#!/usr/bin/perl

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

my $study = "mopead";
my $prefix = "mop";
my %std = load_study($study);
#unless ($itype) {$itype='t1';}
#my %dtype = ("t1" => "mri", );
my $src_dir = '/nas/corachan/MOPEAD/';
#my $raw_dir = $std{'DATA'}.'/raw';
my $conv_file = $std{'DATA'}.'/converted_fmri.csv';
my $ids_file = $std{'DATA'}.'/ids.csv';
my $names_file =$std{'DATA'}.'/ni_names.csv';
my $proj_file = $std{'DATA'}.'/'.$study.'.csv';
my @other_exts = ("nii.gz","json");
my $series = 12;
my $tag = "ep2d_bold_p2_resting_state";
my $aptag = "ep2d_fid_basic_bold_p2_AP";
my $patag = "ep2d_fid_basic_bold_p2_PA";
check_or_make("$std{'DATA'}/fmri");
#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!
my @newones;
foreach my $guy (@not_conv){
        if(exists($idsinfo{$guy})){
                my $count = $series;
                my @conv_files = find(file => 'name' => "*$tag*.nii.gz", in => $std{'DATA'}.'/niftis/'.$guy.'/');
                #dump @conv_files;
                foreach my $nii_file (@conv_files){
                        my $order = 'fslval '.$nii_file.' dim4';
                        my $xinfo = qx/$order/;
                        if($xinfo>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/;
                                        $order = sprintf "cp %s %s/%s%04ds%04d.%s", $file_name, $std{'fMRI'}, $prefix, $idsinfo{$guy}, $count, $ext;
                                        print "$order\n";
                                        system($order);
                                }
                        push @newones, $guy;
                        $count++;                       
                        }
                }
                #Convierto lasimagenes para corregir (A>>P y P>>A)
                print "Getting A>>P\n";
                my $count = $series;
                @conv_files = find(file => 'name' => "*$aptag*.nii.gz", in => $std{'DATA'}.'/niftis/'.$guy.'/');
                foreach my $nii_file (@conv_files){
                        foreach my $ext (@other_exts){
                                (my $file_name = $nii_file) =~ s/nii.gz$/$ext/;
                                my $order = sprintf "cp %s %s/%s%04ds%04d_a2p.%s", $file_name, $std{'fMRI'}, $prefix, $idsinfo{$guy}, $count, $ext;
                                print "$order\n";
                                system($order);
                        }
                        $count++;
                }
                print "Getting P>>A\n";
                my $count = $series;
                @conv_files = find(file => 'name' => "*$patag*.nii.gz", in => $std{'DATA'}.'/niftis/'.$guy.'/');
                foreach my $nii_file (@conv_files){
                        foreach my $ext (@other_exts){
                                (my $file_name = $nii_file) =~ s/nii.gz$/$ext/;
                                my $order = sprintf "cp %s %s/%s%04ds%04d_p2a.%s", $file_name, $std{'fMRI'}, $prefix, $idsinfo{$guy}, $count, $ext;
                                print "$order\n";
                                system($order);
                        }
                        $count++;
                }

        }
}

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