pnmatrix 1.2.4
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- checksums.yaml +7 -0
- data/ext/nmatrix/binary_format.txt +53 -0
- data/ext/nmatrix/data/complex.h +388 -0
- data/ext/nmatrix/data/data.cpp +274 -0
- data/ext/nmatrix/data/data.h +651 -0
- data/ext/nmatrix/data/meta.h +64 -0
- data/ext/nmatrix/data/ruby_object.h +386 -0
- data/ext/nmatrix/extconf.rb +70 -0
- data/ext/nmatrix/math/asum.h +99 -0
- data/ext/nmatrix/math/cblas_enums.h +36 -0
- data/ext/nmatrix/math/cblas_templates_core.h +507 -0
- data/ext/nmatrix/math/gemm.h +241 -0
- data/ext/nmatrix/math/gemv.h +178 -0
- data/ext/nmatrix/math/getrf.h +255 -0
- data/ext/nmatrix/math/getrs.h +121 -0
- data/ext/nmatrix/math/imax.h +82 -0
- data/ext/nmatrix/math/laswp.h +165 -0
- data/ext/nmatrix/math/long_dtype.h +62 -0
- data/ext/nmatrix/math/magnitude.h +54 -0
- data/ext/nmatrix/math/math.h +751 -0
- data/ext/nmatrix/math/nrm2.h +165 -0
- data/ext/nmatrix/math/rot.h +117 -0
- data/ext/nmatrix/math/rotg.h +106 -0
- data/ext/nmatrix/math/scal.h +71 -0
- data/ext/nmatrix/math/trsm.h +336 -0
- data/ext/nmatrix/math/util.h +162 -0
- data/ext/nmatrix/math.cpp +1368 -0
- data/ext/nmatrix/nm_memory.h +60 -0
- data/ext/nmatrix/nmatrix.cpp +285 -0
- data/ext/nmatrix/nmatrix.h +476 -0
- data/ext/nmatrix/ruby_constants.cpp +151 -0
- data/ext/nmatrix/ruby_constants.h +106 -0
- data/ext/nmatrix/ruby_nmatrix.c +3130 -0
- data/ext/nmatrix/storage/common.cpp +77 -0
- data/ext/nmatrix/storage/common.h +183 -0
- data/ext/nmatrix/storage/dense/dense.cpp +1096 -0
- data/ext/nmatrix/storage/dense/dense.h +129 -0
- data/ext/nmatrix/storage/list/list.cpp +1628 -0
- data/ext/nmatrix/storage/list/list.h +138 -0
- data/ext/nmatrix/storage/storage.cpp +730 -0
- data/ext/nmatrix/storage/storage.h +99 -0
- data/ext/nmatrix/storage/yale/class.h +1139 -0
- data/ext/nmatrix/storage/yale/iterators/base.h +143 -0
- data/ext/nmatrix/storage/yale/iterators/iterator.h +131 -0
- data/ext/nmatrix/storage/yale/iterators/row.h +450 -0
- data/ext/nmatrix/storage/yale/iterators/row_stored.h +140 -0
- data/ext/nmatrix/storage/yale/iterators/row_stored_nd.h +169 -0
- data/ext/nmatrix/storage/yale/iterators/stored_diagonal.h +124 -0
- data/ext/nmatrix/storage/yale/math/transpose.h +110 -0
- data/ext/nmatrix/storage/yale/yale.cpp +2074 -0
- data/ext/nmatrix/storage/yale/yale.h +203 -0
- data/ext/nmatrix/types.h +55 -0
- data/ext/nmatrix/util/io.cpp +279 -0
- data/ext/nmatrix/util/io.h +115 -0
- data/ext/nmatrix/util/sl_list.cpp +627 -0
- data/ext/nmatrix/util/sl_list.h +144 -0
- data/ext/nmatrix/util/util.h +78 -0
- data/lib/nmatrix/blas.rb +378 -0
- data/lib/nmatrix/cruby/math.rb +744 -0
- data/lib/nmatrix/enumerate.rb +253 -0
- data/lib/nmatrix/homogeneous.rb +241 -0
- data/lib/nmatrix/io/fortran_format.rb +138 -0
- data/lib/nmatrix/io/harwell_boeing.rb +221 -0
- data/lib/nmatrix/io/market.rb +263 -0
- data/lib/nmatrix/io/point_cloud.rb +189 -0
- data/lib/nmatrix/jruby/decomposition.rb +24 -0
- data/lib/nmatrix/jruby/enumerable.rb +13 -0
- data/lib/nmatrix/jruby/error.rb +4 -0
- data/lib/nmatrix/jruby/math.rb +501 -0
- data/lib/nmatrix/jruby/nmatrix_java.rb +840 -0
- data/lib/nmatrix/jruby/operators.rb +283 -0
- data/lib/nmatrix/jruby/slice.rb +264 -0
- data/lib/nmatrix/lapack_core.rb +181 -0
- data/lib/nmatrix/lapack_plugin.rb +44 -0
- data/lib/nmatrix/math.rb +953 -0
- data/lib/nmatrix/mkmf.rb +100 -0
- data/lib/nmatrix/monkeys.rb +137 -0
- data/lib/nmatrix/nmatrix.rb +1172 -0
- data/lib/nmatrix/rspec.rb +75 -0
- data/lib/nmatrix/shortcuts.rb +1163 -0
- data/lib/nmatrix/version.rb +39 -0
- data/lib/nmatrix/yale_functions.rb +118 -0
- data/lib/nmatrix.rb +28 -0
- data/spec/00_nmatrix_spec.rb +892 -0
- data/spec/01_enum_spec.rb +196 -0
- data/spec/02_slice_spec.rb +407 -0
- data/spec/03_nmatrix_monkeys_spec.rb +80 -0
- data/spec/2x2_dense_double.mat +0 -0
- data/spec/4x4_sparse.mat +0 -0
- data/spec/4x5_dense.mat +0 -0
- data/spec/blas_spec.rb +215 -0
- data/spec/elementwise_spec.rb +311 -0
- data/spec/homogeneous_spec.rb +100 -0
- data/spec/io/fortran_format_spec.rb +88 -0
- data/spec/io/harwell_boeing_spec.rb +98 -0
- data/spec/io/test.rua +9 -0
- data/spec/io_spec.rb +159 -0
- data/spec/lapack_core_spec.rb +482 -0
- data/spec/leakcheck.rb +16 -0
- data/spec/math_spec.rb +1363 -0
- data/spec/nmatrix_yale_resize_test_associations.yaml +2802 -0
- data/spec/nmatrix_yale_spec.rb +286 -0
- data/spec/rspec_monkeys.rb +56 -0
- data/spec/rspec_spec.rb +35 -0
- data/spec/shortcuts_spec.rb +474 -0
- data/spec/slice_set_spec.rb +162 -0
- data/spec/spec_helper.rb +172 -0
- data/spec/stat_spec.rb +214 -0
- data/spec/test.pcd +20 -0
- data/spec/utm5940.mtx +83844 -0
- metadata +295 -0
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/////////////////////////////////////////////////////////////////////
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// = NMatrix
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//
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// A linear algebra library for scientific computation in Ruby.
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// NMatrix is part of SciRuby.
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//
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// NMatrix was originally inspired by and derived from NArray, by
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// Masahiro Tanaka: http://narray.rubyforge.org
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//
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// == Copyright Information
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//
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// SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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// NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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//
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// Please see LICENSE.txt for additional copyright notices.
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//
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// == Contributing
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//
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// By contributing source code to SciRuby, you agree to be bound by
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// our Contributor Agreement:
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//
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// * https://github.com/SciRuby/sciruby/wiki/Contributor-Agreement
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//
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// == row_stored_nd.h
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//
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// Yale storage row-by-row nondiagonal-storage iterator
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//
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#ifndef YALE_ITERATORS_ROW_STORED_ND_H
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# define YALE_ITERATORS_ROW_STORED_ND_H
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#include <ruby.h>
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#include <type_traits>
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#include <typeinfo>
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#include <stdexcept>
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namespace nm { namespace yale_storage {
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/*
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* Constants
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*/
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const float GROWTH_CONSTANT = 1.5;
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/*
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* Forward declarations
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*/
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template <typename D, typename RefType, typename YaleRef> class row_iterator_T;
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/*
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* Iterator for visiting each stored element in a row, including diagonals.
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*/
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template <typename D,
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typename RefType,
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typename YaleRef = typename std::conditional<
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std::is_const<RefType>::value,
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const nm::YaleStorage<D>,
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nm::YaleStorage<D>
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>::type,
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typename RowRef = typename std::conditional<
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std::is_const<RefType>::value,
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const row_iterator_T<D,RefType,YaleRef>,
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row_iterator_T<D,RefType,YaleRef>
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>::type>
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class row_stored_nd_iterator_T {
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protected:
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RowRef& r;
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size_t p_;
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public:
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row_stored_nd_iterator_T(RowRef& row, size_t pp)
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: r(row),
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p_(pp) // do we start at the diagonal?
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{
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}
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// DO NOT IMPLEMENT THESE FUNCTIONS. They prevent C++ virtual slicing
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//template <typename T> row_stored_nd_iterator_T(T const& rhs);
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//template <typename T> row_stored_nd_iterator_T<D,RefType,YaleRef,RowRef> const& operator=(T const& rhs);
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// Next two functions are to ensure we can still cast between nd iterators.
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row_stored_nd_iterator_T(row_stored_nd_iterator_T<D,RefType,YaleRef,RowRef> const& rhs)
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: r(rhs.r), p_(rhs.p_)
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{ }
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row_stored_nd_iterator_T<D,RefType,YaleRef,RowRef> const& operator=(row_stored_nd_iterator_T<D,RefType,YaleRef,RowRef> const& rhs) {
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if (&r != &(rhs.r))
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throw std::logic_error("can't assign iterator from another row iterator");
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p_ = rhs.p_;
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return *this;
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}
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virtual size_t p() const { return p_; }
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virtual bool end() const {
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return p_ > r.p_last;
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}
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row_stored_nd_iterator_T<D,RefType,YaleRef,RowRef>& operator++() {
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if (end()) throw std::out_of_range("cannot increment row stored iterator past end of stored row");
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++p_;
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return *this;
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}
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row_stored_nd_iterator_T<D,RefType,YaleRef,RowRef> operator++(int dummy) const {
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row_stored_nd_iterator_T<D,RefType,YaleRef,RowRef> r(*this);
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return ++r;
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}
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virtual size_t j() const {
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if (end()) throw std::out_of_range("cannot dereference (get j()) for an end pointer");
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return r.ija(p_) - r.offset(1);
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}
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// Need to declare all row_stored_nd_iterator_T friends of each other.
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template <typename E, typename ERefType, typename EYaleRef, typename ERowRef> friend class row_stored_nd_iterator_T;
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virtual bool operator==(const row_stored_nd_iterator_T<D,RefType>& rhs) const {
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if (r.i() != rhs.r.i()) return false;
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if (end()) return rhs.end();
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else if (rhs.end()) return false;
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return j() == rhs.j();
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}
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// There is something wrong with this function.
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virtual bool operator!=(const row_stored_nd_iterator_T<D,RefType>& rhs) const {
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if (r.i() != rhs.r.i()) return true;
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if (end()) return !rhs.end();
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else if (rhs.end()) return true;
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return j() != rhs.j();
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}
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template <typename E, typename ERefType = typename std::conditional<std::is_const<RefType>::value, const E, E>::type>
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bool operator<(const row_stored_nd_iterator_T<E,ERefType>& rhs) const {
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if (r < rhs.r) return true;
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if (r > rhs.r) return false;
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// r == rhs.r
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if (end()) return false;
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if (rhs.end()) return true;
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return j() < rhs.j();
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}
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// De-reference the iterator
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RefType& operator*() {
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return r.a(p_);
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}
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RefType& operator*() const {
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return r.a(p_);
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}
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// Ruby VALUE de-reference
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VALUE operator~() const {
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return nm_rb_dereference<D>(**this);
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}
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inline virtual VALUE rb_j() const { return LONG2NUM(j()); }
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};
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} } // end of namespace nm::yale_storage
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#endif // YALE_ITERATORS_ROW_STORED_ND_H
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/////////////////////////////////////////////////////////////////////
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// = NMatrix
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//
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// A linear algebra library for scientific computation in Ruby.
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// NMatrix is part of SciRuby.
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//
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// NMatrix was originally inspired by and derived from NArray, by
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// Masahiro Tanaka: http://narray.rubyforge.org
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//
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// == Copyright Information
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//
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// SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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// NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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//
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// Please see LICENSE.txt for additional copyright notices.
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//
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// == Contributing
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//
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// By contributing source code to SciRuby, you agree to be bound by
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// our Contributor Agreement:
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//
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// * https://github.com/SciRuby/sciruby/wiki/Contributor-Agreement
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//
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// == stored_diagonal_iterator.h
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//
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// Yale storage diagonal-storage iterator
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//
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#ifndef YALE_ITERATORS_STORED_DIAGONAL_H
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# define YALE_ITERATORS_STORED_DIAGONAL_H
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#include <ruby.h>
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#include <type_traits>
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#include <typeinfo>
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namespace nm { namespace yale_storage {
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/*
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* Iterate across the stored diagonal.
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*/
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template <typename D,
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typename RefType,
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typename YaleRef = typename std::conditional<
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std::is_const<RefType>::value,
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const nm::YaleStorage<D>,
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nm::YaleStorage<D>
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>::type>
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class stored_diagonal_iterator_T : public basic_iterator_T<D,RefType,YaleRef> {
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using basic_iterator_T<D,RefType,YaleRef>::p_;
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using basic_iterator_T<D,RefType,YaleRef>::y;
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using basic_iterator_T<D,RefType,YaleRef>::offset;
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using basic_iterator_T<D,RefType,YaleRef>::shape;
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public:
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stored_diagonal_iterator_T(YaleRef& obj, size_t d = 0)
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: basic_iterator_T<D,RefType,YaleRef>(obj, // y
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std::max(obj.offset(0), obj.offset(1)) + d - obj.offset(0), // i_
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std::max(obj.offset(0), obj.offset(1)) + d) // p_
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{
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// std::cerr << "sdbegin: d=" << d << ", p_=" << p_ << ", i()=" << i() << ", j()=" << j() << std::endl;
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// p_ can range from max(y.offset(0), y.offset(1)) to min(y.real_shape(0), y.real_shape(1))
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}
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size_t d() const {
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return p_ - std::max(offset(0), offset(1));
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}
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stored_diagonal_iterator_T<D,RefType,YaleRef>& operator++() {
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if (i() < shape(0)) ++p_;
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return *this;
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}
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stored_diagonal_iterator_T<D,RefType,YaleRef> operator++(int dummy) const {
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stored_diagonal_iterator_T<D,RefType,YaleRef> iter(*this);
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return ++iter;
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}
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// Indicates if we're at the end of the iteration.
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bool end() const {
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return p_ >= std::min( shape(0) + offset(0), shape(1) + offset(1) );
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}
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// i() and j() are how we know if we're past-the-end. i will be shape(0) and j will be 0.
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size_t i() const {
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return p_ - offset(0);
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}
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size_t j() const {
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return p_ - offset(1);
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}
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template <typename E, typename ERefType = typename std::conditional<std::is_const<RefType>::value, const E, E>::type>
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bool operator!=(const stored_diagonal_iterator_T<E,ERefType>& rhs) const { return d() != rhs.d(); }
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template <typename E, typename ERefType = typename std::conditional<std::is_const<RefType>::value, const E, E>::type>
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bool operator==(const stored_diagonal_iterator_T<E,ERefType>& rhs) const { return !(*this != rhs); }
|
98
|
+
|
99
|
+
template <typename E, typename ERefType = typename std::conditional<std::is_const<RefType>::value, const E, E>::type>
|
100
|
+
bool operator<(const stored_diagonal_iterator_T<E,ERefType>& rhs) const { return d() < rhs.d(); }
|
101
|
+
|
102
|
+
template <typename E, typename ERefType = typename std::conditional<std::is_const<RefType>::value, const E, E>::type>
|
103
|
+
bool operator<=(const stored_diagonal_iterator_T<E,ERefType>& rhs) const {
|
104
|
+
return d() <= rhs.d();
|
105
|
+
}
|
106
|
+
|
107
|
+
template <typename E, typename ERefType = typename std::conditional<std::is_const<RefType>::value, const E, E>::type>
|
108
|
+
bool operator>(const stored_diagonal_iterator_T<E,ERefType>& rhs) const {
|
109
|
+
return d() > rhs.d();
|
110
|
+
}
|
111
|
+
|
112
|
+
template <typename E, typename ERefType = typename std::conditional<std::is_const<RefType>::value, const E, E>::type>
|
113
|
+
bool operator>=(const stored_diagonal_iterator_T<E,ERefType>& rhs) const {
|
114
|
+
return d() >= rhs.d();
|
115
|
+
}
|
116
|
+
|
117
|
+
RefType& operator*() { return y.a(p_); }
|
118
|
+
RefType& operator*() const { return y.a(p_); }
|
119
|
+
|
120
|
+
};
|
121
|
+
|
122
|
+
} } // end of namespace nm::yale_storage
|
123
|
+
|
124
|
+
#endif // YALE_ITERATORS_STORED_DIAGONAL_H
|
@@ -0,0 +1,110 @@
|
|
1
|
+
/////////////////////////////////////////////////////////////////////
|
2
|
+
// = NMatrix
|
3
|
+
//
|
4
|
+
// A linear algebra library for scientific computation in Ruby.
|
5
|
+
// NMatrix is part of SciRuby.
|
6
|
+
//
|
7
|
+
// NMatrix was originally inspired by and derived from NArray, by
|
8
|
+
// Masahiro Tanaka: http://narray.rubyforge.org
|
9
|
+
//
|
10
|
+
// == Copyright Information
|
11
|
+
//
|
12
|
+
// SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
|
13
|
+
// NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
|
14
|
+
//
|
15
|
+
// Please see LICENSE.txt for additional copyright notices.
|
16
|
+
//
|
17
|
+
// == Contributing
|
18
|
+
//
|
19
|
+
// By contributing source code to SciRuby, you agree to be bound by
|
20
|
+
// our Contributor Agreement:
|
21
|
+
//
|
22
|
+
// * https://github.com/SciRuby/sciruby/wiki/Contributor-Agreement
|
23
|
+
//
|
24
|
+
// == transpose.h
|
25
|
+
//
|
26
|
+
// Functions for Yale math: transposing
|
27
|
+
//
|
28
|
+
|
29
|
+
#ifndef YALE_MATH_TRANSPOSE_H
|
30
|
+
# define YALE_MATH_TRANSPOSE_H
|
31
|
+
|
32
|
+
namespace nm { namespace yale_storage {
|
33
|
+
|
34
|
+
/*
|
35
|
+
* Transposes a generic Yale matrix (old or new). Specify new by setting RDiag = true.
|
36
|
+
*
|
37
|
+
* Based on transp from SMMP (same as symbmm and numbmm).
|
38
|
+
*
|
39
|
+
* This is not named in the same way as most yale_storage functions because it does not act on a YALE_STORAGE
|
40
|
+
* object.
|
41
|
+
*/
|
42
|
+
|
43
|
+
template <typename AD, typename BD, bool DiagA, bool Move>
|
44
|
+
void transpose_yale(const size_t n, const size_t m,
|
45
|
+
const size_t* ia, const size_t* ja, const AD* a, const AD& a_default,
|
46
|
+
size_t* ib, size_t* jb, BD* b, const BD& b_default) {
|
47
|
+
|
48
|
+
size_t index;
|
49
|
+
|
50
|
+
// Clear B
|
51
|
+
for (size_t i = 0; i < m+1; ++i) ib[i] = 0;
|
52
|
+
|
53
|
+
if (Move)
|
54
|
+
for (size_t i = 0; i < m+1; ++i) b[i] = b_default;
|
55
|
+
|
56
|
+
if (DiagA) ib[0] = m + 1;
|
57
|
+
else ib[0] = 0;
|
58
|
+
|
59
|
+
/* count indices for each column */
|
60
|
+
|
61
|
+
for (size_t i = 0; i < n; ++i) {
|
62
|
+
for (size_t j = ia[i]; j < ia[i+1]; ++j) {
|
63
|
+
++(ib[ja[j]+1]);
|
64
|
+
}
|
65
|
+
}
|
66
|
+
|
67
|
+
for (size_t i = 0; i < m; ++i) {
|
68
|
+
ib[i+1] = ib[i] + ib[i+1];
|
69
|
+
}
|
70
|
+
|
71
|
+
/* now make jb */
|
72
|
+
|
73
|
+
for (size_t i = 0; i < n; ++i) {
|
74
|
+
|
75
|
+
for (size_t j = ia[i]; j < ia[i+1]; ++j) {
|
76
|
+
index = ja[j];
|
77
|
+
jb[ib[index]] = i;
|
78
|
+
|
79
|
+
if (Move && a[j] != a_default)
|
80
|
+
b[ib[index]] = a[j];
|
81
|
+
|
82
|
+
++(ib[index]);
|
83
|
+
}
|
84
|
+
}
|
85
|
+
|
86
|
+
/* now fixup ib */
|
87
|
+
|
88
|
+
for (size_t i = m; i >= 1; --i) {
|
89
|
+
ib[i] = ib[i-1];
|
90
|
+
}
|
91
|
+
|
92
|
+
|
93
|
+
if (DiagA) {
|
94
|
+
if (Move) {
|
95
|
+
size_t j = std::min(n,m);
|
96
|
+
|
97
|
+
for (size_t i = 0; i < j; ++i) {
|
98
|
+
b[i] = a[i];
|
99
|
+
}
|
100
|
+
}
|
101
|
+
ib[0] = m + 1;
|
102
|
+
|
103
|
+
} else {
|
104
|
+
ib[0] = 0;
|
105
|
+
}
|
106
|
+
}
|
107
|
+
|
108
|
+
} } // end of namespace nm::yale_storage
|
109
|
+
|
110
|
+
#endif
|