#! /usr/bin/perl
#

# March, 2007: Initial implementation. - Claude Lepage
#
# Copyright Alan C. Evans
# Professor of Neurology
# McGill University
#

use strict;
use warnings "all";

use Getopt::Tabular;
use MNI::Startup;
use MNI::FileUtilities qw(check_output_dirs);


# --- set the help & usage strings ---
my $help = <<HELP;
Compute the mean curvature on the mid-surface.
HELP

my $usage = <<USAGE;
Usage: $ProgramName [options] mid.obj output.txt
       $ProgramName -help to list options

USAGE

Getopt::Tabular::SetHelp( $help, $usage );

my $fwhm = 0;
my $transform_xfm = undef;

my @options =
  ( @DefaultArgs,     # from MNI::Startup
    ['-fwhm', 'string', 1, \$fwhm, 'blurring kernel in mm'],
    ['-transform', 'string', 1, \$transform_xfm, 
     'transformation from native to stereotaxic (if surfaces in stx space)'],
  );

GetOptions( \@options, \@ARGV )
  or exit 1;
die "$usage\n" unless @ARGV == 2;

my $mid = shift;
my $output = shift;

# These are temporary files.
MNI::FileUtilities::check_output_dirs("${TmpDir}")
  or exit 1;

# Make sure there is only one way to compute the thickness.

if( defined $transform_xfm ) {
  my $mid_trans = "${TmpDir}/mid_trans.obj";
  my $inv_trans = "${TmpDir}/inv_trans.xfm";
  &run( "xfminvert", $transform_xfm, $inv_trans );
  &run( "transform_objects", $mid, $inv_trans, $mid_trans );
  $mid = $mid_trans;
}

&run( "depth_potential", "-mean_curvature", $mid, $output );

# Blur the cortical mean curvature on the mid-surface in new space.

if( $fwhm gt 0 ) {
  my $output_blurred = "${TmpDir}/mc_blurred.txt";
  &run( "depth_potential", "-smooth", $fwhm, $output, $mid, $output_blurred );
  &run( "mv", "-f", $output_blurred, $output );
}


#Execute a system call.

sub run {
  print "@_\n";
  system(@_)==0 or die "Command @_ failed with status: $?";
}