my $input = $ARGV[0];
open(INFILE,"$input") or die "cannot open file $input!\n";
my $output = $ARGV[1];
my %total_hash_keys=();
my %tri_hash = ();
#set bin width
my $grid = 2;
my $step = 0;
my $block_size = 10000;
my $block_no = 0;

my @points;
while(<INFILE>){my @array = split(/\t/,$_); push @points, [@array];} 
close(INFILE);

#construct hash table
for(my $i=0;$i<@points;$i++){
  for(my $j=$i+1;$j<@points;$j++){
    for(my $k=$j+1;$k<@points;$k++){
      $step++;
      my @pt1 = (${$points[$i]}[0],${$points[$i]}[1],${$points[$i]}[2]);
      my @pt2 = (${$points[$j]}[0],${$points[$j]}[1],${$points[$j]}[2]);
      my @pt3 = (${$points[$k]}[0],${$points[$k]}[1],${$points[$k]}[2]; 
 
      #simplified calculation for the value of the hash;
      my @matrix = (@pt1,@pt2,@pt3);
      for(my $res=0;$res<@points;$res++){
        #transform coor, and bin the new coor as a generated key
        my @old_xyz = @{$points[$res]};
        my @new_xyz = transform(@old_xyz,@matrix);
        foreach(@new_xyz){$_ = int($_/$grid); }
        my $key = $new_xyz[0]."_".$new_xyz[1]."_".$new_xyz[2];
        foreach(@matrix){$_ = sprintf "%.3f",$_;}
        my $value = "";
        for(my $temp=0;$temp<@matrix;$temp++){$value .= $matrix[$temp]."_"; } 
        $total_hash_keys{$key}=0;
        push @{$tri_hash{$key}},$value;
      }
      if(($step % $block_size) == 0){#write to disk file
        $block_no = int($step/$block_size);
        my $tmp_hash_file = "tmp_hash".$block_no;
        open(OUTFILE,">$tmp_hash_file") or die "cannot write to file $tmp_hash_file!\n";
        foreach(keys %tri_hash){
          print OUTFILE "$_\t";
          print OUTFILE "@{$tri_hash{$_}}\n";
        }
        %tri_hash = ();#free memory
      }
    }#for k
  }#for j
}#for i

my $total_file_no = int($step/$block_size);

open(OUTFILE,">$output") or die "cannot write to file $output!\n";
while(($my_key,$my_value)=each %total_hash_keys){
  print OUTFILE $my_key."=>";
  for(my $i=1;$i<$total_file_no + 1;$i++){
    my $hash_file = "tmp_hash".$i; open(INFILE,"$hash_file") or die;
    while(<INFILE>){
      my @array = split(/\t/,$_);
      if($array[0] eq $my_key){
        chomp ($array[1]);
        print OUTFILE $array[1];
        last;
       }
     }
     close(INFILE);
   }
   print OUTFILE "\n";
}

sub transform{
        my ($x,$y,$z,@t) = @_;
        my $new_x=$x*$t[0]+$y*$t[3]+$z*$t[6];
        my $new_y=$x*$t[1]+$y*$t[4]+$z*$t[7];
        my $new_z=$x*$t[2]+$y*$t[5]+$z*$t[8];
        return ($new_x,$new_y,$new_z);
}