set_noalias(other.eval()); } - - template - IMP_EIGEN_STRONG_INLINE void _set_selector(const OtherDerived& other, const internal::false_type&) { _set_noalias(other); } - - /** \internal Like _set() but additionally makes the assumption that no aliasing effect can happen (which - * is the case when creating a new matrix) so one can enforce lazy evaluation. - * - * \sa operator=(const MatrixBase&), _set() - */ - template - IMP_EIGEN_STRONG_INLINE Derived& _set_noalias(const DenseBase& other) - { - // I don't think we need this resize call since the lazyAssign will anyways resize - // and lazyAssign will be called by the assign selector. - //_resize_to_match(other); - // the 'false' below means to enforce lazy evaluation. We don't use lazyAssign() because - // it wouldn't allow to copy a row-vector into a column-vector. - return internal::assign_selector::run(this->derived(), other.derived()); - } - - template - IMP_EIGEN_STRONG_INLINE void _init2(Index nbRows, Index nbCols, typename internal::enable_if::type* = 0) - { - IMP_EIGEN_STATIC_ASSERT(bool(NumTraits::IsInteger) && - bool(NumTraits::IsInteger), - FLOATING_POINT_ARGUMENT_PASSED__INTEGER_WAS_EXPECTED) - resize(nbRows,nbCols); - } - template - IMP_EIGEN_STRONG_INLINE void _init2(const Scalar& val0, const Scalar& val1, typename internal::enable_if::type* = 0) - { - IMP_EIGEN_STATIC_ASSERT_VECTOR_SPECIFIC_SIZE(PlainObjectBase, 2) - m_storage.data()[0] = val0; - m_storage.data()[1] = val1; - } - - template - friend struct internal::matrix_swap_impl; - - /** \internal generic implementation of swap for dense storage since for dynamic-sized matrices of same type it is enough to swap the - * data pointers. - */ - template - void _swap(DenseBase const & other) - { - enum { SwapPointers = internal::is_same::value && Base::SizeAtCompileTime==Dynamic }; - internal::matrix_swap_impl::run(this->derived(), other.const_cast_derived()); - } - - public: -#ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - static IMP_EIGEN_STRONG_INLINE void _check_template_params() - { - IMP_EIGEN_STATIC_ASSERT((IMP_EIGEN_IMPLIES(MaxRowsAtCompileTime==1 && MaxColsAtCompileTime!=1, (Options&RowMajor)==RowMajor) - && IMP_EIGEN_IMPLIES(MaxColsAtCompileTime==1 && MaxRowsAtCompileTime!=1, (Options&RowMajor)==0) - && ((RowsAtCompileTime == Dynamic) || (RowsAtCompileTime >= 0)) - && ((ColsAtCompileTime == Dynamic) || (ColsAtCompileTime >= 0)) - && ((MaxRowsAtCompileTime == Dynamic) || (MaxRowsAtCompileTime >= 0)) - && ((MaxColsAtCompileTime == Dynamic) || (MaxColsAtCompileTime >= 0)) - && (MaxRowsAtCompileTime == RowsAtCompileTime || RowsAtCompileTime==Dynamic) - && (MaxColsAtCompileTime == ColsAtCompileTime || ColsAtCompileTime==Dynamic) - && (Options & (DontAlign|RowMajor)) == Options), - INVALID_MATRIX_TEMPLATE_PARAMETERS) - } -#endif - -private: - enum { ThisConstantIsPrivateInPlainObjectBase }; -}; - -namespace internal { - -template -struct conservative_resize_like_impl -{ - typedef typename Derived::Index Index; - static void run(DenseBase& _this, Index rows, Index cols) - { - if (_this.rows() == rows && _this.cols() == cols) return; - IMP_EIGEN_STATIC_ASSERT_DYNAMIC_SIZE(Derived) - - if ( ( Derived::IsRowMajor && _this.cols() == cols) || // row-major and we change only the number of rows - (!Derived::IsRowMajor && _this.rows() == rows) ) // column-major and we change only the number of columns - { - internal::check_rows_cols_for_overflow::run(rows, cols); - _this.derived().m_storage.conservativeResize(rows*cols,rows,cols); - } - else - { - // The storage order does not allow us to use reallocation. - typename Derived::PlainObject tmp(rows,cols); - const Index common_rows = (std::min)(rows, _this.rows()); - const Index common_cols = (std::min)(cols, _this.cols()); - tmp.block(0,0,common_rows,common_cols) = _this.block(0,0,common_rows,common_cols); - _this.derived().swap(tmp); - } - } - - static void run(DenseBase& _this, const DenseBase& other) - { - if (_this.rows() == other.rows() && _this.cols() == other.cols()) return; - - // Note: Here is space for improvement. Basically, for conservativeResize(Index,Index), - // neither RowsAtCompileTime or ColsAtCompileTime must be Dynamic. If only one of the - // dimensions is dynamic, one could use either conservativeResize(Index rows, NoChange_t) or - // conservativeResize(NoChange_t, Index cols). For these methods new static asserts like - // IMP_EIGEN_STATIC_ASSERT_DYNAMIC_ROWS and IMP_EIGEN_STATIC_ASSERT_DYNAMIC_COLS would be good. - IMP_EIGEN_STATIC_ASSERT_DYNAMIC_SIZE(Derived) - IMP_EIGEN_STATIC_ASSERT_DYNAMIC_SIZE(OtherDerived) - - if ( ( Derived::IsRowMajor && _this.cols() == other.cols()) || // row-major and we change only the number of rows - (!Derived::IsRowMajor && _this.rows() == other.rows()) ) // column-major and we change only the number of columns - { - const Index new_rows = other.rows() - _this.rows(); - const Index new_cols = other.cols() - _this.cols(); - _this.derived().m_storage.conservativeResize(other.size(),other.rows(),other.cols()); - if (new_rows>0) - _this.bottomRightCorner(new_rows, other.cols()) = other.bottomRows(new_rows); - else if (new_cols>0) - _this.bottomRightCorner(other.rows(), new_cols) = other.rightCols(new_cols); - } - else - { - // The storage order does not allow us to use reallocation. - typename Derived::PlainObject tmp(other); - const Index common_rows = (std::min)(tmp.rows(), _this.rows()); - const Index common_cols = (std::min)(tmp.cols(), _this.cols()); - tmp.block(0,0,common_rows,common_cols) = _this.block(0,0,common_rows,common_cols); - _this.derived().swap(tmp); - } - } -}; - -// Here, the specialization for vectors inherits from the general matrix case -// to allow calling .conservativeResize(rows,cols) on vectors. -template -struct conservative_resize_like_impl - : conservative_resize_like_impl -{ - using conservative_resize_like_impl::run; - - typedef typename Derived::Index Index; - static void run(DenseBase& _this, Index size) - { - const Index new_rows = Derived::RowsAtCompileTime==1 ? 1 : size; - const Index new_cols = Derived::RowsAtCompileTime==1 ? size : 1; - _this.derived().m_storage.conservativeResize(size,new_rows,new_cols); - } - - static void run(DenseBase& _this, const DenseBase& other) - { - if (_this.rows() == other.rows() && _this.cols() == other.cols()) return; - - const Index num_new_elements = other.size() - _this.size(); - - const Index new_rows = Derived::RowsAtCompileTime==1 ? 1 : other.rows(); - const Index new_cols = Derived::RowsAtCompileTime==1 ? other.cols() : 1; - _this.derived().m_storage.conservativeResize(other.size(),new_rows,new_cols); - - if (num_new_elements > 0) - _this.tail(num_new_elements) = other.tail(num_new_elements); - } -}; - -template -struct matrix_swap_impl -{ - static inline void run(MatrixTypeA& a, MatrixTypeB& b) - { - a.base().swap(b); - } -}; - -template -struct matrix_swap_impl -{ - static inline void run(MatrixTypeA& a, MatrixTypeB& b) - { - static_cast(a).m_storage.swap(static_cast(b).m_storage); - } -}; - -} // end namespace internal - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_DENSESTORAGEBASE_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/ProductBase.h b/modules/algebra/include/eigen3/Eigen/src/Core/ProductBase.h deleted file mode 100644 index 9979dce174..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/ProductBase.h +++ /dev/null @@ -1,290 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2009-2010 Gael Guennebaud -// -// 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 IMP_EIGEN_PRODUCTBASE_H -#define IMP_EIGEN_PRODUCTBASE_H - -namespace IMP_Eigen { - -/** \class ProductBase - * \ingroup Core_Module - * - */ - -namespace internal { -template -struct traits > -{ - typedef MatrixXpr XprKind; - typedef typename remove_all<_Lhs>::type Lhs; - typedef typename remove_all<_Rhs>::type Rhs; - typedef typename scalar_product_traits::ReturnType Scalar; - typedef typename promote_storage_type::StorageKind, - typename traits::StorageKind>::ret StorageKind; - typedef typename promote_index_type::Index, - typename traits::Index>::type Index; - enum { - RowsAtCompileTime = traits::RowsAtCompileTime, - ColsAtCompileTime = traits::ColsAtCompileTime, - MaxRowsAtCompileTime = traits::MaxRowsAtCompileTime, - MaxColsAtCompileTime = traits::MaxColsAtCompileTime, - Flags = (MaxRowsAtCompileTime==1 ? RowMajorBit : 0) - | EvalBeforeNestingBit | EvalBeforeAssigningBit | NestByRefBit, - // Note that EvalBeforeNestingBit and NestByRefBit - // are not used in practice because nested is overloaded for products - CoeffReadCost = 0 // FIXME why is it needed ? - }; -}; -} - -#define IMP_EIGEN_PRODUCT_PUBLIC_INTERFACE(Derived) \ - typedef ProductBase Base; \ - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(Derived) \ - typedef typename Base::LhsNested LhsNested; \ - typedef typename Base::_LhsNested _LhsNested; \ - typedef typename Base::LhsBlasTraits LhsBlasTraits; \ - typedef typename Base::ActualLhsType ActualLhsType; \ - typedef typename Base::_ActualLhsType _ActualLhsType; \ - typedef typename Base::RhsNested RhsNested; \ - typedef typename Base::_RhsNested _RhsNested; \ - typedef typename Base::RhsBlasTraits RhsBlasTraits; \ - typedef typename Base::ActualRhsType ActualRhsType; \ - typedef typename Base::_ActualRhsType _ActualRhsType; \ - using Base::m_lhs; \ - using Base::m_rhs; - -template -class ProductBase : public MatrixBase -{ - public: - typedef MatrixBase Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(ProductBase) - - typedef typename Lhs::Nested LhsNested; - typedef typename internal::remove_all::type _LhsNested; - typedef internal::blas_traits<_LhsNested> LhsBlasTraits; - typedef typename LhsBlasTraits::DirectLinearAccessType ActualLhsType; - typedef typename internal::remove_all::type _ActualLhsType; - typedef typename internal::traits::Scalar LhsScalar; - - typedef typename Rhs::Nested RhsNested; - typedef typename internal::remove_all::type _RhsNested; - typedef internal::blas_traits<_RhsNested> RhsBlasTraits; - typedef typename RhsBlasTraits::DirectLinearAccessType ActualRhsType; - typedef typename internal::remove_all::type _ActualRhsType; - typedef typename internal::traits::Scalar RhsScalar; - - // Diagonal of a product: no need to evaluate the arguments because they are going to be evaluated only once - typedef CoeffBasedProduct FullyLazyCoeffBaseProductType; - - public: - -#ifndef IMP_EIGEN_NO_MALLOC - typedef typename Base::PlainObject BasePlainObject; - typedef Matrix DynPlainObject; - typedef typename internal::conditional<(BasePlainObject::SizeAtCompileTime==Dynamic) || (BasePlainObject::SizeAtCompileTime*int(sizeof(Scalar)) < int(IMP_EIGEN_STACK_ALLOCATION_LIMIT)), - BasePlainObject, DynPlainObject>::type PlainObject; -#else - typedef typename Base::PlainObject PlainObject; -#endif - - ProductBase(const Lhs& a_lhs, const Rhs& a_rhs) - : m_lhs(a_lhs), m_rhs(a_rhs) - { - imp_eigen_assert(a_lhs.cols() == a_rhs.rows() - && "invalid matrix product" - && "if you wanted a coeff-wise or a dot product use the respective explicit functions"); - } - - inline Index rows() const { return m_lhs.rows(); } - inline Index cols() const { return m_rhs.cols(); } - - template - inline void evalTo(Dest& dst) const { dst.setZero(); scaleAndAddTo(dst,Scalar(1)); } - - template - inline void addTo(Dest& dst) const { scaleAndAddTo(dst,Scalar(1)); } - - template - inline void subTo(Dest& dst) const { scaleAndAddTo(dst,Scalar(-1)); } - - template - inline void scaleAndAddTo(Dest& dst, const Scalar& alpha) const { derived().scaleAndAddTo(dst,alpha); } - - const _LhsNested& lhs() const { return m_lhs; } - const _RhsNested& rhs() const { return m_rhs; } - - // Implicit conversion to the nested type (trigger the evaluation of the product) - operator const PlainObject& () const - { - m_result.resize(m_lhs.rows(), m_rhs.cols()); - derived().evalTo(m_result); - return m_result; - } - - const Diagonal diagonal() const - { return FullyLazyCoeffBaseProductType(m_lhs, m_rhs); } - - template - const Diagonal diagonal() const - { return FullyLazyCoeffBaseProductType(m_lhs, m_rhs); } - - const Diagonal diagonal(Index index) const - { return FullyLazyCoeffBaseProductType(m_lhs, m_rhs).diagonal(index); } - - // restrict coeff accessors to 1x1 expressions. No need to care about mutators here since this isnt a Lvalue expression - typename Base::CoeffReturnType coeff(Index row, Index col) const - { -#ifdef IMP_EIGEN2_SUPPORT - return lhs().row(row).cwiseProduct(rhs().col(col).transpose()).sum(); -#else - IMP_EIGEN_STATIC_ASSERT_SIZE_1x1(Derived) - imp_eigen_assert(this->rows() == 1 && this->cols() == 1); - Matrix result = *this; - return result.coeff(row,col); -#endif - } - - typename Base::CoeffReturnType coeff(Index i) const - { - IMP_EIGEN_STATIC_ASSERT_SIZE_1x1(Derived) - imp_eigen_assert(this->rows() == 1 && this->cols() == 1); - Matrix result = *this; - return result.coeff(i); - } - - const Scalar& coeffRef(Index row, Index col) const - { - IMP_EIGEN_STATIC_ASSERT_SIZE_1x1(Derived) - imp_eigen_assert(this->rows() == 1 && this->cols() == 1); - return derived().coeffRef(row,col); - } - - const Scalar& coeffRef(Index i) const - { - IMP_EIGEN_STATIC_ASSERT_SIZE_1x1(Derived) - imp_eigen_assert(this->rows() == 1 && this->cols() == 1); - return derived().coeffRef(i); - } - - protected: - - LhsNested m_lhs; - RhsNested m_rhs; - - mutable PlainObject m_result; -}; - -// here we need to overload the nested rule for products -// such that the nested type is a const reference to a plain matrix -namespace internal { -template -struct nested, N, PlainObject> -{ - typedef typename GeneralProduct::PlainObject const& type; -}; -template -struct nested, N, PlainObject> -{ - typedef typename GeneralProduct::PlainObject const& type; -}; -} - -template -class ScaledProduct; - -// Note that these two operator* functions are not defined as member -// functions of ProductBase, because, otherwise we would have to -// define all overloads defined in MatrixBase. Furthermore, Using -// "using Base::operator*" would not work with MSVC. -// -// Also note that here we accept any compatible scalar types -template -const ScaledProduct -operator*(const ProductBase& prod, const typename Derived::Scalar& x) -{ return ScaledProduct(prod.derived(), x); } - -template -typename internal::enable_if::value, - const ScaledProduct >::type -operator*(const ProductBase& prod, const typename Derived::RealScalar& x) -{ return ScaledProduct(prod.derived(), x); } - - -template -const ScaledProduct -operator*(const typename Derived::Scalar& x,const ProductBase& prod) -{ return ScaledProduct(prod.derived(), x); } - -template -typename internal::enable_if::value, - const ScaledProduct >::type -operator*(const typename Derived::RealScalar& x,const ProductBase& prod) -{ return ScaledProduct(prod.derived(), x); } - -namespace internal { -template -struct traits > - : traits, - typename NestedProduct::_LhsNested, - typename NestedProduct::_RhsNested> > -{ - typedef typename traits::StorageKind StorageKind; -}; -} - -template -class ScaledProduct - : public ProductBase, - typename NestedProduct::_LhsNested, - typename NestedProduct::_RhsNested> -{ - public: - typedef ProductBase, - typename NestedProduct::_LhsNested, - typename NestedProduct::_RhsNested> Base; - typedef typename Base::Scalar Scalar; - typedef typename Base::PlainObject PlainObject; -// IMP_EIGEN_PRODUCT_PUBLIC_INTERFACE(ScaledProduct) - - ScaledProduct(const NestedProduct& prod, const Scalar& x) - : Base(prod.lhs(),prod.rhs()), m_prod(prod), m_alpha(x) {} - - template - inline void evalTo(Dest& dst) const { dst.setZero(); scaleAndAddTo(dst, Scalar(1)); } - - template - inline void addTo(Dest& dst) const { scaleAndAddTo(dst, Scalar(1)); } - - template - inline void subTo(Dest& dst) const { scaleAndAddTo(dst, Scalar(-1)); } - - template - inline void scaleAndAddTo(Dest& dst, const Scalar& a_alpha) const { m_prod.derived().scaleAndAddTo(dst,a_alpha * m_alpha); } - - const Scalar& alpha() const { return m_alpha; } - - protected: - const NestedProduct& m_prod; - Scalar m_alpha; -}; - -/** \internal - * Overloaded to perform an efficient C = (A*B).lazy() */ -template -template -Derived& MatrixBase::lazyAssign(const ProductBase& other) -{ - other.derived().evalTo(derived()); - return derived(); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_PRODUCTBASE_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/Random.h b/modules/algebra/include/eigen3/Eigen/src/Core/Random.h deleted file mode 100644 index b393550665..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/Random.h +++ /dev/null @@ -1,152 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008 Gael Guennebaud -// -// 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 IMP_EIGEN_RANDOM_H -#define IMP_EIGEN_RANDOM_H - -namespace IMP_Eigen { - -namespace internal { - -template struct scalar_random_op { - IMP_EIGEN_EMPTY_STRUCT_CTOR(scalar_random_op) - template - inline const Scalar operator() (Index, Index = 0) const { return random(); } -}; - -template -struct functor_traits > -{ enum { Cost = 5 * NumTraits::MulCost, PacketAccess = false, IsRepeatable = false }; }; - -} // end namespace internal - -/** \returns a random matrix expression - * - * The parameters \a rows and \a cols are the number of rows and of columns of - * the returned matrix. Must be compatible with this MatrixBase type. - * - * This variant is meant to be used for dynamic-size matrix types. For fixed-size types, - * it is redundant to pass \a rows and \a cols as arguments, so Random() should be used - * instead. - * - * Example: \include MatrixBase_random_int_int.cpp - * Output: \verbinclude MatrixBase_random_int_int.out - * - * This expression has the "evaluate before nesting" flag so that it will be evaluated into - * a temporary matrix whenever it is nested in a larger expression. This prevents unexpected - * behavior with expressions involving random matrices. - * - * \sa MatrixBase::setRandom(), MatrixBase::Random(Index), MatrixBase::Random() - */ -template -inline const CwiseNullaryOp::Scalar>, Derived> -DenseBase::Random(Index rows, Index cols) -{ - return NullaryExpr(rows, cols, internal::scalar_random_op()); -} - -/** \returns a random vector expression - * - * The parameter \a size is the size of the returned vector. - * Must be compatible with this MatrixBase type. - * - * \only_for_vectors - * - * This variant is meant to be used for dynamic-size vector types. For fixed-size types, - * it is redundant to pass \a size as argument, so Random() should be used - * instead. - * - * Example: \include MatrixBase_random_int.cpp - * Output: \verbinclude MatrixBase_random_int.out - * - * This expression has the "evaluate before nesting" flag so that it will be evaluated into - * a temporary vector whenever it is nested in a larger expression. This prevents unexpected - * behavior with expressions involving random matrices. - * - * \sa MatrixBase::setRandom(), MatrixBase::Random(Index,Index), MatrixBase::Random() - */ -template -inline const CwiseNullaryOp::Scalar>, Derived> -DenseBase::Random(Index size) -{ - return NullaryExpr(size, internal::scalar_random_op()); -} - -/** \returns a fixed-size random matrix or vector expression - * - * This variant is only for fixed-size MatrixBase types. For dynamic-size types, you - * need to use the variants taking size arguments. - * - * Example: \include MatrixBase_random.cpp - * Output: \verbinclude MatrixBase_random.out - * - * This expression has the "evaluate before nesting" flag so that it will be evaluated into - * a temporary matrix whenever it is nested in a larger expression. This prevents unexpected - * behavior with expressions involving random matrices. - * - * \sa MatrixBase::setRandom(), MatrixBase::Random(Index,Index), MatrixBase::Random(Index) - */ -template -inline const CwiseNullaryOp::Scalar>, Derived> -DenseBase::Random() -{ - return NullaryExpr(RowsAtCompileTime, ColsAtCompileTime, internal::scalar_random_op()); -} - -/** Sets all coefficients in this expression to random values. - * - * Example: \include MatrixBase_setRandom.cpp - * Output: \verbinclude MatrixBase_setRandom.out - * - * \sa class CwiseNullaryOp, setRandom(Index), setRandom(Index,Index) - */ -template -inline Derived& DenseBase::setRandom() -{ - return *this = Random(rows(), cols()); -} - -/** Resizes to the given \a newSize, and sets all coefficients in this expression to random values. - * - * \only_for_vectors - * - * Example: \include Matrix_setRandom_int.cpp - * Output: \verbinclude Matrix_setRandom_int.out - * - * \sa MatrixBase::setRandom(), setRandom(Index,Index), class CwiseNullaryOp, MatrixBase::Random() - */ -template -IMP_EIGEN_STRONG_INLINE Derived& -PlainObjectBase::setRandom(Index newSize) -{ - resize(newSize); - return setRandom(); -} - -/** Resizes to the given size, and sets all coefficients in this expression to random values. - * - * \param nbRows the new number of rows - * \param nbCols the new number of columns - * - * Example: \include Matrix_setRandom_int_int.cpp - * Output: \verbinclude Matrix_setRandom_int_int.out - * - * \sa MatrixBase::setRandom(), setRandom(Index), class CwiseNullaryOp, MatrixBase::Random() - */ -template -IMP_EIGEN_STRONG_INLINE Derived& -PlainObjectBase::setRandom(Index nbRows, Index nbCols) -{ - resize(nbRows, nbCols); - return setRandom(); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_RANDOM_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/Redux.h b/modules/algebra/include/eigen3/Eigen/src/Core/Redux.h deleted file mode 100644 index 7b8d2cfcaf..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/Redux.h +++ /dev/null @@ -1,409 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008 Gael Guennebaud -// Copyright (C) 2006-2008 Benoit Jacob -// -// 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 IMP_EIGEN_REDUX_H -#define IMP_EIGEN_REDUX_H - -namespace IMP_Eigen { - -namespace internal { - -// TODO -// * implement other kind of vectorization -// * factorize code - -/*************************************************************************** -* Part 1 : the logic deciding a strategy for vectorization and unrolling -***************************************************************************/ - -template -struct redux_traits -{ -public: - enum { - PacketSize = packet_traits::size, - InnerMaxSize = int(Derived::IsRowMajor) - ? Derived::MaxColsAtCompileTime - : Derived::MaxRowsAtCompileTime - }; - - enum { - MightVectorize = (int(Derived::Flags)&ActualPacketAccessBit) - && (functor_traits::PacketAccess), - MayLinearVectorize = MightVectorize && (int(Derived::Flags)&LinearAccessBit), - MaySliceVectorize = MightVectorize && int(InnerMaxSize)>=3*PacketSize - }; - -public: - enum { - Traversal = int(MayLinearVectorize) ? int(LinearVectorizedTraversal) - : int(MaySliceVectorize) ? int(SliceVectorizedTraversal) - : int(DefaultTraversal) - }; - -public: - enum { - Cost = ( Derived::SizeAtCompileTime == Dynamic - || Derived::CoeffReadCost == Dynamic - || (Derived::SizeAtCompileTime!=1 && functor_traits::Cost == Dynamic) - ) ? Dynamic - : Derived::SizeAtCompileTime * Derived::CoeffReadCost - + (Derived::SizeAtCompileTime-1) * functor_traits::Cost, - UnrollingLimit = IMP_EIGEN_UNROLLING_LIMIT * (int(Traversal) == int(DefaultTraversal) ? 1 : int(PacketSize)) - }; - -public: - enum { - Unrolling = Cost != Dynamic && Cost <= UnrollingLimit - ? CompleteUnrolling - : NoUnrolling - }; -}; - -/*************************************************************************** -* Part 2 : unrollers -***************************************************************************/ - -/*** no vectorization ***/ - -template -struct redux_novec_unroller -{ - enum { - HalfLength = Length/2 - }; - - typedef typename Derived::Scalar Scalar; - - static IMP_EIGEN_STRONG_INLINE Scalar run(const Derived &mat, const Func& func) - { - return func(redux_novec_unroller::run(mat,func), - redux_novec_unroller::run(mat,func)); - } -}; - -template -struct redux_novec_unroller -{ - enum { - outer = Start / Derived::InnerSizeAtCompileTime, - inner = Start % Derived::InnerSizeAtCompileTime - }; - - typedef typename Derived::Scalar Scalar; - - static IMP_EIGEN_STRONG_INLINE Scalar run(const Derived &mat, const Func&) - { - return mat.coeffByOuterInner(outer, inner); - } -}; - -// This is actually dead code and will never be called. It is required -// to prevent false warnings regarding failed inlining though -// for 0 length run() will never be called at all. -template -struct redux_novec_unroller -{ - typedef typename Derived::Scalar Scalar; - static IMP_EIGEN_STRONG_INLINE Scalar run(const Derived&, const Func&) { return Scalar(); } -}; - -/*** vectorization ***/ - -template -struct redux_vec_unroller -{ - enum { - PacketSize = packet_traits::size, - HalfLength = Length/2 - }; - - typedef typename Derived::Scalar Scalar; - typedef typename packet_traits::type PacketScalar; - - static IMP_EIGEN_STRONG_INLINE PacketScalar run(const Derived &mat, const Func& func) - { - return func.packetOp( - redux_vec_unroller::run(mat,func), - redux_vec_unroller::run(mat,func) ); - } -}; - -template -struct redux_vec_unroller -{ - enum { - index = Start * packet_traits::size, - outer = index / int(Derived::InnerSizeAtCompileTime), - inner = index % int(Derived::InnerSizeAtCompileTime), - alignment = (Derived::Flags & AlignedBit) ? Aligned : Unaligned - }; - - typedef typename Derived::Scalar Scalar; - typedef typename packet_traits::type PacketScalar; - - static IMP_EIGEN_STRONG_INLINE PacketScalar run(const Derived &mat, const Func&) - { - return mat.template packetByOuterInner(outer, inner); - } -}; - -/*************************************************************************** -* Part 3 : implementation of all cases -***************************************************************************/ - -template::Traversal, - int Unrolling = redux_traits::Unrolling -> -struct redux_impl; - -template -struct redux_impl -{ - typedef typename Derived::Scalar Scalar; - typedef typename Derived::Index Index; - static IMP_EIGEN_STRONG_INLINE Scalar run(const Derived& mat, const Func& func) - { - imp_eigen_assert(mat.rows()>0 && mat.cols()>0 && "you are using an empty matrix"); - Scalar res; - res = mat.coeffByOuterInner(0, 0); - for(Index i = 1; i < mat.innerSize(); ++i) - res = func(res, mat.coeffByOuterInner(0, i)); - for(Index i = 1; i < mat.outerSize(); ++i) - for(Index j = 0; j < mat.innerSize(); ++j) - res = func(res, mat.coeffByOuterInner(i, j)); - return res; - } -}; - -template -struct redux_impl - : public redux_novec_unroller -{}; - -template -struct redux_impl -{ - typedef typename Derived::Scalar Scalar; - typedef typename packet_traits::type PacketScalar; - typedef typename Derived::Index Index; - - static Scalar run(const Derived& mat, const Func& func) - { - const Index size = mat.size(); - imp_eigen_assert(size && "you are using an empty matrix"); - const Index packetSize = packet_traits::size; - const Index alignedStart = internal::first_aligned(mat); - enum { - alignment = bool(Derived::Flags & DirectAccessBit) || bool(Derived::Flags & AlignedBit) - ? Aligned : Unaligned - }; - const Index alignedSize2 = ((size-alignedStart)/(2*packetSize))*(2*packetSize); - const Index alignedSize = ((size-alignedStart)/(packetSize))*(packetSize); - const Index alignedEnd2 = alignedStart + alignedSize2; - const Index alignedEnd = alignedStart + alignedSize; - Scalar res; - if(alignedSize) - { - PacketScalar packet_res0 = mat.template packet(alignedStart); - if(alignedSize>packetSize) // we have at least two packets to partly unroll the loop - { - PacketScalar packet_res1 = mat.template packet(alignedStart+packetSize); - for(Index index = alignedStart + 2*packetSize; index < alignedEnd2; index += 2*packetSize) - { - packet_res0 = func.packetOp(packet_res0, mat.template packet(index)); - packet_res1 = func.packetOp(packet_res1, mat.template packet(index+packetSize)); - } - - packet_res0 = func.packetOp(packet_res0,packet_res1); - if(alignedEnd>alignedEnd2) - packet_res0 = func.packetOp(packet_res0, mat.template packet(alignedEnd2)); - } - res = func.predux(packet_res0); - - for(Index index = 0; index < alignedStart; ++index) - res = func(res,mat.coeff(index)); - - for(Index index = alignedEnd; index < size; ++index) - res = func(res,mat.coeff(index)); - } - else // too small to vectorize anything. - // since this is dynamic-size hence inefficient anyway for such small sizes, don't try to optimize. - { - res = mat.coeff(0); - for(Index index = 1; index < size; ++index) - res = func(res,mat.coeff(index)); - } - - return res; - } -}; - -// NOTE: for SliceVectorizedTraversal we simply bypass unrolling -template -struct redux_impl -{ - typedef typename Derived::Scalar Scalar; - typedef typename packet_traits::type PacketScalar; - typedef typename Derived::Index Index; - - static Scalar run(const Derived& mat, const Func& func) - { - imp_eigen_assert(mat.rows()>0 && mat.cols()>0 && "you are using an empty matrix"); - const Index innerSize = mat.innerSize(); - const Index outerSize = mat.outerSize(); - enum { - packetSize = packet_traits::size - }; - const Index packetedInnerSize = ((innerSize)/packetSize)*packetSize; - Scalar res; - if(packetedInnerSize) - { - PacketScalar packet_res = mat.template packet(0,0); - for(Index j=0; j(j,i)); - - res = func.predux(packet_res); - for(Index j=0; j::run(mat, func); - } - - return res; - } -}; - -template -struct redux_impl -{ - typedef typename Derived::Scalar Scalar; - typedef typename packet_traits::type PacketScalar; - enum { - PacketSize = packet_traits::size, - Size = Derived::SizeAtCompileTime, - VectorizedSize = (Size / PacketSize) * PacketSize - }; - static IMP_EIGEN_STRONG_INLINE Scalar run(const Derived& mat, const Func& func) - { - imp_eigen_assert(mat.rows()>0 && mat.cols()>0 && "you are using an empty matrix"); - Scalar res = func.predux(redux_vec_unroller::run(mat,func)); - if (VectorizedSize != Size) - res = func(res,redux_novec_unroller::run(mat,func)); - return res; - } -}; - -} // end namespace internal - -/*************************************************************************** -* Part 4 : public API -***************************************************************************/ - - -/** \returns the result of a full redux operation on the whole matrix or vector using \a func - * - * The template parameter \a BinaryOp is the type of the functor \a func which must be - * an associative operator. Both current STL and TR1 functor styles are handled. - * - * \sa DenseBase::sum(), DenseBase::minCoeff(), DenseBase::maxCoeff(), MatrixBase::colwise(), MatrixBase::rowwise() - */ -template -template -IMP_EIGEN_STRONG_INLINE typename internal::result_of::Scalar)>::type -DenseBase::redux(const Func& func) const -{ - typedef typename internal::remove_all::type ThisNested; - return internal::redux_impl - ::run(derived(), func); -} - -/** \returns the minimum of all coefficients of \c *this. - * \warning the result is undefined if \c *this contains NaN. - */ -template -IMP_EIGEN_STRONG_INLINE typename internal::traits::Scalar -DenseBase::minCoeff() const -{ - return this->redux(IMP_Eigen::internal::scalar_min_op()); -} - -/** \returns the maximum of all coefficients of \c *this. - * \warning the result is undefined if \c *this contains NaN. - */ -template -IMP_EIGEN_STRONG_INLINE typename internal::traits::Scalar -DenseBase::maxCoeff() const -{ - return this->redux(IMP_Eigen::internal::scalar_max_op()); -} - -/** \returns the sum of all coefficients of *this - * - * \sa trace(), prod(), mean() - */ -template -IMP_EIGEN_STRONG_INLINE typename internal::traits::Scalar -DenseBase::sum() const -{ - if(SizeAtCompileTime==0 || (SizeAtCompileTime==Dynamic && size()==0)) - return Scalar(0); - return this->redux(IMP_Eigen::internal::scalar_sum_op()); -} - -/** \returns the mean of all coefficients of *this -* -* \sa trace(), prod(), sum() -*/ -template -IMP_EIGEN_STRONG_INLINE typename internal::traits::Scalar -DenseBase::mean() const -{ - return Scalar(this->redux(IMP_Eigen::internal::scalar_sum_op())) / Scalar(this->size()); -} - -/** \returns the product of all coefficients of *this - * - * Example: \include MatrixBase_prod.cpp - * Output: \verbinclude MatrixBase_prod.out - * - * \sa sum(), mean(), trace() - */ -template -IMP_EIGEN_STRONG_INLINE typename internal::traits::Scalar -DenseBase::prod() const -{ - if(SizeAtCompileTime==0 || (SizeAtCompileTime==Dynamic && size()==0)) - return Scalar(1); - return this->redux(IMP_Eigen::internal::scalar_product_op()); -} - -/** \returns the trace of \c *this, i.e. the sum of the coefficients on the main diagonal. - * - * \c *this can be any matrix, not necessarily square. - * - * \sa diagonal(), sum() - */ -template -IMP_EIGEN_STRONG_INLINE typename internal::traits::Scalar -MatrixBase::trace() const -{ - return derived().diagonal().sum(); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_REDUX_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/Ref.h b/modules/algebra/include/eigen3/Eigen/src/Core/Ref.h deleted file mode 100644 index ed2b8ba76d..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/Ref.h +++ /dev/null @@ -1,278 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2012 Gael Guennebaud -// -// 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 IMP_EIGEN_REF_H -#define IMP_EIGEN_REF_H - -namespace IMP_Eigen { - -template class RefBase; -template,OuterStride<> >::type > class Ref; - -/** \class Ref - * \ingroup Core_Module - * - * \brief A matrix or vector expression mapping an existing expressions - * - * \tparam PlainObjectType the equivalent matrix type of the mapped data - * \tparam Options specifies whether the pointer is \c #Aligned, or \c #Unaligned. - * The default is \c #Unaligned. - * \tparam StrideType optionally specifies strides. By default, Ref implies a contiguous storage along the inner dimension (inner stride==1), - * but accept a variable outer stride (leading dimension). - * This can be overridden by specifying strides. - * The type passed here must be a specialization of the Stride template, see examples below. - * - * This class permits to write non template functions taking Eigen's object as parameters while limiting the number of copies. - * A Ref<> object can represent either a const expression or a l-value: - * \code - * // in-out argument: - * void foo1(Ref x); - * - * // read-only const argument: - * void foo2(const Ref& x); - * \endcode - * - * In the in-out case, the input argument must satisfies the constraints of the actual Ref<> type, otherwise a compilation issue will be triggered. - * By default, a Ref can reference any dense vector expression of float having a contiguous memory layout. - * Likewise, a Ref can reference any column major dense matrix expression of float whose column's elements are contiguously stored with - * the possibility to have a constant space inbetween each column, i.e.: the inner stride mmust be equal to 1, but the outer-stride (or leading dimension), - * can be greater than the number of rows. - * - * In the const case, if the input expression does not match the above requirement, then it is evaluated into a temporary before being passed to the function. - * Here are some examples: - * \code - * MatrixXf A; - * VectorXf a; - * foo1(a.head()); // OK - * foo1(A.col()); // OK - * foo1(A.row()); // compilation error because here innerstride!=1 - * foo2(A.row()); // The row is copied into a contiguous temporary - * foo2(2*a); // The expression is evaluated into a temporary - * foo2(A.col().segment(2,4)); // No temporary - * \endcode - * - * The range of inputs that can be referenced without temporary can be enlarged using the last two template parameter. - * Here is an example accepting an innerstride!=1: - * \code - * // in-out argument: - * void foo3(Ref > x); - * foo3(A.row()); // OK - * \endcode - * The downside here is that the function foo3 might be significantly slower than foo1 because it won't be able to exploit vectorization, and will involved more - * expensive address computations even if the input is contiguously stored in memory. To overcome this issue, one might propose to overloads internally calling a - * template function, e.g.: - * \code - * // in the .h: - * void foo(const Ref& A); - * void foo(const Ref >& A); - * - * // in the .cpp: - * template void foo_impl(const TypeOfA& A) { - * ... // crazy code goes here - * } - * void foo(const Ref& A) { foo_impl(A); } - * void foo(const Ref >& A) { foo_impl(A); } - * \endcode - * - * - * \sa PlainObjectBase::Map(), \ref TopicStorageOrders - */ - -namespace internal { - -template -struct traits > - : public traits > -{ - typedef _PlainObjectType PlainObjectType; - typedef _StrideType StrideType; - enum { - Options = _Options, - Flags = traits >::Flags | NestByRefBit - }; - - template struct match { - enum { - HasDirectAccess = internal::has_direct_access::ret, - StorageOrderMatch = PlainObjectType::IsVectorAtCompileTime || Derived::IsVectorAtCompileTime || ((PlainObjectType::Flags&RowMajorBit)==(Derived::Flags&RowMajorBit)), - InnerStrideMatch = int(StrideType::InnerStrideAtCompileTime)==int(Dynamic) - || int(StrideType::InnerStrideAtCompileTime)==int(Derived::InnerStrideAtCompileTime) - || (int(StrideType::InnerStrideAtCompileTime)==0 && int(Derived::InnerStrideAtCompileTime)==1), - OuterStrideMatch = Derived::IsVectorAtCompileTime - || int(StrideType::OuterStrideAtCompileTime)==int(Dynamic) || int(StrideType::OuterStrideAtCompileTime)==int(Derived::OuterStrideAtCompileTime), - AlignmentMatch = (_Options!=Aligned) || ((PlainObjectType::Flags&AlignedBit)==0) || ((traits::Flags&AlignedBit)==AlignedBit), - ScalarTypeMatch = internal::is_same::value, - MatchAtCompileTime = HasDirectAccess && StorageOrderMatch && InnerStrideMatch && OuterStrideMatch && AlignmentMatch && ScalarTypeMatch - }; - typedef typename internal::conditional::type type; - }; - -}; - -template -struct traits > : public traits {}; - -} - -template class RefBase - : public MapBase -{ - typedef typename internal::traits::PlainObjectType PlainObjectType; - typedef typename internal::traits::StrideType StrideType; - -public: - - typedef MapBase Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(RefBase) - - inline Index innerStride() const - { - return StrideType::InnerStrideAtCompileTime != 0 ? m_stride.inner() : 1; - } - - inline Index outerStride() const - { - return StrideType::OuterStrideAtCompileTime != 0 ? m_stride.outer() - : IsVectorAtCompileTime ? this->size() - : int(Flags)&RowMajorBit ? this->cols() - : this->rows(); - } - - RefBase() - : Base(0,RowsAtCompileTime==Dynamic?0:RowsAtCompileTime,ColsAtCompileTime==Dynamic?0:ColsAtCompileTime), - // Stride<> does not allow default ctor for Dynamic strides, so let' initialize it with dummy values: - m_stride(StrideType::OuterStrideAtCompileTime==Dynamic?0:StrideType::OuterStrideAtCompileTime, - StrideType::InnerStrideAtCompileTime==Dynamic?0:StrideType::InnerStrideAtCompileTime) - {} - - IMP_EIGEN_INHERIT_ASSIGNMENT_OPERATORS(RefBase) - -protected: - - typedef Stride StrideBase; - - template - void construct(Expression& expr) - { - if(PlainObjectType::RowsAtCompileTime==1) - { - imp_eigen_assert(expr.rows()==1 || expr.cols()==1); - ::new (static_cast(this)) Base(expr.data(), 1, expr.size()); - } - else if(PlainObjectType::ColsAtCompileTime==1) - { - imp_eigen_assert(expr.rows()==1 || expr.cols()==1); - ::new (static_cast(this)) Base(expr.data(), expr.size(), 1); - } - else - ::new (static_cast(this)) Base(expr.data(), expr.rows(), expr.cols()); - - if(Expression::IsVectorAtCompileTime && (!PlainObjectType::IsVectorAtCompileTime) && ((Expression::Flags&RowMajorBit)!=(PlainObjectType::Flags&RowMajorBit))) - ::new (&m_stride) StrideBase(expr.innerStride(), StrideType::InnerStrideAtCompileTime==0?0:1); - else - ::new (&m_stride) StrideBase(StrideType::OuterStrideAtCompileTime==0?0:expr.outerStride(), - StrideType::InnerStrideAtCompileTime==0?0:expr.innerStride()); - } - - StrideBase m_stride; -}; - - -template class Ref - : public RefBase > -{ - private: - typedef internal::traits Traits; - template - inline Ref(const PlainObjectBase& expr, - typename internal::enable_if::MatchAtCompileTime),Derived>::type* = 0); - public: - - typedef RefBase Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(Ref) - - - #ifndef IMP_EIGEN_PARSED_BY_DOXYGEN - template - inline Ref(PlainObjectBase& expr, - typename internal::enable_if::MatchAtCompileTime),Derived>::type* = 0) - { - IMP_EIGEN_STATIC_ASSERT(static_cast(Traits::template match::MatchAtCompileTime), STORAGE_LAYOUT_DOES_NOT_MATCH); - Base::construct(expr.derived()); - } - template - inline Ref(const DenseBase& expr, - typename internal::enable_if::MatchAtCompileTime),Derived>::type* = 0) - #else - template - inline Ref(DenseBase& expr) - #endif - { - IMP_EIGEN_STATIC_ASSERT(static_cast(internal::is_lvalue::value), THIS_EXPRESSION_IS_NOT_A_LVALUE__IT_IS_READ_ONLY); - IMP_EIGEN_STATIC_ASSERT(static_cast(Traits::template match::MatchAtCompileTime), STORAGE_LAYOUT_DOES_NOT_MATCH); - enum { THIS_EXPRESSION_IS_NOT_A_LVALUE__IT_IS_READ_ONLY = Derived::ThisConstantIsPrivateInPlainObjectBase}; - Base::construct(expr.const_cast_derived()); - } - - IMP_EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Ref) - -}; - -// this is the const ref version -template class Ref - : public RefBase > -{ - typedef internal::traits Traits; - public: - - typedef RefBase Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(Ref) - - template - inline Ref(const DenseBase& expr, - typename internal::enable_if::ScalarTypeMatch),Derived>::type* = 0) - { -// std::cout << match_helper::HasDirectAccess << "," << match_helper::OuterStrideMatch << "," << match_helper::InnerStrideMatch << "\n"; -// std::cout << int(StrideType::OuterStrideAtCompileTime) << " - " << int(Derived::OuterStrideAtCompileTime) << "\n"; -// std::cout << int(StrideType::InnerStrideAtCompileTime) << " - " << int(Derived::InnerStrideAtCompileTime) << "\n"; - construct(expr.derived(), typename Traits::template match::type()); - } - - inline Ref(const Ref& other) : Base(other) { - // copy constructor shall not copy the m_object, to avoid unnecessary malloc and copy - } - - template - inline Ref(const RefBase& other) { - construct(other.derived(), typename Traits::template match::type()); - } - - protected: - - template - void construct(const Expression& expr,internal::true_type) - { - Base::construct(expr); - } - - template - void construct(const Expression& expr, internal::false_type) - { - m_object.lazyAssign(expr); - Base::construct(m_object); - } - - protected: - TPlainObjectType m_object; -}; - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_REF_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/Replicate.h b/modules/algebra/include/eigen3/Eigen/src/Core/Replicate.h deleted file mode 100644 index 581f6aee16..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/Replicate.h +++ /dev/null @@ -1,177 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2009-2010 Gael Guennebaud -// -// 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 IMP_EIGEN_REPLICATE_H -#define IMP_EIGEN_REPLICATE_H - -namespace IMP_Eigen { - -/** - * \class Replicate - * \ingroup Core_Module - * - * \brief Expression of the multiple replication of a matrix or vector - * - * \param MatrixType the type of the object we are replicating - * - * This class represents an expression of the multiple replication of a matrix or vector. - * It is the return type of DenseBase::replicate() and most of the time - * this is the only way it is used. - * - * \sa DenseBase::replicate() - */ - -namespace internal { -template -struct traits > - : traits -{ - typedef typename MatrixType::Scalar Scalar; - typedef typename traits::StorageKind StorageKind; - typedef typename traits::XprKind XprKind; - enum { - Factor = (RowFactor==Dynamic || ColFactor==Dynamic) ? Dynamic : RowFactor*ColFactor - }; - typedef typename nested::type MatrixTypeNested; - typedef typename remove_reference::type _MatrixTypeNested; - enum { - RowsAtCompileTime = RowFactor==Dynamic || int(MatrixType::RowsAtCompileTime)==Dynamic - ? Dynamic - : RowFactor * MatrixType::RowsAtCompileTime, - ColsAtCompileTime = ColFactor==Dynamic || int(MatrixType::ColsAtCompileTime)==Dynamic - ? Dynamic - : ColFactor * MatrixType::ColsAtCompileTime, - //FIXME we don't propagate the max sizes !!! - MaxRowsAtCompileTime = RowsAtCompileTime, - MaxColsAtCompileTime = ColsAtCompileTime, - IsRowMajor = MaxRowsAtCompileTime==1 && MaxColsAtCompileTime!=1 ? 1 - : MaxColsAtCompileTime==1 && MaxRowsAtCompileTime!=1 ? 0 - : (MatrixType::Flags & RowMajorBit) ? 1 : 0, - Flags = (_MatrixTypeNested::Flags & HereditaryBits & ~RowMajorBit) | (IsRowMajor ? RowMajorBit : 0), - CoeffReadCost = _MatrixTypeNested::CoeffReadCost - }; -}; -} - -template class Replicate - : public internal::dense_xpr_base< Replicate >::type -{ - typedef typename internal::traits::MatrixTypeNested MatrixTypeNested; - typedef typename internal::traits::_MatrixTypeNested _MatrixTypeNested; - public: - - typedef typename internal::dense_xpr_base::type Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(Replicate) - - template - inline explicit Replicate(const OriginalMatrixType& a_matrix) - : m_matrix(a_matrix), m_rowFactor(RowFactor), m_colFactor(ColFactor) - { - IMP_EIGEN_STATIC_ASSERT((internal::is_same::type,OriginalMatrixType>::value), - THE_MATRIX_OR_EXPRESSION_THAT_YOU_PASSED_DOES_NOT_HAVE_THE_EXPECTED_TYPE) - imp_eigen_assert(RowFactor!=Dynamic && ColFactor!=Dynamic); - } - - template - inline Replicate(const OriginalMatrixType& a_matrix, Index rowFactor, Index colFactor) - : m_matrix(a_matrix), m_rowFactor(rowFactor), m_colFactor(colFactor) - { - IMP_EIGEN_STATIC_ASSERT((internal::is_same::type,OriginalMatrixType>::value), - THE_MATRIX_OR_EXPRESSION_THAT_YOU_PASSED_DOES_NOT_HAVE_THE_EXPECTED_TYPE) - } - - inline Index rows() const { return m_matrix.rows() * m_rowFactor.value(); } - inline Index cols() const { return m_matrix.cols() * m_colFactor.value(); } - - inline Scalar coeff(Index rowId, Index colId) const - { - // try to avoid using modulo; this is a pure optimization strategy - const Index actual_row = internal::traits::RowsAtCompileTime==1 ? 0 - : RowFactor==1 ? rowId - : rowId%m_matrix.rows(); - const Index actual_col = internal::traits::ColsAtCompileTime==1 ? 0 - : ColFactor==1 ? colId - : colId%m_matrix.cols(); - - return m_matrix.coeff(actual_row, actual_col); - } - template - inline PacketScalar packet(Index rowId, Index colId) const - { - const Index actual_row = internal::traits::RowsAtCompileTime==1 ? 0 - : RowFactor==1 ? rowId - : rowId%m_matrix.rows(); - const Index actual_col = internal::traits::ColsAtCompileTime==1 ? 0 - : ColFactor==1 ? colId - : colId%m_matrix.cols(); - - return m_matrix.template packet(actual_row, actual_col); - } - - const _MatrixTypeNested& nestedExpression() const - { - return m_matrix; - } - - protected: - MatrixTypeNested m_matrix; - const internal::variable_if_dynamic m_rowFactor; - const internal::variable_if_dynamic m_colFactor; -}; - -/** - * \return an expression of the replication of \c *this - * - * Example: \include MatrixBase_replicate.cpp - * Output: \verbinclude MatrixBase_replicate.out - * - * \sa VectorwiseOp::replicate(), DenseBase::replicate(Index,Index), class Replicate - */ -template -template -const Replicate -DenseBase::replicate() const -{ - return Replicate(derived()); -} - -/** - * \return an expression of the replication of \c *this - * - * Example: \include MatrixBase_replicate_int_int.cpp - * Output: \verbinclude MatrixBase_replicate_int_int.out - * - * \sa VectorwiseOp::replicate(), DenseBase::replicate(), class Replicate - */ -template -const typename DenseBase::ReplicateReturnType -DenseBase::replicate(Index rowFactor,Index colFactor) const -{ - return Replicate(derived(),rowFactor,colFactor); -} - -/** - * \return an expression of the replication of each column (or row) of \c *this - * - * Example: \include DirectionWise_replicate_int.cpp - * Output: \verbinclude DirectionWise_replicate_int.out - * - * \sa VectorwiseOp::replicate(), DenseBase::replicate(), class Replicate - */ -template -const typename VectorwiseOp::ReplicateReturnType -VectorwiseOp::replicate(Index factor) const -{ - return typename VectorwiseOp::ReplicateReturnType - (_expression(),Direction==Vertical?factor:1,Direction==Horizontal?factor:1); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_REPLICATE_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/ReturnByValue.h b/modules/algebra/include/eigen3/Eigen/src/Core/ReturnByValue.h deleted file mode 100644 index 30cdd1365c..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/ReturnByValue.h +++ /dev/null @@ -1,99 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2009-2010 Gael Guennebaud -// Copyright (C) 2009-2010 Benoit Jacob -// -// 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 IMP_EIGEN_RETURNBYVALUE_H -#define IMP_EIGEN_RETURNBYVALUE_H - -namespace IMP_Eigen { - -/** \class ReturnByValue - * \ingroup Core_Module - * - */ - -namespace internal { - -template -struct traits > - : public traits::ReturnType> -{ - enum { - // We're disabling the DirectAccess because e.g. the constructor of - // the Block-with-DirectAccess expression requires to have a coeffRef method. - // Also, we don't want to have to implement the stride stuff. - Flags = (traits::ReturnType>::Flags - | EvalBeforeNestingBit) & ~DirectAccessBit - }; -}; - -/* The ReturnByValue object doesn't even have a coeff() method. - * So the only way that nesting it in an expression can work, is by evaluating it into a plain matrix. - * So internal::nested always gives the plain return matrix type. - * - * FIXME: I don't understand why we need this specialization: isn't this taken care of by the EvalBeforeNestingBit ?? - */ -template -struct nested, n, PlainObject> -{ - typedef typename traits::ReturnType type; -}; - -} // end namespace internal - -template class ReturnByValue - : internal::no_assignment_operator, public internal::dense_xpr_base< ReturnByValue >::type -{ - public: - typedef typename internal::traits::ReturnType ReturnType; - - typedef typename internal::dense_xpr_base::type Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(ReturnByValue) - - template - inline void evalTo(Dest& dst) const - { static_cast(this)->evalTo(dst); } - inline Index rows() const { return static_cast(this)->rows(); } - inline Index cols() const { return static_cast(this)->cols(); } - -#ifndef IMP_EIGEN_PARSED_BY_DOXYGEN -#define Unusable YOU_ARE_TRYING_TO_ACCESS_A_SINGLE_COEFFICIENT_IN_A_SPECIAL_EXPRESSION_WHERE_THAT_IS_NOT_ALLOWED_BECAUSE_THAT_WOULD_BE_INEFFICIENT - class Unusable{ - Unusable(const Unusable&) {} - Unusable& operator=(const Unusable&) {return *this;} - }; - const Unusable& coeff(Index) const { return *reinterpret_cast(this); } - const Unusable& coeff(Index,Index) const { return *reinterpret_cast(this); } - Unusable& coeffRef(Index) { return *reinterpret_cast(this); } - Unusable& coeffRef(Index,Index) { return *reinterpret_cast(this); } - template Unusable& packet(Index) const; - template Unusable& packet(Index, Index) const; -#endif -}; - -template -template -Derived& DenseBase::operator=(const ReturnByValue& other) -{ - other.evalTo(derived()); - return derived(); -} - -template -template -Derived& DenseBase::lazyAssign(const ReturnByValue& other) -{ - other.evalTo(derived()); - return derived(); -} - - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_RETURNBYVALUE_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/Reverse.h b/modules/algebra/include/eigen3/Eigen/src/Core/Reverse.h deleted file mode 100644 index 4d284bbfd0..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/Reverse.h +++ /dev/null @@ -1,224 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2006-2008 Benoit Jacob -// Copyright (C) 2009 Ricard Marxer -// Copyright (C) 2009-2010 Gael Guennebaud -// -// 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 IMP_EIGEN_REVERSE_H -#define IMP_EIGEN_REVERSE_H - -namespace IMP_Eigen { - -/** \class Reverse - * \ingroup Core_Module - * - * \brief Expression of the reverse of a vector or matrix - * - * \param MatrixType the type of the object of which we are taking the reverse - * - * This class represents an expression of the reverse of a vector. - * It is the return type of MatrixBase::reverse() and VectorwiseOp::reverse() - * and most of the time this is the only way it is used. - * - * \sa MatrixBase::reverse(), VectorwiseOp::reverse() - */ - -namespace internal { - -template -struct traits > - : traits -{ - typedef typename MatrixType::Scalar Scalar; - typedef typename traits::StorageKind StorageKind; - typedef typename traits::XprKind XprKind; - typedef typename nested::type MatrixTypeNested; - typedef typename remove_reference::type _MatrixTypeNested; - enum { - RowsAtCompileTime = MatrixType::RowsAtCompileTime, - ColsAtCompileTime = MatrixType::ColsAtCompileTime, - MaxRowsAtCompileTime = MatrixType::MaxRowsAtCompileTime, - MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime, - - // let's enable LinearAccess only with vectorization because of the product overhead - LinearAccess = ( (Direction==BothDirections) && (int(_MatrixTypeNested::Flags)&PacketAccessBit) ) - ? LinearAccessBit : 0, - - Flags = int(_MatrixTypeNested::Flags) & (HereditaryBits | LvalueBit | PacketAccessBit | LinearAccess), - - CoeffReadCost = _MatrixTypeNested::CoeffReadCost - }; -}; - -template struct reverse_packet_cond -{ - static inline PacketScalar run(const PacketScalar& x) { return preverse(x); } -}; - -template struct reverse_packet_cond -{ - static inline PacketScalar run(const PacketScalar& x) { return x; } -}; - -} // end namespace internal - -template class Reverse - : public internal::dense_xpr_base< Reverse >::type -{ - public: - - typedef typename internal::dense_xpr_base::type Base; - IMP_EIGEN_DENSE_PUBLIC_INTERFACE(Reverse) - using Base::IsRowMajor; - - // next line is necessary because otherwise const version of operator() - // is hidden by non-const version defined in this file - using Base::operator(); - - protected: - enum { - PacketSize = internal::packet_traits::size, - IsColMajor = !IsRowMajor, - ReverseRow = (Direction == Vertical) || (Direction == BothDirections), - ReverseCol = (Direction == Horizontal) || (Direction == BothDirections), - OffsetRow = ReverseRow && IsColMajor ? PacketSize : 1, - OffsetCol = ReverseCol && IsRowMajor ? PacketSize : 1, - ReversePacket = (Direction == BothDirections) - || ((Direction == Vertical) && IsColMajor) - || ((Direction == Horizontal) && IsRowMajor) - }; - typedef internal::reverse_packet_cond reverse_packet; - public: - - inline Reverse(const MatrixType& matrix) : m_matrix(matrix) { } - - IMP_EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Reverse) - - inline Index rows() const { return m_matrix.rows(); } - inline Index cols() const { return m_matrix.cols(); } - - inline Index innerStride() const - { - return -m_matrix.innerStride(); - } - - inline Scalar& operator()(Index row, Index col) - { - imp_eigen_assert(row >= 0 && row < rows() && col >= 0 && col < cols()); - return coeffRef(row, col); - } - - inline Scalar& coeffRef(Index row, Index col) - { - return m_matrix.const_cast_derived().coeffRef(ReverseRow ? m_matrix.rows() - row - 1 : row, - ReverseCol ? m_matrix.cols() - col - 1 : col); - } - - inline CoeffReturnType coeff(Index row, Index col) const - { - return m_matrix.coeff(ReverseRow ? m_matrix.rows() - row - 1 : row, - ReverseCol ? m_matrix.cols() - col - 1 : col); - } - - inline CoeffReturnType coeff(Index index) const - { - return m_matrix.coeff(m_matrix.size() - index - 1); - } - - inline Scalar& coeffRef(Index index) - { - return m_matrix.const_cast_derived().coeffRef(m_matrix.size() - index - 1); - } - - inline Scalar& operator()(Index index) - { - imp_eigen_assert(index >= 0 && index < m_matrix.size()); - return coeffRef(index); - } - - template - inline const PacketScalar packet(Index row, Index col) const - { - return reverse_packet::run(m_matrix.template packet( - ReverseRow ? m_matrix.rows() - row - OffsetRow : row, - ReverseCol ? m_matrix.cols() - col - OffsetCol : col)); - } - - template - inline void writePacket(Index row, Index col, const PacketScalar& x) - { - m_matrix.const_cast_derived().template writePacket( - ReverseRow ? m_matrix.rows() - row - OffsetRow : row, - ReverseCol ? m_matrix.cols() - col - OffsetCol : col, - reverse_packet::run(x)); - } - - template - inline const PacketScalar packet(Index index) const - { - return internal::preverse(m_matrix.template packet( m_matrix.size() - index - PacketSize )); - } - - template - inline void writePacket(Index index, const PacketScalar& x) - { - m_matrix.const_cast_derived().template writePacket(m_matrix.size() - index - PacketSize, internal::preverse(x)); - } - - const typename internal::remove_all::type& - nestedExpression() const - { - return m_matrix; - } - - protected: - typename MatrixType::Nested m_matrix; -}; - -/** \returns an expression of the reverse of *this. - * - * Example: \include MatrixBase_reverse.cpp - * Output: \verbinclude MatrixBase_reverse.out - * - */ -template -inline typename DenseBase::ReverseReturnType -DenseBase::reverse() -{ - return derived(); -} - -/** This is the const version of reverse(). */ -template -inline const typename DenseBase::ConstReverseReturnType -DenseBase::reverse() const -{ - return derived(); -} - -/** This is the "in place" version of reverse: it reverses \c *this. - * - * In most cases it is probably better to simply use the reversed expression - * of a matrix. However, when reversing the matrix data itself is really needed, - * then this "in-place" version is probably the right choice because it provides - * the following additional features: - * - less error prone: doing the same operation with .reverse() requires special care: - * \code m = m.reverse().eval(); \endcode - * - this API allows to avoid creating a temporary (the current implementation creates a temporary, but that could be avoided using swap) - * - it allows future optimizations (cache friendliness, etc.) - * - * \sa reverse() */ -template -inline void DenseBase::reverseInPlace() -{ - derived() = derived().reverse().eval(); -} - -} // end namespace IMP_Eigen - -#endif // IMP_EIGEN_REVERSE_H diff --git a/modules/algebra/include/eigen3/Eigen/src/Core/Select.h b/modules/algebra/include/eigen3/Eigen/src/Core/Select.h deleted file mode 100644 index 97bcedaa68..0000000000 --- a/modules/algebra/include/eigen3/Eigen/src/Core/Select.h +++ /dev/null @@ -1,162 +0,0 @@ -// This file is part of Eigen, a lightweight C++ template library -// for linear algebra. -// -// Copyright (C) 2008-2010 Gael Guennebaud -// -// 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 IMP_EIGEN_SELECT_H -#define IMP_EIGEN_SELECT_H - -namespace IMP_Eigen { - -/** \class Select - * \ingroup Core_Module - * - * \brief Expression of a coefficient wise version of the C++ ternary operator ?: - * - * \param ConditionMatrixType the type of the \em condition expression which must be a boolean matrix - * \param ThenMatrixType the type of the \em then expression - * \param ElseMatrixType the type of the \em else expression - * - * This class represents an expression of a coefficient wise version of the C++ ternary operator ?:. - * It is the return type of DenseBase::select() and most of the time this is the only way it is used. - * - * \sa DenseBase::select(const DenseBase&, const DenseBase&) const - */ - -namespace internal { -template -struct traits > - : traits -{ - typedef typename traits::Scalar Scalar; - typedef Dense StorageKind; - typedef typename traits::XprKind XprKind; - typedef typename ConditionMatrixType::Nested ConditionMatrixNested; - typedef typename ThenMatrixType::Nested ThenMatrixNested; - typedef typename ElseMatrixType::Nested ElseMatrixNested; - enum { - RowsAtCompileTime = ConditionMatrixType::RowsAtCompileTime, - ColsAtCompileTime = ConditionMatrixType::ColsAtCompileTime, - MaxRowsAtCompileTime = ConditionMatrixType::MaxRowsAtCompileTime, - MaxColsAtCompileTime = ConditionMatrixType::MaxColsAtCompileTime, - Flags = (unsigned int)ThenMatrixType::Flags & ElseMatrixType::Flags & HereditaryBits, - CoeffReadCost = traits::type>::CoeffReadCost - + IMP_EIGEN_SIZE_MAX(traits::type>::CoeffReadCost, - traits::type>::CoeffReadCost) - }; -}; -} - -template -class Select : internal::no_assignment_operator, - public internal::dense_xpr_base< Select >::type -{ - public: - - typedef typename internal::dense_xpr_base