#!/usr/bin/perl

use strict; use warnings;
use NEURO qw(load_study);
use File::Find::Rule;
use Data::Dump qw(dump);

my $study = "bioface";
my %std = load_study($study);
#unless ($itype) {$itype='t1';}
#my %dtype = ("t1" => "mri", );
my $src_dir = '/nas/bioface_raw';
#my $raw_dir = $std{'DATA'}.'/raw';
my $conv_file = $std{'DATA'}.'/converted_dti.csv';
my $ids_file = $std{'DATA'}.'/ids.csv';
my $names_file =$std{'DATA'}.'/ni_names.csv';
my $proj_file = $std{'DATA'}.'/bioface.csv';
my @other_exts = ("nii.gz","bval","bvec","json");
my @b0_exts = ("nii.gz","json");
my $tag = "DTIep2d_diff_mddw_48dir_p3_AP";
my $b0_tag = "DTIep2d_diff_mddw_4b0_PA";
#Leo la DB
my %idsinfo;
open IDS, "<$ids_file" or die $!;
while(<IDS>){
        chomp;
        my ($key, $value) = split(/,\s?/);
        $idsinfo{$key} = $value;
}
close IDS;
#Leo los que ya he descomprimido
my @orig_str = qx/ls $src_dir/;
chomp @orig_str;
#Leo los que se han convertido
my @conv_str;
open CONV, "<$conv_file" or die $!;
chomp (@conv_str = <CONV>);
close CONV;
#Y a ver cuantos faltan por convertir!
my %conv_str = map { $_ => 1 } @conv_str;
my @not_conv = grep !$conv_str{$_}, @orig_str;
# y a convertirlos!
foreach my $guy (@not_conv){
        if(exists($idsinfo{$guy})){
#DTIep2d_diff_mddw_48dir_p3_AP
                my $order = 'dcm2niix -z i -b y -o '.$std{'DATA'}.'/tmp/ '.$src_dir.'/'.$guy;
                print "$order\n";
                system($order);
                my @conv_files = find(file => 'name' => "*$tag*.nii.gz", in => $std{'DATA'}.'/tmp/');
                #dump @conv_files;
                foreach my $nii_file (@conv_files){
                        $order = 'fslinfo '.$nii_file;
                        my %xinfo;
                        foreach (qx/$order/){
                                my ( $key, $value ) = /(\S+)\s+(\S+)\s*.*/;
                                $xinfo{$key} =$value;
                        }
                        if($xinfo{"dim4"}>1){
                                print "Choosing and moving files\n";
                                my $file_name = $nii_file;
                                foreach my $ext (@other_exts){
                                        ($file_name = $nii_file) =~ s/nii.gz$/$ext/;
                                        if (-e $file_name) {
                                                $order = sprintf "mv \"%s\" %s/dti/bfa%04ds0020.%s", $file_name, $std{'DATA'}, $idsinfo{$guy}, $ext;
                                                print "$order\n";
                                                system($order);
                                        }
                                }
                        }
                }
                   print "Getting P>>A B0\n";
#DTIep2d_diff_mddw_4b0_PA
                @conv_files = find(file => 'name' => "*$b0_tag*.nii.gz", in => $std{'DATA'}.'/tmp/');
                foreach my $nii_file (@conv_files){
                        foreach my $ext (@b0_exts){
                                (my $file_name = $nii_file) =~ s/nii.gz$/$ext/;
                                $order = sprintf "mv \"%s\" %s/dti/bfa%04d_p2a_b0.%s", $file_name, $std{'DATA'}, $idsinfo{$guy}, $ext;
                                print "$order\n";
                                system($order);
                        }
                }
                print "Cleaning house\n";
                $order = "rm $std{'DATA'}/tmp/*";
                system($order);
        }
}


#actualizo los convertidos
push(@conv_str, @not_conv);
open CONV, ">$conv_file" or die $!;
print CONV "$_\n" foreach @conv_str;
close CONV;