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
@@ -0,0 +1,730 @@
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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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// == storage.cpp
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//
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// Code that is used by or involves more then one storage type.
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/*
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* Standard Includes
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*/
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/*
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* Project Includes
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*/
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#include "data/data.h"
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#include "storage.h"
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#include "common.h"
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/*
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* Macros
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*/
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/*
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* Global Variables
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*/
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extern "C" {
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const char* const STYPE_NAMES[nm::NUM_STYPES] = {
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"dense",
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"list",
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"yale"
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};
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} // end extern "C" block
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/*
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* Forward Declarations
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*/
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namespace nm {
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/*
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* Functions
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*/
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/////////////////////////
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// Templated Functions //
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/////////////////////////
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namespace dense_storage {
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template <typename LDType, typename RDType>
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static void cast_copy_list_contents(LDType* lhs, const LIST* rhs, RDType* default_val,
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size_t& pos, const size_t* shape, size_t dim, size_t max_elements, size_t recursions);
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template <typename LDType, typename RDType>
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static void cast_copy_list_default(LDType* lhs, RDType* default_val, size_t& pos,
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const size_t* shape, size_t dim, size_t max_elements, size_t recursions);
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/*
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* Convert (by creating a copy) from list storage to dense storage.
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*/
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template <typename LDType, typename RDType>
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DENSE_STORAGE* create_from_list_storage(const LIST_STORAGE* rhs, dtype_t l_dtype) {
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nm_list_storage_register(rhs);
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// allocate and copy shape
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size_t* shape = NM_ALLOC_N(size_t, rhs->dim);
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memcpy(shape, rhs->shape, rhs->dim * sizeof(size_t));
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DENSE_STORAGE* lhs = nm_dense_storage_create(l_dtype, shape, rhs->dim, NULL, 0);
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// Position in lhs->elements.
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size_t pos = 0;
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size_t max_elements = nm_storage_count_max_elements(rhs);
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//static void dense_storage_cast_copy_list_contents_template(LDType* lhs, const LIST* rhs, RDType* default_val, size_t& pos, const size_t* shape, size_t dim, size_t max_elements, size_t recursions)
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// recursively copy the contents
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if (rhs->src == rhs)
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cast_copy_list_contents<LDType,RDType>(reinterpret_cast<LDType*>(lhs->elements),
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rhs->rows,
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reinterpret_cast<RDType*>(rhs->default_val),
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pos, shape, lhs->dim, max_elements, rhs->dim-1);
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else {
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LIST_STORAGE *tmp = nm_list_storage_copy(rhs);
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cast_copy_list_contents<LDType,RDType>(reinterpret_cast<LDType*>(lhs->elements),
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tmp->rows,
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reinterpret_cast<RDType*>(tmp->default_val),
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pos, shape, lhs->dim, max_elements, tmp->dim-1);
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nm_list_storage_delete(tmp);
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}
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nm_list_storage_unregister(rhs);
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return lhs;
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}
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/*
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* Create/allocate dense storage, copying into it the contents of a Yale matrix.
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*/
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template <typename LDType, typename RDType>
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DENSE_STORAGE* create_from_yale_storage(const YALE_STORAGE* rhs, dtype_t l_dtype) {
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nm_yale_storage_register(rhs);
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// Position in rhs->elements.
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IType* rhs_ija = reinterpret_cast<YALE_STORAGE*>(rhs->src)->ija;
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RDType* rhs_a = reinterpret_cast<RDType*>(reinterpret_cast<YALE_STORAGE*>(rhs->src)->a);
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// Allocate and set shape.
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size_t* shape = NM_ALLOC_N(size_t, rhs->dim);
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shape[0] = rhs->shape[0];
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shape[1] = rhs->shape[1];
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DENSE_STORAGE* lhs = nm_dense_storage_create(l_dtype, shape, rhs->dim, NULL, 0);
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LDType* lhs_elements = reinterpret_cast<LDType*>(lhs->elements);
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// Position in dense to write to.
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size_t pos = 0;
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LDType LCAST_ZERO = rhs_a[rhs->src->shape[0]];
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// Walk through rows. For each entry we set in dense, increment pos.
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for (size_t i = 0; i < shape[0]; ++i) {
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IType ri = i + rhs->offset[0];
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if (rhs_ija[ri] == rhs_ija[ri+1]) { // Check boundaries of row: is row empty? (Yes.)
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// Write zeros in each column.
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for (size_t j = 0; j < shape[1]; ++j) { // Move to next dense position.
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// Fill in zeros and copy the diagonal entry for this empty row.
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if (ri == j + rhs->offset[1]) lhs_elements[pos] = static_cast<LDType>(rhs_a[ri]);
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else lhs_elements[pos] = LCAST_ZERO;
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++pos;
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}
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} else { // Row contains entries: write those in each column, interspersed with zeros.
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// Get the first ija position of the row (as sliced)
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IType ija = nm::yale_storage::binary_search_left_boundary(rhs, rhs_ija[ri], rhs_ija[ri+1]-1, rhs->offset[1]);
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// What column is it?
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IType next_stored_rj = rhs_ija[ija];
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for (size_t j = 0; j < shape[1]; ++j) {
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IType rj = j + rhs->offset[1];
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if (rj == ri) { // at a diagonal in RHS
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lhs_elements[pos] = static_cast<LDType>(rhs_a[ri]);
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} else if (rj == next_stored_rj) { // column ID was found in RHS
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lhs_elements[pos] = static_cast<LDType>(rhs_a[ija]); // Copy from rhs.
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// Get next.
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++ija;
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// Increment to next column ID (or go off the end).
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if (ija < rhs_ija[ri+1]) next_stored_rj = rhs_ija[ija];
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else next_stored_rj = rhs->src->shape[1];
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} else { // rj < next_stored_rj
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// Insert zero.
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lhs_elements[pos] = LCAST_ZERO;
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}
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// Move to next dense position.
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++pos;
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}
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}
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}
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nm_yale_storage_unregister(rhs);
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return lhs;
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}
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/*
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* Copy list contents into dense recursively.
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*/
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template <typename LDType, typename RDType>
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static void cast_copy_list_contents(LDType* lhs, const LIST* rhs, RDType* default_val, size_t& pos, const size_t* shape, size_t dim, size_t max_elements, size_t recursions) {
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NODE *curr = rhs->first;
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int last_key = -1;
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nm_list_storage_register_list(rhs, recursions);
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for (size_t i = 0; i < shape[dim - 1 - recursions]; ++i, ++pos) {
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if (!curr || (curr->key > (size_t)(last_key+1))) {
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if (recursions == 0) lhs[pos] = static_cast<LDType>(*default_val);
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else cast_copy_list_default<LDType,RDType>(lhs, default_val, pos, shape, dim, max_elements, recursions-1);
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++last_key;
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} else {
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if (recursions == 0) lhs[pos] = static_cast<LDType>(*reinterpret_cast<RDType*>(curr->val));
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else cast_copy_list_contents<LDType,RDType>(lhs, (const LIST*)(curr->val),
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default_val, pos, shape, dim, max_elements, recursions-1);
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last_key = curr->key;
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curr = curr->next;
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}
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}
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nm_list_storage_unregister_list(rhs, recursions);
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--pos;
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}
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/*
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* Copy a set of default values into dense.
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*/
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template <typename LDType,typename RDType>
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static void cast_copy_list_default(LDType* lhs, RDType* default_val, size_t& pos, const size_t* shape, size_t dim, size_t max_elements, size_t recursions) {
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for (size_t i = 0; i < shape[dim - 1 - recursions]; ++i, ++pos) {
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if (recursions == 0) lhs[pos] = static_cast<LDType>(*default_val);
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else cast_copy_list_default<LDType,RDType>(lhs, default_val, pos, shape, dim, max_elements, recursions-1);
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}
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--pos;
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}
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} // end of namespace dense_storage
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namespace list_storage {
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template <typename LDType, typename RDType>
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static bool cast_copy_contents_dense(LIST* lhs, const RDType* rhs, RDType* zero, size_t& pos, size_t* coords, const size_t* shape, size_t dim, size_t recursions);
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/*
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* Creation of list storage from dense storage.
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*/
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template <typename LDType, typename RDType>
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LIST_STORAGE* create_from_dense_storage(const DENSE_STORAGE* rhs, dtype_t l_dtype, void* init) {
|
271
|
+
nm_dense_storage_register(rhs);
|
272
|
+
|
273
|
+
LDType* l_default_val = NM_ALLOC_N(LDType, 1);
|
274
|
+
RDType* r_default_val = NM_ALLOCA_N(RDType, 1); // clean up when finished with this function
|
275
|
+
|
276
|
+
// allocate and copy shape and coords
|
277
|
+
size_t *shape = NM_ALLOC_N(size_t, rhs->dim),
|
278
|
+
*coords = NM_ALLOC_N(size_t, rhs->dim);
|
279
|
+
|
280
|
+
memcpy(shape, rhs->shape, rhs->dim * sizeof(size_t));
|
281
|
+
memset(coords, 0, rhs->dim * sizeof(size_t));
|
282
|
+
|
283
|
+
// set list default_val to 0
|
284
|
+
if (init) *l_default_val = *reinterpret_cast<LDType*>(init);
|
285
|
+
else {
|
286
|
+
if (l_dtype == RUBYOBJ) *l_default_val = INT2FIX(0);
|
287
|
+
else *l_default_val = 0;
|
288
|
+
}
|
289
|
+
|
290
|
+
// need test default value for comparing to elements in dense matrix
|
291
|
+
if (rhs->dtype == l_dtype || rhs->dtype != RUBYOBJ) *r_default_val = static_cast<RDType>(*l_default_val);
|
292
|
+
else *r_default_val = nm::rubyobj_from_cval(l_default_val, l_dtype);
|
293
|
+
|
294
|
+
|
295
|
+
LIST_STORAGE* lhs = nm_list_storage_create(l_dtype, shape, rhs->dim, l_default_val);
|
296
|
+
|
297
|
+
nm_list_storage_register(lhs);
|
298
|
+
|
299
|
+
size_t pos = 0;
|
300
|
+
|
301
|
+
if (rhs->src == rhs)
|
302
|
+
list_storage::cast_copy_contents_dense<LDType,RDType>(lhs->rows,
|
303
|
+
reinterpret_cast<const RDType*>(rhs->elements),
|
304
|
+
r_default_val,
|
305
|
+
pos, coords, rhs->shape, rhs->dim, rhs->dim - 1);
|
306
|
+
else {
|
307
|
+
DENSE_STORAGE* tmp = nm_dense_storage_copy(rhs);
|
308
|
+
list_storage::cast_copy_contents_dense<LDType,RDType>(lhs->rows,
|
309
|
+
reinterpret_cast<const RDType*>(tmp->elements),
|
310
|
+
r_default_val,
|
311
|
+
pos, coords, rhs->shape, rhs->dim, rhs->dim - 1);
|
312
|
+
|
313
|
+
nm_dense_storage_delete(tmp);
|
314
|
+
}
|
315
|
+
|
316
|
+
nm_list_storage_unregister(lhs);
|
317
|
+
nm_dense_storage_unregister(rhs);
|
318
|
+
|
319
|
+
return lhs;
|
320
|
+
}
|
321
|
+
|
322
|
+
|
323
|
+
|
324
|
+
/*
|
325
|
+
* Creation of list storage from yale storage.
|
326
|
+
*/
|
327
|
+
template <typename LDType, typename RDType>
|
328
|
+
LIST_STORAGE* create_from_yale_storage(const YALE_STORAGE* rhs, dtype_t l_dtype) {
|
329
|
+
// allocate and copy shape
|
330
|
+
nm_yale_storage_register(rhs);
|
331
|
+
|
332
|
+
size_t *shape = NM_ALLOC_N(size_t, rhs->dim);
|
333
|
+
shape[0] = rhs->shape[0]; shape[1] = rhs->shape[1];
|
334
|
+
|
335
|
+
RDType* rhs_a = reinterpret_cast<RDType*>(reinterpret_cast<YALE_STORAGE*>(rhs->src)->a);
|
336
|
+
RDType R_ZERO = rhs_a[ rhs->src->shape[0] ];
|
337
|
+
|
338
|
+
// copy default value from the zero location in the Yale matrix
|
339
|
+
LDType* default_val = NM_ALLOC_N(LDType, 1);
|
340
|
+
*default_val = static_cast<LDType>(R_ZERO);
|
341
|
+
|
342
|
+
LIST_STORAGE* lhs = nm_list_storage_create(l_dtype, shape, rhs->dim, default_val);
|
343
|
+
|
344
|
+
if (rhs->dim != 2) rb_raise(nm_eStorageTypeError, "Can only convert matrices of dim 2 from yale.");
|
345
|
+
|
346
|
+
IType* rhs_ija = reinterpret_cast<YALE_STORAGE*>(rhs->src)->ija;
|
347
|
+
|
348
|
+
NODE *last_row_added = NULL;
|
349
|
+
// Walk through rows and columns as if RHS were a dense matrix
|
350
|
+
for (IType i = 0; i < shape[0]; ++i) {
|
351
|
+
IType ri = i + rhs->offset[0];
|
352
|
+
|
353
|
+
NODE *last_added = NULL;
|
354
|
+
|
355
|
+
// Get boundaries of beginning and end of row
|
356
|
+
IType ija = rhs_ija[ri],
|
357
|
+
ija_next = rhs_ija[ri+1];
|
358
|
+
|
359
|
+
// Are we going to need to add a diagonal for this row?
|
360
|
+
bool add_diag = false;
|
361
|
+
if (rhs_a[ri] != R_ZERO) add_diag = true; // non-zero and located within the bounds of the slice
|
362
|
+
|
363
|
+
if (ija < ija_next || add_diag) {
|
364
|
+
ija = nm::yale_storage::binary_search_left_boundary(rhs, ija, ija_next-1, rhs->offset[1]);
|
365
|
+
|
366
|
+
LIST* curr_row = list::create();
|
367
|
+
|
368
|
+
LDType* insert_val;
|
369
|
+
|
370
|
+
while (ija < ija_next) {
|
371
|
+
// Find first column in slice
|
372
|
+
IType rj = rhs_ija[ija];
|
373
|
+
IType j = rj - rhs->offset[1];
|
374
|
+
|
375
|
+
// Is there a nonzero diagonal item between the previously added item and the current one?
|
376
|
+
if (rj > ri && add_diag) {
|
377
|
+
// Allocate and copy insertion value
|
378
|
+
insert_val = NM_ALLOC_N(LDType, 1);
|
379
|
+
*insert_val = static_cast<LDType>(rhs_a[ri]);
|
380
|
+
|
381
|
+
// Insert the item in the list at the appropriate location.
|
382
|
+
// What is the appropriate key? Well, it's definitely right(i)==right(j), but the
|
383
|
+
// rj index has already been advanced past ri. So we should treat ri as the column and
|
384
|
+
// subtract offset[1].
|
385
|
+
if (last_added) last_added = list::insert_after(last_added, ri - rhs->offset[1], insert_val);
|
386
|
+
else last_added = list::insert(curr_row, false, ri - rhs->offset[1], insert_val);
|
387
|
+
|
388
|
+
// don't add again!
|
389
|
+
add_diag = false;
|
390
|
+
}
|
391
|
+
|
392
|
+
// now allocate and add the current item
|
393
|
+
insert_val = NM_ALLOC_N(LDType, 1);
|
394
|
+
*insert_val = static_cast<LDType>(rhs_a[ija]);
|
395
|
+
|
396
|
+
if (last_added) last_added = list::insert_after(last_added, j, insert_val);
|
397
|
+
else last_added = list::insert(curr_row, false, j, insert_val);
|
398
|
+
|
399
|
+
++ija; // move to next entry in Yale matrix
|
400
|
+
}
|
401
|
+
|
402
|
+
if (add_diag) {
|
403
|
+
|
404
|
+
// still haven't added the diagonal.
|
405
|
+
insert_val = NM_ALLOC_N(LDType, 1);
|
406
|
+
*insert_val = static_cast<LDType>(rhs_a[ri]);
|
407
|
+
|
408
|
+
// insert the item in the list at the appropriate location
|
409
|
+
if (last_added) last_added = list::insert_after(last_added, ri - rhs->offset[1], insert_val);
|
410
|
+
else last_added = list::insert(curr_row, false, ri - rhs->offset[1], insert_val);
|
411
|
+
|
412
|
+
// no need to set add_diag to false because it'll be reset automatically in next iteration.
|
413
|
+
}
|
414
|
+
|
415
|
+
// Now add the list at the appropriate location
|
416
|
+
if (last_row_added) last_row_added = list::insert_after(last_row_added, i, curr_row);
|
417
|
+
else last_row_added = list::insert(lhs->rows, false, i, curr_row);
|
418
|
+
}
|
419
|
+
|
420
|
+
// end of walk through rows
|
421
|
+
}
|
422
|
+
|
423
|
+
nm_yale_storage_unregister(rhs);
|
424
|
+
|
425
|
+
return lhs;
|
426
|
+
}
|
427
|
+
|
428
|
+
|
429
|
+
/* Copy dense into lists recursively
|
430
|
+
*
|
431
|
+
* FIXME: This works, but could probably be cleaner (do we really need to pass coords around?)
|
432
|
+
*/
|
433
|
+
template <typename LDType, typename RDType>
|
434
|
+
static bool cast_copy_contents_dense(LIST* lhs, const RDType* rhs, RDType* zero, size_t& pos, size_t* coords, const size_t* shape, size_t dim, size_t recursions) {
|
435
|
+
|
436
|
+
nm_list_storage_register_list(lhs, recursions);
|
437
|
+
|
438
|
+
NODE *prev = NULL;
|
439
|
+
LIST *sub_list;
|
440
|
+
bool added = false, added_list = false;
|
441
|
+
//void* insert_value;
|
442
|
+
|
443
|
+
for (coords[dim-1-recursions] = 0; coords[dim-1-recursions] < shape[dim-1-recursions]; ++coords[dim-1-recursions], ++pos) {
|
444
|
+
|
445
|
+
if (recursions == 0) {
|
446
|
+
// create nodes
|
447
|
+
|
448
|
+
if (rhs[pos] != *zero) {
|
449
|
+
// is not zero
|
450
|
+
|
451
|
+
// Create a copy of our value that we will insert in the list
|
452
|
+
LDType* insert_value = NM_ALLOC_N(LDType, 1);
|
453
|
+
*insert_value = static_cast<LDType>(rhs[pos]);
|
454
|
+
|
455
|
+
if (!lhs->first) prev = list::insert(lhs, false, coords[dim-1-recursions], insert_value);
|
456
|
+
else prev = list::insert_after(prev, coords[dim-1-recursions], insert_value);
|
457
|
+
|
458
|
+
added = true;
|
459
|
+
}
|
460
|
+
// no need to do anything if the element is zero
|
461
|
+
|
462
|
+
} else { // create lists
|
463
|
+
// create a list as if there's something in the row in question, and then delete it if nothing turns out to be there
|
464
|
+
sub_list = list::create();
|
465
|
+
|
466
|
+
added_list = list_storage::cast_copy_contents_dense<LDType,RDType>(sub_list, rhs, zero, pos, coords, shape, dim, recursions-1);
|
467
|
+
|
468
|
+
if (!added_list) list::del(sub_list, recursions-1);
|
469
|
+
else if (!lhs->first) prev = list::insert(lhs, false, coords[dim-1-recursions], sub_list);
|
470
|
+
else prev = list::insert_after(prev, coords[dim-1-recursions], sub_list);
|
471
|
+
|
472
|
+
// added = (added || added_list);
|
473
|
+
}
|
474
|
+
}
|
475
|
+
|
476
|
+
nm_list_storage_unregister_list(lhs, recursions);
|
477
|
+
|
478
|
+
coords[dim-1-recursions] = 0;
|
479
|
+
--pos;
|
480
|
+
|
481
|
+
return added;
|
482
|
+
}
|
483
|
+
|
484
|
+
} // end of namespace list_storage
|
485
|
+
|
486
|
+
|
487
|
+
namespace yale_storage { // FIXME: Move to yale.cpp
|
488
|
+
/*
|
489
|
+
* Creation of yale storage from dense storage.
|
490
|
+
*/
|
491
|
+
template <typename LDType, typename RDType>
|
492
|
+
YALE_STORAGE* create_from_dense_storage(const DENSE_STORAGE* rhs, dtype_t l_dtype, void* init) {
|
493
|
+
|
494
|
+
if (rhs->dim != 2) rb_raise(nm_eStorageTypeError, "can only convert matrices of dim 2 to yale");
|
495
|
+
|
496
|
+
nm_dense_storage_register(rhs);
|
497
|
+
|
498
|
+
IType pos = 0;
|
499
|
+
IType ndnz = 0;
|
500
|
+
|
501
|
+
// We need a zero value. This should nearly always be zero, but sometimes you might want false or nil.
|
502
|
+
LDType L_INIT(0);
|
503
|
+
if (init) {
|
504
|
+
if (l_dtype == RUBYOBJ) L_INIT = *reinterpret_cast<VALUE*>(init);
|
505
|
+
else L_INIT = *reinterpret_cast<LDType*>(init);
|
506
|
+
}
|
507
|
+
RDType R_INIT = static_cast<RDType>(L_INIT);
|
508
|
+
|
509
|
+
RDType* rhs_elements = reinterpret_cast<RDType*>(rhs->elements);
|
510
|
+
|
511
|
+
// First, count the non-diagonal nonzeros
|
512
|
+
for (size_t i = rhs->shape[0]; i-- > 0;) {
|
513
|
+
for (size_t j = rhs->shape[1]; j-- > 0;) {
|
514
|
+
pos = rhs->stride[0]*(i + rhs->offset[0]) + rhs->stride[1]*(j + rhs->offset[1]);
|
515
|
+
if (i != j && rhs_elements[pos] != R_INIT) ++ndnz;
|
516
|
+
|
517
|
+
// move forward 1 position in dense matrix elements array
|
518
|
+
}
|
519
|
+
}
|
520
|
+
|
521
|
+
// Copy shape for yale construction
|
522
|
+
size_t* shape = NM_ALLOC_N(size_t, 2);
|
523
|
+
shape[0] = rhs->shape[0];
|
524
|
+
shape[1] = rhs->shape[1];
|
525
|
+
|
526
|
+
size_t request_capacity = shape[0] + ndnz + 1;
|
527
|
+
|
528
|
+
// Create with minimum possible capacity -- just enough to hold all of the entries
|
529
|
+
YALE_STORAGE* lhs = nm_yale_storage_create(l_dtype, shape, 2, request_capacity);
|
530
|
+
|
531
|
+
if (lhs->capacity < request_capacity)
|
532
|
+
rb_raise(nm_eStorageTypeError, "conversion failed; capacity of %ld requested, max allowable is %ld", (unsigned long)request_capacity, (unsigned long)(lhs->capacity));
|
533
|
+
|
534
|
+
LDType* lhs_a = reinterpret_cast<LDType*>(lhs->a);
|
535
|
+
IType* lhs_ija = lhs->ija;
|
536
|
+
|
537
|
+
// Set the zero position in the yale matrix
|
538
|
+
lhs_a[shape[0]] = L_INIT;
|
539
|
+
|
540
|
+
// Start just after the zero position.
|
541
|
+
IType ija = shape[0]+1;
|
542
|
+
pos = 0;
|
543
|
+
|
544
|
+
// Copy contents
|
545
|
+
for (IType i = 0; i < rhs->shape[0]; ++i) {
|
546
|
+
// indicate the beginning of a row in the IJA array
|
547
|
+
lhs_ija[i] = ija;
|
548
|
+
|
549
|
+
for (IType j = 0; j < rhs->shape[1]; ++j) {
|
550
|
+
pos = rhs->stride[0] * (i + rhs->offset[0]) + rhs->stride[1] * (j + rhs->offset[1]); // calc position with offsets
|
551
|
+
|
552
|
+
if (i == j) { // copy to diagonal
|
553
|
+
lhs_a[i] = static_cast<LDType>(rhs_elements[pos]);
|
554
|
+
} else if (rhs_elements[pos] != R_INIT) { // copy nonzero to LU
|
555
|
+
lhs_ija[ija] = j; // write column index
|
556
|
+
lhs_a[ija] = static_cast<LDType>(rhs_elements[pos]);
|
557
|
+
|
558
|
+
++ija;
|
559
|
+
}
|
560
|
+
}
|
561
|
+
}
|
562
|
+
|
563
|
+
lhs_ija[shape[0]] = ija; // indicate the end of the last row
|
564
|
+
lhs->ndnz = ndnz;
|
565
|
+
|
566
|
+
nm_dense_storage_unregister(rhs);
|
567
|
+
|
568
|
+
return lhs;
|
569
|
+
}
|
570
|
+
|
571
|
+
/*
|
572
|
+
* Creation of yale storage from list storage.
|
573
|
+
*/
|
574
|
+
template <typename LDType, typename RDType>
|
575
|
+
YALE_STORAGE* create_from_list_storage(const LIST_STORAGE* rhs, nm::dtype_t l_dtype) {
|
576
|
+
if (rhs->dim != 2) rb_raise(nm_eStorageTypeError, "can only convert matrices of dim 2 to yale");
|
577
|
+
|
578
|
+
if (rhs->dtype == RUBYOBJ) {
|
579
|
+
VALUE init_val = *reinterpret_cast<VALUE*>(rhs->default_val);
|
580
|
+
if (rb_funcall(init_val, rb_intern("!="), 1, Qnil) == Qtrue && rb_funcall(init_val, rb_intern("!="), 1, Qfalse) == Qtrue && rb_funcall(init_val, rb_intern("!="), 1, INT2FIX(0)) == Qtrue)
|
581
|
+
rb_raise(nm_eStorageTypeError, "list matrix of Ruby objects must have default value equal to 0, nil, or false to convert to yale");
|
582
|
+
} else if (strncmp(reinterpret_cast<const char*>(rhs->default_val), "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0", DTYPE_SIZES[rhs->dtype]))
|
583
|
+
rb_raise(nm_eStorageTypeError, "list matrix of non-Ruby objects must have default value of 0 to convert to yale");
|
584
|
+
|
585
|
+
nm_list_storage_register(rhs);
|
586
|
+
|
587
|
+
size_t ndnz = nm_list_storage_count_nd_elements(rhs);
|
588
|
+
// Copy shape for yale construction
|
589
|
+
size_t* shape = NM_ALLOC_N(size_t, 2);
|
590
|
+
shape[0] = rhs->shape[0];
|
591
|
+
shape[1] = rhs->shape[1];
|
592
|
+
|
593
|
+
size_t request_capacity = shape[0] + ndnz + 1;
|
594
|
+
YALE_STORAGE* lhs = nm_yale_storage_create(l_dtype, shape, 2, request_capacity);
|
595
|
+
|
596
|
+
if (lhs->capacity < request_capacity)
|
597
|
+
rb_raise(nm_eStorageTypeError, "conversion failed; capacity of %ld requested, max allowable is %ld", (unsigned long)request_capacity, (unsigned long)(lhs->capacity));
|
598
|
+
|
599
|
+
// Initialize the A and IJA arrays
|
600
|
+
init<LDType>(lhs, rhs->default_val);
|
601
|
+
|
602
|
+
IType* lhs_ija = lhs->ija;
|
603
|
+
LDType* lhs_a = reinterpret_cast<LDType*>(lhs->a);
|
604
|
+
|
605
|
+
IType ija = lhs->shape[0]+1;
|
606
|
+
|
607
|
+
// Copy contents
|
608
|
+
for (NODE* i_curr = rhs->rows->first; i_curr; i_curr = i_curr->next) {
|
609
|
+
|
610
|
+
// Shrink reference
|
611
|
+
int i = i_curr->key - rhs->offset[0];
|
612
|
+
if (i < 0 || i >= (int)rhs->shape[0]) continue;
|
613
|
+
|
614
|
+
for (NODE* j_curr = ((LIST*)(i_curr->val))->first; j_curr; j_curr = j_curr->next) {
|
615
|
+
|
616
|
+
// Shrink reference
|
617
|
+
int j = j_curr->key - rhs->offset[1];
|
618
|
+
if (j < 0 || j >= (int)rhs->shape[1]) continue;
|
619
|
+
|
620
|
+
LDType cast_jcurr_val = *reinterpret_cast<RDType*>(j_curr->val);
|
621
|
+
if (i_curr->key - rhs->offset[0] == j_curr->key - rhs->offset[1])
|
622
|
+
lhs_a[i_curr->key - rhs->offset[0]] = cast_jcurr_val; // set diagonal
|
623
|
+
else {
|
624
|
+
lhs_ija[ija] = j_curr->key - rhs->offset[1]; // set column value
|
625
|
+
|
626
|
+
lhs_a[ija] = cast_jcurr_val; // set cell value
|
627
|
+
|
628
|
+
++ija;
|
629
|
+
// indicate the beginning of a row in the IJA array
|
630
|
+
for (size_t i = i_curr->key - rhs->offset[0] + 1; i < rhs->shape[0] + rhs->offset[0]; ++i) {
|
631
|
+
lhs_ija[i] = ija;
|
632
|
+
}
|
633
|
+
|
634
|
+
}
|
635
|
+
}
|
636
|
+
|
637
|
+
}
|
638
|
+
|
639
|
+
lhs_ija[rhs->shape[0]] = ija; // indicate the end of the last row
|
640
|
+
lhs->ndnz = ndnz;
|
641
|
+
|
642
|
+
nm_list_storage_unregister(rhs);
|
643
|
+
|
644
|
+
return lhs;
|
645
|
+
}
|
646
|
+
|
647
|
+
} // end of namespace yale_storage
|
648
|
+
} // end of namespace nm
|
649
|
+
|
650
|
+
extern "C" {
|
651
|
+
|
652
|
+
/*
|
653
|
+
* The following functions represent stype casts -- conversions from one
|
654
|
+
* stype to another. Each of these is the C accessor for a templated C++
|
655
|
+
* function.
|
656
|
+
*/
|
657
|
+
|
658
|
+
|
659
|
+
STORAGE* nm_yale_storage_from_dense(const STORAGE* right, nm::dtype_t l_dtype, void* init) {
|
660
|
+
NAMED_LR_DTYPE_TEMPLATE_TABLE(ttable, nm::yale_storage::create_from_dense_storage, YALE_STORAGE*, const DENSE_STORAGE* rhs, nm::dtype_t l_dtype, void*);
|
661
|
+
|
662
|
+
if (!ttable[l_dtype][right->dtype]) {
|
663
|
+
rb_raise(nm_eDataTypeError, "casting between these dtypes is undefined");
|
664
|
+
return NULL;
|
665
|
+
}
|
666
|
+
|
667
|
+
return (STORAGE*)ttable[l_dtype][right->dtype]((const DENSE_STORAGE*)right, l_dtype, init);
|
668
|
+
}
|
669
|
+
|
670
|
+
STORAGE* nm_yale_storage_from_list(const STORAGE* right, nm::dtype_t l_dtype, void* dummy) {
|
671
|
+
NAMED_LR_DTYPE_TEMPLATE_TABLE(ttable, nm::yale_storage::create_from_list_storage, YALE_STORAGE*, const LIST_STORAGE* rhs, nm::dtype_t l_dtype);
|
672
|
+
|
673
|
+
if (!ttable[l_dtype][right->dtype]) {
|
674
|
+
rb_raise(nm_eDataTypeError, "casting between these dtypes is undefined");
|
675
|
+
return NULL;
|
676
|
+
}
|
677
|
+
|
678
|
+
return (STORAGE*)ttable[l_dtype][right->dtype]((const LIST_STORAGE*)right, l_dtype);
|
679
|
+
}
|
680
|
+
|
681
|
+
STORAGE* nm_dense_storage_from_list(const STORAGE* right, nm::dtype_t l_dtype, void* dummy) {
|
682
|
+
NAMED_LR_DTYPE_TEMPLATE_TABLE(ttable, nm::dense_storage::create_from_list_storage, DENSE_STORAGE*, const LIST_STORAGE* rhs, nm::dtype_t l_dtype);
|
683
|
+
|
684
|
+
if (!ttable[l_dtype][right->dtype]) {
|
685
|
+
rb_raise(nm_eDataTypeError, "casting between these dtypes is undefined");
|
686
|
+
return NULL;
|
687
|
+
}
|
688
|
+
|
689
|
+
return (STORAGE*)ttable[l_dtype][right->dtype]((const LIST_STORAGE*)right, l_dtype);
|
690
|
+
}
|
691
|
+
|
692
|
+
STORAGE* nm_dense_storage_from_yale(const STORAGE* right, nm::dtype_t l_dtype, void* dummy) {
|
693
|
+
NAMED_LR_DTYPE_TEMPLATE_TABLE(ttable, nm::dense_storage::create_from_yale_storage, DENSE_STORAGE*, const YALE_STORAGE* rhs, nm::dtype_t l_dtype);
|
694
|
+
|
695
|
+
const YALE_STORAGE* casted_right = reinterpret_cast<const YALE_STORAGE*>(right);
|
696
|
+
|
697
|
+
if (!ttable[l_dtype][right->dtype]) {
|
698
|
+
rb_raise(nm_eDataTypeError, "casting between these dtypes is undefined");
|
699
|
+
return NULL;
|
700
|
+
}
|
701
|
+
|
702
|
+
return reinterpret_cast<STORAGE*>(ttable[l_dtype][right->dtype](casted_right, l_dtype));
|
703
|
+
}
|
704
|
+
|
705
|
+
STORAGE* nm_list_storage_from_dense(const STORAGE* right, nm::dtype_t l_dtype, void* init) {
|
706
|
+
NAMED_LR_DTYPE_TEMPLATE_TABLE(ttable, nm::list_storage::create_from_dense_storage, LIST_STORAGE*, const DENSE_STORAGE*, nm::dtype_t, void*);
|
707
|
+
|
708
|
+
if (!ttable[l_dtype][right->dtype]) {
|
709
|
+
rb_raise(nm_eDataTypeError, "casting between these dtypes is undefined");
|
710
|
+
return NULL;
|
711
|
+
}
|
712
|
+
|
713
|
+
return (STORAGE*)ttable[l_dtype][right->dtype]((DENSE_STORAGE*)right, l_dtype, init);
|
714
|
+
}
|
715
|
+
|
716
|
+
STORAGE* nm_list_storage_from_yale(const STORAGE* right, nm::dtype_t l_dtype, void* dummy) {
|
717
|
+
NAMED_LR_DTYPE_TEMPLATE_TABLE(ttable, nm::list_storage::create_from_yale_storage, LIST_STORAGE*, const YALE_STORAGE* rhs, nm::dtype_t l_dtype);
|
718
|
+
|
719
|
+
const YALE_STORAGE* casted_right = reinterpret_cast<const YALE_STORAGE*>(right);
|
720
|
+
|
721
|
+
if (!ttable[l_dtype][right->dtype]) {
|
722
|
+
rb_raise(nm_eDataTypeError, "casting between these dtypes is undefined");
|
723
|
+
return NULL;
|
724
|
+
}
|
725
|
+
|
726
|
+
return (STORAGE*)ttable[l_dtype][right->dtype](casted_right, l_dtype);
|
727
|
+
}
|
728
|
+
|
729
|
+
} // end of extern "C"
|
730
|
+
|