nu_correct_norm.in

#! @PERL@
 
#---------------------------------------------------------------------------
#@COPYRIGHT :
#             Copyright 1998, Alex P. Zijdenbos
#             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: nu_correct_norm.in,v $
#$Revision: 1.2 $
#$Author: claude $
#$Date: 2006-05-05 01:21:32 $
#$State: Exp $
#---------------------------------------------------------------------------

use warnings "all";

use MNI::Startup;
use MNI::Spawn;
use MNI::FileUtilities qw(check_output_dirs);
use MNI::PathUtilities qw(replace_dir);
use Getopt::Tabular;
use IO::File;

use strict;

# User-modifiable globals
my $Inputfile;
my $Outputfile;

# Other globals
my($Usage, $Help);

&Initialize;

my $TmpFile = replace_dir ($TmpDir, $Inputfile);
$TmpFile =~ s/\.(gz|z|Z)$//;

Spawn(['nu_correct', $Inputfile, $TmpFile]);

Spawn(['normalize_mri', '-nolg', '-inormalize', '-const 1000 -ratioOfMedians',
       $TmpFile, $Outputfile]);

# ------------------------------ MNI Header ----------------------------------
#@NAME       : Initialize
#@INPUT      : 
#@OUTPUT     : 
#@RETURNS    : 
#@DESCRIPTION: 
#@METHOD     : 
#@GLOBALS    : 
#@CALLS      : 
#@CREATED    : 98/11/29, Alex Zijdenbos
#@MODIFIED   : 
#-----------------------------------------------------------------------------
sub Initialize
{
   $, = ' ';     # set output field separator

   # First, announce ourselves to stdout (for ease in later dissection
   # of log files) -- unless STDOUT is a tty.
   self_announce if $Verbose;

   # Set defaults for the global variables.
   $Verbose      = 1;
   $Execute      = 1;
   $Clobber      = 0;
   $KeepTmp      = 0;

   &CreateInfoText;

   my(@argTbl) = (@DefaultArgs);
   
   my(@leftOverArgs);

   GetOptions (\@argTbl, \@ARGV, \@leftOverArgs) || die "\n";
   if (@leftOverArgs != 2) {
       warn $Usage;
       die "Incorrect number of arguments\n";
   }

   ($Inputfile, $Outputfile) = @leftOverArgs;

   die "Output file $Outputfile exists! Use -clobber to overwrite\n"
       if (-e $Outputfile && ! $Clobber);

   RegisterPrograms([qw(nu_correct normalize_mri)]) || die;

   AddDefaultArgs('nu_correct',     ($Verbose) ? ['-verbose'] : ['-quiet']);
   AddDefaultArgs('normalize_mri',  ($Verbose) ? ['-verbose'] : ['-quiet']);

   AddDefaultArgs('nu_correct',     ['-clobber']);
   AddDefaultArgs('normalize_mri',  ['-clobber']);

   &check_output_dirs($TmpDir) if $Execute;

   # Be strict about having programs registered
   MNI::Spawn::SetOptions (strict => 2);
}

# ------------------------------ MNI Header ----------------------------------
#@NAME       : CreateInfoText
#@INPUT      : 
#@OUTPUT     : 
#@RETURNS    : 
#@DESCRIPTION: 
#@METHOD     : 
#@GLOBALS    : 
#@CALLS      : 
#@CREATED    : 98/11/29, Alex Zijdenbos
#@MODIFIED   : 
#-----------------------------------------------------------------------------
sub CreateInfoText
{
    $Usage = <<USAGE;
Usage: $ProgramName [options] <input.mnc> <output.mnc> 
       $ProgramName -help for details
USAGE

    $Help = <<HELP;

$ProgramName nu_corrects and normalizes <input.mnc>.
The global intensity normalization targets an absolute median value of 1000.
HELP

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