#!/usr/bin/perl
# Copyright 2019 O. Sotolongo <asqwerty@gmail.com>
use strict; use warnings;

use File::Find::Rule;
use NEURO4 qw(print_help load_project check_or_make centiloid_fbb cut_shit);
use Data::Dump qw(dump);
use File::Remove 'remove';
use File::Basename qw(basename);

my $wcut = 0;
my $cfile="";

@ARGV = ("-h") unless @ARGV;

while (@ARGV and $ARGV[0] =~ /^-/) {
    $_ = shift;
    last if /^--$/;
    if (/^-cut/) { $cfile = shift; chomp($cfile); $wcut = 1;}
    if (/^-h$/) { print_help $ENV{'PIPEDIR'}.'/doc/pet_metrics.hlp'; exit;}
}
 
my $study = shift;
unless ($study) { print_help $ENV{'PIPEDIR'}.'/doc/pet_metrics.hlp'; exit;}
my %std = load_project($study);
my $w_dir=$std{'WORKING'};
my $data_dir=$std{'DATA'};
my $db = $data_dir.'/'.$study.'_pet.csv';
my $outdir = "$std{'DATA'}/slurm";
check_or_make($outdir);
our @subjects = cut_shit($db, $data_dir."/".$cfile);

my $ofile = $data_dir."/".$study."_fbb_cl.csv";
foreach my $subj (sort @subjects){
        #Making sbatch scripts
        # Get FBB image into MNI space
        my $order = $ENV{'PIPEDIR'}."/bin/fbb2std.sh ".$subj." ".$w_dir;
        my $orderfile = $outdir.'/'.$subj.'_fbb_reg.sh';
        open ORD, ">$orderfile";
        print ORD '#!/bin/bash'."\n";
        print ORD '#SBATCH -J fbb_metrics_'.$study."\n";
        print ORD '#SBATCH --time=4:0:0'."\n"; #si no ha terminado en X horas matalo
        print ORD '#SBATCH -c 8'."\n"; #para limitar el numero de ejecuciones por maquina
        print ORD '#SBATCH --mail-type=FAIL,TIME_LIMIT,STAGE_OUT'."\n"; #no quieres que te mande email de todo
        print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";
        print ORD '#SBATCH -o '.$outdir.'/fbb2std-'.$subj.'-%j'."\n";
        print ORD "srun $order\n";
        close ORD;
        system("sbatch $orderfile");
}
my $order = $ENV{'PIPEDIR'}."/bin/fbb_cl_masks.pl ".$study." ".($wcut?"-cut $cfile":"");
my $orderfile = $outdir.'/fbb_masks.sh';
open ORD, ">$orderfile";
print ORD '#!/bin/bash'."\n";
print ORD '#SBATCH -J fbb_metrics_'.$study."\n";
print ORD '#SBATCH --time=24:0:0'."\n"; #si no ha terminado en X horas matalo
print ORD '#SBATCH --mail-type=FAIL,END'."\n"; #email cuando termine o falle
print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";
print ORD '#SBATCH -o '.$outdir.'/fbbmasks-%j'."\n";
print ORD "srun $order\n";
close ORD;
my $xorder = 'sbatch --dependency=singleton'.' '.$orderfile;
exec($xorder);