#!/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 NEURO4 qw(load_project print_help);
my $full = 0;
@ARGV = ("-h") unless @ARGV;
while (@ARGV and $ARGV[0] =~ /^-/) {
    $_ = shift;
    last if /^--$/;
    if (/^-f/) {$full = 1}
    if (/^-h/) { print_help $ENV{'PIPEDIR'}.'/doc/make_fbb_report.hlp'; exit;}
}
my $study = shift;
unless ($study) { print_help $ENV{'PIPEDIR'}.'/doc/make_pet_report.hlp'; exit;}

my %std = load_project($study);

my $w_dir=$std{'WORKING'};
my $d_dir=$std{'DATA'};

# Redirect ouput to logfile (do it only when everything is fine)
my $debug = "$d_dir/.debug_report.log";
open STDOUT, ">$debug" or die "Can't redirect stdout";
open STDERR, ">&STDOUT" or die "Can't dup stdout";

my $order = "slicesdir -o ";
my @names = find(file => 'name' => "*_fbb.nii.gz", in => $w_dir);
foreach my $name (sort @names){
	(my $struc = $name) =~ s/fbb/struc/; 
	$order .= $name.' '.$struc." ";
	if ($full) {
		(my $base = $name) =~ s/\.nii\.gz$//;
		$base=basename($base);
		my @regs = find(file => 'name' => "$base*reg.nii.gz", in => $w_dir);
		dump @regs;	
		foreach my $reg (sort @regs){
			$order .= $reg.' '.$struc." ";
		}
	}
}
chdir $w_dir;
print "$order\n";
system($order);
dirmove('slicesdir', 'fbbs');