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README.md

RubyROOT

Ruby binding of ROOT (CERN)

  • Version: 0.2.10
  • Author: Hirokazu Odaka

Introduction

RubyROOT is a Ruby binding of ROOT, which is a data analysis framework developed by CERN. RubyROOT provides a minimun set of Ruby interface to useful ROOT classes including histograms, trees, graphs, and canvases. By using this extension library, we get a powerful data analysis environment based on the flexibility of Ruby.

ROOT already has a well-designed Ruby binding, "RubyRoot", in the package. But this seems not possible to be built with Ruby 2.0. Thus, we have started developing of this library.

Currently, this Ruby wapper offers the following ROOT classes:
TApplication, TArrow, TAttAxis, TAttBBox2D, TAttFill, TAttLine, TAttMarker, TAttPad, TAttText, TAxis, TBox, TBranch, TCanvas, TChain, TCollection, TColor, TDirectory, TDirectoryFile, TEllipse, TF1, TFile, TFormula, TGraph, TGraphAsymmErrors, TGraphErrors, TH1, TH1C, TH1D, TH1F, TH1I, TH1S, TH2, TH2C, TH2D, TH2F, TH2I, TH2S, TH3, TH3C, TH3D, TH3F, TH3I, TH3S, TKey, TLatex, TLeaf, TLegend, TLine, TList, TLorentzRotation, TLorentzVector, TMap, TMarker, TNamed, TObjArray, TObjString, TObject, TPair, TPad, TPaletteAxis, TPave, TRint, TROOT, TRandom, TRandom3, TRotation, TSeqCollection, TString, TStyle, TSpline, TText, TTree, TVirtualPad, TVector2, TVector3.

Contact

  • Hirokazu Odaka
  • RIKEN
  • hirokazu.odaka(AT)riken.jp

GitHub

https://github.com/odakahirokazu/RubyROOT/

Supported Platform

  • Mac OS X
  • (Linux: not tested)

Note for Linux users

It should be possible to install RubyROOT on Linux though we have not tested yet. You need to install the same software descibed below and then please try the same way. It might be necessary to modify CMake files in this package.

Note for ROOT5 users

If you want to use ROOT5, you can use version 0.1.21, which is the latest version compatible to ROOT5. Version 0.2 and later support ROOT6 only.

Test environment

The author's developing/testing environment is as follows:

  • iMac 27-inch late 2015
  • macOS Sierra (10.12.6)
  • Apple LLVM version 9.0.0 (clang-900.0.37)
  • CMake 3.9.4
  • ruby 2.4.2p198 (2017-09-14 revision 59899)
  • ROOT 6.10/06
  • SWIG Version 3.0.12

Contributions Are Welcome

Contributions of any kind including documentation, testing, and coding are very welcome.

Licence

RubyROOT is distributed under the GNU General Public License version 3.

Installation

Required Software

(1) C++ compliler

(2) CMake

version 3.8 or later

This package uses CMake (Cross platform make) for easy installation.

(3) Ruby

version 2.3.1 or later, but version 2.4 won't work

(4) SWIG

version 3.0.10 or later

SWIG (Simplified Wrapper and Interface Generator) provides an easy way to generate extended libraries of various scripting languages.

(5) ROOT

version 6.08/00 or later

A data analysis framework.

Installation Guide

On Mac OS X with Homebrew, the easiest way is as follows.

(1) Update Homebrew.

$ brew update

(2) Install required software via Homebrew.

$ brew install cmake
$ brew install swig

(3) Check your Ruby version, or install Ruby.

If you want to use a specific version of Ruby, we recommend using rbenv. Rbenv provides nice Ruby environemt, in which you can easily/safely choose different Ruby versions. It can easily introduced using Homebrew on OS X.

$ brew install ruby-build
$ brew install rbenv
$ rbenv init

To initialize rbenv, write the following line in .bashrc or .zshrc.

eval "$(rbenv init -)"

Then, in a new shell, install Ruby as follows.

$ rbenv install -l

This will show like this =>

Available versions:
  1.8.6-p383
  1.8.6-p420
  1.8.7-p249
  ...
  2.3.0
  2.3.1
  2.3.2
  2.3.3
  ...

Then, select the latest stable version: 2.3.3, for example.

$ rbenv install 2.3.3
$ rbenv rehash
$ rbenv global 2.3.3

(4) Install ROOT.

$ brew install root

(5) Obtain RubyROOT via GitHub.

$ git clone git://github.com/odakahirokazu/RubyROOT.git

(6) Build & install.

$ ls
  RubyROOT ...

$ mkdir RubyROOT-build
$ cd RubyROOT-build
$ cmake ../RubyROOT -DCMAKE_INSTALL_PREFIX=<your_install_destination>

By default, CMAKE_INSTALL_PREFIX is set to $HOME; the ruby extention library will be installed in $HOME/lib/ruby. You may use following options:

  • ENABLE_MINUIT2 (enable Minuit2, default=ON)

After successful cmake, just do make and make install.

$ make
$ make install

(7) Set environment variable.

Write the following line in .bashrc or .zshrc.

export RUBYLIB=<your_install_destination>/lib/ruby:$RUBYLIB

Usage

Getting Started: Histogram and File

The first example is to handle a histogram and a file. You can get a script example from examples/write_hist.rb.

require 'RubyROOT'

Root::TFile.open('hist.root', 'RECREATE') do
  h = Root::TH1D.create('hist', 'Histogram', 100, -5.0, 5.0)
  1.upto(h.GetNbinsX){|i| h.SetBinContent(i, i*4.0) }
  h.SetBinContent(32, 547.2)
  h.FillRandom("gaus", 15000)
  h.Write
end

This script makes a histogram named "hist" with 100 bins in a range from -5.0 to +5.0. Then, certain values are assiend. It also fill 15000 values sampled from a Gaussian distribution with sigma=1. Finally, the created histogram is saved to a new file called "hist.root".

A Ruby script using ROOT needs to require RubyROOT.rb. Most of classes and methods are members of Root module, so you can use a ROOT class with the module name like Root::TFile. You can also include the module in order to access the ROOT classes without specifying the module name explicitly.

include Root
h = TH1D.create('hist', 'Histogram', 100, -5.0, 5.0)

ROOT file

To open a ROOT file, you can use TFile.open(file_name, option). Without a block, this method returns a file object opened. If a block is given to the method like the above example, the file obejct is passed as a block variable and can be used in the block. After the block process, the file is automatically closed by calling TFile.Close(). In this case, open method returns nil. The next two code have the same effect.

openning file without a block
f = TFile.open('data.root')
# do something
f.Close
openning file with a block
TFile.open('data.root') do |f|
  # do something
end

Making a histogram

Histograms are frequently used data in our analysis. To make a histogram, you can use create methods like

h = TH1D.create(name, title, number_of_bins, lower_edge, upper_edge)

This has the same effect as C++ code below:

TH1* h = new TH1D(name, title, number_of_bins, lower_edge, upper_edge);

Although Ruby classes normally have new method to allocate a new object, you should use create method to make a new histogram object.

The histogram created by RubyROOT can be handled by the same way as C++ functions:

h.Fill(value)
h.Fill(value, weight)
h.SetBinContent(bin, counts)
value = h.GetBinContent(bin)

To write the histogram to the file, you can use TH1#Write() or TFile#Write(). If you need to change the ownership of the object, you can use TH1#SetDirectory(directory).

h.SetDirectory(f)
h.Write
About create method for experts

In fact, it is possible to call new methods to make a histogram as TH1D.new, but this causes a conflict between Ruby's garbage collection and memory management by ROOT.

Reading a histogram in a file

Now you have gotten a file hist.root containing a histogram after execution of write_hist.rb. The second example script examples/read_hist.rb tells us how to read this file.

Root::TFile.open('hist.root') do |f|
  h = f.Get('hist')
  for i in 1..h.GetNbinsX
    puts "%4d %6.1f" % [i, h.GetBinContent(i)]
  end
end

This simple script opens hist.root and gets the histogram object hist by calling TFile#Get() method. Then, it dumps the bin labels and value contents of all bins. You will get this:

   1    4.0
   2    8.0
   3   12.0
...
  49  774.0
  50  791.0
  51  798.0
...
  98  392.0
  99  396.0
 100  400.0

Drawing a histogram

See examples/draw_hist.rb as an example to draw a histogram. To draw something in a canvas, you need to include RootApp module. A canvas should also be created by TCanvas.create(name, title, width, height) method. After invoking TH1#Draw() and TCanvas#Update(), call run_app() to run ROOT TApplication. Please note that to quit the application properly, you need to select "Quit ROOT" from the pulldown menu "File". If you closed the canvas window by pushing the close button, the application would be still running. In this case, you can quit the application via Ruby application or kill command in the shell.

#!/usr/bin/env ruby

require 'RubyROOT'
include RootApp

Root::TFile.open('hist.root') do |f|
  c1 = Root::TCanvas.create("c1", "canvas1", 640, 480)
  h = f.Get('hist')
  h.Draw
  h.SetLineColor(2)
  h.GetXaxis.SetTitle("values")
  h.GetXaxis.SetTitleOffset(1.2)
  h.GetXaxis.CenterTitle
  h.GetYaxis.SetTitle("counts")
  h.GetYaxis.CenterTitle
  h.GetYaxis.SetTitleOffset(1.35)
  h.SetTitle("Histogram drawn by RubyROOT")
  c1.Update
  run_app
end

This script will draw a histogram like this.

Histogram sample

2D and 3D histograms

RubyROOT supports 1D, 2D and 3D histograms (TH1, TH1C, TH1D, TH1F, TH1I, TH1S, TH2, TH2C, TH2D, TH2F, TH2I, TH2S, TH3, TH3C, TH3D, TH3F, TH3I, TH3S). See examples/hist2d.rb.

2D Histogram sample

Tree

A tree is also useful data structure provided in ROOT, which is very similar to a table. Usage of the TTree class in the normal C++ mode is a little bit complicated compared with histograms. In RubyROOT, API is redesigned to fit the Ruby language.

Writing a tree

Let's see a script examples/write_tree.rb. This creates a tree (i.e. table) with value columns of event_id, position, and energy, and then save it to a file.

random = Root::TRandom3.new

Root::TFile.open("tree.root", "RECREATE") do
  tree = Root::TTree.create("tree", "tree")
  row = tree.define(event_id: 'I', position: 'F', energy: 'F')
  1000.times do |i|
    row.event_id = i+1
    row.position = random.Uniform(-12.8, +12.8)
    row.energy = random.Gaus(511.0, 2.5)
    tree.Fill
  end
  tree.GetEntries.times{|i| tree.Show i }
  tree.Write
end

A tree object is also generated by calling TTree.create() like a histogram. To define branches, you can use TTree#define() with keyword arguments that specify pairs of the name and type of branches.

row = tree.define(event_id: 'I', position: 'F', energy: 'F')

This defines three branches (or columns):

  • event_id (type: signed 4-byte integer),
  • position (type: single-precision floating point), and
  • energy (type: single-precision floating point).

A character specifying a type is the same as ROOT's definition (e.g. 'D' for double-precision floating point, 's' for unsigned 2-byte (short) integer.) This method returns a buffer object that contains the branch (column) data for an entry (a single row). You can assign a value to the data buffer as row.energy = value and call TTree#Fill() to fill the data into the tree.

Reading a tree

RubyROOT also provides an easy way to read a tree as shown in examples/read_tree.rb.

Root::TFile.open("tree.root") do |f|
  tree = f.Get("tree")
  tree.read.each do |t|
    puts "%4d  %7.2f  %7.2f" % [t.event_id, t.position, t.energy]
  end
end

The tree saved in a file can be obtained by TFile#Get(). TTree#read() returns an enumerable object that scans all entires (rows), so each method with a block can be accessible to the contents of each entry via the branch name like t.energy.

Graph

Making a graph is easy. See examples/graph.rb. A TGraph object is created by TGraph.create(x_values, y_values).

require 'RubyROOT'
include RootApp

### data definition
x = [1.0, 2.3, 3.1, 4.0, 5.0]
y = [1.2, 2.1, 10.2, 3.2, 4.0]

### make a graph and draw it
graph = Root::TGraph.create(x, y)
graph.SetName("graph1")
c1 = Root::TCanvas.create
graph.Draw("APL")
c1.Update
run_app

RubyROOT also provides TGraphErrors and TGraphAsymmErrors. See examples/graph_with_error_bars.rb and examples/graph_with_asymmetric_error_bars.rb. All arguments are given as Array.

graph1 = TGraphErrors.create(x_values, y_values, x_errors, y_errors)
graph2 = TGraphAsymmErrors.create(x_values, y_values, x_lower_errors, x_upper_errors, y_lower_errors, y_upper_errors)

To write a graph into a file, the graph object must have a name. See write_graph.rb.

graph = Root::TGraphErrors.create(x, y, xe, ye)
graph.SetName("graph1")

Functions

Class TF1 is used for a mathematical function. See function.rb. This script makes a TF1 object that represents a function f(x)=(x-1)^2-2. This class allows us to use new method to create an object. Then, the function is evaluated at three x-values, 0.0, 1.0, and 2.0. To draw it, just call TF1#Draw() method.

f = Root::TF1.new("func", "(x-1)^2-2", -3.0, +4.0)
puts "f(x)=#{f.Eval(0.0)} for x=0.0"
puts "f(x)=#{f.Eval(1.0)} for x=1.0"
puts "f(x)=#{f.Eval(2.0)} for x=2.0"
f.Draw

Function defined in Ruby code

You can also define a function in a Ruby code session. function_in_ruby.rb tells us how to do it. You can use a function object generator Root::func which accepts a block returning a user-defined function value of a given argument x.

acos_extended = Root::func{|x|
  n = ((x+1.0)/2.0)
  cycle = (n>0.0) ? n.to_i : -(n.abs.to_i)-1
  Math::acos(x-cycle*2.0)-Math::PI*cycle
}

f = Root::TF1.create("func", acos_extended, -5.0, 5.0, 1)

The block given to Root::func describes an arbitray user-defined function. In this example, we try to define an extended version of arccos(x) that has a limitless domain of definition while normal arcsos(x) accepts a value ranging from -1 to +1. As shown below, the function is extended to outside of [-1, 1]. The normal version of acos(x) created by TF1.new is superposed in blue color.

Extend acos(x)

Comments for experts

The function object generator Root::func is defined in RubyROOT.rb as

def func(&f)
  lambda {|x, p| f.(x[0]) }
end

So you can define the function obejct by directly using lambda. You can find it in function_in_ruby2.rb.

acos_extended = lambda{|xs, ps|
  x = xs[0]
  n = ((x+1.0)/2.0)
  cycle = (n>0.0) ? n.to_i : -(n.abs.to_i)-1
  Math::acos(x-cycle*2.0)-Math::PI*cycle
}

Frequently Asked Questions

Installation

I failed to install Ruby via rbenv.

Try the latest versions of rbenv and ruby-build you can obtain via homebrew.

For version 2.0.0-p451, I needed to set RUBY_CONFIGURE_OPTS like this:

RUBY_CONFIGURE_OPTS="--with-readline-dir=/usr/local" rbenv install 2.0.0-p451

This workaround forces ruby-build to use readline provided by OS X system, which is actually libedit (readline compatible library). This problem seems to be resolved in version 2.0.0-p481.

I failed to build RubyROOT, the error message says something about Minuit2.

In the default setting, RubyROOT requires Minuit2 with ROOT. If you did not set minuit2 enabled (via --enable-minuit2 option) when you installed ROOT, use cmake option -DENABLE_MINUIT2=OFF at RubyROOT's cmake as follows:

cmake ../RubyROOT -DENABLE_MINUIT2=OFF <other options>

Note that homebrew formula of ROOT6 normally sets minuit2 enabled.

Data Analysis using RubyROOT

When should I use create method insted of new method?

You should use create when you make a histogram, tree, canvas, or graph. These create methods are provided if default new methods cause some problems within the Ruby environment or have incovenient API as Ruby interface. To make a histogram or tree object, you should use create method in order to avoid a conflict with Ruby's garbage collection. In the case of graphs, create method makes a graph objects directly from Ruby native Array while new method can be used for making a graph only from C++-based DoubleArray.

Can I use a tree including a variable-length array?

Yes, you can. See examples/write_tree_variable_length.rb and examples/read_tree_variable_length.rb.

How can I get a parameter and error value of the mizimization result?

You can use methods below:

  • Minuit2FunctionMinimizer#GetParameter(index)
  • Minuit2FunctionMinimizer#GetError(index)

See also examples/minimization.rb.

Can I use color constants defined in ROOT?

Yes. But they are renamed in order to obey a Ruby grammar that the first character of a constant is capital. You can use: KWhite, KBlack, KGray, KRed, KGreen, KBlue, KYellow, KMagenta, KCyan, KOrange, KSpring, KTeal, KAzure, KViolet, KPink.


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