//============================ 
// Getting the code 
//===========================

1. If you do not use a MAC system, open all the ".sh" scripts and remove the ".bak" down below by the "sed" command.

2. You need to run in two steps in order to get the stack plots (I will explain latter why):

3. To start, please put your root files in the "data" directory.

//==================================
//  Normalizing the plots 
//==================================

1. Please go to the config directory. In the directory, you will find the following files:

DYJetsToLL_10To50.in		DYJetsToLL_j4.in		Wjets_j1.in			changeInputFiles.sh
DYJetsToLL_j0.in		NormalizeHistos.in		Wjets_j2.in			data_singleMu.in
DYJetsToLL_j1.in		QCD_Pt-20toInf_MuEnriched.in	Wjets_j3.in			files.log
DYJetsToLL_j2.in		WWinclusive.in			Wjets_j4.in			style.in
DYJetsToLL_j3.in		WZinclusive.in			ZZinclusive.in			ttbar.in

* The "NormalizeHistos.in" contains the list of files you want to normalize to cross section and luminosity. 

* The files with names of SM processes, are configuration files for the BGs. The file data_singleMu.in is for data. 

* Please open any of the files and get familiar with the different settings. 
You will see that there are settings for the normalization process, the stacking process and to plot efficiencies. 

2. Your output ROOT files from the TNT_Analyzer already have the correct input name in the config files. 
For example: rootfile: FILE/DYJetsToLL_M-5to50_Asympt25ns.root.

3. Nevertheless, please make sure that each config file you list in the "NormalizeHistos.in" has a matching input ROOT file 
in the "data" directory.

4. To run the code, do:  

> sh RunNormalizeHistos.sh outputDirectory

"outputDirectory" is just a name, it can be anything you'd like. 
This might take a few minutes since currently we have many histograms per file. 
After running the code, go to the "outputDirectory" and you'll find a set of subdirectories. 
The subdirectories correspond to the cuts ran over and/or the 
cuts you wanted to make the histograms for. Keep in mind that the cuts are applied 
sequestially on the EDAnalyzer. Therefore, cut3 (e.g RecoMuon2Nmin) has also 
cuts 1 and 2 already applied. You have control over the subdirectories you'd like to run over. 

The subdirectories can be added or removed from an input file called "directories.in" stored inside the "config" directory. 
You also have control over the processes you'd like to include (e.g data, ttbar, wjets etc).
The processes can be found at "config/NormalizeHistos.in". Be aware that data is not normalized to anything, 
but you need to run over it, in order to get the proper format of the plots, to be used latter when making the stack 
plots or the plots normalized to unity.

//==================================
//  hadd non-inclusive samples 
//==================================

Many times you have several MC samples binned on pT or with a different jet multiplicity. 
You need to normalize them first and then you can add then to make the plot. 
For example, imagine a W+jets sample divided as w1jets, w2jets, w3jets etc. 
Each process has its own cross section, you need to properly normalize 
each plot using the "RunNormalizeHistos.sh". Neverhtless, you most likely want to plot only a 
single W+jets process and not one per jet multiplicity. 
Therefore, after normalizing each process, you can combine all the W+Jets processes, using an script called "add.sh". 
The script is very simple to use, only make sure you take a look at it before you use it. 
The same applies for other cases, for example, diboson samples. If you run over the test root files in this package, 
you can all all the dibison samples, per cathegory: WW, WZ, ZZ, buy doing:

> sh add.sh ZZ outputDirectory
> sh add.sh WW outputDirectory
> sh add.sh WZ outputDirectory

So, you'll get only one file for all the ZZ processes, one for all the WW and one for all the WZ ones.


//==============================
// Output log files
//==============================

After running the normalization step, you will get a set of output log files, per each cut. 
The log files can be found inside the directory "LogFiles".

//=================================
//  Making the stacks
//=================================

b. To make the stack plots you can run in the following way: 

sh RunStackHistos.sh outputDirectory outputDirectoryStacks

The first parameter "outputDirectory" is the name of the directory where the normalized histos are and the second parameter 
"outputDirectoryStacks" can be anything you'd like. After running this, a directory called "outputDirectoryStacks" with thr output 
of all the stack histos will be created. Inside this directoy, you'll find a set of subdirectories, one per cut, each with 
a set of stacked plots in "PDF" format and a root file "StackedPlots.root". The plots in PDF format, are the ones that were 
defined in the file "config/style.in". If can add or remove plots in this file, depending on your needs.  

//================================
// Making plots norlized to Unity
//================================

You also can make overlaid plots of the different processes normalized to unity. In order to do that, you need to run:

> sh RunUnitPlotter.sh outputDirectory outputDirectoryUnity

The "RunUnitPlotter.sh" script uses as input the "StackPlotter.in" to determine which processes to run over. 
It also used the "directories.in" to determine which subdiretories (cuts) the user wants to make plots for.

//================================
// Efficiency tables
//================================

You can also make efficiency tables! To run the code do:

> sh RunMakeEfficiencyTable.sh > Table.log

The processes you'd like to make the efficiency table for, are defined at "config/LogProcesses.in". The code uses the output log files 
obtained after the normalization step. The table is printed in a very close, but not perfect, LaTex format. 
You need to change by had a few things, such as the number of columns in the "tabular" part and 
also use meaningful names for the cuts. The cuts apper with the name of the sub-directory.

//==============================
//  Configuration
//==============================

As mentioned before, inside the configuration directory, you'll fine the configuration files for data and MC samples. 
You can set colors, line styles, line colors, leged for the different processes etc. 
Also, you can define if you'd like the stacked plots to be on linear of log scale using the "setLogScale" flag. In order to 
to this last part, you need to change the flag in all the config files. There is an script called "changeInputFiles.sh" 
in order to do this. Finally, if you'd like to make MC only plots,you need to ser the "usedata" flag to False in all the 
config files (use the "changeInputFiles.sh") script. 

//============================
// IMPORTANT REMARK
//===========================

This code is under development. This version is very complete but it is not perfect yet. 
I will include several features in the next few weeks, such as tools to process 2D and 3D plots among others.