#!/usr/bin/perl
# Copyright 2019 O. Sotolongo <asqwerty@gmail.com>
use strict; use warnings;
 
use File::Find::Rule;
use NEURO qw(print_help get_pair load_study achtung shit_done get_lut check_or_make centiloid_fbb);
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 $ENV{'PIPEDIR'}.'/doc/pet_metrics.hlp'; exit;}
my %std = load_study($study);
my $w_dir=$std{'WORKING'};
my $data_dir=$std{'DATA'};
my $outdir = "$std{'DATA'}/slurm";
check_or_make($outdir);
our %subjects;

my @plist = find(file => 'name' => "*_fbb.nii.gz", '!name' => "*tmp*", in => $w_dir);
my $ofile = $data_dir."/".$study."_fbb_cl.csv";
my $patt = '([A-Z,a-z]{1,4})(\d{1,6})_fbb';

my @pets;

if ($cfile){
	my %cuts = get_pair($data_dir."/".$cfile);
	foreach my $cut (keys %cuts){
		if(grep {/$cut/} @plist){
			$pets[$cut] = $plist[$cut];
		}
	}
}else{
	@pets = @plist;
}


foreach my $pet (sort @pets){   
    (my $dg,my $subject) = $pet =~ /$patt/;
    if($subject){
		$subjects{$subject}{'dg'} = $dg;
		$subjects{$subject}{'pet'} = $pet;
	}
}

foreach my $subject (sort keys %subjects){
	my $norm;
	my $dg = $subjects{$subject}{'dg'};
	my $subj = $dg.$subject;
	#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, ">$orderfile";
	print ORD '#!/bin/bash'."\n";
	print ORD '#SBATCH -J fbb2std_'.$study."\n";
	print ORD '#SBATCH --time=4:0:0'."\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='."$ENV{'USER'}\n";
	print ORD '#SBATCH -o '.$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 fbb2std_'.$study."\n";
print ORD '#SBATCH --time=24:0:0'."\n"; #si no ha terminado en X horas matalo
print ORD '#SBATCH --mail-type=FAIL,END'."\n"; #email cuando termine o falle
print ORD '#SBATCH --mail-user='."$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);