Index: BOL/Multi_atlas/METRICS/epstopdf
===================================================================
--- BOL/Multi_atlas/METRICS/epstopdf	(revision 4342)
+++ 	(revision )
@@ -1,421 +1,0 @@
-#!/usr/bin/env perl
-use strict;
-
-# Change by Thomas Esser, Sept. 1998: The above lines allows us to find
-# perl along $PATH rather than guessing a fixed location. The above
-# construction should work with most shells.
-
-# A script to transform an EPS file so that:
-#   a) it is guarenteed to start at the 0,0 coordinate
-#   b) it sets a page size exactly corresponding to the BoundingBox
-# This means that when Ghostscript renders it, the result needs no
-# cropping, and the PDF MediaBox is correct.
-#   c) the result is piped to Ghostscript and a PDF version written
-#
-# It needs a Level 2 PS interpreter.
-# If the bounding box is not right, of course, you have problems...
-#
-# The only thing I have not allowed for is the case of
-# "%%BoundingBox: (atend)", which is more complicated.
-#
-# Sebastian Rahtz, for Elsevier Science
-#
-# now with extra tricks from Hans Hagen's texutil.
-#
-# History
-#  1999/05/06 v2.5 (Heiko Oberdiek)
-#    * New options: --hires, --exact, --filter, --help.
-#    * Many cosmetics: title, usage, ...
-#    * New code for debug, warning, error
-#    * Detecting of cygwin perl
-#    * Scanning for %%{Hires,Exact,}BoundingBox.
-#    * Scanning only the header in order not to get a wrong
-#      BoundingBox of an included file.
-#    * (atend) supported.
-#    * uses strict; (earlier error detecting).
-#    * changed first comment from '%!PS' to '%!';
-#    * corrected (atend) pattern: '\s*\(atend\)'
-#    * using of $bbxpat in all BoundingBox cases,
-#      correct the first white space to '...Box:\s*$bb...'
-#    * corrected first line (one line instead of two before 'if 0;';
-#  2000/11/05 v2.6 (Heiko Oberdiek)
-#    * %%HiresBoundingBox corrected to %%HiResBoundingBox
-#  2001/03/05 v2.7 (Heiko Oberdiek)
-#    * Newline before grestore for the case that there is no
-#      whitespace at the end of the eps file.
-#  2002/02/18 v2.8draft (Gerben Wierda)
-#    * Handle different eol styles transparantly
-#    * Applied fix from Peder Axensten for Freehand bug
-#  2002/02/21 v2.8draft (Gerben Wierda)
-#    * Fixed bug where last line of buffer was not copied out (ugh!)
-#  2003/04/22 v2.9draft (Gerben Wierda)
-#    * Fixed bug where with cr-eol files everything up to the first %!
-#    * in the first 2048 bytes was gobbled (double ugh!)
-#  2004/03/17 v2.9.1draft (Gerben Wierda)
-#    * No autorotate page
-#  2005/09/29 v2.9.2draft (Gerben Wierda)
-#    * Quote OutFilename
-#  2005/10/01 v2.9.3draft (Gerben Wierda)
-#    * Quote OutFilename
-#  2005/10/06 v2.9.4gw (Gerben Wierda)
-#    * This has become the official version for now
-#  2005/10/06 v2.9.5gw (Gerben Wierda)
-#    * Fixed a horrendous bug in the (atend) handling code
-#
-
-### program identification
-my $program = "epstopdf";
-my $filedate="2006/01/29";
-my $fileversion="2.9.5gw";
-my $copyright = "Copyright 1998-2006 by Sebastian Rahtz et al.";
-my $title = "\U$program\E $fileversion, $filedate - $copyright\n";
-
-### ghostscript command name
-my $GS = "gs";
-$GS = "gswin32c" if $^O eq 'MSWin32';
-$GS = "gswin32c" if $^O =~ /cygwin/;
-
-### options
-$::opt_help=0;
-$::opt_debug=0;
-$::opt_compress=1;
-$::opt_gs=1;
-$::opt_hires=0;
-$::opt_exact=0;
-$::opt_filter=0;
-$::opt_outfile="";
-
-### usage
-my @bool = ("false", "true");
-my $usage = <<"END_OF_USAGE";
-${title}Syntax:  $program [options] <eps file>
-Options:
-  --help:           print usage
-  --outfile=<file>: write result to <file>
-  --(no)filter:     read standard input   (default: $bool[$::opt_filter])
-  --(no)gs:         run ghostscript       (default: $bool[$::opt_gs])
-  --(no)compress:   use compression       (default: $bool[$::opt_compress])
-  --(no)hires:      scan HiResBoundingBox (default: $bool[$::opt_hires])
-  --(no)exact:      scan ExactBoundingBox (default: $bool[$::opt_exact])
-  --(no)debug:      debug informations    (default: $bool[$::opt_debug])
-Examples for producing 'test.pdf':
-  * $program test.eps
-  * produce postscript | $program --filter >test.pdf
-  * produce postscript | $program -f -d -o=test.pdf
-Example: look for HiResBoundingBox and produce corrected PostScript:
-  * $program -d --nogs -hires test.ps>testcorr.ps
-END_OF_USAGE
-
-### process options
-use Getopt::Long;
-GetOptions (
-  "help!",
-  "debug!",
-  "filter!",
-  "compress!",
-  "gs!",
-  "hires!",
-  "exact!",
-  "outfile=s",
-) or die $usage;
-
-### help functions
-sub debug {
-  print STDERR "* @_\n" if $::opt_debug;
-}
-sub warning {
-  print STDERR "==> Warning: @_!\n";
-}
-sub error {
-  die "$title!!! Error: @_!\n";
-}
-sub errorUsage {
-  die "$usage\n!!! Error: @_!\n";
-}
-
-### option help
-die $usage if $::opt_help;
-
-### get input filename
-my $InputFilename = "";
-if ($::opt_filter) {
-  @ARGV == 0 or
-    die errorUsage "Input file cannot be used with filter option";
-  $InputFilename = "-";
-  debug "Input file: standard input";
-}
-else {
-  @ARGV > 0 or die errorUsage "Input filename missing";
-  @ARGV < 2 or die errorUsage "Unknown option or too many input files";
-  $InputFilename = $ARGV[0];
-  -f $InputFilename or error "'$InputFilename' does not exist";
-  debug "Input filename:", $InputFilename;
-}
-
-### option compress
-my $GSOPTS = "";
-$GSOPTS = "-dUseFlateCompression=false " unless $::opt_compress;
-
-### option BoundingBox types
-my $BBName = "%%BoundingBox:";
-!($::opt_hires and $::opt_exact) or
-  error "Options --hires and --exact cannot be used together";
-$BBName = "%%HiResBoundingBox:" if $::opt_hires;
-$BBName = "%%ExactBoundingBox:" if $::opt_exact;
-debug "BoundingBox comment:", $BBName;
-
-### option outfile
-my $OutputFilename = $::opt_outfile;
-if ($OutputFilename eq "") {
-  if ($::opt_gs) {
-    $OutputFilename = $InputFilename;
-    if (!$::opt_filter) {
-      $OutputFilename =~ s/\.[^\.]*$//;
-      $OutputFilename .= ".pdf";
-    }
-  }
-  else {
-    $OutputFilename = "-"; # standard output
-  }
-}
-if ($::opt_filter) {
-  debug "Output file: standard output";
-}
-else {
-  debug "Output filename:", $OutputFilename;
-}
-
-### option gs
-if ($::opt_gs) {
-  debug "Ghostscript command:", $GS;
-  debug "Compression:", ($::opt_compress) ? "on" : "off";
-}
-
-### open input file
-open(IN,"<$InputFilename") or error "Cannot open",
-  ($::opt_filter) ? "standard input" : "'$InputFilename'";
-binmode IN;
-
-### open output file
-if ($::opt_gs) {
-  my $pipe = "$GS -q -sDEVICE=pdfwrite $GSOPTS -dAutoRotatePages=/None" .
-          " -sOutputFile='$OutputFilename' - -c quit";
-  debug "Ghostscript pipe:", $pipe;
-  open(OUT,"|$pipe") or error "Cannot open Ghostscript for piped input";
-}
-else {
-  open(OUT,">$OutputFilename") or error "Cannot write '$OutputFilename";
-}
-
-# reading a cr-eol file on a lf-eol system makes it impossible to parse
-# the header and besides it will read the intire file into yor line by line
-# scalar. this is also true the other way around.
-
-### scan a block, try to determine eol style
-
-my $buf;
-my $buflen;
-my @bufarray;
-my @parsedbufarray; # for mytell/myseek
-my $bufarraypos;
-
-# We assume 2048 is big enough.
-my $EOLSCANBUFSIZE = 2048;
-
-$buflen = read( IN, $buf, $EOLSCANBUFSIZE);
-if ($buflen > 0) {
-  my $crlfpos;
-  my $lfpos;
-  my $crpos;
-
-  # remove binary junk before header
-  # if there is no header, we assume the file starts with ascii style and
-  # we look for a eol style anyway, to prevent possible loading of the
-  # entire file
-  if ($buf =~ /%!/) {
-    # throw away binary junk before %!
-    $buf =~ s/(.*?)%!/%!/o;
-  }
-  $lfpos = index( $buf, "\n");
-  $crpos = index( $buf, "\r");
-  $crlfpos = index( $buf, "\r\n");
-
-  if ($crpos > 0 and ($lfpos == -1 or $lfpos > $crpos+1)) {
-    # The first eol was a cr and it was not immediately followed by a lf
-    $/ = "\r";
-    debug "The first eol character was a CR ($crpos) and not immediately followed by a LF ($lfpos)";
-  }
-
-  # Now we have set the correct eol-character. Get one more line and add
-  # it to our buffer. This will make the buffer contain an entire line
-  # at the end. Then split the buffer in an array. We will draw lines from
-  # that array until it is empty, then move again back to <IN>
-  $buf .= <IN> unless eof( IN);
-  $buflen = length( $buf);
-  $bufarraypos = 0;
-
-  # Some extra magic is needed here: if we set $/ to \r, Perl's re engine
-  # still thinks eol is \n in regular expressions (not very nice) so we
-  # cannot split on ^, but have to split on \r and reappend those.
-  if ($/ eq "\r") {
-    @bufarray = split( /\r/ms, $buf); # split on \r
-    grep( $_ .= "\r", @bufarray); # re-append \r to each array item
-  }
-  else {
-    @bufarray = split( /^/ms, $buf);
-  }
-}
-
-### getline
-sub getline {
-  if ($#bufarray >= 0) {
-    $_ = shift( @bufarray);
-    unshift( @parsedbufarray, $_); # for myseek and mytell
-    $bufarraypos += length( $_);
-    # debug "getline from array. bufarraypos = $bufarraypos";
-    # debug "*** READ: $_";
-  }
-  else {
-    $_ = <IN>;
-  }
-  return( defined( $_));
-}
-
-### mytell and myseek, work on <IN> only
-sub mytell {
-  if ($#bufarray) {
-    # debug "Telling ARRAY position $bufarraypos";
-    return $bufarraypos;
-  }
-  else {
-    my $pos = tell( IN);
-    # debug "Telling FILE position $pos";
-    return $pos;
-  }
-}
-
-sub myseek {
-  my $pos = shift;
-  # debug "Seeking to position $pos in input";
-  if ($pos < $buflen) {
-    # debug "myseek position $pos < buffer size $buflen";
-    # We were still parsing the array, reset to the end of buf and
-    # move to the right line in the array.
-    # Now, move stuff from the @parsedbufarray back until we are back at $pos
-    my $tmpline;
-    while ($bufarraypos > $pos) {
-      # debug "myseek bufarray position $bufarraypos > position $pos";
-      # we test on parsedbufarray to prevent an infinite loop on
-      # a programming error (DEVELOP only)
-      die "Programming error 1\n" unless $#parsedbufarray;
-      $tmpline = shift( @parsedbufarray);
-      $bufarraypos -= length( $tmpline);
-      unshift( @bufarray, $tmpline);
-      debug "*** UNREAD: $tmpline";
-    }
-    # debug "Returning to ARRAY size position $buflen (bufarraypos = $bufarraypos)";
-    return seek( IN, $buflen, 0);
-  }
-  else {
-    # debug "Seeking to FILE position $pos";
-    return seek( IN, $pos, 0);
-  }
-}
-
-### scan first line
-my $header = 0;
-getline();
-if (/%!/) {
-  # throw away binary junk before %!
-  s/(.*)%!/%!/o;
-}
-$header = 1 if /^%/;
-debug "Scanning header for BoundingBox";
-print OUT;
-
-### variables and pattern for BoundingBox search
-my $bbxpatt = '[0-9eE\.\-]';
-               # protect backslashes: "\\" gets '\'
-my $BBValues = "\\s*($bbxpatt+)\\s+($bbxpatt+)\\s+($bbxpatt+)\\s+($bbxpatt+)";
-my $BBCorrected = 0;
-
-sub CorrectBoundingBox {
-  my ($llx, $lly, $urx, $ury) = @_;
-  debug "Old BoundingBox:", $llx, $lly, $urx, $ury;
-  my ($width, $height) = ($urx - $llx, $ury - $lly);
-  my ($xoffset, $yoffset) = (-$llx, -$lly);
-  debug "New BoundingBox: 0 0", $width, $height;
-  debug "Offset:", $xoffset, $yoffset;
-
-  print OUT "%%BoundingBox: 0 0 $width $height\n";
-  print OUT "<< /PageSize [$width $height] >> setpagedevice\n";
-  print OUT "gsave $xoffset $yoffset translate\n";
-}
-
-### scan header
-if ($header) {
-  HEADER: while (getline()) {
-    ### Fix for freehand bug ### by Peder Axensten
-    next HEADER if(!/\S/);
-
-    ### end of header
-    if (!/^%/ or /^%%EndComments/) {
-      print OUT;
-      last;
-    }
-
-    ### BoundingBox with values
-    if (/^$BBName$BBValues/) {
-      CorrectBoundingBox $1, $2, $3, $4;
-      $BBCorrected = 1;
-      last;
-    }
-
-    ### BoundingBox with (atend)
-    if (/^$BBName\s*\(atend\)/) {
-      debug $BBName, "(atend)";
-      if ($::opt_filter) {
-        warning "Cannot look for BoundingBox in the trailer",
-                "with option --filter";
-        last;
-      }
-      my $pos = mytell();
-      debug "Current file position:", $pos;
-
-      # looking for %%BoundingBox
-      while (getline()) {
-        # skip over included documents
-        if (/^%%BeginDocument/) {
-          while (getline()) {
-            last if /^%%EndDocument/;
-          }
-        }
-        if (/^$BBName$BBValues/) {
-          CorrectBoundingBox $1, $2, $3, $4;
-          $BBCorrected = 1;
-          last;
-        }
-      }
-
-      # go back
-      myseek( $pos) or error "Cannot go back to line '$BBName (atend)'";
-      last;
-    }
-
-    # print header line
-    print OUT;
-  }
-}
-
-### print rest of file
-while (getline()) {
-  print OUT;
-}
-
-### close files
-close(IN);
-print OUT "\ngrestore\n" if $BBCorrected;
-close(OUT);
-warning "BoundingBox not found" unless $BBCorrected;
-debug "Ready.";
-;
