#!/usr/bin/perl -w
#---------------------------------------------------------------------------
#@COPYRIGHT :
#             Copyright 1996, John G. Sled, 
#             McConnell Brain Imaging Centre,
#             Montreal Neurological Institute, McGill University.
#             Permission to use, copy, modify, and distribute this
#             software and its documentation for any purpose and without
#             fee is hereby granted, provided that the above copyright
#             notice appear in all copies.  The author and McGill University
#             make no representations about the suitability of this
#             software for any purpose.  It is provided "as is" without
#             express or implied warranty.
#---------------------------------------------------------------------------- 
#$RCSfile: field2imp.in,v $
#$Revision: 1.1 $
#$Author: bert $
#$Date: 2003/04/16 14:29:34 $
#$State: Exp $
#---------------------------------------------------------------------------
# ------------------------------ MNI Header ----------------------------------
#@NAME       : field2imp
#@INPUT      : 
#@OUTPUT     : 
#@RETURNS    : 
#@DESCRIPTION: create a compact representation of the given field
#@METHOD     : 
#@GLOBALS    : 
#@CALLS      : 
#@CREATED    : August 28, 1996      J.G.Sled  
#@MODIFIED   : 
#  $Id: field2imp.in,v 1.1 2003/04/16 14:29:34 bert Exp $
#-----------------------------------------------------------------------------
use MNI::Startup qw(nocputimes);
use MNI::Spawn;
use MNI::FileUtilities qw(check_output_dirs);
use MNI::PathUtilities qw(split_path);
use Getopt::Tabular;

# these values are chosen to be less smooth than most fields
$lambda = 0.01;
$distance = 50;
$subsample = 4;

&Initialize;

   # Set global variables for calling various programs
MNI::Spawn::SetOptions (strict  => 2);
&RegisterPrograms([qw(spline_smooth)]);

Spawn(['spline_smooth', '-full_support', '-distance', $distance, '-b_spline',
             '-lambda', $lambda, '-subsample', $subsample, '-novolume',
             $input_volume, '-compact', $output_imp, '-clobber']);


# ------------------------------ MNI Header ----------------------------------
#@NAME       : &SetHelp
#@INPUT      : none
#@OUTPUT     : none
#@RETURNS    : nothing
#@DESCRIPTION: Sets the $Help and $Usage globals, and registers them
#              with ParseArgs so that user gets useful error and help
#              messages.
#@METHOD     : 
#@GLOBALS    : $Help, $Usage
#@CALLS      : 
#@CREATED    : 
#@MODIFIED   : 
#-----------------------------------------------------------------------------
sub SetHelp
{
   $Version = '1.10';
   $LongVersion = 'Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37';

   $Usage = <<USAGE;
$ProgramName, version $Version

Usage: $ProgramName [-help] input.mnc output.imp
USAGE

   $Help = <<HELP;

$ProgramName is a script that reduces a MINC volume into a compact spline
representation. 

HELP
   
   Getopt::Tabular::SetHelp ($Help, $Usage);       
}

# ------------------------------ MNI Header ----------------------------------
#@NAME       : &SetupArgTables
#@INPUT      : none
#@OUTPUT     : none
#@RETURNS    : References to the two option tables:
#                @pref_args
#@DESCRIPTION: Defines the tables of command line (and config file) 
#              options that we pass to ParseArgs.
#@METHOD     : 
#@GLOBALS    : makes references to many globals (almost all of 'em in fact)
#              even though most of them won't have been defined when
#              this is called
#@CALLS      : 
#@CREATED    : 
#@MODIFIED   : 
#-----------------------------------------------------------------------------
sub SetupArgTables
{
   my (@pref_args);

   sub print_version
   {
      print "Program $ProgramName, built from:\n$LongVersion\n";
      exit;
   }

   # Preferences -- these shouldn't affect the results

   @pref_args = 
      (["General Options", "section"],
       ["-verbose|-quiet", "boolean", 0, \$Verbose, 
	"be noisy [default; opposite is -quiet]" ],
       ["-execute|-noexecute", "boolean", 0, \$Execute, 
	"actually execute planned commands [default]"],
       ["-clobber|-noclobber", "boolean", 0, \$Clobber,
	"overwrite output files [default: -noclobber]"],
       ["-version", "call", undef, \&print_version,
        "print version and quit"] );

   (\@pref_args);
}

# ------------------------------ MNI Header ----------------------------------
#@NAME       : &ValidateArgs
#@INPUT      : 
#@OUTPUT     : 
#@RETURNS    : 
#@DESCRIPTION: Checks global variables for inconsistencies caused by bad
#               combinations of arguments
#@METHOD     : 
#@GLOBALS    : 
#@CALLS      : 
#@CREATED    : 
#@MODIFIED   : 
#-----------------------------------------------------------------------------
sub ValidateArgs
{
   # check whether $output_volume can be over written
   ((-e $output_imp || -e "$output_imp.gz" ) && ! $Clobber) &&
      (die("Clobber option not given.  Cannot overwrite file:\n"
              ." $output_imp\n"));

   &check_output_dirs($output_directory);
}

# ------------------------------ MNI Header ----------------------------------
#@NAME       : &Initialize
#@INPUT      : 
#@OUTPUT     : 
#@RETURNS    : 
#@DESCRIPTION: Sets global variables, parses command line.  Dies on
#              any error.
#@METHOD     : 
#@GLOBALS    : preferences: $Verbose, $Execute, $Clobber, $Debug, $KeepTmp
#              
#@CALLS      : &SetSpawnOptions
#              &SetupArgTables
#              &ParseArgs::Parse
#@CREATED    : 
#@MODIFIED   : 
#-----------------------------------------------------------------------------
sub Initialize
{
   my ($pref_tbl, @reducedARGV);

   # Set defaults for the global variables.  These can be overridden by 
   # the command line.
   $Verbose      = 1;

   &SetHelp;
 
   # Parse command line arguments
   ($pref_tbl) = &SetupArgTables;
   GetOptions($pref_tbl, \@ARGV, \@reducedARGV)
         || exit 1;

   if (@reducedARGV != 2) 
   { 
      print STDERR "Leftover args: @reducedARGV\n" if @reducedARGV;
      print STDERR $Usage;
      die "Incorrect number of arguments\n";
   }
   ($input_volume, $output_imp) = @reducedARGV;

   # expand some arguments
   ($output_directory) = split_path($output_imp);

   # validate argument combinations and check filenames
   ValidateArgs;

}