#!/usr/bin/perl
#
# suma_change_spec
#
# A script to automate the changing of SUMA's Spec. files.
#
# written by Xander Meadow
# 1/8/04
#
# Modified for new SUMA files by XM
# 2/11/04
#
#
# This code may be freely distributed, and modified as needed.  Please
# contact xmeadow@uchicago.edu with any questions or improvements for the
# script.
##############################################################################

use Getopt::Long;

# if no arguments presented, print out help message.
if(!$ARGV[0]) {
	$help=1;
}else {
	$help=0;
}

GetOptions(\%args, "input=s", "state=s", "domainparent=s", "output=s", "remove","anatomical");

# if not all of the necessary flags are present, print out help message.
if (!($args{input} && $args{state})) {
	$help=1;
}

# help message
if ($help) {
 print "suma_change_spec:\n";
 print " This program changes SUMA's surface specification (Spec) files.\n";
 print " At minimum, the flags input and state are required.\n";
 print "Available flags:\n";
 print "  input: Which is the SUMA Spec file you want to change.\n";
 print "  state: The state within the Spec file you want to change.\n";
 print "  domainparent: The new Domain Parent for the state within the ";
 print "\n\tSpec file you want to change.\n";
 print "  output: The name to which your new Spec file will be temporarily";
 print "\n\twritten to. (this flag is optional, if omitted the new Spec\n";
 print "\tfile will be temporarily written to 'input_file.change').\n";
 print "  remove: This flag will remove the automatically created backup.\n";
 print "  anatomical: This will add 'Anatomical = Y' to the selected\n";
 print "\tSurfaceState.\n";
 print "Usage:\n";
 print " This program will take the user given flags and create a spec file,\n";
 print " named from the output flag or <input>.change.  It will then take\n";
 print " this new spec file and overwrite the original input file.  If the -remove\n";
 print " flag is not used the original input file can be found at ";
 print "<inputfile>.bkp.\n If the -remove is used the .bkp file will be ";
 print " automatically deleted.\n\n";
 print " ex. suma_change_spec -input <file> -state <statename> \n";
 print "\t-domainparent <new_parent> -anatomical\n";
 exit;
}

# open read in and write out files.
open(IN,$args{input});
if (!(-e $args{input})) {
	print "ERROR!! Input file $args{input} does not exist\n";
	exit;
}
if ($args{output}) {
	open(OUT,">$args{output}");
}
else {
	open(OUT,">$args{input}.change");
}

# initialize variables.
$mark=0;
$holder="";

# read in input file.
while (<IN>) {
  chomp($_);

# Check to see if the line read in is either LocalDomainParent or
# Surface state line.
  if ($mark == 0) {
	switch: for ($_) {
	  /LocalDomainParent = / && do {
		$holder=$_;
		$mark=1;	
	  };
	  /SurfaceState = / && do {
		$mark=1;
	  };
	}
  }

# If the read in line is not a LocalDomainParent line, print it out.
  if (!($holder)) {
	print OUT "$_\n";
  }

# If mark equals 2, then the previous line was either a LocalDomainParent
# line or a SurfaceState line.  Either way now the script must check to
# see if this is the correct state to be making changes to.
  if ($mark == 2) {
	switch: for ($_) {
	    /$args{state}/ && do {
		if ($holder) {
		  if ($args{domainparent}) {
		   print OUT "\tLocalDomainParent = $args{domainparent}\n";
		  } else {
		   print OUT "$holder\n";
		  }
		  print OUT "$_\n";
		  $holder="";
		  $mark=0;
		}
		if ($args{anatomical}) {
		  print OUT "\tAnatomical = Y\n";
		}
		$mark=0;
	    };
	  }
# If this is not the correct SurfaceState, then print out the held
# LocalDomainParent line as well as the current SurfaceState line.
# Also, clear the holder variable.
	if ($holder) {
	  print OUT "$holder\n";
	  print OUT "$_\n";
	  $holder="";
	  $mark=0;
	}
  }

# This is required to allow to a new input $_ to be read in, that $_ should
# be the SurfaceState information.
  if ($mark == 1) { $mark=2; }
}

# Close the read in and write out files.
close(IN);
close(OUT);

# Move the original input file to a backup file, unless the user has requested
# no backup file be created, then if there was an output file, change its 
# name to the original input file.  If there wasn't an output file, move the
# input.change file's name to the original input file.
if (!($args{remove})) {
`mv $args{input} $args{input}.bkp`;
}
if ($args{output}) {
  `mv $args{output} $args{input}`;
}
else {
  `mv $args{input}.change $args{input}`;
}