An Introduction to Root I/O

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1 An Introduction to Root I/O C Coleman-Smith Duke Physics cec24@phy.duke.edu March 31, 2010

2 Outline Getting Started With Root What is root What can root do Compiling, installing, getting help Macros & Functions CINT commands Macros Functions Compiling Loading and Storing Data TFile TTree Processing Data Example files are available on my internal webspace: (Duke Physics) Root Intro March 31, / 1

3 What is root? What is root? Designed to be a Particle Physics data analysis framework, work started in mid 90 s by Rene Brun & Fons Radmakers. A series of libraries, structures and classes designed for analysis of large data sets. Open Source, download from You interact with root via the Intepreter CINT Aim is to make doing physics easy, stop re-inventing the wheel! What can you do with it? Work with large data sets: cut, sample, visualise Store these sets in a machine independant fashion, thus easily share your work. Work interactively with your data, great power from a few commands. The same things you already do, but better. cec24@phy.duke.edu (Duke Physics) Root Intro March 31, / 1

4 What is root (2) This sounds too good to be true! All C++, you can code it as C but you ll miss some elegance. The framework is HUGE, subscribes to the There s more than one way to do it school. The interpreter is trying to interpret C++, this is a horrible idea. It crashes, a lot. How to get help: 1 Read the documentation: Make sure to turn the Show Inherited button on. 2 Ask us: cec24@phy.duke.edu, ht25@phy.duke.edu 3 Ask on the forum, Rene usually responds in a few days: cec24@phy.duke.edu (Duke Physics) Root Intro March 31, / 1

5 Installing Download latest production version, configure, build, install Useful config flags:./configure --prefix=/usr/local --disable-builtin-freetype --disable-builtin-ftgl --disable-builtin-pcre --enable-gsl-shared --disable-builtin-zlib Assuming you installed to /usr/local setup the required environmental variables by adding this to your.bashrc source /usr/local/root/bin/thisroot.sh Or (Duke Physics) Root Intro March 31, / 1

6 First Run On starting root you begin at the CINT command-line. no splash: root -l help:? quit:.q (do this often) load a macro:.l <macroname> execute:.x <macroname> compile:.l <macroname>++ cec24@phy.duke.edu (Duke Physics) Root Intro March 31, / 1

$h> void example1(void){ // c++ commands cout << "Hello World" << endl; /* but you can also run c code */ printf("%s\n", "bello fnurld"); To run this macro, start root and execute it with.x example1.$

7 Macros The canonical Hello-World example (example1.c), note that you can mix calls from the C and C++ stdlibs, /* need to include C headers */ # include <stdio.h> void example1(void){ // c++ commands cout << "Hello World" << endl; /* but you can also run c code */ printf("%s\n", "bello fnurld"); To run this macro, start root and execute it with.x example1.c Single function macros must have the same function name as their filename or the interpreter will not know which function to run. cec24@phy.duke.edu (Duke Physics) Root Intro March 31, / 1

8 Macros(2) Functions Macros can contain many functions,.l <filename> will load them all, you can call them as you would in real code: fn_name(foo,bar,baz) /** * note that you don t *need* to include ANY headers * also you don t need to declare fn prototypes (yay) */ void example2(int baz){ cout << foo(baz) << endl; int foo(int bar){ // a stupid function return 3+bar; int flob(int qux){ // you can call other functions return foo(qux); // you can even be recursive! (up to 128 depth) int wibble(int x, int y){ cout << x << endl; if(x > 1) { wibble(x-1, y+1); else { return(y); cec24@phy.duke.edu (Duke Physics) Root Intro March 31, / 1

9 Compiling Macros Macros and fns are compiled to bytecode by CINT and then executed, slow. const double pi = ; int example3(void){ cout << "the sqrt of 2 is: " << sqrt(2.0) << endl; cout << "the sin of pi/4 is: " << sin(pi/4) << endl; return(0); Above won t compile, need to include all the headers: # include <iostream> # include <cmath> // c++ headers const double pi = ; int example3(void){ cout << "the sqrt of 2 is: " << sqrt(2.0) << endl; cout << "the sin of pi/4 is: " << sin(pi/4) << endl; return(0); Be very careful with memory leaks in large compiled scripts cec24@phy.duke.edu (Duke Physics) Root Intro March 31, / 1

10 TFile TFile Acts as the interface for saving and loading your root objects from the disk: The data is stored in a machine-independant binary format. void write_tfile(char* filename){ // create filename, or if it exists overwrite it TFile *rootfile = TFile::Open(filename, "RECREATE", "a demo file:ccs"); TObjString *stringy = new TObjString("surely you re joking mr Feynman"); TObjString *stringy2 = new TObjString("my foot! you re on my foot mr Feynman"); stringy->write(); stringy2->write(); delete rootfile; Open the file with TFile::Open(filename, "MODE", "title") To save objects to this file do Object->Write() To close SAFELY, delete the pointer. It s safest to set the MODE string to RECREATE for making a new file. Didn t use new method to create the file, or close method to close it, these cause strange behaviour. When objects are written to a TFile a key is created in the file s dictionary, one retrieves objects by their keys. cec24@phy.duke.edu (Duke Physics) Root Intro March 31, / 1

11 TFile (2) Reading To read objects from a open file, you need to set a key pointer to each object and then cast the return of key->readobj(). void open_tfile(char* filename){ // this is a big C++ y TFile *infile = TFile::Open(filename); TKey *key; // need this to read TObjects from files TIter next(infile->getlistofkeys()); TObjString *instring; // loop over all keys in the file while (key = (TKey*)next()){ instring = (TObjString*)key->ReadObj(); cout << instring->getstring() << endl; delete infile; // and close the file You can use the CINT command.ls to list the keys in an open TFile. If you you know the name of the TObject in the file, in this case a histogram you can do TFile *rootfile = TFile::Open("./rootfile.root"); TH1F *my-saved-histogram = (TH1F*)rootfile->Get("histogram1"); // do histogram things here delete rootfile The latter method is more common. Open question: How to read and correctly cast a file of N objects of m different (unknown beforehand) types? cec24@phy.duke.edu (Duke Physics) Root Intro March 31, / 1

12 TTree The TTree class is the most important class in ROOT for data manipulation. Designed to store tuples of data. Each tree consists of multiple branches and each branch holds one data field (integer, floating point, array, object, structure). You can have as many branches as you like and store as many data points as disk space allows. The TTree class has many methods to allow easy: cutting; sorting and graphing of data stored in trees. TTree* tree = new TTree("tree", "example-tree"); /* setup variables to fill tree, MUST be root types */ Int_t local_id; Char_t particlename[128]; Double_t energy, array[3]; tree->branch("particleid", &local_id, "particleid/i"); tree->branch("particlename", particlename, "particlename/c"); tree->branch("energy", &energy, "energy/d"); tree->branch("momentum", array, "array[3]/d"); while(...){ // get values from your input data and set them to your branch ptrs local_id = data[i].id; energy = data[i].energy;... tree->fill(); // this set of values will be added to the tree The branch variables need to be the root types: Int_t, Double_t, Float_t cec24@phy.duke.edu (Duke Physics) Root Intro March 31, / 1

13 TTree2 The name you give to a TTree on creation will be its key on disk, the title field is not important. Once you ve created a tree, you can write it to the currently open TFile with tree->write(); If you open a TFile (with ptr rootfile) with a tree (named mytree) in it you can make a pointer to it by: TTree* tptr = (TTree*)rootfile->Get("mytree"); The Print() method will print info about the branches in a tree. The Draw("branchspec", "cutspec", "options") method is a wonderful way to visualise your data. This lets you plot the branches with cuts applied. tptr->draw("branch1:branch2", "branch1<10", "CONTZ") You can also dive into the tree with the TTreeViewer object, this is creates a GUI interface to the Draw(...) command. TTreeViewer* tv = new TTreeViewer("mytree"); cec24@phy.duke.edu (Duke Physics) Root Intro March 31, / 1

14 Processing Data How to loop over branches in a tree to do some analysis // processing data void process_tree(char* branch1, char* branch2, char* filename){ TFile *rfile = TFile::Open(filename); TTree *t = (TTree*)rfile->Get("tree"); Double_t b1val, b2val; // setup the branches we want to loop over TBranch *branch1 = t->getbranch(branch1); TBranch *branch2 = t->getbranch(branch2); branch1->setaddress(&b1val); branch2->setaddress(&b2val); for(int i; i < t->getentries(); i++){ branch1->getentry(i); branch2->getentry(i); /* now b1val and b2val are set to the * i th entries of branch1 and branch2 * do data processing here... */ delete rfile; // close the original file /* do anything else here, like save your results to a new tree*/ cec24@phy.duke.edu (Duke Physics) Root Intro March 31, / 1

15 What Next Read the tutorials Read the users guide Add a custom class as a subclass of TObject. Would let you store specific meta-data in your TFiles. See the Event class. This is hard, but possibly worth it. There are interfaces to Pythia6 Neural Networks Image Processing libraries FFTW You could use the python or ruby interfaces. And of course you can make excellent graphs... cec24@phy.duke.edu (Duke Physics) Root Intro March 31, / 1

16 Thanks Thanks to Taritree Wongjirad & Ben Cerio for some useful discussions. Thanks to Sean Stave (TUNL) for some excellent advice and the Star example. (Duke Physics) Root Intro March 31, / 1

Introduction to ROOT. M. Eads PHYS 474/790B. Friday, January 17, 14

Introduction to ROOT. M. Eads PHYS 474/790B. Friday, January 17, 14 Introduction to ROOT What is ROOT? ROOT is a software framework containing a large number of utilities useful for particle physics: More stuff than you can ever possibly need (or want)! 2 ROOT is written