#!/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: make_template.in,v $
#$Revision: 1.4 $
#$Author: claude $
#$Date: 2006/05/05 02:13:44 $
#$State: Exp $
#---------------------------------------------------------------------------
# ------------------------------ MNI Header ----------------------------------
#@NAME       : make_template
#@INPUT      : 
#@OUTPUT     : 
#@RETURNS    : 
#@DESCRIPTION: 
#@            
#@METHOD     : 
#@GLOBALS    : 
#@CALLS      : 
#@CREATED    : August 15, 1996      J.G.Sled  
#@MODIFIED   : 
#  $Id: make_template.in,v 1.4 2006/05/05 02:13:44 claude Exp $
#-----------------------------------------------------------------------------

use MNI::Startup qw(nocputimes);
use MNI::Spawn;
use MNI::MincUtilities qw(:geometry);
use Getopt::Tabular;
use POSIX qw(:math_h);

# Start main program ------------------------------------------------
&Initialize;
self_announce;

&MakeTemplate($input_volume, $output_volume, $shrink_factor);

#  End of Main Program
#-----------------------------------------------------------------------------

# ------------------------------ MNI Header ----------------------------------
#@NAME       : ShrinkVolume
#@INPUT      : volume, shrink factor
#@OUTPUT     : 
#@RETURNS    : 
#@DESCRIPTION: reduce sampling in finest sampling direction by given factor
#              reduce other sampling directions only if reduced sampling is 
#               less.  Uses nearest neighbour resampling.
#@METHOD     : 
#@GLOBALS    : Standard ($Execute, ...)
#@CALLS      : 
#@CREATED    : 96/05/29 J.G.Sled
#@MODIFIED   : 
#-----------------------------------------------------------------------------
sub MakeTemplate
{
   my ($input_volume, $output_volume, $shink_factor) = @_;
   my (@step, @length, $newstep);

   volume_params($input_volume, undef, \@step, \@length, undef, undef);
   
   if($shrink_factor > 1) {
      # find smallest step size
      $newstep = (abs($step[0]) < abs($step[1])) ? $step[0] : $step[1]; 
      $newstep = (abs($step[2]) < abs($newstep)) ? $step[2] : $newstep;

      $newstep = abs($newstep * $shrink_factor);
      
      for($i = 0; $i < 3; $i++) {
         if(abs($step[$i]) < $newstep) {
            $step[$i] = $step[$i] * $shrink_factor;
            $length[$i] = POSIX::ceil(($length[$i]-1)/$shrink_factor)+1;
         }
      }
   }
   
   # generate volume
   Spawn(['mincresample', $input_volume, $output_volume, '-nearest_neighbour',
         '-step', @step, '-nelements', @length, '-clobber']);

}


# ------------------------------ MNI Header ----------------------------------
#@NAME       : SetupArgTables
#@INPUT      : none
#@OUTPUT     : none
#@RETURNS    : References to the two option tables:
#                @pref_args
#                @protocol_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, @protocol_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]" ],
       ["-clobber|-noclobber", "boolean", 0, \$Clobber,
	"overwrite output files [default: -noclobber]"],
       ["-version", "call", undef, \&print_version,
        "print version and quit"]);

   # Protocol (data-specific) options 

   @protocol_args = 
      (["General Options","section"],
       ["-shrink", "integer", 1, \$shrink_factor, 
        "specify a smaller workspace; the"
        ." sampling in each dimension is reduced to that of the finest"
        ." sampling divided by factor or the current sampling which ever"
        ." is less. (suggest 2 or 3)", "<factor>"]); 
   
   (\@pref_args, \@protocol_args);
}

# ------------------------------ 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 = '1.12.0';
   $LongVersion = 'Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08';

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

Usage: $ProgramName [-help] [options] input_volume.mnc template.mnc
USAGE

   $Help = <<HELP;

$ProgramName is a script that creates a template based on the given volume

HELP

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

# ------------------------------ 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 $output_volume || -e "$output_volume.gz" ) && ! $Clobber) &&
      (die("Clobber option not given.  Cannot overwrite file:\n"
              ." $output_volume\n"));

   # check that appropriate files and directories exist
   (-r $input_volume) || die("Cannot read input file: $input_volume\n");
   (defined $user_mask_volume && !(-r $user_mask_volume)) &&
      die("Cannot read mask volume file: $user_mask_volume\n");
   
   ($shrink_factor < 1) &&
      die("Shrink factor must be greater than or equal to one.\n");
}


# ------------------------------ 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, $protocol_tbl, @args);

   # Set defaults for the global variables.  These can be overridden by 
   # the command line.
   $Verbose      = 0;

   SetHelp;
 
   # make_template specific parameters
   $shrink_factor = 1;

   # Parse command line arguments
   ($pref_tbl, $protocol_tbl) = SetupArgTables;

   GetOptions([@$pref_tbl, @$protocol_tbl], \@ARGV, \@args) || exit 1;
   if (@args != 2) 
   { 
      print STDERR $Usage;
      die "Incorrect number of arguments\n";
   }
   ($input_volume, $output_volume) = @args;

   # validate argument combinations and check filenames
   ValidateArgs;

   # Set global variables for calling various programs
   MNI::Spawn::SetOptions (strict  => 2);

   RegisterPrograms([qw(mincresample dd mv)]);
}