[Rcpp-commits] r3780 - in pkg/RcppArmadillo: . inst inst/include/armadillo_bits man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Sep 25 13:52:40 CEST 2012
Author: edd
Date: 2012-09-25 13:52:39 +0200 (Tue, 25 Sep 2012)
New Revision: 3780
Modified:
pkg/RcppArmadillo/ChangeLog
pkg/RcppArmadillo/DESCRIPTION
pkg/RcppArmadillo/inst/NEWS.Rd
pkg/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/SpMat_bones.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/SpMat_iterators_meat.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/SpSubview_bones.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/SpSubview_iterators_meat.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/SpSubview_meat.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/arma_ostream_meat.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/diskio_meat.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/fn_accu.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/fn_dot.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/fn_n_unique.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/fn_trace.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/operator_div.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/operator_minus.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/operator_plus.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/operator_schur.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/operator_times.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/span.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/spglue_minus_meat.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/spglue_plus_meat.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/spglue_times_meat.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/spop_max_meat.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/spop_min_meat.hpp
pkg/RcppArmadillo/inst/include/armadillo_bits/spop_sum_meat.hpp
pkg/RcppArmadillo/man/RcppArmadillo-package.Rd
Log:
Release 0.3.4.2 with Armadillo 3.4.2
Modified: pkg/RcppArmadillo/ChangeLog
===================================================================
--- pkg/RcppArmadillo/ChangeLog 2012-09-22 19:25:15 UTC (rev 3779)
+++ pkg/RcppArmadillo/ChangeLog 2012-09-25 11:52:39 UTC (rev 3780)
@@ -1,3 +1,9 @@
+2012-09-25 Dirk Eddelbuettel <edd at debian.org>
+
+ * DESCRIPTION: Release 0.3.4.2
+
+ * inst/include/*: Upgraded to new release 3.4.2 of Armadillo
+
2012-09-18 Dirk Eddelbuettel <edd at debian.org>
* DESCRIPTION: Release 0.3.4.1
Modified: pkg/RcppArmadillo/DESCRIPTION
===================================================================
--- pkg/RcppArmadillo/DESCRIPTION 2012-09-22 19:25:15 UTC (rev 3779)
+++ pkg/RcppArmadillo/DESCRIPTION 2012-09-25 11:52:39 UTC (rev 3780)
@@ -1,7 +1,7 @@
Package: RcppArmadillo
Type: Package
Title: Rcpp integration for Armadillo templated linear algebra library
-Version: 0.3.4.1
+Version: 0.3.4.2
Date: $Date$
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel <edd at debian.org>
@@ -21,7 +21,7 @@
(due to speed and/or integration capabilities), rather than another language.
.
The RcppArmadillo package includes the header files from the templated
- Armadillo library (currently version 3.4.1). Thus users do not need to
+ Armadillo library (currently version 3.4.2). Thus users do not need to
install Armadillo itself in order to use RcppArmadillo.
.
This Armadillo integration provides a nice illustration of the
Modified: pkg/RcppArmadillo/inst/NEWS.Rd
===================================================================
--- pkg/RcppArmadillo/inst/NEWS.Rd 2012-09-22 19:25:15 UTC (rev 3779)
+++ pkg/RcppArmadillo/inst/NEWS.Rd 2012-09-25 11:52:39 UTC (rev 3780)
@@ -2,6 +2,16 @@
\title{News for Package 'RcppArmadillo'}
\newcommand{\cpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
+\section{Changes in RcppArmadillo version 0.3.4.2 (2012-09-25)}{
+ \itemize{
+ \item Upgraded to Armadillo release 3.4.2
+ \itemize{
+ \item minor fixes for handling sparse submatrix views
+ \item minor speedups for sparse matrices
+ }
+ }
+}
+
\section{Changes in RcppArmadillo version 0.3.4.1 (2012-09-18)}{
\itemize{
\item Upgraded to Armadillo release 3.4.1
Modified: pkg/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp
===================================================================
--- pkg/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp 2012-09-22 19:25:15 UTC (rev 3779)
+++ pkg/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp 2012-09-25 11:52:39 UTC (rev 3780)
@@ -1991,7 +1991,7 @@
fill(eT(0));
// Iterate over each nonzero element and set it.
- for(typename SpProxy<T1>::const_iterator_type it = p.begin(); it.pos() < p.get_n_nonzero(); ++it)
+ for(typename SpProxy<T1>::const_iterator_type it = p.begin(); it != p.end(); ++it)
{
at(it.row(), it.col()) = (*it);
}
@@ -2013,7 +2013,7 @@
fill(eT(0));
- for(typename SpProxy<T1>::const_iterator_type it = p.begin(); it.pos() < p.get_n_nonzero(); ++it)
+ for(typename SpProxy<T1>::const_iterator_type it = p.begin(); it != p.end(); ++it)
{
at(it.row(), it.col()) = (*it);
}
@@ -2035,7 +2035,7 @@
arma_debug_assert_same_size(n_rows, n_cols, p.get_n_rows(), p.get_n_cols(), "addition");
- for(typename SpProxy<T1>::const_iterator_type it = p.begin(); it.pos() < p.get_n_nonzero(); ++it)
+ for(typename SpProxy<T1>::const_iterator_type it = p.begin(); it != p.end(); ++it)
{
at(it.row(), it.col()) += (*it);
}
@@ -2057,7 +2057,7 @@
arma_debug_assert_same_size(n_rows, n_cols, p.get_n_rows(), p.get_n_cols(), "subtraction");
- for(typename SpProxy<T1>::const_iterator_type it = p.begin(); it.pos() < p.get_n_nonzero(); ++it)
+ for(typename SpProxy<T1>::const_iterator_type it = p.begin(); it != p.end(); ++it)
{
at(it.row(), it.col()) -= (*it);
}
@@ -2101,7 +2101,7 @@
// We have to zero everything that isn't being used.
arrayops::inplace_set(memptr(), eT(0), (it.col() * n_rows) + it.row());
- while(it.pos() < p.get_n_nonzero())
+ while(it != p.end())
{
const uword cur_loc = (it.col() * n_rows) + it.row();
@@ -2109,7 +2109,7 @@
++it;
- const uword next_loc = (it.pos() == p.get_n_nonzero())
+ const uword next_loc = (it == p.end())
? (p.get_n_cols() * n_rows)
: (it.col() * n_rows) + it.row();
Modified: pkg/RcppArmadillo/inst/include/armadillo_bits/SpMat_bones.hpp
===================================================================
--- pkg/RcppArmadillo/inst/include/armadillo_bits/SpMat_bones.hpp 2012-09-22 19:25:15 UTC (rev 3779)
+++ pkg/RcppArmadillo/inst/include/armadillo_bits/SpMat_bones.hpp 2012-09-25 11:52:39 UTC (rev 3780)
@@ -47,6 +47,8 @@
/**
* The row indices of each value. row_indices[i] is the row of values[i].
+ * The length of this array is n_nonzero + 1; the final value ensures the
+ * integrity of iterators.
*/
const uword* const row_indices;
@@ -305,13 +307,13 @@
inline iterator_base(const SpMat& in_M);
inline iterator_base(const SpMat& in_M, const uword col, const uword pos);
- inline eT operator*() const;
+ inline arma_hot eT operator*() const;
- inline bool operator==(const iterator_base& rhs) const;
- inline bool operator!=(const iterator_base& rhs) const;
+ inline arma_hot bool operator==(const iterator_base& rhs) const;
+ inline arma_hot bool operator!=(const iterator_base& rhs) const;
- inline bool operator==(const typename SpSubview<eT>::iterator_base& rhs) const;
- inline bool operator!=(const typename SpSubview<eT>::iterator_base& rhs) const;
+ inline arma_hot bool operator==(const typename SpSubview<eT>::iterator_base& rhs) const;
+ inline arma_hot bool operator!=(const typename SpSubview<eT>::iterator_base& rhs) const;
// Don't hold location internally; call "dummy" methods to get that information.
arma_inline uword row() const { return M.row_indices[internal_pos]; }
@@ -330,13 +332,15 @@
inline const_iterator(const SpMat& in_M, uword initial_pos = 0); // Assumes initial_pos is valid.
//! Once initialized, will be at the first nonzero value after the given position (using forward columnwise traversal).
inline const_iterator(const SpMat& in_M, uword in_row, uword in_col);
+ //! If you know the exact position of the iterator. in_row is a dummy argument.
+ inline const_iterator(const SpMat& in_M, uword in_row, uword in_col, uword in_pos);
inline const_iterator(const const_iterator& other);
- inline const_iterator& operator++();
- inline void operator++(int);
+ inline arma_hot const_iterator& operator++();
+ inline arma_hot void operator++(int);
- inline const_iterator& operator--();
- inline void operator--(int);
+ inline arma_hot const_iterator& operator--();
+ inline arma_hot void operator--(int);
};
/**
@@ -351,16 +355,17 @@
inline iterator(SpMat& in_M, uword initial_pos = 0) : const_iterator(in_M, initial_pos) { }
inline iterator(SpMat& in_M, uword in_row, uword in_col) : const_iterator(in_M, in_row, in_col) { }
+ inline iterator(SpMat& in_M, uword in_row, uword in_col, uword in_pos) : const_iterator(in_M, in_row, in_col, in_pos) { }
inline iterator(const const_iterator& other) : const_iterator(other) { }
- inline SpValProxy<SpMat<eT> > operator*();
+ inline arma_hot SpValProxy<SpMat<eT> > operator*();
// overloads needed for return type correctness
- inline iterator& operator++();
- inline void operator++(int);
+ inline arma_hot iterator& operator++();
+ inline arma_hot void operator++(int);
- inline iterator& operator--();
- inline void operator--(int);
+ inline arma_hot iterator& operator--();
+ inline arma_hot void operator--(int);
};
class const_row_iterator : public iterator_base
@@ -372,11 +377,11 @@
inline const_row_iterator(const SpMat& in_M, uword in_row, uword in_col);
inline const_row_iterator(const const_row_iterator& other);
- inline const_row_iterator& operator++();
- inline void operator++(int);
+ inline arma_hot const_row_iterator& operator++();
+ inline arma_hot void operator++(int);
- inline const_row_iterator& operator--();
- inline void operator--(int);
+ inline arma_hot const_row_iterator& operator--();
+ inline arma_hot void operator--(int);
uword internal_row; // Hold row internally because we use internal_pos differently.
uword actual_pos; // Actual position in matrix.
@@ -395,21 +400,21 @@
inline row_iterator(SpMat& in_M, uword in_row, uword in_col) : const_row_iterator(in_M, in_row, in_col) { }
inline row_iterator(const row_iterator& other) : const_row_iterator(other) { }
- inline SpValProxy<SpMat<eT> > operator*();
+ inline arma_hot SpValProxy<SpMat<eT> > operator*();
// overloads required for return type correctness
- inline row_iterator& operator++();
- inline void operator++(int);
+ inline arma_hot row_iterator& operator++();
+ inline arma_hot void operator++(int);
- inline row_iterator& operator--();
- inline void operator--(int);
+ inline arma_hot row_iterator& operator--();
+ inline arma_hot void operator--(int);
};
inline iterator begin();
inline const_iterator begin() const;
- inline iterator end();
- inline const_iterator end() const;
+ inline iterator end();
+ inline const_iterator end() const;
inline iterator begin_col(const uword col_num);
inline const_iterator begin_col(const uword col_num) const;
Modified: pkg/RcppArmadillo/inst/include/armadillo_bits/SpMat_iterators_meat.hpp
===================================================================
--- pkg/RcppArmadillo/inst/include/armadillo_bits/SpMat_iterators_meat.hpp 2012-09-22 19:25:15 UTC (rev 3779)
+++ pkg/RcppArmadillo/inst/include/armadillo_bits/SpMat_iterators_meat.hpp 2012-09-25 11:52:39 UTC (rev 3780)
@@ -44,6 +44,7 @@
template<typename eT>
inline
+arma_hot
eT
SpMat<eT>::iterator_base::operator*() const
{
@@ -54,6 +55,7 @@
template<typename eT>
inline
+arma_hot
bool
SpMat<eT>::iterator_base::operator==(const iterator_base& rhs) const
{
@@ -64,6 +66,7 @@
template<typename eT>
inline
+arma_hot
bool
SpMat<eT>::iterator_base::operator!=(const iterator_base& rhs) const
{
@@ -74,6 +77,7 @@
template<typename eT>
inline
+arma_hot
bool
SpMat<eT>::iterator_base::operator==(const typename SpSubview<eT>::iterator_base& rhs) const
{
@@ -84,6 +88,7 @@
template<typename eT>
inline
+arma_hot
bool
SpMat<eT>::iterator_base::operator!=(const typename SpSubview<eT>::iterator_base& rhs) const
{
@@ -101,6 +106,13 @@
SpMat<eT>::const_iterator::const_iterator(const SpMat<eT>& in_M, uword initial_pos)
: iterator_base(in_M, 0, initial_pos)
{
+ // Corner case for empty matrices.
+ if(in_M.n_nonzero == 0)
+ {
+ iterator_base::internal_col = in_M.n_cols;
+ return;
+ }
+
// Determine which column we should be in.
while(iterator_base::M.col_ptrs[iterator_base::internal_col + 1] <= iterator_base::internal_pos)
{
@@ -135,6 +147,16 @@
template<typename eT>
inline
+SpMat<eT>::const_iterator::const_iterator(const SpMat<eT>& in_M, const uword /* in_row */, const uword in_col, const uword in_pos)
+ : iterator_base(in_M, in_col, in_pos)
+ {
+ // Nothing to do.
+ }
+
+
+
+template<typename eT>
+inline
SpMat<eT>::const_iterator::const_iterator(const typename SpMat<eT>::const_iterator& other)
: iterator_base(other.M, other.internal_col, other.internal_pos)
{
@@ -145,6 +167,7 @@
template<typename eT>
inline
+arma_hot
typename SpMat<eT>::const_iterator&
SpMat<eT>::const_iterator::operator++()
{
@@ -169,6 +192,7 @@
template<typename eT>
inline
+arma_hot
void
SpMat<eT>::const_iterator::operator++(int)
{
@@ -179,10 +203,11 @@
template<typename eT>
inline
+arma_hot
typename SpMat<eT>::const_iterator&
SpMat<eT>::const_iterator::operator--()
{
- iterator_base::M.print("M");
+ //iterator_base::M.print("M");
// printf("decrement from %d, %d, %d\n", iterator_base::internal_pos, iterator_base::internal_col, iterator_base::row());
@@ -206,6 +231,7 @@
template<typename eT>
inline
+arma_hot
void
SpMat<eT>::const_iterator::operator--(int)
{
@@ -220,6 +246,7 @@
template<typename eT>
inline
+arma_hot
SpValProxy<SpMat<eT> >
SpMat<eT>::iterator::operator*()
{
@@ -234,6 +261,7 @@
template<typename eT>
inline
+arma_hot
typename SpMat<eT>::iterator&
SpMat<eT>::iterator::operator++()
{
@@ -245,6 +273,7 @@
template<typename eT>
inline
+arma_hot
void
SpMat<eT>::iterator::operator++(int)
{
@@ -255,6 +284,7 @@
template<typename eT>
inline
+arma_hot
typename SpMat<eT>::iterator&
SpMat<eT>::iterator::operator--()
{
@@ -266,6 +296,7 @@
template<typename eT>
inline
+arma_hot
void
SpMat<eT>::iterator::operator--(int)
{
@@ -288,6 +319,13 @@
, internal_row(0)
, actual_pos(0)
{
+ // Corner case for empty matrix.
+ if(in_M.n_nonzero == 0)
+ {
+ iterator_base::internal_col = in_M.n_cols;
+ return;
+ }
+
// We don't count zeroes in our position count, so we have to find the nonzero
// value corresponding to the given initial position. We assume initial_pos
// is valid.
@@ -385,6 +423,7 @@
*/
template<typename eT>
inline
+arma_hot
typename SpMat<eT>::const_row_iterator&
SpMat<eT>::const_row_iterator::operator++()
{
@@ -436,6 +475,7 @@
*/
template<typename eT>
inline
+arma_hot
void
SpMat<eT>::const_row_iterator::operator++(int)
{
@@ -449,6 +489,7 @@
*/
template<typename eT>
inline
+arma_hot
typename SpMat<eT>::const_row_iterator&
SpMat<eT>::const_row_iterator::operator--()
{
@@ -490,6 +531,7 @@
*/
template<typename eT>
inline
+arma_hot
void
SpMat<eT>::const_row_iterator::operator--(int)
{
@@ -502,6 +544,7 @@
template<typename eT>
inline
+arma_hot
SpValProxy<SpMat<eT> >
SpMat<eT>::row_iterator::operator*()
{
@@ -516,6 +559,7 @@
template<typename eT>
inline
+arma_hot
typename SpMat<eT>::row_iterator&
SpMat<eT>::row_iterator::operator++()
{
@@ -527,6 +571,7 @@
template<typename eT>
inline
+arma_hot
void
SpMat<eT>::row_iterator::operator++(int)
{
@@ -537,6 +582,7 @@
template<typename eT>
inline
+arma_hot
typename SpMat<eT>::row_iterator&
SpMat<eT>::row_iterator::operator--()
{
@@ -548,6 +594,7 @@
template<typename eT>
inline
+arma_hot
void
SpMat<eT>::row_iterator::operator--(int)
{
Modified: pkg/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp
===================================================================
--- pkg/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp 2012-09-22 19:25:15 UTC (rev 3779)
+++ pkg/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp 2012-09-25 11:52:39 UTC (rev 3780)
@@ -25,12 +25,15 @@
, n_elem(0)
, n_nonzero(0)
, vec_state(0)
- , values(NULL)
- , row_indices(NULL)
+ , values(memory::acquire_chunked<eT>(1))
+ , row_indices(memory::acquire_chunked<uword>(1))
, col_ptrs(memory::acquire<uword>(1))
{
arma_extra_debug_sigprint_this(this);
-
+
+ access::rw(values[0]) = 0;
+ access::rw(row_indices[0]) = 0;
+
access::rw(col_ptrs[0]) = 0; // No elements.
}
@@ -264,7 +267,7 @@
arma_debug_assert_same_size(n_rows, n_cols, x.n_rows, x.n_cols, "addition");
// Iterate over nonzero values of other matrix.
- for (const_iterator it = x.begin(); it.pos() < x.n_nonzero; it++)
+ for (const_iterator it = x.begin(); it != x.end(); it++)
{
get_value(it.row(), it.col()) += *it;
}
@@ -284,7 +287,7 @@
arma_debug_assert_same_size(n_rows, n_cols, x.n_rows, x.n_cols, "subtraction");
// Iterate over nonzero values of other matrix.
- for (const_iterator it = x.begin(); it.pos() < x.n_nonzero; it++)
+ for (const_iterator it = x.begin(); it != x.end(); it++)
{
get_value(it.row(), it.col()) -= *it;
}
@@ -326,7 +329,7 @@
iterator it = begin();
const_iterator x_it = x.begin();
- while (it.pos() < n_nonzero && x_it.pos() < x.n_nonzero)
+ while (it != end() && x_it != x.end())
{
// One of these will be further advanced than the other (or they will be at the same place).
if ((it.row() == x_it.row()) && (it.col() == x_it.col()))
@@ -362,7 +365,7 @@
}
// If we are not at the end of our matrix, then we must terminate the remaining elements.
- while (it.pos() < n_nonzero)
+ while (it != end())
{
(*it) = 0;
@@ -390,7 +393,7 @@
, n_elem(0)
, n_nonzero(0)
, vec_state(0)
- , values(NULL)
+ , values(NULL) // extra element is set when mem_resize is called
, row_indices(NULL)
, col_ptrs(NULL)
{
@@ -424,7 +427,7 @@
typename SpMat<T>::const_iterator y_it = Y.begin();
uword cur_pos = 0;
- while ((x_it.pos() < X.n_nonzero) || (y_it.pos() < Y.n_nonzero))
+ while ((x_it != X.end()) || (y_it != Y.end()))
{
if(x_it == y_it) // if we are at the same place
{
@@ -501,7 +504,7 @@
, n_elem(0)
, n_nonzero(0)
, vec_state(0)
- , values(NULL)
+ , values(NULL) // extra element is set when mem_resize is called in operator=()
, row_indices(NULL)
, col_ptrs(NULL)
{
@@ -518,21 +521,63 @@
const SpMat<eT>&
SpMat<eT>::operator=(const Base<eT, T1>& x)
{
- //No easy init function, will have to generate matrix manually.
arma_extra_debug_sigprint();
const Proxy<T1> p(x.get_ref());
const uword x_n_rows = p.get_n_rows();
const uword x_n_cols = p.get_n_cols();
-
+ const uword x_n_elem = p.get_n_elem();
+
init(x_n_rows, x_n_cols);
-
+
+ // Count number of nonzero elements in base object.
+ uword n = 0;
+ if(Proxy<T1>::prefer_at_accessor == true)
+ {
+ for(uword j = 0; j < x_n_cols; ++j)
+ {
+ for(uword i = 0; i < x_n_rows; ++i)
+ {
+ if(p.at(i, j) != eT(0))
+ ++n;
+ }
+ }
+ }
+ else
+ {
+ for(uword i = 0; i < x_n_elem; ++i)
+ {
+ if(p[i] != eT(0))
+ {
+ ++n;
+ }
+ }
+ }
+
+ mem_resize(n);
+
+ // Now the memory is resized correctly; add nonzero elements.
+ n = 0;
for(uword j = 0; j < x_n_cols; ++j)
- for(uword i = 0; i < x_n_rows; ++i)
{
- at(i,j) = p.at(i,j); // let SpValProxy handle 0's.
+ for(uword i = 0; i < x_n_rows; ++i)
+ {
+ if(p.at(i, j) != eT(0))
+ {
+ access::rw(values[n]) = p.at(i, j);
+ access::rw(row_indices[n]) = i;
+ access::rw(col_ptrs[j + 1])++;
+ ++n;
+ }
+ }
}
+
+ // Sum column counts to be column pointers.
+ for(uword c = 1; c <= n_cols; ++c)
+ {
+ access::rw(col_ptrs[c]) += col_ptrs[c - 1];
+ }
return *this;
}
@@ -592,7 +637,7 @@
{
const_iterator it = begin();
- while(it.pos() < n_nonzero)
+ while(it != end())
{
const eT value = (*it);
@@ -604,7 +649,7 @@
// Now add all partial sums to the matrix.
for(uword i = 0; i < n_rows; ++i)
{
- if(partial_sums[i] != 0)
+ if(partial_sums[i] != eT(0))
{
access::rw(z.values[cur_pos]) = partial_sums[i];
access::rw(z.row_indices[cur_pos]) = i;
@@ -677,10 +722,10 @@
const_iterator it = begin();
uword new_n_nonzero = 0;
- while(it.pos() < n_nonzero())
+ while(it != end())
{
// prefer_at_accessor == false can't save us any work here
- if(((*it) * x.at(it.row(), it.col())) != 0)
+ if(((*it) * p.at(it.row(), it.col())) != eT(0))
{
++new_n_nonzero;
}
@@ -692,11 +737,11 @@
const_iterator c_it = begin();
uword cur_pos = 0;
- while(c_it.pos() < n_nonzero)
+ while(c_it != end())
{
// prefer_at_accessor == false can't save us any work here
- const eT val = (*c_it) * x(c_it.row(), c_it.col());
- if(val != 0)
+ const eT val = (*c_it) * p.at(c_it.row(), c_it.col());
+ if(val != eT(0))
{
access::rw(tmp.values[cur_pos]) = val;
access::rw(tmp.row_indices[cur_pos]) = c_it.row();
@@ -731,7 +776,7 @@
, n_elem(0)
, n_nonzero(0)
, vec_state(0)
- , values(NULL)
+ , values(NULL) // extra element added when mem_resize is called
, row_indices(NULL)
, col_ptrs(NULL)
{
@@ -757,14 +802,26 @@
if(alias == false)
{
init(in_n_rows, in_n_cols);
-
+
+ const uword x_n_nonzero = X.n_nonzero;
+
+ mem_resize(x_n_nonzero);
+
typename SpSubview<eT>::const_iterator it = X.begin();
- while(it.pos() < X.n_nonzero)
+ while(it != X.end())
{
- at(it.row(), it.col()) = (*it);
+ access::rw(row_indices[it.pos()]) = it.row();
+ access::rw(values[it.pos()]) = (*it);
+ ++access::rw(col_ptrs[it.col() + 1]);
++it;
}
+
+ // Now sum column pointers.
+ for(uword c = 1; c <= n_cols; ++c)
+ {
+ access::rw(col_ptrs[c]) += col_ptrs[c - 1];
+ }
}
else
{
@@ -788,19 +845,11 @@
arma_debug_assert_same_size(n_rows, n_cols, X.n_rows, X.n_cols, "addition");
- const uword in_n_cols = X.n_cols;
- const uword in_n_rows = X.n_rows;
+ typename SpSubview<eT>::const_iterator it = X.begin();
- const_iterator it = const_iterator(X.m, X.aux_row1, X.aux_col1);
-
- while(it.col < (X.aux_col1 + in_n_cols))
+ while(it != X.end())
{
- // Is it within the proper range?
- if((it.row >= X.aux_row1) && (it.row < (X.aux_row1 + in_n_rows)))
- {
- at(it.row - X.aux_row1, it.col - X.aux_col1) += (*it);
- }
-
+ at(it.row(), it.col()) += (*it);
++it;
}
@@ -818,19 +867,11 @@
arma_debug_assert_same_size(n_rows, n_cols, X.n_rows, X.n_cols, "subtraction");
- const uword in_n_cols = X.n_cols;
- const uword in_n_rows = X.n_rows;
+ typename SpSubview<eT>::const_iterator it = X.begin();
- const_iterator it = const_iterator(X.m, X.aux_row1, X.aux_col1);
-
- while(it.col < (X.aux_col1 + in_n_cols))
+ while(it != X.end())
{
- // Is it within the proper range?
- if((it.row >= X.aux_row1) && (it.row < (X.aux_row1 + in_n_rows)))
- {
- at(it.row - X.aux_row1, it.col - X.aux_col1) -= (*it);
- }
-
+ at(it.row(), it.col()) -= (*it);
++it;
}
@@ -865,28 +906,32 @@
arma_extra_debug_sigprint();
arma_debug_assert_same_size(n_rows, n_cols, x.n_rows, x.n_cols, "element-wise multiplication");
-
- // We want to iterate over whichever has fewer nonzero points.
- if (n_nonzero <= x.n_nonzero)
+
+ iterator it = begin();
+ typename SpSubview<eT>::const_iterator xit = x.begin();
+
+ while((it != end()) || (xit != x.end()))
{
- // Use our iterator.
- for (iterator it = begin(); it.pos() < n_nonzero; it++)
+ if((xit.row() == it.row()) && (xit.col() == it.col()))
{
- (*it) *= x(it.row(), it.col());
+ (*it) *= (*xit);
+ ++it;
+ ++xit;
}
- }
- else
- {
- // Use their iterator. A little more complex...
- const_iterator it = const_iterator(x.m, x.aux_row1, x.aux_col1);
- while((it.col() < (x.aux_col1 + x.n_cols)))
+ else
{
- if((it.row() >= x.aux_row1) && (it.row() < (x.aux_row1 + x.n_rows)))
+ if((xit.col() > it.col()) || ((xit.col() == it.col()) && (xit.row() > it.row())))
{
- at(it.row() - x.aux_row1, it.col() - x.aux_col1) *= (*it);
+ // xit is "ahead"
+ (*it) = eT(0); // erase element; x has a zero here
+ it.internal_pos--; // update iterator so it still works
+ ++it;
}
-
- ++it;
+ else
+ {
+ // it is "ahead"
+ ++xit;
+ }
}
}
@@ -925,7 +970,7 @@
, n_elem(0)
, n_nonzero(0)
, vec_state(0)
- , values(NULL)
+ , values(NULL) // extra value set in operator=()
, row_indices(NULL)
, col_ptrs(NULL)
{
@@ -943,17 +988,50 @@
{
arma_extra_debug_sigprint();
+ const uword x_n_rows = x.n_rows;
+ const uword x_n_cols = x.n_cols;
+
// Set the size correctly.
- init(x.n_rows, x.n_cols);
-
- for(uword col = 0; col < x.n_cols; col++)
+ init(x_n_rows, x_n_cols);
+
+ // Count number of nonzero elements.
+ uword n = 0;
+ for(uword c = 0; c < x_n_cols; ++c)
{
- for(uword row = 0; row < x.n_rows; row++)
+ for(uword r = 0; r < x_n_rows; ++r)
{
- // Add any nonzero values.
- at(row, col) = x.at(row, col);
+ if(x.at(r, c) != eT(0))
+ {
+ ++n;
+ }
}
}
+
+ // Resize memory appropriately.
+ mem_resize(n);
+
+ n = 0;
+ for(uword c = 0; c < x_n_cols; ++c)
+ {
+ for(uword r = 0; r < x_n_rows; ++r)
+ {
+ const eT val = x.at(r, c);
+
+ if(val != eT(0))
+ {
+ access::rw(values[n]) = val;
+ access::rw(row_indices[n]) = r;
+ ++access::rw(col_ptrs[c + 1]);
+ ++n;
+ }
+ }
+ }
+
+ // Fix column counts into column pointers.
+ for(uword c = 1; c <= n_cols; ++c)
+ {
+ access::rw(col_ptrs[c]) += col_ptrs[c - 1];
+ }
return *this;
}
@@ -977,7 +1055,7 @@
{
for(uword row = 0; row < n_rows; ++row)
{
- at(row, col) += x(row, col);
+ at(row, col) += x.at(row, col);
}
}
@@ -1000,7 +1078,7 @@
{
for(uword row = 0; row < n_rows; ++row)
{
- at(row, col) -= x(row, col);
+ at(row, col) -= x.at(row, col);
}
}
@@ -1053,7 +1131,7 @@
{
for(uword row = 0; row < n_rows; ++row)
{
- at(row, col) *= x(row, col);
+ at(row, col) *= x.at(row, col);
}
}
@@ -1076,7 +1154,7 @@
{
for(uword row = 0; row < n_rows; ++row)
{
- at(row, col) /= x(row, col);
+ at(row, col) /= x.at(row, col);
}
}
@@ -1094,7 +1172,7 @@
, n_elem(0)
, n_nonzero(0)
, vec_state(0)
- , values(NULL)
+ , values(NULL) // set in application of sparse operation
, row_indices(NULL)
, col_ptrs(NULL)
{
@@ -1218,7 +1296,7 @@
, n_elem(0)
, n_nonzero(0)
, vec_state(0)
- , values(NULL)
+ , values(NULL) // extra element set in application of sparse glue
, row_indices(NULL)
, col_ptrs(NULL)
{
@@ -1363,8 +1441,25 @@
SpMat<eT>::operator()(const uword row_num, const span& col_span)
{
arma_extra_debug_sigprint();
-
- return SpSubview<eT>(*this, row_num, col_span.a, col_span.b - col_span.a + 1);
+
+ const bool col_all = col_span.whole;
+
+ const uword local_n_cols = n_cols;
+
+ const uword in_col1 = col_all ? 0 : col_span.a;
+ const uword in_col2 = col_span.b;
+ const uword submat_n_cols = col_all ? local_n_cols : in_col2 - in_col1 + 1;
+
+ arma_debug_check
+ (
+ (row_num >= n_rows)
+ ||
+ ( col_all ? false : ((in_col1 > in_col2) || (in_col2 >= local_n_cols)) )
+ ,
+ "SpMat::operator(): indices out of bounds or incorrectly used"
+ );
+
+ return SpSubview<eT>(*this, row_num, in_col1, 1, submat_n_cols);
}
@@ -1375,8 +1470,25 @@
SpMat<eT>::operator()(const uword row_num, const span& col_span) const
{
arma_extra_debug_sigprint();
-
- return SpSubview<eT>(*this, row_num, col_span.a, col_span.b - col_span.a + 1);
+
+ const bool col_all = col_span.whole;
+
+ const uword local_n_cols = n_cols;
+
+ const uword in_col1 = col_all ? 0 : col_span.a;
+ const uword in_col2 = col_span.b;
+ const uword submat_n_cols = col_all ? local_n_cols : in_col2 - in_col1 + 1;
+
+ arma_debug_check
+ (
+ (row_num >= n_rows)
+ ||
+ ( col_all ? false : ((in_col1 > in_col2) || (in_col2 >= local_n_cols)) )
+ ,
+ "SpMat::operator(): indices out of bounds or incorrectly used"
+ );
+
+ return SpSubview<eT>(*this, row_num, in_col1, 1, submat_n_cols);
}
@@ -1411,8 +1523,25 @@
SpMat<eT>::operator()(const span& row_span, const uword col_num)
{
arma_extra_debug_sigprint();
-
- return SpSubview<eT>(*this, row_span.a, col_num, row_span.b - row_span.a + 1, 0);
+
+ const bool row_all = row_span.whole;
+
+ const uword local_n_rows = n_rows;
+
+ const uword in_row1 = row_all ? 0 : row_span.a;
+ const uword in_row2 = row_span.b;
+ const uword submat_n_rows = row_all ? local_n_rows : in_row2 - in_row1 + 1;
+
+ arma_debug_check
+ (
+ (col_num >= n_cols)
+ ||
+ ( row_all ? false : ((in_row1 > in_row2) || (in_row2 >= local_n_rows)) )
+ ,
+ "SpMat::operator(): indices out of bounds or incorrectly used"
+ );
+
+ return SpSubview<eT>(*this, in_row1, col_num, submat_n_rows, 1);
}
@@ -1423,8 +1552,25 @@
SpMat<eT>::operator()(const span& row_span, const uword col_num) const
{
arma_extra_debug_sigprint();
-
- return SpSubview<eT>(*this, row_span.a, col_num, row_span.b - row_span.a + 1, 0);
+
+ const bool row_all = row_span.whole;
+
+ const uword local_n_rows = n_rows;
+
+ const uword in_row1 = row_all ? 0 : row_span.a;
+ const uword in_row2 = row_span.b;
+ const uword submat_n_rows = row_all ? local_n_rows : in_row2 - in_row1 + 1;
+
+ arma_debug_check
+ (
+ (col_num >= n_cols)
+ ||
+ ( row_all ? false : ((in_row1 > in_row2) || (in_row2 >= local_n_rows)) )
+ ,
+ "SpMat::operator(): indices out of bounds or incorrectly used"
+ );
+
+ return SpSubview<eT>(*this, in_row1, col_num, submat_n_rows, 1);
}
@@ -1722,7 +1868,6 @@
uword cur_col = in_col1;
for (uword i = in_col2 + 1; i <= n_cols; ++i, ++cur_col)
{
- std::cout << "i " << i << " n_cols " << n_cols << std::endl;
new_col_ptrs[cur_col] = col_ptrs[i] - diff;
}
@@ -2499,11 +2644,12 @@
// columns and rows. We'll have to store a new set of column vectors.
uword* new_col_ptrs = memory::acquire<uword>(in_cols + 1);
- uword* new_row_indices = memory::acquire_chunked<uword>(n_nonzero);
+ uword* new_row_indices = memory::acquire_chunked<uword>(n_nonzero + 1);
+ access::rw(new_row_indices[n_nonzero]) = 0;
arrayops::inplace_set(new_col_ptrs, uword(0), in_cols + 1);
- for(const_iterator it = begin(); it.pos() < n_nonzero; it++)
+ for(const_iterator it = begin(); it != end(); it++)
{
uword vector_position = (it.col() * n_rows) + it.row();
new_row_indices[it.pos()] = vector_position % in_rows;
@@ -2557,8 +2703,11 @@
memory::release(values);
memory::release(row_indices);
- access::rw(values) = NULL;
- access::rw(row_indices) = NULL;
+ access::rw(values) = memory::acquire_chunked<eT>(1);
+ access::rw(row_indices) = memory::acquire_chunked<uword>(1);
+
+ access::rw(values[0]) = 0;
+ access::rw(row_indices[0]) = 0;
}
access::rw(n_nonzero) = 0;
@@ -3123,11 +3272,14 @@
{
memory::release(values);
memory::release(row_indices);
-
- access::rw(values) = NULL;
- access::rw(row_indices) = NULL;
}
+ access::rw(values) = memory::acquire_chunked<eT>(1);
+ access::rw(row_indices) = memory::acquire_chunked<uword>(1);
+
+ access::rw(values[0]) = 0;
+ access::rw(row_indices[0]) = 0;
+
memory::release(col_ptrs);
// Set the new size accordingly.
@@ -3226,7 +3378,7 @@
while (line_stream >> val)
{
// Only add nonzero elements.
- if (val != 0)
+ if (val != eT(0))
{
get_value(row, col) = val;
}
@@ -3256,13 +3408,19 @@
{
init(x.n_rows, x.n_cols);
- // values and row_indices are null.
- access::rw(values) = memory::acquire_chunked<eT> (x.n_nonzero);
- access::rw(row_indices) = memory::acquire_chunked<uword>(x.n_nonzero);
+ // values and row_indices may not be null.
+ if (values != NULL)
+ {
+ memory::release(values);
+ memory::release(row_indices);
+ }
+ access::rw(values) = memory::acquire_chunked<eT> (x.n_nonzero + 1);
+ access::rw(row_indices) = memory::acquire_chunked<uword>(x.n_nonzero + 1);
+
// Now copy over the elements.
- arrayops::copy(access::rwp(values), x.values, x.n_nonzero);
- arrayops::copy(access::rwp(row_indices), x.row_indices, x.n_nonzero);
+ arrayops::copy(access::rwp(values), x.values, x.n_nonzero + 1);
+ arrayops::copy(access::rwp(row_indices), x.row_indices, x.n_nonzero + 1);
arrayops::copy(access::rwp(col_ptrs), x.col_ptrs, x.n_cols + 1);
access::rw(n_nonzero) = x.n_nonzero;
@@ -3285,8 +3443,11 @@
memory::release(values);
memory::release(row_indices);
- access::rw(values) = NULL;
- access::rw(row_indices) = NULL;
+ access::rw(values) = memory::acquire_chunked<eT> (1);
+ access::rw(row_indices) = memory::acquire_chunked<uword>(1);
+
+ access::rw(values[0]) = 0;
+ access::rw(row_indices[0]) = 0;
}
else
{
@@ -3296,8 +3457,11 @@
if(n_alloc < new_n_nonzero)
{
- eT* new_values = memory::acquire_chunked<eT> (new_n_nonzero);
- uword* new_row_indices = memory::acquire_chunked<uword>(new_n_nonzero);
+ eT* new_values = memory::acquire_chunked<eT> (new_n_nonzero + 1);
+ uword* new_row_indices = memory::acquire_chunked<uword>(new_n_nonzero + 1);
+
+ access::rw(new_values[new_n_nonzero]) = 0;
+ access::rw(new_row_indices[new_n_nonzero]) = 0;
if(n_nonzero > 0)
{
@@ -3391,7 +3555,7 @@
typename SpMat<eT>::iterator
SpMat<eT>::end()
{
- return iterator(*this, n_nonzero);
+ return iterator(*this, 0, n_cols, n_nonzero);
}
@@ -3401,7 +3565,7 @@
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/rcpp -r 3780
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