#! /usr/bin/env perl
#
# Compute the percentages of classified CSF, WM, GM.
# 
# Note: This is for the whole head, including brain stem and cerebellum,
#       so not ideal to represent the WM and GM we want.
#
# Claude Lepage - claude@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 $transform_xfm = undef;

$me = &basename($0);

$Help = <<HELP;
| Compute the percentages of classified CSF, WM, GM.
| 
| Problems or comments should be sent to: claude\@bic.mni.mcgill.ca
HELP

$Usage = "Usage: $me cls.mnc [info_file.txt]\n\n";

# Check arguments
&Getopt::Tabular::SetHelp($Help, $Usage);

die $Usage if( !( $#ARGV == 1 || $#ARGV == 2 ) );

my $cls = shift(@ARGV);
my $mask = shift(@ARGV);
my $info_file = shift(@ARGV);

# check for files
die "$me: Couldn't find input file: $cls\n\n" if (!-e $cls);

my $tmpdir = &tempdir( "classify_qc-XXXXXX", TMPDIR => 1, CLEANUP => 1 );

if( ( $mask ne "none" ) and ( -e $mask ) ) {
  my $cls_masked = "${tmpdir}/cls_masked.mnc";
  `minccalc -quiet -clobber -expression 'if(A[1]>0.5){A[0]}else{0}' $cls $mask $cls_masked`;
  $cls = $cls_masked;
}

my $csf_vol;
chomp( $csf_vol = `mincstats -quiet -count -mask $cls -mask_binvalue 1 $cls` );

my $gm_vol;
chomp( $gm_vol = `mincstats -quiet -count -mask $cls -mask_binvalue 2 $cls` );

my $wm_vol;
chomp( $wm_vol = `mincstats -quiet -count -mask $cls -mask_binvalue 3 $cls` );

my $total_vol = $csf_vol + $gm_vol + $wm_vol;

my $csf_pct = 100.0 * $csf_vol / $total_vol;
my $gm_pct = 100.0 * $gm_vol / $total_vol;
my $wm_pct = 100.0 * $wm_vol / $total_vol;

if( defined $info_file ) {
  open PIPE, ">$info_file";
  print PIPE sprintf( "classified image CSF %5.2f%%  GM %5.2f%%  WM %5.2f%%\n", 
                      $csf_pct, $gm_pct, $wm_pct );
  close PIPE;
} else {
  print sprintf( "classified image CSF %5.2f%%  GM %5.2f%%  WM %5.2f%%\n", 
                 $csf_pct, $gm_pct, $wm_pct );
}