#!/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 $atlas = 1;                                                                                        
@ARGV = ("-h") unless @ARGV;                                                                          
while (@ARGV and $ARGV[0] =~ /^-/) {                                                                  
    $_ = shift;                                                                                       
    last if /^--$/;                                                                                   
    if (/^-l/) { $attach = 0;}                                                                                                                                                
    if (/^-sd/) { $with_sd = 1;}                                                                      
    if (/^-h/) { print_help $ENV{'PIPEDIR'}.'/doc/dti_metrics.hlp'; exit;}                            
}
my $study = shift;                                                                                    
unless ($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 $roi_list = $ENV{'PIPEDIR'}.'/lib/jhu.labels.list';                                                                                                                                      
my $roi_dir = $ENV{'PIPEDIR'}.'/lib/jhu/';                                                            
my $jhu = "JHU_labels_custom_tmp";                                                                    
my %masks = get_pair $roi_list;                                                                       
my @dti_fas = find(file => 'name' => "*_dti_FA.nii.gz", in => $w_dir);                                                         
my %csv;                                                                                              
                                                                                                      
my $ofile = $data_dir."/".$study."_dti.csv";                                                          
open OF, ">$ofile";                                                                                   
                                                                                                      
print OF "Subject"; 
foreach my $rmask (sort keys %masks){                                                                 
        if($with_sd){                                                                                 
                print OF ";$masks{$rmask}","_FA_Mean;","$masks{$rmask}","_FA_STD";                    
        }else{                                                                                        
                print OF ";$masks{$rmask}","_FA";                                                     
        }                                                                                             
}                                                                                                     
print OF "\n";                                                                                        
                                                                                                      
foreach my $dti (sort @dti_fas){                                                                      
        (my $a,my $subject) = $dti =~ /(\w{1,3})(\d{1,6})_dti_FA/;                                                                               
        if($subject){                                                                                 
                foreach my $rmask (sort keys %masks){                                                 
                        my ($m_index) = $rmask =~ /.*_(\d+)$/;                                        
                        if($m_index){                                                                 
                                my $order = "fslmaths ".$w_dir."/.tmp_".$a.$subject."/".$jhu." -uthr ".$m_index." -thr ".$m_index." -div ".$m_index." ".$w_dir."/.tmp_".$a.$subject."/JHU_labels_".$rmask."_tmp";                                                                                                 
                        print "$order\n";                                                             
                        system($order);                                                               
                        } else {
                        my $order = "fslmaths ".$w_dir."/.tmp_".$a.$subject."/".$jhu." -uthr ".$m_index." -thr ".$m_index." ".$w_dir."/.tmp_".$a.$subject."/JHU_labels_".$rmask."_tmp";                     
                        print "$order\n";                                                                                                                                                                   
                        system($order);                                                               
                        }                                                                             
                }                                                                                     
                print OF "$subject";                                                                  
                foreach my $rmask (sort keys %masks){                                                 
                        my $order = "fslstats ".$dti." -k ".$w_dir."/.tmp_".$a.$subject."/JHU_labels_".$rmask."_tmp -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";                                                    
                        }
                }                                                                                     
                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;                                                    
}