#!/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 $net_path;
@ARGV = ("-h") unless @ARGV;
while (@ARGV and $ARGV[0] =~ /^-/) {
    $_ = shift;
    last if /^--$/;
    if (/^-path/) {$net_path = shift;}
    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_thresholds_".$net_path.".csv";
open OF, ">$ofile";
print OF "Threshold";
my %pollos;
foreach my $dti (sort @dti_fas){
	(my $a,my $subject) = $dti =~ /(\w{1,4})(\d{1,6})_dti_FA/;
	my $name = $a.$subject;
	my $img_path = $w_dir.'/'.$name.'_probtrack_'.$net_path.'/fdt_paths.nii.gz';
	if(-f $img_path){
		$pollos{$name} = $dti;
		print OF ";$name";
	}
}
print OF "\n";
for (my $thr = 0.05; $thr<1; $thr+=0.05){ 
	print OF "$thr"; print "$thr\n";
	foreach my $pollo (sort keys %pollos){
		my $img_path = $w_dir.'/'.$pollo.'_probtrack_'.$net_path.'/fdt_paths.nii.gz';
		my $order = $ENV{'PIPEDIR'}.'/bin/track2mask.sh '.$img_path.' '.$thr;
		system($order);
		my $mask_path = $w_dir.'/'.$pollo.'_probtrack_'.$net_path.'/fdt_paths_mask.nii.gz'; 
		$order = "fslstats ".$pollos{$pollo}." -k ".$mask_path." -M -S";
		(my $mean, my $std) = map{/(\d+\.\d*)\s*(\d+\.\d*)/} qx/$order/;
		print OF ";$mean";
	}
	print OF "\n";
}
close OF;
achtung basename($ENV{_}), $ofile, $study;