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lib/Algorithm/LinearManifoldDataClusterer.pm  view on Meta::CPAN

package Algorithm::LinearManifoldDataClusterer;

#------------------------------------------------------------------------------------
# Copyright (c) 2015 Avinash Kak. All rights reserved.  This program is free
# software.  You may modify and/or distribute it under the same terms as Perl itself.
# This copyright notice must remain attached to the file.
#
# Algorithm::LinearManifoldDataClusterer is a Perl module for clustering data that
# resides on a low-dimensional manifold in a high-dimensional measurement space.
# -----------------------------------------------------------------------------------

use 5.10.0;
use strict;
use warnings;
use Carp;
use List::Util qw(reduce any);
use File::Basename;
use Math::Random;
use Graphics::GnuplotIF;
use Math::GSL::Matrix;
use POSIX (); 

our $VERSION = '1.01';

# Constructor:
sub new { 
    my ($class, %args) = @_;
    my @params = keys %args;
    croak "\nYou have used a wrong name for a keyword argument " .
          "--- perhaps a misspelling\n" 
          if check_for_illegal_params(@params) == 0;
    bless {
        _datafile                     =>   $args{datafile} || croak("datafile required"),
        _mask                         =>   $args{mask}     || croak("mask required"),
        _K                            =>   $args{K}        || 0,
        _P                            =>   $args{P}        || 0,
        _terminal_output              =>   $args{terminal_output} || 0,
        _max_iterations               =>   $args{max_iterations} || 0,
        _delta_reconstruction_error   =>   $args{delta_reconstruction_error} || 0.001,
        _delta_normalized_error       =>   undef,
        _cluster_search_multiplier    =>   $args{cluster_search_multiplier} || 1,
        _visualize_each_iteration     =>   $args{visualize_each_iteration} == 0 ? 0 : 1,
        _show_hidden_in_3D_plots      =>   $args{show_hidden_in_3D_plots} == 0 ? 0 : 1,
        _make_png_for_each_iteration  =>   $args{make_png_for_each_iteration} == 0 ? 0 : 1,
        _debug                        =>   $args{debug} || 0,
        _N                            =>   0,
        _KM                           =>   $args{K} * $args{cluster_search_multiplier},
        _data_hash                    =>   {},
        _data_tags                    =>   [],
        _data_dimensions              =>   0,
        _final_clusters               =>   [],
        _auto_retry_flag              =>   0,
        _num_iterations_actually_used =>   undef,
        _scale_factor                 =>   undef,
        _data_tags_to_cluster_label_hash  => {},
        _final_reference_vecs_for_all_subspaces => [],
        _reconstruction_error_as_a_function_of_iteration => [],
        _final_trailing_eigenvec_matrices_for_all_subspaces => [],
        _subspace_construction_error_as_a_function_of_iteration => [],
    }, $class;
}

sub get_data_from_csv {
    my $self = shift;
    my $filename = $self->{_datafile} || die "you did not specify a file with the data to be clustered";
    my $mask = $self->{_mask};