Index: trunk/doc/README
===================================================================
--- trunk/doc/README	(revision 4)
+++ trunk/doc/README	(revision 4)
@@ -0,0 +1,169 @@
+
+Using ExRootAnalysis package for PGS data analysis
+==================================================
+
+
+Author: Pavel Demin
+
+
+
+
+Introductory remarks
+====================
+
+
+The ExRootAnalysis is a package designed to simplify ROOT tree production and
+analysis. The purpose of this tutorial is to present current functionality of
+this software.
+
+
+
+
+Quick start with ExRootAnalysis
+===============================
+
+Make sure that ROOT is installed and ROOTSYS, PATH, LD_LIBRARY_PATH,
+DYLD_LIBRARY_PATH are configured correctly.
+
+Command to unpack the source code:
+
+   tar -zxf ExRootAnalysis.tar.gz
+
+Commands to create shared library for interactive ROOT session:
+
+   cd ExRootAnalysis
+
+   make
+
+Commands to create static library for linking with PGS:
+
+   cd ExRootAnalysis
+
+   make static
+
+
+
+
+Simple analysis using TTree::Draw
+=================================
+
+
+Now we can start ROOT and look at the data stored in the ROOT tree.
+
+Start ROOT and load shared library:
+
+   root
+   gSystem->Load("lib/libExRootAnalysis.so");
+
+Open ROOT tree file and do some basic analysis using Draw or TBrowser:
+
+   TFile::Open("pgs_events.root");
+   LHCO->Draw("Electron.PT");
+   TBrowser browser;
+
+Note 1: LHCO - tree name, it can be learnt e.g. from TBrowser
+
+Note 2: Electron - branch name; PT - variable (leaf) of this branch
+
+Complete description of all branches can be found in
+
+   ExRootAnalysis/doc/RootTreeDescription.html
+
+
+
+
+Macro-based analysis
+====================
+
+
+Analysis macro consists of histogram booking, event loop (histogram filling),
+histogram display
+
+Basic analysis macro:
+
+{
+  // Load shared library
+  gSystem->Load("lib/libExRootAnalysis.so");
+  gSystem->Load("libPhysics");
+
+  // Create chain of root trees
+  TChain chain("LHCO");
+  chain.Add("pgs_events.root");
+  
+  // Create object of class ExRootTreeReader
+  ExRootTreeReader *treeReader = new ExRootTreeReader(&chain);
+  Long64_t numberOfEntries = treeReader->GetEntries();
+  
+  // Get pointers to branches used in this analysis
+  TClonesArray *branchJet = treeReader->UseBranch("Jet");
+  TClonesArray *branchElectron = treeReader->UseBranch("Electron");
+  
+  // Book histograms
+  TH1 *histJetPT = new TH1F("jet_pt", "jet P_{T}", 100, 0.0, 100.0);
+  TH1 *histMass = new TH1F("mass", "M_{inv}(e_{1}, e_{2})", 100, 40.0, 140.0);
+
+  // Loop over all events
+  for(Int_t entry = 0; entry < numberOfEntries; ++entry) {
+
+    // Load selected branches with data from specified event
+    treeReader->ReadEntry(entry);
+  
+    // If event contains at least 1 jet
+    if(branchJet->GetEntries() > 0) {
+
+      // Take first jet
+      TRootJet *jet = (TRootJet*) branchJet->At(0);
+      
+      // Plot jet transverse momentum
+      histJetPT->Fill(jet->PT);
+      
+      // Print jet transverse momentum
+      cout << jet->PT << endl;
+    }
+
+    TRootElectron *elec1, *elec2;
+    TLorentzVector vec1, vec2;
+
+    // If event contains at least 2 electrons
+    if(branchElectron->GetEntries() > 1) {
+
+      // Take first two electrons
+      elec1 = (TRootElectron *) branchElectron->At(0);
+      elec2 = (TRootElectron *) branchElectron->At(1);
+
+      // Create two 4-vectors for the electrons
+      vec1.SetPtEtaPhiM(elec1->PT, elec1->Eta, elec1->Phi, 0.0);
+      vec2.SetPtEtaPhiM(elec2->PT, elec2->Eta, elec2->Phi, 0.0);
+
+      // Plot their invariant mass
+      histMass->Fill((vec1 + vec2).M());
+    }
+  }
+
+  // Show resulting histograms
+  histJetPT->Draw();
+  histMass->Draw();
+}
+
+
+
+
+More advanced macro-based analysis
+==================================
+
+
+ExRootAnalysis/test contains macro Example.C using class ExRootTreeReader to
+access data and class ExRootResult to manage histograms booking and output
+
+Here are commands to run this macro:
+
+   cd ExRootAnalysis/test
+   $EDITOR test.list
+   root
+   gSystem->Load("../lib/libExRootAnalysis.so");
+   .X Example.C("test.list");
+
+Note: file test.list should contain list of root files that you would like to
+analyse (one root file per line)
+
+
Index: trunk/doc/awk/branches_gen.awk
===================================================================
--- trunk/doc/awk/branches_gen.awk	(revision 4)
+++ trunk/doc/awk/branches_gen.awk	(revision 4)
@@ -0,0 +1,54 @@
+BEGIN {
+  print "<html>"
+  
+  print "<head>"
+  print "  <meta HTTP-EQUIV=\"Content-Type\" CONTENT=\"text/html; charset=iso-8859-1\">"
+  print "  <meta NAME=\"keywords\" CONTENT=\"root, tree, ntuple, format, description\">"
+  print "  <title>root tree description</title>"
+  print "</head>"
+
+  print "<body>"
+  
+  print "<H1>root tree description</H1>"
+  print "<hr>"
+  print "<H2>Branches</H2>"
+  print "<hr>"
+
+  print "<table style=\"border: 1px dotted;\" align=\"center\" border=\"0\" cellpadding=\"7\" cellspacing=\"3\" widt=\"95%\">"
+  print "<tr><td><b>Branch</b></td>"
+  print "<td><b>Definition</b></td>"
+  print "<td><b>Class</b></td></tr>"
+
+  even = 1;
+  previous_line = ""
+}
+
+function print_line(previous_line, current_line, even) {
+  if(even) print "<tr bgcolor=\"#eeeeee\">"
+ 	else print "<tr bgcolor=\"#ffffff\">"
+  split(current_line, a, "\"");
+  print "  <td>"a[2]"</td>"
+  split(previous_line, a, "// ");
+  print "  <td>"a[2]"</td>"
+  split(current_line, a, ",");
+  split(a[2], b, "::");
+  gsub(" ", "", b[1]);
+ 
+  if(b[1] == "ExRootGen" || b[1] == "ExRootSimParticle") b[1] = "ExRootGenParticle";
+ 
+  print "  <td><a href=\"#"b[1]"\">"b[1]"</a></td>";
+  print "</tr>";
+}
+
+/NewBranch/ {
+  print_line(previous_line, $0, even);
+  even = !even;
+}
+
+{
+  previous_line = $0
+}
+
+END {
+  print "</table>"
+}
Index: trunk/doc/awk/classes_gen.awk
===================================================================
--- trunk/doc/awk/classes_gen.awk	(revision 4)
+++ trunk/doc/awk/classes_gen.awk	(revision 4)
@@ -0,0 +1,55 @@
+BEGIN {  
+  print "<hr>"
+  print "<H2>Classes</H2>"
+  print "<hr>"
+
+  print "<table style=\"border: 1px dotted;\" align=\"center\" border=\"0\" cellpadding=\"7\" cellspacing=\"3\" widt=\"95%\">"
+  print "<tr><td><b>Parameter</b></td>"
+  print "<td><b>Definition</b></td>"
+  print "<td><b>How it was calculated</b></td></tr>"
+
+}
+
+function print_line(name, comment, even, end) {
+  if(name != ""){
+   	if(even) print "<tr bgcolor=\"#eeeeee\">"
+   	else print "<tr bgcolor=\"#ffffff\">"
+    print "  <td>"name"</td>"
+    split(comment, a, "|");
+    print "  <td>"a[1]"</td>"
+    print "  <td>"a[2]"</td>"
+    print "</tr>"
+  }
+}
+
+/^ *class ExRoot/{
+  print_line(name, comment, even, 1);
+  even = 1;
+  name = "";
+  comment = "";
+  split($2, a, ":");
+  print "<tr bgcolor=\"#ffffff\"><td colspan=3><hr><a name=\""a[1]"\"><H3>"a[1]"</H3><hr></td></tr>"
+}
+
+/: public ExRoot[^S]/{
+  name = sprintf("<a href=\"#%s\">%s</a>", $4, $4);
+  split($2, a, ":");
+  comment = sprintf("%s inherits all %s parameters", a[1], $4);
+}
+
+/^ *[A-Za-z_]* [A-Za-z].*; \/\/ / {
+  print_line(name, comment, even, 0);
+  split($2, a, ";");
+  name = a[1];
+  split($0, a, "// ");
+  comment = a[2];
+  even = !even;
+}
+
+/^ +\/\/ /{split($0, a, "// "); comment = comment" "a[2]}
+END {
+  print_line(name, comment, even, 1);
+  print "</table>"
+  print "</body></html>"
+}
+
Index: trunk/doc/awk/script.sh
===================================================================
--- trunk/doc/awk/script.sh	(revision 4)
+++ trunk/doc/awk/script.sh	(revision 4)
@@ -0,0 +1,16 @@
+#! /bin/sh
+
+if [ $# -ne 1 ]
+then
+  echo " Usage: $0 output_file"
+  echo " output_file - output file in HTML format."
+  exit
+fi
+
+awk -f branches_gen.awk \
+  ../../test/ExRootLHEFConverter.cpp \
+  ../../test/ExRootSTDHEPConverter.cpp \
+  ../../test/ExRootLHCOlympicsConverter.cpp > $1
+awk -f classes_gen.awk \
+  ../../ExRootAnalysis/ExRootClasses.h >> $1
+
Index: trunk/doc/awk/script_with_pgs.sh
===================================================================
--- trunk/doc/awk/script_with_pgs.sh	(revision 4)
+++ trunk/doc/awk/script_with_pgs.sh	(revision 4)
@@ -0,0 +1,14 @@
+#! /bin/sh
+
+if [ $# -ne 1 ]
+then
+  echo " Usage: $0 output_file"
+  echo " output_file - output file in HTML format."
+  exit
+fi
+
+awk -f branches_gen.awk \
+  ../../test/ExRootLHEFConverter.cpp \
+  ../../pgs/ExRootAnalysis.cc > $1
+awk -f classes_gen.awk ../../ExRootAnalysis/ExRootClasses.h >> $1
+
Index: trunk/doc/epstosmth
===================================================================
--- trunk/doc/epstosmth	(revision 4)
+++ trunk/doc/epstosmth	(revision 4)
@@ -0,0 +1,335 @@
+#!/usr/bin/env perl
+
+# Copyright 1998-2001 by Sebastian Rahtz et al.
+# epstopdf is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# epstopdf is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with epstopdf; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+
+use strict;
+
+# 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.
+#  2006/05/09 v2.8 (David W. Rankin, Jr.)
+#    * option --pdfvers to specify the Ghostscript command to set
+#      the PDF version output.
+
+my $IsWin32 = ($^O =~ /MSWin32/i);
+
+### program identification
+my $program = "epstosmth";
+my $filedate="2006/05/09";
+my $fileversion="2.8";
+my $copyright = "Copyright 1998-2001 by Sebastian Rahtz et al.";
+my $title = "\U$program\E $fileversion, $filedate - $copyright\n";
+
+### ghostscript command name
+my $GS = "gs";
+$GS = "gswin32c" if $^O eq 'MSWin32';
+
+if ($IsWin32) {
+  $GS = `kpsecheck --ghostscript`;
+  $GS =~ m/^dll\s*:\s*(.+)/mio;
+  $GS = $1;
+  $GS =~ s/gsdll32.dll/gswin32c.exe/io;
+  if ($GS eq "") {
+    $GS = "gswin32c.exe";
+  }
+  $GS = "\"$GS\"" if ($GS =~ m/\s/);
+}
+
+### options
+$::opt_help=0;
+$::opt_debug=0;
+$::opt_compress=1;
+$::opt_gs=1;
+$::opt_hires=0;
+$::opt_exact=0;
+$::opt_filter=0;
+$::opt_outfile="";
+$::opt_pdfvers="";
+$::opt_gsdev="pdfwrite";
+$::opt_gsopt="";
+
+### 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)pdfvers:    PDF Version for Output (default: [GhostScript's default])
+  --(no)hires:      scan HiResBoundingBox  (default: $bool[$::opt_hires])
+  --(no)exact:      scan ExactBoundingBox  (default: $bool[$::opt_exact])
+  --(no)debug:      debug informations     (default: $bool[$::opt_debug])
+  --gsdev=<dev>:    select gs device
+  --gsopt=<opts>:   additional gs options
+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!",
+  "pdfvers=s",
+  "outfile=s",
+  "gsdev=s",
+  "gsopt=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 $GSOPTS = "$::opt_gsopt ";
+
+debug "gs opts:", $GSOPTS;
+
+$GSOPTS .= "-dUseFlateCompression=false " unless $::opt_compress;
+
+### option pdfvers (GhostScript PDF Compatability options)
+$GSOPTS .= "-dCompatibilityLevel=$::opt_pdfvers " unless $::opt_pdfvers eq "";
+
+### 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) {
+      $OutputFilename =~ s/\.[^\.]*$//;
+      if ($::opt_gsdev =~ m/^pdf/) {
+        $OutputFilename .= '.pdf';
+      } elsif ($::opt_gsdev =~ m/^png/) {
+        $OutputFilename .= '.png';
+      } elsif ($::opt_gsdev =~ m/^jpeg/) {
+        $OutputFilename .= '.jpg';
+      } else {
+        $OutputFilename .= ($::opt_gsdev eq "" ? ".pdf" : ".$::opt_gsdev");
+      }
+    }
+  }
+  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=$::opt_gsdev $GSOPTS " .
+          "-sOutputFile=$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";
+}
+
+### scan first line
+my $header = 0;
+$_ = <IN>;
+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) {
+  while (<IN>) {
+
+    ### 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 = tell(IN);
+      debug "Current file position:", $pos;
+
+      # looking for %%BoundingBox
+      while (<IN>) {
+        # skip over included documents
+        if (/^%%BeginDocument/) {
+          while (<IN>) {
+            last if /^%%EndDocument/;
+          }
+        }
+        if (/^$BBName$BBValues/) {
+          CorrectBoundingBox $1, $2, $3, $4;
+          $BBCorrected = 1;
+          last;
+        }
+      }
+
+      # go back
+      seek(IN, $pos, 0) or error "Cannot go back to line '$BBName (atend)'";
+      last;
+    }
+
+    # print header line
+    print OUT;
+  }
+}
+
+### print rest of file
+while (<IN>) {
+  print OUT;
+}
+
+### close files
+close(IN);
+print OUT "\ngrestore\n" if $BBCorrected;
+close(OUT);
+warning "BoundingBox not found" unless $BBCorrected;
+debug "Ready.";
+;