#!/usr/bin/perl

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

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

my $study;
my $cfile;
my $debug=1;
my $corr=1;
my $legacy=0;
my $cuda=1;
my $atlas=0; 
my $mode=0;
my $s2t=0;
my $network;
@ARGV = ("-h") unless @ARGV;
while (@ARGV and $ARGV[0] =~ /^-/) {
    $_ = shift;
    last if /^--$/;
    if (/^-cut/) { $cfile = shift; chomp($cfile);}
    if (/^-slow/) {$cuda=0;}
    if (/^-single/) {$mode=1;}
    if (/^-s2t/) {$s2t=1;}
    if (/^-uofm/) {$atlas="uofm"; $network = shift; chomp($network); $network =~ s/\_/\//g;}
    if (/^-h/) { print_help $ENV{'PIPEDIR'}.'/doc/dti_reg.hlp'; exit;}
}
$study = shift;
unless ($study) { print_help $ENV{'PIPEDIR'}.'/doc/dti_reg.hlp'; exit;}

my %std = load_study($study);

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

# Redirect ouput to logfile (do it only when everything is fine)
my $logfile = "$std{'DATA'}/.debug_dti_tracks.log";
open STDOUT, ">$logfile" or die "Can't redirect stdout";
open STDERR, ">&STDOUT" or die "Can't dup stdout";
$debug ? open DBG, ">$logfile" :0;

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

my $w_dir=$std{'WORKING'};
my $dti_dir=$std{'DTI'};
my $mri_dir=$std{'MRI'};
my $db = $std{'DATABASE'};
my $data_dir=$std{'DATA'};

#open slurm file
#my $orderfile = "$std{'DATA'}/dti_track_orders.sh";
#my $conffile = "$std{'DATA'}/dti_track_orders.conf";
my $outdir = "$std{'DATA'}/slurm";
check_or_make($outdir);
#my $jobname = "track_$study";

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

print "Collecting needed files\n";

my %dtis;

if ($cfile){
	my %cuts = get_pair($data_dir."/".$cfile);
	foreach my $cut (keys %cuts){
		if(grep {/$cut/} %plist){
			$dtis{$cut} = $plist{$cut};
		}
	}
}else{
	%dtis = %plist;
}
#open CNF, ">$conffile";
#my $count = 0;
foreach my $subject (sort keys %dtis){
	#Compulsory: el DTI debe haber pasado el preproc
	my $dti_fa = $w_dir.'/'.$dtis{$subject}.$subject.'_dti_FA.nii.gz';
	print "$dti_fa\n";
	#Compulsory: Necesito tambien la segmentacion de freesurfer de este pollo
	my $aseg = $subj_dir.'/'.$study.'_'.$dtis{$subject}.$subject.'/mri/aseg.mgz';
	print "$aseg\n";
	if((-e $dti_fa) && (-e $aseg)){
		my $order;
		unless($atlas){
			if($cuda){
				if($s2t){
					$order = $pipe_dir."/bin/dti_bedtrack_seek.sh ".$study." ".$dtis{$subject}.$subject." ".$w_dir;
				}else{
					#$order = $count."\t".$pipe_dir."/bin/dti_bedtrack_cuda.sh ".$study." ".$dtis{$subject}.$subject." ".$w_dir;
					$order = $pipe_dir."/bin/dti_bedtrack_cuda.sh ".$study." ".$dtis{$subject}.$subject." ".$w_dir." ".$mode;
				}else{
					#$order = $count."\t".$pipe_dir."/bin/dti_bedtrack.sh ".$study." ".$dtis{$subject}.$subject." ".$w_dir;
					$order = $pipe_dir."/bin/dti_bedtrack.sh ".$study." ".$dtis{$subject}.$subject." ".$w_dir." ".$mode;
				}
			}
		}else{
			if($s2t){
				$order = $pipe_dir."/bin/dti_bedtrack_seek.sh ".$study." ".$dtis{$subject}.$subject." ".$w_dir." ".$pipe_dir."/lib/".$atlas;
			}else{
				$order = $pipe_dir."/bin/dti_bedtrack_nodes.sh ".$study." ".$dtis{$subject}.$subject." ".$w_dir." ".$pipe_dir."/lib/".$atlas."/".$network." ".$mode;
			}
		}
		#$count++;
		#print CNF "$order\n";
		my $orderfile = $outdir.'/'.$subject.'dti_orders.sh';
                open ORD, ">$orderfile";
		print ORD '#!/bin/bash'."\n";
                print ORD '#SBATCH -J dti_track_'.$subject."\n";
                print ORD '#SBATCH --time=1:0:0'."\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.'/dti_track-slurm-%j'."\n";
		if($cuda){ print ORD '#SBATCH -p cuda'."\n";}
		print ORD "srun $order\n";
                close ORD;
                my $pid = fork();
                if ($pid == 0){
                        exec("sbatch $orderfile");
                }
                elsif (!defined($pid)){
                        die "could not fork";
		}
		$debug ? print DBG "$order\n" :0;
	}
}
#close CNF;

#open ORD, ">$orderfile";
#print ORD '#!/bin/bash'."\n";
#print ORD '#SBATCH --time=0'."\n";
#print ORD '#SBATCH -J '.$track_study."\n";
#print ORD '#SBATCH -n '.$count."\n";
#print ORD '#SBATCH -o '.$outdir.'/dti_track-slurm-%j'."\n";
#print ORD '#SBATCH --mail-type=ALL'."\n";                                                             
#print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";
#if($cuda){print ORD '#SBATCH -p cuda'."\n";}
#print ORD "srun --exclusive --multi-prog ".$conffile."\n";
#close ORD;

$debug ? close DBG:0;   
#exec("sbatch -o $w_dir/dti_track.out $orderfile");