#! /usr/bin/env perl
#
# Volumetric Feature Extractor
#
# Oliver Lyttelton oliver@bic.mni.mcgill.ca

#
# Copyright Alan C. Evans
# Professor of Neurology
# McGill University
#

use strict;
use warnings "all";
use Getopt::Tabular;
use File::Basename;
use File::Temp qw/ tempdir /;


my($Help, $Usage, $me);
my(@opt_table, %opt, $source, $target, $outxfm, @args, $tmpdir);

$me = &basename($0);
%opt = (
   'verbose'   => 0,
   'clobber'   => 0,
   'asymmetry' => 0
   );

$Help = <<HELP;
|    $me extracts a volumetric feature sets with options to 
|    vary the extraction space (native or tal) the blurring kernel,
|    the registration space (tal or nl tal) and the sampling 
|    resolution
| 
| Problems or comments should be sent to: oliver\@bic.mni.mcgill.ca
HELP

$Usage = "Usage: $me [options] input.mnc output.mnc\n".
         "       $me -help to list options\n\n";

@opt_table = (
   ["-verbose", "boolean", 0, \$opt{verbose},
      "be verbose" ],
   ["-clobber", "boolean", 0, \$opt{clobber},
      "clobber existing check files" ],
    ["-extract_class", "string", 1, \$opt{extract_class},
      "Choose class for non-binary classified image" ],
   ["-native_xfm", "string", 1, \$opt{native_trans},
      "supply native transformation for extraction space" ],
   ["-native_sum_file", "string", 1, \$opt{native_sum},
      "print out the sum of native voxels" ],
   ["-asymm", "boolean", 0, \$opt{asymmetry},
      "flip and diff the files for evaluation of asymmetries" ],      
   ["-blurfwhm", "string",1,\$opt{blur}, 
      "optional blurring kernel" ],
   ["-nl_xfm", "string", 1, \$opt{nl_trans},
      "non-linear registration transformation" ],
   ["-downsample", "string",1,\$opt{blur},
      "specify downsampling factor" ],   
   );

# Check arguments
&Getopt::Tabular::SetHelp($Help, $Usage);
&GetOptions (\@opt_table, \@ARGV) || exit 1;
die $Usage if($#ARGV != 1);
my $input = shift(@ARGV);
my $output = shift(@ARGV);


# check for files
die "$me: Couldn't find input file: $input\n" if (!-e $input);
if(-e $output && !$opt{clobber}){
   die "$me: $output exists, -clobber to overwrite\n";
   }

# make tmpdir
$tmpdir = &tempdir( "$me-XXXXXXXX", TMPDIR => 1, CLEANUP => 1 );

my $pretransform_file = $opt{native_trans}; 
my $transform_file = $opt{nl_trans};
my $FWHM = 0;
if ($opt{blur}) {$FWHM = $opt{blur}; }
my $do_symm = $opt{asymmetry};
my $downsample = $opt{downsample};
my $native_sum;
if ($opt{native_sum}){ $native_sum = "${opt{native_sum}}";}

                
#set up internal variables
my $pre_trans_output = "${tmpdir}/pretrans.mnc";
my $extract_file = "${tmpdir}/class.mnc";
my $blur_file = "${tmpdir}/blur.mnc";
my $positive_file =  "${tmpdir}/positive.mnc";
my $flip_file = "${tmpdir}/flip.mnc";
my $diff_file = "${tmpdir}/diff.mnc";
my $post_blur_output = "${tmpdir}/posttrans.mnc";
my $resample_file = "${tmpdir}/resample.mnc";
my $source_file = $input;
 
#Optional pre-blurring transformation
  	if ($pretransform_file) {
	    #perform_pre_blurring_transformation step
		&do_cmd("mincresample", "-clobber", "-transform",
			$pretransform_file, "-like", $source_file,
			$source_file, $pre_trans_output);
		$source_file =$pre_trans_output;
	}
    
    if($native_sum){
        #measure total 
		&do_cmd("mincstats -sum ${source_file}> ${native_sum}");
	}
	
#Optional Select_Class step
     if ($opt{extract_class}) {
	    #extract class
         &do_cmd("minccalc","-clobber", "-expression","if(abs(A[0]-${opt{extract_class}})<0.5){out=1;}else{out=0;}",$source_file, $extract_file );
		 $source_file = $extract_file;
	}
    
#Optional Blurring stage                                                                          
  	if ($FWHM!=0) {
	    #perform_pre_blurring step
         &do_cmd("mincblur","-clobber", "-fwhm",$FWHM,$source_file, $blur_file );
          $source_file = "${blur_file}_blur.mnc";
         &do_cmd("minccalc","-clobber", "-expression","if(A[0]<0){out=0;}else{out=A[0];}",$source_file, $positive_file );
		 $source_file =$positive_file;
	}
    
 
	
#Reverse Optional pre-blurring transformation
  	if ($pretransform_file) {
	    #perform_pre_blurring_transformation step
        &do_cmd("mincresample", "-clobber","-invert_transformation","-transform",
			$pretransform_file, "-like", $source_file,
			$source_file, $post_blur_output);
		$source_file =$post_blur_output;
	} 
        
		                                                         
#Optional Resampling step	
 	if ($transform_file) {
	    #perform_resampling step
		&do_cmd("mincresample", "-clobber", "-transform",
			$transform_file, "-like", $source_file,
			$source_file, $resample_file);		
        $source_file = $resample_file;
}

#Optional Asymmetry stages                                                                      
  	if ($do_symm) {
	    #perform_symmetry step
		&do_cmd("flip_volume",$source_file, $flip_file);
        #perform_symmetry step
        &do_cmd("mincmath","-clobber","-sub",$source_file,$flip_file,$diff_file);
		$source_file = $diff_file;

	}



#Optional Downsampling step	
if ($downsample){&do_cmd("downsample.exe",$downsample, $source_file, $output); 
}else{
      &do_cmd("cp", $source_file, $output);
     if (substr($source_file,-3) eq ".gz"){
         &do_cmd("mv", $output, "${output}.gz");
         &do_cmd("gzip","-d", "${output}.gz");
        }
  }


sub do_cmd { 
   print STDOUT "@_\n" if $opt{verbose};
   system(@_) == 0 or die;
}