use strict;
use warnings;
use feature 'say';
use PDL;

my $x = pdl
[
 [0, 1, 2],
 [3, 4, 5],
 [6, 7, 8],
 [0, 1, 2],
 [0, 1, 2],
 [6, 7, 8],
];

my @index;
my @keys;
my %count;

for ( 0 .. $x-> dim( 1 ) - 1 ) {
    my $ref = $x-> slice( [], $_ )-> get_dataref;
    next if $count{ $$ref } ++;
    push @index, $_;
    push @keys, $$ref;
}

my $uniq   = $x-> dice( 'X', pdl \@index );
my $counts = pdl @count{ @keys };

say $uniq;
say $counts;
say $uniq-> append( $counts-> transpose );

##</code><code>##

>perl pdl180220.pl

[
 [0 1 2]
 [3 4 5]
 [6 7 8]
]

[3 1 2]

[
 [0 1 2 3]
 [3 4 5 1]
 [6 7 8 2]
]