#!/usr/bin/perl

use strict; use warnings;
use Data::Dump qw(dump);
use File::Find::Rule;
use File::Copy::Recursive qw(dirmove);

use NEURO qw(populate check_subj load_study print_help get_petdata get_pair achtung shit_done check_or_make);

#my $study;
my $cfile;
my $sok = 0;

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

my %std = load_study($study);

my $subj_dir = $ENV{'SUBJECTS_DIR'};

#Run this script ONLY on "Detritus"
#or change the paths to the correct ones

my $w_dir=$std{'WORKING'};
#my $pet_dir = $spect?$std{'SPECT'}:$std{'PET-FDG'};
my $pet_dir = $std{'PET-FBB'};
#my $petnc_dir = $std{'FBB-NC'};
my $db = $std{'DATABASE'};
my $data_dir=$std{'DATA'};
my $outdir = "$std{'DATA'}/slurm";
check_or_make($outdir);

my %plist = populate($db);
my @ok_pets;

print "Collecting needed files\n";
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;
}

my $err_file = $data_dir."/.fbb_errors.debug";
open ERRF, ">$err_file" or die "Could not open error file!";

foreach my $subject (sort keys %pets){
	my @names = find(file => 'name' => "$pets{$subject}$subject*", '!name' => '*_*', 'name' => '*.nii.gz', in => $pet_dir);	
	dump @names;
	if(@names){
		my @mri = find(file => 'name' => "brain.mgz", in => $subj_dir."/".$study."_".$pets{$subject}.$subject."/mri");
		if(@mri){
			push @ok_pets, $subject;
		}else{
			print ERRF "Subject $subject has no MRI brain extracted!!!\n";
		}
	}		
}

foreach my $subject (@ok_pets){
	#my @mri = find(file => 'name' => $pets{$subject}.$subject."_brain.nii.gz", in => "$w_dir/");
	my $orderfile = $outdir.'/'.$subject.'_get_subj.sh';
	my $order = $ENV{'PIPEDIR'}."/bin/get_fs_subj.sh ".$study." ".$pets{$subject}.$subject." ".$w_dir;
	open ORD, ">$orderfile";
	print ORD '#!/bin/bash'."\n";
	print ORD '#SBATCH -J fbb_correct_'.$study."\n";
	print ORD '#SBATCH --time=1:0:0'."\n"; #si no ha terminado en X horas matalo
	print ORD '#SBATCH --mail-type=FAIL,STAGE_OUT'."\n"; #no quieres que te mande email de todo
	print ORD '#SBATCH -o '.$outdir.'/fbb_get_subj-%j'."\n";
	print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";
	print ORD "srun $order\n";
	close ORD;
	my $jobid = `sbatch $orderfile`;
	$jobid = ( split ' ', $jobid )[ -1 ];
	$order = $ENV{'PIPEDIR'}."/bin/fbbtemp_reg.sh ".$study." ".$pets{$subject}.$subject." ".$pet_dir." ".$w_dir;
	$orderfile = $outdir.'/'.$subject.'_fbb_reg.sh';
	open ORD, ">$orderfile";
	print ORD '#!/bin/bash'."\n";
	print ORD '#SBATCH -J fbb_correct_'.$study."\n";
	print ORD '#SBATCH --time=1:0:0'."\n"; #si no ha terminado en X horas matalo
	print ORD '#SBATCH --mail-type=FAIL,STAGE_OUT'."\n"; #no quieres que te mande email de todo
	print ORD '#SBATCH -o '.$outdir.'/fbb_reg-%j'."\n";
	print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";
	print ORD "srun $order\n";
	close ORD;
	my $xorder = 'sbatch --depend=afterok:'.$jobid.' '.$orderfile;
	system("$xorder");
}

my $order = $ENV{'PIPEDIR'}."/bin/make_fbb_report.pl ".$study;
my $orderfile = $outdir.'/fbb_report.sh';
open ORD, ">$orderfile";
print ORD '#!/bin/bash'."\n";
print ORD '#SBATCH -J fbb_correct_'.$study."\n";
print ORD '#SBATCH --time=2:0:0'."\n"; #si no ha terminado en X horas matalo
print ORD '#SBATCH --mail-type=FAIL,END'."\n"; #email cuando termine o falle
print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";
print ORD '#SBATCH -o '.$outdir.'/fbb_rep-%j'."\n";
print ORD "srun $order\n";
close ORD;
my $xorder = 'sbatch --dependency=singleton'.' '.$orderfile;
exec($xorder);