/*  samples.h

    Tim Behrens, Saad Jbabdi, Stam Sotiropoulos, Moises Hernandez  - FMRIB Image Analysis Group

    Copyright (C) 2005 University of Oxford  */

/*  Part of FSL - FMRIB's Software Library
    http://www.fmrib.ox.ac.uk/fsl
    fsl@fmrib.ox.ac.uk
    
    Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
    Imaging of the Brain), Department of Clinical Neurology, Oxford
    University, Oxford, UK
    
    
    LICENCE
    
    FMRIB Software Library, Release 5.0 (c) 2012, The University of
    Oxford (the "Software")
    
    The Software remains the property of the University of Oxford ("the
    University").
    
    The Software is distributed "AS IS" under this Licence solely for
    non-commercial use in the hope that it will be useful, but in order
    that the University as a charitable foundation protects its assets for
    the benefit of its educational and research purposes, the University
    makes clear that no condition is made or to be implied, nor is any
    warranty given or to be implied, as to the accuracy of the Software,
    or that it will be suitable for any particular purpose or for use
    under any specific conditions. Furthermore, the University disclaims
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    by or on behalf of Licensee to third parties or (2) use of the
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#include "newmat.h"
#include "newimage/newimageall.h"
#include "xfibresoptions.h"


using namespace Xfibres;

////////////////////////////////////////////
//       MCMC SAMPLE STORAGE
////////////////////////////////////////////

class Samples{
  	xfibresOptions& opts;
  	Matrix m_dsamples;
  	Matrix m_d_stdsamples;
  	Matrix m_S0samples;
  	Matrix m_f0samples;

	//   // storing signal
	//   Matrix m_mean_sig;
	//   Matrix m_std_sig;
	//   Matrix m_sig2;

  	vector<Matrix> m_thsamples;
  	vector<Matrix> m_phsamples;
  	vector<Matrix> m_fsamples;
  	vector<Matrix> m_lamsamples;

  	//for storing means
  	RowVector m_mean_dsamples;
  	RowVector m_mean_d_stdsamples;
  	RowVector m_mean_S0samples;
  	RowVector m_mean_f0samples;
  	RowVector m_mean_tausamples;
  	vector<Matrix> m_dyadic_vectors;
  	vector<RowVector> m_mean_fsamples;
  	vector<RowVector> m_mean_lamsamples;

  	//float m_sum_d;  changed GPU version
  	//float m_sum_d_std;  changed GPU version
  	//float m_sum_S0;  changed GPU version
  	//float m_sum_f0;  changed GPU version
  	//float m_sum_tau;  changed GPU version
  	//vector<SymmetricMatrix> m_dyad;  changed GPU version
  	//vector<float> m_sum_f;  changed GPU version
  	//vector<float> m_sum_lam;  changed GPU version
  	//ColumnVector m_vec;  changed GPU version

  	/////////////// GPU version /////////////////////
  	float *m_sum_d;
  	float *m_sum_S0;
  	float *m_sum_d_std;
  	float *m_sum_f0;
  	float *m_sum_tau;

  	vector<SymmetricMatrix> *m_dyad;
  	vector<float>  *m_sum_f;
  	vector<float> *m_sum_lam;
  	ColumnVector *m_vec;
  	////////////////////////////////////////////////
  
  	int m_nsamps;

	public:

  	Samples(int nvoxels,int nmeasures);
    
	void record(float rd,float rf0,float rtau,float rdstd,float rs0,float *rth,float *rph, float *rf, int vox, int samp);
  
  	void finish_voxel(int vox);
  
  	void save(int idpart);
};