#!/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 $old=0;
my $chop=0;
@ARGV = ("-h") unless @ARGV;
while (@ARGV and $ARGV[0] =~ /^-/) {
    $_ = shift;
    last if /^--$/;
    if (/^-cut/) { $cfile = shift; chomp($cfile);}
    if (/^-nocorr/) {$corr=0;} 
    if (/^-legacy/) {$legacy=1;}
    if (/^-old/) {$old=1;}
    if (/^-chop/) {$old=1; $chop=1;}
    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'};
#my $pipe_dir = "/nas/software/neuro.dev/bin/";
# Redirect ouput to logfile (do it only when everything is fine)
my $logfile = "$std{'DATA'}/.debug_dti_register.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'};

my $outdir = "$std{'DATA'}/slurm";
check_or_make($outdir);

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;
}

my $count = 0;
my @jobs_list;
foreach my $subject (sort keys %dtis){
        if($subject){
                my @names = find(file => 'name' => "$dtis{$subject}$subject*.nii.gz", in => $dti_dir);
                my @t1_names = find(file => 'name' => "$dtis{$subject}$subject*.nii.gz", in => $mri_dir);
                if(@names && @t1_names){
                        my $order;
                        unless($old){
                                if($corr){
                                        if($legacy){
                                                $order = $pipe_dir."/bin/dti_proc_legacy.sh ".$names[0]." ".$t1_names[0]." ".$dtis{$subject}.$subject." ".$w_dir;
                                        }else{
                                                $order = $pipe_dir."/bin/dti_proc_epi.sh ".$study." ".$names[0]." ".$t1_names[0]." ".$dtis{$subject}.$subject." ".$w_dir;
                                        }
                                }else{
                                        if($legacy){
                                                $order = $pipe_dir."/bin/dti_proc_nocorr_legacy.sh ".$names[0]." ".$t1_names[0]." ".$dtis{$subject}.$subject." ".$w_dir;
                                        }else{
                                                $order = $pipe_dir."/bin/dti_proc_nocorr.sh ".$names[0]." ".$t1_names[0]." ".$dtis{$subject}.$subject." ".$w_dir;
                                        }
                                }
                        }else{
                                if($chop){
                                        $order = $pipe_dir."/bin/dti_proc_x.sh ".$names[0]." ".$t1_names[0]." ".$dtis{$subject}.$subject." ".$w_dir;
                                }else{
                                        $order = $pipe_dir."/bin/dti_proc_deprecated.sh ".$names[0]." ".$dtis{$subject}.$subject." ".$w_dir;
                                }
                        }
                        my $orderfile = $outdir.'/'.$subject.'dti_orders.sh';
                        open ORD, ">$orderfile";
                        print ORD '#!/bin/bash'."\n";
                        print ORD '#SBATCH -J dti_reg-'.$study."\n";
                        print ORD '#SBATCH --time=15:0:0'."\n"; #si no ha terminado en X horas matalo
                        print ORD '#SBATCH -c 4'."\n";
                        print ORD '#SBATCH --mail-type=FAIL,STAGE_OUT'."\n"; #no quieres que te mande email de todo
                        print ORD '#SBATCH -o '.$outdir.'/dti_reg-slurm-%j'."\n";
                        unless($legacy or $old){ print ORD '#SBATCH --gres=gpu:1'."\n"; }
                        print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";
                        unless($legacy or $old){ print ORD '#SBATCH -p cuda'."\n"; }
                        print ORD "srun $order\n";
                        close ORD;
                        my $jobid = `sbatch $orderfile`;
                        $jobid = ( split ' ', $jobid )[ -1 ];
                        push @jobs_list, $jobid;
                        $debug ? print DBG "$order\n" :0;
                }
        }
}
$debug ? close DBG:0;   
my $sjobs = join(',',@jobs_list);
my $orderfile = $outdir.'/dti_reg_end.sh';
open ORD, ">$orderfile";
print ORD '#!/bin/bash'."\n";
print ORD '#SBATCH -J dti_reg-'.$study."\n";
print ORD '#SBATCH --mail-type=END'."\n"; #email cuando termine
print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";
print ORD '#SBATCH -o '.$outdir.'/dti_reg_end-%j'."\n";
print ORD ":\n";
close ORD;
my $order = 'sbatch --depend=afterany:'.$sjobs.' '.$orderfile;
exec($order);