#!/usr/bin/perl

use strict; use warnings;
use File::Basename qw(basename);
use Data::Dump qw(dump);

use NEURO4 qw(populate check_subj load_project print_help check_or_make get_subjects get_list);

my $attach = 0;
my $cfile;

@ARGV = ("-h") unless @ARGV;
while (@ARGV and $ARGV[0] =~ /^-/) {
    $_ = shift;
    last if /^--$/;
    if (/^-a/) { $attach = 1;}
    if (/^-cut/) { $cfile = shift; chomp($cfile);}
    if (/^-h/) { print_help $ENV{'PIPEDIR'}.'/doc/recon.hlp'; exit;}
}

my $study = shift;
unless ($study) { print_help $ENV{'PIPEDIR'}.'/doc/recon.hlp'; exit;}
my $debug = 1;
my $stage = "-autorecon-all";
my %std = load_project($study);
my $data_dir=$std{'DATA'};
my $mri_db = $std{'DATA'}.'/'.$study.'_mri.csv';
my $bids_path = $std{'DATA'}.'/bids';
#open debug file
my $logfile = "$std{'DATA'}/.debug.controlled.log";
$debug ? open DBG, ">$logfile" :0;
#open slurm file
my $orderfile = "$std{'DATA'}/mri_orders.sh";
my $conffile = "$std{'DATA'}/mri_orders.conf";
my $outdir = "$std{'DATA'}/slurm";
check_or_make($outdir);

#get subjects from database or file
my @plist;
my @iplist = get_subjects($mri_db);

if ($cfile){
        my @cuts = get_list($data_dir."/".$cfile);
        foreach my $cut (sort @cuts){
                if(grep {/$cut/} @iplist){
                        push @plist, $cut;
                }
        }
}else{
        @plist = @iplist;
}
foreach my $pkey (sort @plist){
        my $subj = $study."_".$pkey;
        my %nifti = check_subj($std{'DATA'},$subj);
        if($nifti{'T1w'}){
                my $order;
                if($nifti{'T2w'}){
                        $order = "recon-all ".$stage." -i ".$nifti{'T1w'}." -T2 ".$nifti{'T2w'}." -subjid ".$subj;
                }else{
                        $order = "recon-all ".$stage." -i ".$nifti{'T1w'}." -subjid ".$subj;
                }
                my $orderfile = $outdir.'/'.$subj.'fs_orders.sh';
                open ORD, ">$orderfile";
                print ORD '#!/bin/bash'."\n";
                print ORD '#SBATCH -J fs_recon_'.$study."\n";
                print ORD '#SBATCH --time=48:0:0'."\n"; #si no ha terminado en X horas matalo
                print ORD '#SBATCH --mail-type=FAIL,TIME_LIMIT,STAGE_OUT'."\n"; #no quieres que te mande email de todo
                print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";
                print ORD '#SBATCH -p fast'."\n";
                print ORD '#SBATCH -o '.$outdir.'/fs_recon-slurm-'.$subj.'-%j'."\n";
                print ORD "srun $order\n";
                close ORD;
                system("sbatch $orderfile");
        }
}

$debug ? close DBG:0;
$orderfile = $outdir.'/fs_recon_end.sh';
open ORD, ">$orderfile";
print ORD '#!/bin/bash'."\n";
print ORD '#SBATCH -J fs_recon_'.$study."\n";
print ORD '#SBATCH --mail-type=END'."\n"; #email cuando termine
print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";
print ORD '#SBATCH -o '.$outdir.'/fs_recon_end-%j'."\n";
print ORD ":\n";
close ORD;
my $order = 'sbatch --dependency=singleton '.$orderfile;
exec($order);