Mass fit for B->D(Kshh)hh
------------------------

=== Basic instructions ===

Ensure ROOT/RooFit are available

To build:

   make

To run:

   ./bin/run Settings/GeneralSettings.txt

To copy output to binned fit directory

   cd scripts
   ./copyParamTextFiles.sh

=== Directory contents ===

bin      : executable
figs     : figures produced by the fit
Inputs   : PID efficiencies, yields for toy generation
obj      : .o files
output   : text files and root files produced by the fit
scripts  : scripts to process fit output
Settings : fit configuration (datasets, PDFs)
src      : .C, .h files


=== Source files ===

--- Base classes ---

Base : some basic functionality, inherited by many classes
CommonTools : more basic functionality

--- Main fit ---

Fitting : mass fit, plotting, toy studies
InternalStorage : set up yields 
Main : contains 'main'; creates Settings and Fitting objects
Model : sets up fit and generation models, prints yields and purities
Settings : read configuration files
Yields : create yields used in fit (could be RooFormulaVars)

--- Mathematical tools ---

CorrGauss : for smearing of parameters with covariance matrix

--- PDF creation ---

Pdf_Base : base class for PDFs listed below
Pdf_Fit : creation of PDFs used in mass fit
Pdf_Gen : creation of PDFs used for toy generation (could differ from those used in the fit)

--- PDF wrappers ---

Enable different PDFs to be used for each fit component, and facilitate parameter sharing

DoubleCrystalBall : wrapper class for double Crystal Ball
Exponential : wrapper class for exponential
KeysPdf : wrapper class for RooKeysPdf
Linear : wrapper class for RooChebychev

--- RooFit PDFs ---

Lambda : wrapper class for RooKeysPdf to make Lb->Dph shape
PartRecoDstKst : wrapper class for RooKeysPdf to make partially reconstructed shapes

=== Hints ===

To run mass fit toys:

   After running normal data fit: ./bin/run Settings/GeneralSettings.txt
   All necessary files can be found in output/

   If fit range is from 5200,

     mv output/GenTotals_5200.txt Inputs/
     mv output/ratiosFIXED_5200.txt Inputs/
     mv output/*FIXED.txt Settings/PDFShapes/Gen/

   Edit the following text files to point to correct options files
     
     Settings/PDFShapes/ControlFiles_GenPdf.txt
     Inputs/ControlFiles.txt

To turn PDFs for different modes on/off:
    
    In Settings/GeneralSettings.txt:

      * PDFS
      bd_drho true
      bs_dstkst true
      bd_dstkst false
      lb_dppi false
      bu_dkpipi false
      bu_dpipipi false
     
To convert parameters for Binned Fit:
    
    cd scripts
    ./copyParamTextFiles.sh -- moves files from Settings/PDFShapes/Gen/RANGE/ to BinnededFit Settings and applies necessary range correction

    After mass fit toys are run and you have a textfile from ToyReading_MINOS/bias.txt, move this to output/bias_RANGE.txt

      python biascorrection.py

      Output: output/values_biascorr_RANGE.txt

    If this mass fit was from a range other than 5200,
      
      python convertParamsForBinnedFit_BiasCorrect.py

      Output: output/values_biascorr_rangecorr_RANGE.txt
              Need to then copy these values manually in BinnedFit Settings