#!/usr/bin/perl

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

my $study = "mopead";
my %std = load_study($study);

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'}.'/mopead.csv';
my @other_exts = ("nii.gz","json");

#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){
	my $order = 'for x in `find '.$src_dir.'/'.$guy.' -type f`; do if [[ `dckey -k "SeriesDescription" $x 2>&1 | grep ep2d_bold_p2_resting_state` ]]; then dirname $x; fi; done | uniq > '.$std{'DATA'}.'/tmp/tmp_list.dirs; for x in `cat '.$std{'DATA'}.'/tmp/tmp_list.dirs`; do dcm2niix -z y -o '.$std{'DATA'}.'/tmp $x; done; rm '.$std{'DATA'}.'/tmp/tmp_list.dirs';
	print "$order\n";
	system($order);
	my @conv_files = find(file => 'name' => "*.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/;
				$order = sprintf "mv %s %s/fmri/mop%04ds0012.%s", $file_name, $std{'DATA'}, $idsinfo{$guy}, $ext;
				print "$order\n";
				system($order);
			}			
		}
	}
	print "Cleaning house\n";
	$order = "rm $std{'DATA'}/tmp/*";
	system($order);
	#Convierto las imagenes para corregir (A>>P y P>>A)
	print "Getting A>>P\n";
	$order = 'for x in `find '.$src_dir.'/'.$guy.' -type f`; do if [[ `dckey -k "SeriesDescription" $x 2>&1 | grep ep2d_fid_basic_bold_p2_AP` ]]; then dcm2niix -z y -o '.$std{'DATA'}.'/tmp $x; fi;done';
	system($order);
	$order = sprintf "mv %s/tmp/*.nii.gz %s/fmri/mop%04d_a2p.nii.gz", $std{'DATA'}, $std{'DATA'}, $idsinfo{$guy};
	print "$order\n";
        system($order);
	print "Getting P>>A\n";                                                                       
        $order = 'for x in `find '.$src_dir.'/'.$guy.' -type f`; do if [[ `dckey -k "SeriesDescription" $x 2>&1 | grep ep2d_fid_basic_bold_p2_PA` ]]; then dcm2niix -z y -o '.$std{'DATA'}.'/tmp $x; fi;done';
	system($order);
        $order = sprintf "mv %s/tmp/*.nii.gz %s/fmri/mop%04d_p2a.nii.gz", $std{'DATA'}, $std{'DATA'}, $idsinfo{$guy};                                                                                       
        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;