#!/usr/bin/perl
# Copyright 2019 O. Sotolongo <asqwerty@gmail.com>
use strict; use warnings;
 
use File::Find::Rule;
use NEURO qw(print_help get_pair load_study achtung shit_done get_lut check_or_make centiloid_fbb);
use Data::Dump qw(dump);
use File::Remove 'remove';
use File::Basename qw(basename);

my $ref_roi =  "voi_WhlCbl_2mm.nii";
my $ctx_roi = "voi_ctx_2mm.nii";

my $roi_paths = $ENV{'PIPEDIR'}.'/lib/Centiloid_Std_VOI/nifti/2mm/';
my $withstd = 0;
my $cfile;

@ARGV = ("-h") unless @ARGV;

while (@ARGV and $ARGV[0] =~ /^-/) {
    $_ = shift;
    last if /^--$/;
    if (/^-cut/) { $cfile = shift; chomp($cfile);}
}
 
my $study = shift;
unless ($study) { print_help $ENV{'PIPEDIR'}.'/doc/pet_metrics.hlp'; exit;}
my %std = load_study($study);
my $w_dir=$std{'WORKING'};
my $data_dir=$std{'DATA'};

our %subjects;

my @plist = find(file => 'name' => "*_fbb.nii.gz", '!name' => "*tmp*", in => $w_dir);
my $ofile = $data_dir."/".$study."_fbb_cl.csv";
my $patt = '([A-Z,a-z]{1,4})(\d{1,6})_fbb';

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;
}

foreach my $pet (sort @pets){   
    (my $dg,my $subject) = $pet =~ /$patt/;
    if($subject){
		$subjects{$subject}{'dg'} = $dg;
		$subjects{$subject}{'pet'} = $pet;
	}
}
my %sdata;
foreach my $subject (sort keys %subjects){
	my $care;
	my $norm;
	my $dg = $subjects{$subject}{'dg'};
	# Apply masks to FBB
	my $roi_mask = $roi_paths.$ctx_roi;
	my $order = "fslstats ".$w_dir."/".$dg.$subject."_fbb_mni -k ".$roi_mask." -M";
	my $ctx = qx/$order/;
	my $roi_mask = $roi_paths.$ctx_roi;
	$order = "fslstats ".$w_dir."/".$dg.$subject."_fbb_mni -k ".$roi_mask." -M";
	print "$order\n";
	my $norm = qx/$order/;
	$subjects{$subject}{$npf.'mean'} = $ctx/$norm;	
}

open OF, ">$ofile";
print OF "Subject; SUVR; Centilod";
print OF "\n";
foreach my $subject (sort keys %subjects){
	print OF "$subject";
	my $mean = $subjects{$subject}{$npf.'mean'};
	print OF ";$mean";
	print OF ";", centiloid_fbb($mean);
	print OF "\n";
}
close OF;