###############################################################################
 *
 *	 .oooooo..o oooooooooo.  ooooo      ooo  .o88o.  o8o      .  
 *	d8P'    `Y8 `888'   `Y8b `888b.     `8'  888 `"  `"'    .o8  
 *	Y88bo.       888     888  8 `88b.    8  o888oo  oooo  .o888oo
 *	 `"Y8888o.   888oooo888'  8   `88b.  8   888    `888    888  
 *	     `"Y88b  888    `88b  8     `88b.8   888     888    888  
 *	oo     .d8P  888    .88P  8       `888   888     888    888 .
 *	8""88888P'  o888bood8P'  o8o        `8  o888o   o888o   "888"
 *
 *		SBNfit, fitter, oscillator, covariance matrix maker, collapser
 *			originally for sterile decays at SBL facilities
 *			but actually pretty generic. Now More!
 *
 *		If you have any questions, queries or comments please contact the authors;
 *			 markrl@nevis.columbia.edu 
 *
 *The authors make no guarrentee of the behaviour, stability or bug-free-ness of this code.
 *Use is at own risk.
################################################################################
Installation and such
Should be a standard;

cmake .. 
make 

from build directory. CmakeLists were quickly written and not tested anywhere!
Probably need root compiled with Cmake for now or FindROOT.cmake.
Will update as required



To run example N (there are 5 examples)
I think they currently are hardcoded to work in build/examples only.

./exampledemo --xml ../../xml/uboone.xml --test 2
./exampledemo --xml ../../xml/sbn.xml --test 1


sbn.xml and uboone.xml are included in xml folder, but easily modified



############################################################################
##############		Whats What! ########################################
############################################################################

##### SBNconfig.h/.cxx ####

SBNconfig is the base class that reads in a .xml file using tinyxml
(included). This contains all info on bins, modes and detctors. Each file must
have at LEAST one mode and one detector and one channel. (e.g neutrino mode and microboone).
Each channel must have at least one subchannel, but can have as many as you
want. In calculating chi^2 all subchannels are collapesed down to one
"channel". All subchannels must have same binning, but this can vary between
channels. You can quickly turn off any componant by toggling the "use=1"
attribute.
The two main classes that inherit from this are SBNspec and SBNchi.

##### SBNspec.h/.cxx #####

SBNspec is initilzed from a xml file. It can either be passed the location of
a root file (whose contents match the xml file naming conventions!) or just an
xml file in which case it is initilised empty (but having all the xml named
channels/subchannels..etc..).
An initilised SBNspec contains a vector of TH1's, one for every
subchannel/channel/mode/detector that was in the xml. You can scale or
normalise any channel using the supplied functions and the .xml names.
So if you want to scale all the SBND_elike histograms, you can just write
hist.Scale("SBND_elike", VALUE);
It also has some basic functionality for scaling a histogram by an energy
dependant function:
hist.Scale("uBooNE",TF1);
All model dependant bits should be included in an inherited class.

SBNspec->CompressVector() collapses down the subclass histograms into a vector
of correct length to be fed into a CHI^2 calc.

SBNspec->WriteOut("filename.root") quickly dumps all the histograms into a
root file for debugging/checking

##### SBNchi.h/.cxx #####

SBNchi is the class you use if you already have a covariance matrix. The
location of the root file containing it should be incuded in the xml file on
initilisation. It must be initilized with a SBNspec as the background. If the
covariance matrix and SBNspec have different structures (e.g your covariance
matrix has extra modes/subchannels..etc.. than your spectrum, you can use
different xml files provided that you correctly toggle them using the
"use=0/1" xml attribute). Its much less error prone if your SBNspecs and covariance
matrices can be initilised using the same xml file.

SBNchi contains functions to correctly select only the rows and columns that
you want to use. Calculates the statistical bit from your inputted background
SBNspec and contains a generic algorithm for collapsing down the large
extended covariance matrix down containing ALL subchannels (for any number of
subchannels) to a smaller one used in chi^2 calculations. 

To calculate a chi^2 after initilization, you can either pass in a signal
SBNspec:
SBNchi->CalcChi(SBNspec sig_spec);
or a vector of appropiate length
SBNchi->CalcChi(std::vector<double>);
WARNING: by passing a vector you loose some checks on xml config consistancy.

##### SBNosc.h/.cxx #####

SBNosc is a daughter class to SBNspec. It basically is a spectrum that has
built in 3+N oscillation capabilities. The oscillation amplitudes are found i
prob.h as well as a legacy structure to hold oscillation paramaters
neutrinoModel (must update this).
SBNosc requires that you have precomputed SBNspecs for a range of mass
frequencies sitting in data/precomp. For any 3+1,3+2 or 3+3 model if
calculates all the mass-splitting frequencies and can either permantly
oscillate the internal spectra using the parameters in the given
neutrinoModel; You can set if its appearance only, disapearance only, both....etc..

SBNosc->OscillateThis();  
or it can just spit out a vector
std::vector<double >  SBNosc->Oscillate();  
if you are just passing it lots of a SBNchi for example.








TODO: 
make it so the absolute path for data/ is taken in by cmake.