#!/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: sharpen_volume.in,v $
#$Revision: 1.1 $
#$Author: bert $
#$Date: 2003/04/16 14:29:34 $
#$State: Exp $
#---------------------------------------------------------------------------
# ------------------------------ MNI Header ----------------------------------
#@NAME       : sharpen_volume
#@INPUT      : 
#@OUTPUT     : 
#@RETURNS    : 
#@DESCRIPTION: modifies intensities so as to produce a sharper histogram
#@METHOD     : 
#@GLOBALS    : 
#@CALLS      : 
#@CREATED    : February 28, 1996 
#@MODIFIED   : 
#-----------------------------------------------------------------------------
use MNI::Startup qw(nocputimes);
use MNI::Spawn;
use MNI::FileUtilities;
use Getopt::Tabular;

&Initialize;

&Spawn(['volume_hist', '-bins', $bins, '-auto_range', '-mask', $mask_volume,
         $source_volume, "$base_name.hist", '-clobber', '-text', '-select',
         1, '-quiet', @window_option]);
$min_bin = 0;
$max_bin = 1;
open(FILE, "$base_name.hist");
while(<FILE>) {
   if(/domain: +([-e\d\.]+) +([-e\d\.]+)/) {
      $min_bin = $1;
      $max_bin = $2;
   }
}
close(FILE);

&Spawn(['sharpen_hist', '-clobber', @blur_option, '-fwhm', $filter_fwhm,
       '-noise', $noise_level, '-quiet', '-range', $min_bin, $max_bin,
        "$base_name.hist", "$base_name.sharp"]);
&Spawn(['minclookup', '-continuous', '-range', $min_bin, $max_bin, '-clobber',
       '-lookup_table', "$base_name.sharp", $source_volume, $output_volume]);

(defined $save_histogram) && &Spawn("cp $base_name.hist $save_histogram");


# ------------------------------ MNI Header ----------------------------------
#@NAME       : &Initialize
#@INPUT      : none
#@OUTPUT     : none
#@RETURNS    : 
#@DESCRIPTION: 
#@METHOD     : 
#@GLOBALS    : 
#@CALLS      : 
#@CREATED    : 
#@MODIFIED   : 
#-----------------------------------------------------------------------------
sub Initialize
{
   $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] [options] mask.mnc input.mnc output.mnc
USAGE

   $Help = <<HELP;

$ProgramName is a script that modifies the intensities in a volume such that
   the histogram is sharper.

HELP

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

   $filter_fwhm = .2;
   $noise_level = .01;
   $bins        = 200;
   $blur_flag    = 0;
   $window_flag  = 0;
   undef $save_histogram;

   sub print_version
   {
      print "Program $ProgramName, built from:\n$LongVersion\n";
      exit;
   }
  
   @args_table = 
      (["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"], 
#       ["-tmpdir", "string", 1, \$TmpDir,
#	"temporary working directory"],
#       ["-keeptmp|-nokeeptmp", "boolean", 0, \$KeepTmp,
#	"don't delete temporary files [default: -nokeeptmp]"],
       
       ["Protocol Options","section"],
       ["-fwhm", "float", 1, \$filter_fwhm,
	"<value> fwhm of blur in histogram (default .2)"],
       ["-noise", "float", 1, \$noise_level,
	"<value> noise threshold for deconvolution"],
       ["-bins", "integer", 1, \$bins,
        "<number>  specify number of bins in histogram (default 200)"],
       ["-blur|-deblur", "boolean", undef, \$blur_flag,
	"use blurring.  -deblur: skip deblurring step."],
       ["-parzen|-noparzen", "boolean", undef, \$window_flag,
        "use Parzen window when estimating intensity distribution"],
       ["-save_histogram", "string", 1, \$save_histogram,
        "keep uncorrected histogram"]);

   my (@reducedARGV);
   GetOptions(\@args_table, \@ARGV, \@reducedARGV) || exit 1;
   
   if (@reducedARGV != 3) 
   { 
      print STDERR "Leftover args: @reducedARGV\n" if @reducedARGV;
      print STDERR $Usage;
      die "Incorrect number of arguments\n";
   } 

   ($mask_volume, $source_volume, $output_volume) = @reducedARGV;
   # check whether $output_volume can be over written
   ((-e $output_volume) && ! $Clobber) &&
      (die("Clobber option not given.  Cannot overwrite file:"
              ." $output_volume\n"));

   ($output_volume =~ ?^([\S]+).mnc?) && ($base_name = $1) ||
      die "sharpen_volume failed: output volume does not appear to be"
      ." a minc volume.\n";

   @blur_option = $blur_flag ? ('-blur') : ();
   @window_option = $window_flag ? ('-window') : ();

   # Set global variables for calling various programs
   MNI::Spawn::SetOptions (strict  => 2);
   RegisterPrograms([qw(volume_hist sharpen_hist minclookup cp)]);

}