Math-SparseMatrix-0.03/ 0040755 0124673 0000157 00000000000 10776235034 013446 5 ustar tpederse Math-SparseMatrix-0.03/lib/ 0040755 0124673 0000157 00000000000 10776235034 014214 5 ustar tpederse Math-SparseMatrix-0.03/lib/Math/ 0040755 0124673 0000157 00000000000 10776235034 015105 5 ustar tpederse Math-SparseMatrix-0.03/lib/Math/SparseMatrix.pm 0100644 0124673 0000157 00000033575 10776234722 020102 0 ustar tpederse package Math::SparseMatrix;
=head1 NAME
Math::SparseMatrix - Provides basic sparse matrix operations such as creation, reading from file, reading transpose from file and writing to file.
=cut
use 5.006;
use strict;
use warnings;
require Exporter;
require Math::SparseVector;
use Math::SparseVector;
our @ISA = qw(Exporter);
# Items to export into callers namespace by default. Note: do not export
# names by default without a very good reason. Use EXPORT_OK instead.
# Do not simply export all your public functions/methods/constants.
# This allows declaration use Math::SparseMatrix ':all';
# If you do not need this, moving things directly into @EXPORT or @EXPORT_OK
# will save memory.
our %EXPORT_TAGS = ( 'all' => [ qw(
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our @EXPORT = qw(
);
our $VERSION = '0.03';
sub new {
my $class = shift;
my $rows = shift;
my $cols = shift;
if (!defined $rows || !defined $cols) {
die "Math::SparseMatrix->new error.\n" .
"USAGE: my \$spmatrix = Math::SparseMatrix->new(\$num_rows, \$num_cols);\n";
}
my $self = {
_rows => $rows,
_cols => $cols,
_nnz => 0,
_data => {}
};
bless $self, $class;
return $self;
}
sub set {
my $self = shift;
my ($row, $col, $val) = @_;
if (!defined $row || !defined $col || !defined $val) {
die "Math::SparseMatrix->set error.\n" .
"USAGE: \$spmatrix->set(\$row, \$col, \$val);\n";
}
if ($row < 1 || $row > $self->{_rows}) {
die "Math::SparseMatrix->set error.\n" .
"Row index out of bounds, must be between 1 and " .
$self->{_rows} . " inclusive.\n";
}
if ($col < 1 || $col > $self->{_cols}) {
die "Math::SparseMatrix->set error.\n" .
"Column index out of bounds, must be between 1 and " .
$self->{_cols} . " inclusive.\n";
}
if ($val == 0) {
die "Math::SparseMatrix->set error.\n" .
"Cannot store zero value in a sparse matrix.\n";
}
if (exists $self->{_data}->{$row}) {
# update the number of non-zero elements in the matrix
$self->{_nnz} -= scalar($self->{_data}->{$row}->keys);
$self->{_data}{$row}->set($col,$val);
$self->{_nnz} += scalar($self->{_data}->{$row}->keys);
} else {
$self->{_data}->{$row} = new Math::SparseVector();
$self->{_data}->{$row}->set($col,$val);
$self->{_nnz}++;
}
}
sub get {
my $self = shift;
my ($row, $col) = @_;
if (!defined $row || !defined $col) {
die "Math::SparseMatrix->get error.\n" .
"USAGE: \$val = \$spmatrix->get(\$row, \$col);\n";
}
if ($row < 1 || $row > $self->{_rows}) {
die "Math::SparseMatrix->get error.\n" .
"Row index out of bounds, must be between 1 and " .
$self->{_rows} . " inclusive.\n";
}
if ($col < 1 || $col > $self->{_cols}) {
die "Math::SparseMatrix->get error.\n" .
"Column index out of bounds, must be between 1 and " .
$self->{_cols} . " inclusive.\n";
}
if (exists $self->{_data}->{$row}) {
return $self->{_data}->{$row}->get($col);
} else {
return 0;
}
}
sub createFromFile {
my $class = shift;
my $infile = shift;
if (!defined $infile) {
die "Math::SparseMatrix->createFromFile error.\n" .
"USAGE: my \$spmatrix = Math::SparseMatrix->createFromFile(\$input_file);\n";
}
if (!-f $infile) {
die "Math::SparseMatrix->createFromFile error.\n" .
"Cannot find file $infile.\n";
}
my $self = {
_rows => 0,
_cols => 0,
_nnz => 0,
_data => {}
};
open(INPUT, "< $infile") or
die "Math::SparseMatrix->createFromFile error.\n" .
"Failed to open sparse matrix input file $infile.\n";
# read the number of rows, columns and the non-zero elements in the
# file
my $line = ;
chomp $line;
my ($rows, $cols, $nnz) = split / +/, $line;
$self->{_rows} = $rows;
$self->{_cols} = $cols;
# DO NOT SET THE NUMBER OF NON-ZEROS, THAT IS MANAGED BY THE set(...)
# function, which is called below
# create a Math::SparseMatrix object
bless $self, $class;
# also do error checks on file integrity
my $lineNum = 0;
my $nnzFound = 0;
while ($line = ) {
chomp $line;
$lineNum++;
if ($lineNum > $rows) {
die "Math::SparseMatrix->createFromFile error.\n".
"Number of rows in $infile is greater than that " .
"mentioned in the file header ($rows).";
}
my @tokens = split / +/, $line;
my $index;
# process the pairs in each line
for ($index = 0; $index < @tokens; $index += 2) {
# the column number of the current pair is the column
# number, and the current line number is the row number
$self->set($lineNum, $tokens[$index], $tokens[$index + 1]);
$nnzFound++;
}
}
if ($nnzFound < $nnz) {
die "Math::SparseMatrix->createFromFile error.\n".
"Number of non-zero elements found in $infile is less than that " .
"mentioned in the file header -- $nnzFound < $nnz.\n";
}
if ($nnzFound > $nnz) {
die "Math::SparseMatrix->createFromFile error.\n".
"Number of non-zero elements found in $infile is greater than that " .
"mentioned in the file header -- $nnzFound > $nnz.\n";
}
# now the transposed matrix is loaded and ready to be returned
return $self;
}
sub createTransposeFromFile {
my $class = shift;
my $infile = shift;
if (!defined $infile) {
die "Math::SparseMatrix->createTransposeFromFile error.\n" .
"USAGE: \$my \$spmatrix = Math::SparseMatrix->createTransposeFromFile(\$input_file)\n";
}
if (!-f $infile) {
die "Math::SparseMatrix->createTransposeFromFile error.\n" .
"Cannot find file $infile.\n";
}
my $self = {
_rows => 0,
_cols => 0,
_nnz => 0,
_data => {}
};
open(INPUT, "< $infile") or
die "Math::SparseMatrix->createTransposeFromFile error.\n" .
"Failed to open sparse matrix input file $infile.\n";
# read the number of rows, columns and the non-zero elements in the
# file
my $line = ;
chomp $line;
my ($rows, $cols, $nnz) = split / +/, $line;
# swap number of rows and columns
$self->{_rows} = $cols;
$self->{_cols} = $rows;
# DO NOT SET THE NUMBER OF NON-ZEROS, THAT IS MANAGED BY THE set(...)
# function, which is called below
# create a Math::SparseMatrix object
bless $self, $class;
# also do error checks on file integrity
my $lineNum = 0;
my $nnzFound = 0;
while ($line = ) {
chomp $line;
$lineNum++;
if ($lineNum > $rows) {
die "Math::SparseMatrix->createTransposeFromFile error.\n".
"Number of columns in $infile is greater than that " .
"mentioned in the file header ($rows).";
}
my @tokens = split / +/, $line;
my $index;
# process the pairs in each line
for ($index = 0; $index < @tokens; $index += 2) {
# the column number of the current pair is the row
# number in the transpose, the current line number is
# the column number in the transpose
$self->set($tokens[$index], $lineNum, $tokens[$index + 1]);
$nnzFound++;
}
}
if ($nnzFound < $nnz) {
die "Math::SparseMatrix->createTransposeFromFile error.\n".
"Number of non-zero elements found in $infile is less than that " .
"mentioned in the file header -- $nnzFound < $nnz.\n";
}
if ($nnzFound > $nnz) {
die "Math::SparseMatrix->createTransposeFromFile error.\n".
"Number of non-zero elements found in $infile is greater than that " .
"mentioned in the file header -- $nnzFound > $nnz.\n";
}
# now the transposed matrix is loaded and ready to be returned
return $self;
}
sub writeToFile {
my $self = shift;
my $outfile = shift;
if (!defined $outfile) {
die "Math::SparseMatrix->writeToFile error.\n" .
"USAGE: \$spmatrix->writeToFile (\$output_file);\n";
}
# write it to the output file
open(OUTPUT, "> $outfile") or
die "Math::SparseMatrix->writeToFile error.\n" .
"Failed to create output file $outfile.\n";
print OUTPUT $self->{_rows} . " " . $self->{_cols} . " " .
$self->{_nnz} . "\n";
my $row;
my $linecount = 1;
foreach $row (sort {$a <=> $b} keys %{$self->{_data}}) {
if ($row > $linecount) {
# add empty lines for empty rows
my $i = 0;
my $limit = $row - $linecount;
for ($i = 0; $i < $limit; $i++) {
print OUTPUT "\n";
$linecount++;
}
}
my $vec = $self->{_data}->{$row};
my $line = $vec->stringify();
print OUTPUT $line . "\n";
$linecount++;
}
close OUTPUT;
}
sub printDims {
my $self = shift;
print "Rows: " . $self->{_rows} . ". Cols: " . $self->{_cols} . ".\n";
}
1;
__END__
=head1 DESCRIPTION
Math::SparseMatrix provides simple sparse matrix functionality such as
creation of sparse matrices, writing them out to a file, reading matrices from
files and reading transpose of a matrix stored in a file.
=head1 SYNOPSIS
=over
=item 1. To begin with, Math::SparseMatrix should be included in your Perl program as follows:
# include this module for use in your program
use Math::SparseMatrix;
=item 2. To create an empty sparse matrix object with the required dimensions, use the following constructor:
# create a new sparse matrix with 10 rows and 15 columns
my $spmatrix = Math::SparseMatrix->new(10, 15);
=item 3. To update the values in the sparse matrix, use the "set" function as follows:
# set the value at row 5, column 3 to 10
$spmatrix->set(5, 3, 10);
=item 4. To retrieve a stored value, use the "get" function as follows:
# get the value at row 6, column 5 if present, or zero
$val = $spmatrix->get(6, 5);
=item 5. A sparse matrix can be written out to a file in the supported format (explained below) as follows:
# write out the sparse matrix to the file "matrix.txt"
$spmatrix->writeToFile("matrix.txt");
=item 6. A new sparse matrix object can be created from a file in the supported format as follows:
# create a matrix object by reading the file "matrix.txt"
my $spmatrix = Math::SparseMatrix->createFromFile("matrix.txt");
=item 7. A new sparse matrix that is the transpose of the matrix stored in the given input file can be created as follows:
# create the transpose of the matrix stored in "matrix.txt"
my $spmatrix = Math::SparseMatrix->createTransposeFromFile("matrix.txt");
=item 8. Finally, to generate the transpose of a matrix stored in a file, read the transpose as in #7 above and write out the read transpose to a new file as in #5 above.
# create the transpose of the matrix stored in "matrix.txt"
my $spmatrix = Math::SparseMatrix->createTransposeFromFile("matrix.txt");
# write out the created transpose to another file "transpose.txt"
$spmatrix->writeToFile("transpose.txt");
=back
=head1 SPARSE DATA FORMAT
The sparse matrix file format that Math::SparseMatrix expects is described
below with an example.
The first line (or the header line) of the file should contain 3 number
separated by a single space.
The first number is the number of rows in the sparse matrix, the second
number is the number of columns and the third number is the number of non-zero
elements present in the stored matrix.
Each subsequent line represents one row of the sparse matrix, therefore there
should be as many number of lines after the header line as the number of rows
mentioned in the header line. In every line representing a row, there should
be as many pairs of numbers as the number of non-zero elements in that row.
The first number in the pair represents the column number of the non-zero
element (column numbers start with 1). The row number is implicitly provided
by the line
number in the file. The second number in the pair is the actual non-zero
matrix element. Numbers in a pair and multiple pairs should all be separated
by single spaces. If a row does not contain any non-zero element, then an
empty line should be present in the file.
NOTE: There should be no empty lines except those representing empty rows,
neither should there be any comment lines. Commenting is not supported.
Consider the sparse matrix of 5 rows and 4 columns below:
10 0 0 0
0 0 6 8
0 0 0 0
0 21 0 0
7 0 0 9
The sparse file representation for the same is:
5 4 6
1 10
3 6 4 8
2 21
1 7 4 9
Notice the empty line in between for the third row.
=head1 SEE ALSO
Math::SparseVector
=head1 AUTHORS
Ted Pedersen, University of Minnesota, Duluth.
tpederse at d.umn.edu
Mahesh Joshi, Carnegie-Mellon University
maheshj @ cmu.edu
=head1 COPYRIGHT
Copyright (c) 2006-2008, Ted Pedersen and Mahesh Joshi
This program is free software; you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation; either version 2 of the License, or (at your option) any later
version.
This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with
this program; if not, write to
The Free Software Foundation, Inc.,
59 Temple Place - Suite 330,
Boston, MA 02111-1307, USA.
=cut
Math-SparseMatrix-0.03/CHANGES 0100644 0124673 0000157 00000000645 10776234764 014454 0 ustar tpederse Revision history for Perl extension Math::SparseMatrix.
0.03 Sun Apr 06, 2008
- remove garbage Math-SparseMatrix-0.02 directory
0.02 Mon Mar 24, 2008
- relax Perl requirements to 5.6.2
- update Makefile.PL to better support META.yml
- modified SparseMatrix.pm so README can be generated from it
0.01 Sun Jun 18 18:54:21 2006
- original version; created by h2xs 1.23 with options
-AXc -n Math::SparseMatrix
Math-SparseMatrix-0.03/MANIFEST 0100644 0124673 0000157 00000000175 10776235020 014572 0 ustar tpederse CHANGES
INSTALL.pod
lib/Math/SparseMatrix.pm
Makefile.PL
MANIFEST This list of files
META.yml
README
t/Math-SparseMatrix.t
Math-SparseMatrix-0.03/INSTALL.pod 0100644 0124673 0000157 00000003527 10772025650 015261 0 ustar tpederse =head1 NAME
INSTALL Installation instructions for Math::SparseMatrix
=head1 DEPENDENCIES
This module requires these other modules and libraries:
Math::SparseVector
=head1 SYNOPSIS
To install this module type the following:
perl Makefile.PL
make
make test
make install
The exact location of where Math::SparseMatrix will be installed depends
on your system configuration.
If you do not have authority to write into system directories, you can
install Math::SparseMatrix in a local directory that you own and have
permissions to read and write into as follows:
perl Makefile.PL PREFIX=/YOUR/DIR
make
make test
make install
This will install the module into
/YOUR/DIR/lib/perl5/site_perl/Math/SparseMatrix.pm
If you install Math::SparseMatrix in a local directory, you will have to
explicitly set your PERL5LIB environment variable to include:
/YOUR/DIR/lib/perl5/site_perl
if this directory was not already included.
=head1 Authors
Ted Pedersen, University of Minnesota, Duluth.
tpederse at d.umn.edu
Mahesh Joshi, Carnegie Mellon University
maheshj at cmu.edu
=head1 COPYRIGHT
Copyright (c) 2006-2008, Ted Pedersen and Mahesh Joshi
This program is free software; you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation; either version 2 of the License, or (at your option) any later
version.
This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with
this program; if not, write to
The Free Software Foundation, Inc.,
59 Temple Place - Suite 330,
Boston, MA 02111-1307, USA.
Math-SparseMatrix-0.03/t/ 0040755 0124673 0000157 00000000000 10776235034 013711 5 ustar tpederse Math-SparseMatrix-0.03/t/Math-SparseMatrix.t 0100644 0124673 0000157 00000003060 10451243255 017375 0 ustar tpederse # Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl Math-SparseMatrix.t'
#########################
use Test::More tests => 45;
require_ok('Math::SparseVector');
BEGIN { use_ok('Math::SparseMatrix') };
require_ok('Math::SparseMatrix');
#########################
#########################
# creation
$spmatrix = Math::SparseMatrix->new(5, 10);
isa_ok($spmatrix, 'Math::SparseMatrix');
#########################
# get / set
$spmatrix->set(5, 4, 25);
cmp_ok($spmatrix->get(5, 4), '==', 25, 'test get/set');
#########################
# saving to file / reading back
$spmatrix1 = Math::SparseMatrix->new(5, 4);
$spmatrix1->set(1,2,3);
$spmatrix1->set(2,3,5);
$spmatrix1->set(3,1,1);
$spmatrix1->set(4,4,7);
$spmatrix1->set(5,3,25);
$spmatrix1->writeToFile("test.mat");
$spmatrix2 = Math::SparseMatrix->createFromFile("test.mat");
for ($i = 1; $i < 6; $i++) {
for ($j = 1; $j < 5; $j++) {
cmp_ok($spmatrix1->get($i,$j), '==',$spmatrix2->get($i,$j), 'test saving and reading back from file');
}
}
#########################
# reading transpose
$spmatrix3 = Math::SparseMatrix->new(4, 5);
$spmatrix3->set(1,3,1);
$spmatrix3->set(2,1,3);
$spmatrix3->set(3,2,5);
$spmatrix3->set(3,5,25);
$spmatrix3->set(4,4,7);
$spmatrix4 = Math::SparseMatrix->createTransposeFromFile("test.mat");
for ($i = 1; $i < 5; $i++) {
for ($j = 1; $j < 6; $j++) {
cmp_ok($spmatrix3->get($i,$j), '==', $spmatrix4->get($i,$j), 'test saving and reading back from file');
}
}
unlink("test.mat");
Math-SparseMatrix-0.03/META.yml 0100644 0124673 0000157 00000001107 10776235034 014713 0 ustar tpederse --- #YAML:1.0
name: Math-SparseMatrix
version: 0.03
abstract: Provides basic sparse matrix operations such as creation, reading from file, reading transpose from file and writing to file.
license: gpl
author:
- Ted Pedersen ; Mahesh Joshi
generated_by: ExtUtils::MakeMaker version 6.44
distribution_type: module
requires:
Math::SparseVector: 0.01
meta-spec:
url: http://module-build.sourceforge.net/META-spec-v1.3.html
version: 1.3
Math-SparseMatrix-0.03/README 0100644 0124673 0000157 00000012050 10772025423 014314 0 ustar tpederse NAME
Math::SparseMatrix - Provides basic sparse matrix operations such as
creation, reading from file, reading transpose from file and writing to
file.
DESCRIPTION
Math::SparseMatrix provides simple sparse matrix functionality such as
creation of sparse matrices, writing them out to a file, reading
matrices from files and reading transpose of a matrix stored in a file.
SYNOPSIS
1. To begin with, Math::SparseMatrix should be included in your Perl
program as follows:
# include this module for use in your program
use Math::SparseMatrix;
2. To create an empty sparse matrix object with the required dimensions,
use the following constructor:
# create a new sparse matrix with 10 rows and 15 columns
my $spmatrix = Math::SparseMatrix->new(10, 15);
3. To update the values in the sparse matrix, use the "set" function as
follows:
# set the value at row 5, column 3 to 10
$spmatrix->set(5, 3, 10);
4. To retrieve a stored value, use the "get" function as follows:
# get the value at row 6, column 5 if present, or zero
$val = $spmatrix->get(6, 5);
5. A sparse matrix can be written out to a file in the supported format
(explained below) as follows:
# write out the sparse matrix to the file "matrix.txt"
$spmatrix->writeToFile("matrix.txt");
6. A new sparse matrix object can be created from a file in the
supported format as follows:
# create a matrix object by reading the file "matrix.txt"
my $spmatrix = Math::SparseMatrix->createFromFile("matrix.txt");
7. A new sparse matrix that is the transpose of the matrix stored in the
given input file can be created as follows:
# create the transpose of the matrix stored in "matrix.txt"
my $spmatrix = Math::SparseMatrix->createTransposeFromFile("matrix.txt");
8. Finally, to generate the transpose of a matrix stored in a file, read
the transpose as in #7 above and write out the read transpose to a new
file as in #5 above.
# create the transpose of the matrix stored in "matrix.txt"
my $spmatrix = Math::SparseMatrix->createTransposeFromFile("matrix.txt");
# write out the created transpose to another file "transpose.txt"
$spmatrix->writeToFile("transpose.txt");
SPARSE DATA FORMAT
The sparse matrix file format that Math::SparseMatrix expects is
described below with an example.
The first line (or the header line) of the file should contain 3 number
separated by a single space. The first number is the number of rows in
the sparse matrix, the second number is the number of columns and the
third number is the number of non-zero elements present in the stored
matrix.
Each subsequent line represents one row of the sparse matrix, therefore
there should be as many number of lines after the header line as the
number of rows mentioned in the header line. In every line representing
a row, there should be as many pairs of numbers as the number of
non-zero elements in that row. The first number in the pair represents
the column number of the non-zero element (column numbers start with 1).
The row number is implicitly provided by the line number in the file.
The second number in the pair is the actual non-zero matrix element.
Numbers in a pair and multiple pairs should all be separated by single
spaces. If a row does not contain any non-zero element, then an empty
line should be present in the file.
NOTE: There should be no empty lines except those representing empty
rows, neither should there be any comment lines. Commenting is not
supported.
Consider the sparse matrix of 5 rows and 4 columns below:
10 0 0 0
0 0 6 8
0 0 0 0
0 21 0 0
7 0 0 9
The sparse file representation for the same is:
5 4 6
1 10
3 6 4 8
2 21
1 7 4 9
Notice the empty line in between for the third row.
SEE ALSO
Math::SparseVector
AUTHORS
Ted Pedersen, University of Minnesota, Duluth. tpederse at d.umn.edu
Mahesh Joshi, Carnegie-Mellon University maheshj @ cmu.edu
COPYRIGHT
Copyright (c) 2006-2008, Ted Pedersen and Mahesh Joshi
This program is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the
Free Software Foundation; either version 2 of the License, or (at your
option) any later version.
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to
The Free Software Foundation, Inc.,
59 Temple Place - Suite 330,
Boston, MA 02111-1307, USA.
Math-SparseMatrix-0.03/Makefile.PL 0100644 0124673 0000157 00000001575 10772006462 015422 0 ustar tpederse use 5.006;
use ExtUtils::MakeMaker;
# See lib/ExtUtils/MakeMaker.pm for details of how to influence
# the contents of the Makefile that is written.
WriteMakefile(
NAME => 'Math::SparseMatrix',
VERSION_FROM => 'lib/Math/SparseMatrix.pm', # finds $VERSION
PREREQ_PM => {Math::SparseVector => 0.01}, # e.g., Module::Name => 1.1
($] >= 5.005 ? ## Add these new keywords supported since 5.005
(ABSTRACT_FROM => 'lib/Math/SparseMatrix.pm', # retrieve abstract from module
AUTHOR => 'Ted Pedersen ; Mahesh Joshi ') : ()),
# allows make dist to create .tar.gz with correct name/version
'dist' => {'COMPRESS' => 'gzip -9f', 'SUFFIX' => 'gz'},
# allows for automatic creation of META.yml
($ExtUtils::MakeMaker::VERSION ge '6.30_00'?
('LICENSE' => 'gpl', ) : ()),
);