#!/usr/bin/perl

# Copyright 2019 O. Sotolongo <asqwerty@gmail.com>

# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
use strict; use warnings;

use File::Find::Rule;
use NEURO4 qw(print_help load_project shit_done cut_shit check_subj check_or_make);
use Data::Dump qw(dump);
use File::Remove 'remove';
use File::Basename qw(basename);
use File::Copy::Recursive qw(dircopy);

my $fslic = '/nas/usr/local/opt/freesurfer/.license';
my $fmriprep_version = '1.5.6';
my $cfile="";
#my $fs = 0;
my $st = 0;
@ARGV = ("-h") unless @ARGV;

while (@ARGV and $ARGV[0] =~ /^-/) {
    $_ = shift;
    last if /^--$/;
    if (/^-cut/) { $cfile = shift; chomp($cfile);}
#    if (/^-fs/) { $fs = 1};
    if (/^-st/) {$st = 1};
    if (/^-h$/) { print_help $ENV{'PIPEDIR'}.'/doc/dfmriprep.hlp'; exit;}
}
my $study = shift;
unless ($study) { print_help $ENV{'PIPEDIR'}.'/doc/dfmriprep.hlp'; exit;}
my %std = load_project($study);
my $w_dir = $std{'WORKING'};
my $data_dir = $std{'DATA'};
my $bids_dir = $std{'BIDS'};
my $fsdir = $ENV{'SUBJECTS_DIR'};
my $db = $std{'DATA'}.'/'.$study.'_mri.csv';
my $fmriout_dir = $data_dir.'/fmriprep_out';
my $fssubsdir = $fmriout_dir.'/freesurfer';
my $noslicetiming;
if($st){
        $noslicetiming = "";
}else{
        $noslicetiming = "--ignore slicetiming";
}
check_or_make($fmriout_dir);
check_or_make($fssubsdir);
my $outdir = "$std{'DATA'}/slurm";
check_or_make($outdir);

my @subjects = cut_shit($db, $data_dir."/".$cfile);

foreach my $subject (@subjects) {
        my %nifti = check_subj($std{'DATA'},$subject);
        if($nifti{'func'}){
                my $fssd = $fssubsdir.'/sub-'.$subject;
                my $rfssd = $fsdir.'/'.$study.'_'.$subject;
                check_or_make($fssd);
                dircopy($rfssd,$fssd);
                my $orderfile = $outdir.'/'.$subject.'_fmriprep.sh';
                open ORD, ">$orderfile";
                print ORD '#!/bin/bash'."\n";
                print ORD '#SBATCH -J fmriprep_'.$study."\n";
                print ORD '#SBATCH --time=72:0:0'."\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 -o '.$outdir.'/fmriprep-%j'."\n";
                print ORD '#SBATCH -c 20'."\n";
                print ORD '#SBATCH -p fast'."\n";
                print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";
#docker run --rm -it -e DOCKER_VERSION_8395080871=19.03.5 -v /nas/usr/local/opt/freesurfer/.license:/opt/freesurfer/license.txt:ro -v /nas/data/mopead/bids:/data:ro -v /nas/data/mopead/fmriprep_out:/out poldracklab/fmriprep:1.5.0 /data /out participant --participant-label sub-0001 --ignore slicetiming --skip_bids_validation
                print ORD 'srun docker run -t -d --rm -v '.$fslic.':/opt/freesurfer/license.txt:ro -v '.$bids_dir.'/sub-'.$subject.':/data:ro -v '.$fmriout_dir.':/out poldracklab/fmriprep:'.$fmriprep_version.' /data /out participant --participant-label '.$subject.' '.$noslicetiming.' --skip_bids_validation --fs-subjects-dir out/freesurfer';
                close ORD;
                system("sbatch $orderfile");
                #sleep(2);
        }
}
my $orderfile = $outdir.'/fmriprep_end.sh';
open ORD, ">$orderfile";
print ORD '#!/bin/bash'."\n";
print ORD '#SBATCH -J fmriprep_'.$study."\n";
print ORD '#SBATCH --mail-type=END'."\n"; #email cuando termine
print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";
print ORD '#SBATCH -p fast'."\n";
print ORD '#SBATCH -o '.$outdir.'/fmriprep_end-%j'."\n";
print ORD ":\n";
close ORD;
my $order = 'sbatch --dependency=singleton '.$orderfile;
exec($order);