#!/usr/bin/perl

use strict; use warnings;

use File::Find::Rule;
use NEURO qw(print_help get_pair load_study achtung shit_done);
use Data::Dump qw(dump);
use File::Basename qw(basename);

my $attach = 1;
my $with_sd = 0;
my $threshold = 0.25;
#my $atlas;
my $net_path;
#my $netwstr;
@ARGV = ("-h") unless @ARGV;
while (@ARGV and $ARGV[0] =~ /^-/) {
    $_ = shift;
    last if /^--$/;
    if (/^-l/) { $attach = 0;}
    #if (/^-uofm/) {$atlas="uofm"; $network = shift; chomp($network); $netwstr = $network; $network =~ s/\_/\//g;}
    if (/^-thr/) {$threshold = shift;}
    if (/^-path/) {$net_path = shift;}
    if (/^-sd/) { $with_sd = 1;}
    if (/^-h/) { print_help $ENV{'PIPEDIR'}.'/doc/dti_metrics.hlp'; exit;}
}

my $study = shift;
$net_path = "out" unless $net_path;
unless ($study) { print_help $ENV{'PIPEDIR'}.'/doc/dti_metrics.hlp'; exit;}
my %std = load_study($study);

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

my @dti_fas = find(file => 'name' => "*_dti_FA.nii.gz", in => $w_dir);
my %csv;

my $ofile = $data_dir."/".$study."_dti_".$net_path.".csv";
open OF, ">$ofile";
print OF "Subject";
if($with_sd){
	print OF ";$net_path","_FA_Mean;","$net_path","_FA_STD",";$net_path","_MD_Mean;","$net_path","_MD_STD";
}else{
	print OF ";$net_path","_FA",";$net_path","_MD";
}
print OF "\n";

foreach my $dti (sort @dti_fas){
	(my $a,my $subject) = $dti =~ /(\w{1,4})(\d{1,6})_dti_FA/;
	my $tmpmd = $w_dir.'/'.$a.$subject."_dti_MD";
	if($subject){
		print OF "$subject";
		my $img_path = $w_dir.'/'.$a.$subject.'_probtrack_'.$net_path.'/fdt_paths.nii.gz'; 
		my $order = $ENV{'PIPEDIR'}.'/bin/track2mask.sh '.$img_path.' '.$threshold;
		print "$order\n";
		system($order);
		my $mask_path = $w_dir.'/'.$a.$subject.'_probtrack_'.$net_path.'/fdt_paths_mask.nii.gz'; 
		$order = "fslstats ".$dti." -k ".$mask_path." -M -S";
		print "$order\n";
		(my $mean, my $std) = map{/(\d+\.\d*)\s*(\d+\.\d*)/} qx/$order/;
		if($with_sd){
			print OF ";$mean",";$std";
		}else{
			print OF ";$mean";
		}
		$order = "fslstats ".$tmpmd." -k ".$mask_path." -M -S";
		print "$order\n";
		($mean, $std) = map{/(\d+\.\d*)\s*(\d+\.\d*)/} qx/$order/;
		if($with_sd){
			print OF ";$mean",";$std";
		}else{
			print OF ";$mean";
		}
	}
	print OF "\n";
}

close OF;

my $zfile = $ofile.'.gz';
system("gzip -c $ofile > $zfile");

if ($attach){
	shit_done basename($ENV{_}), $study, $zfile;
}else{
	achtung basename($ENV{_}), $ofile, $study;
}