/*  unwarpfns.h

    Mark Jenkinson, FMRIB Image Analysis Group

    Copyright (C) 2000 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
    all responsibility for the use which is made of the Software. It
    further disclaims any liability for the outcomes arising from using
    the Software.
    
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    liabilities asserted by third parties (including claims for
    negligence) which arise directly or indirectly from the use of the
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    transmitted product. You may be held legally responsible for any
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    You are not permitted under this Licence to use this Software
    commercially. Use for which any financial return is received shall be
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    of the source code or the Software into a product for sale or license
    by or on behalf of Licensee to third parties or (2) use of the
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    developing software products for sale or license to a third party or
    (3) use of the Software or any derivative of it for research with the
    final aim of developing non-software products for sale or license to a
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    innovation@isis.ox.ac.uk quoting reference DE/9564. */

#if !defined(__unwarpfns_h)
#define __unwarpfns_h

#include <string>
#include <iostream>
#include <fstream>
#define WANT_STREAM
#define WANT_MATH

#include <vector>
#include <map>
#include <algorithm>
#include "newmatap.h"
#include "newmatio.h"
#include "newimage/newimageall.h"

using namespace NEWIMAGE;
using namespace NEWMAT;

//////////////////////////////////////////////////////////////////////////

int maximum_position(const ColumnVector& vec);

int maximum_position(const Matrix& vec);

void delete_row(Matrix& mat, int r);

void delete_column(Matrix& mat, int c);

void insert_row(Matrix& mat, int r, const Matrix& nrow);

void insert_column(Matrix& mat, int c, const Matrix& ncol);

ColumnVector pava(const ColumnVector& data, const ColumnVector& weights);

ColumnVector pava(const ColumnVector& data);

//////////////////////////////////////////////////////////////////////////

template <class T>
void simple_erode(volume<T>& binaryvol);
  
template <class T>
void simple_dilate(volume<T>& binaryvol);

volume<float> despike_filter2D(const volume<float>& vol, float threshold);

volume<float> median_filter2D(const volume<float>& vol);

volume<float> masked_despike_filter2D(const volume<float>& vol, 
				      const volume<float>& mask,
				      float threshold);

volume<float> masked_median_filter2D(const volume<float>& vol, 
				     const volume<float>& mask);

float basic_mask_threshold(const volume<float>& absmap);

volume<float> make_basic_head_mask(const volume<float>& absmap, float thresh);

volume<float> make_head_mask(const volume<float>& absmap, float thresh); 
volume<float> make_head_mask2D(const volume<float>& absmap, float thresh);

volume<float> make_filled_head_mask(const volume<float>& absmap); 

volume<float> fill_head_mask(const volume<float>& origmask);

void fill_holes(volume<float>& vol, const volume<float>& holemask, 
		const volume<float>& mask); 

volume<float> extrapolate_volume(const volume<float>& datavol,
				 const volume<float>& origmask,
				 const volume<float>& enlargedmask);

volume<float> polynomial_extrapolate(const volume<float>& datavol,
				     const volume<float>& validmask,
				     int n, bool verbose=false);

volume<float> fourier_extrapolate(const volume<float>& datavol,
				  const volume<float>& validmask,
				  int n, bool verbose=false);

void connection_matrices(const volume<float>& phasemap,
			 const volume<int>& label, 
			 Matrix& Qab, Matrix& Pab, Matrix& Nab, double& K);

void connection_matrices(const volume<float>& phasemap,
			 const volume<int>& label, Matrix& Kab);

float calc_cost(const Matrix& Mab, const Matrix& Qab, const Matrix& Pvec, 
		float K); 

float calc_delta_cost(const Matrix& Mab, const Matrix& Qab, const Matrix& Pvec,
		      int j, float d); 

float calc_delta_cost(const Matrix& Mab, const Matrix& Qab, 
		      const Matrix& Pvecon2PI, int signedj); 

float wrap(float theta);

void remove_linear_ramps(const ColumnVector& ramp,
			 volume<float>& ph, const volume<float>& mask);

void restore_linear_ramps(const ColumnVector& ramp,
			  volume<float>& uph, const volume<float>& mask);

ColumnVector estimate_linear_ramps(volume<float>& ph, const volume<float>& mask);

////////////////////////////////////////////////////////////////////////////

volume<float> apply_unwrapping(const volume<float>& phasemap, 
			       const volume<int>& label, 
			       const Matrix& label_offsets);

volume<int> find_phase_labels(const volume<float>& phasemap, 
			      const volume<float>& mask,
			      int n=4);

volume<int> find_phase_labels2D(const volume<float>& phasemap, 
				const volume<float>& mask,
				int n, bool unique3Dlabels); 
 
volume<float> unwrap(const volume<float>& phasemap, 
		     const volume<int>& label, bool verbose=false);

volume<float> unwrap2D(const volume<float>& phasemap, 
		       const volume<int>& label, bool verbose=false);

volume<float> calc_fmap(const volume<float>& phase1, 
			const volume<float>& phase2,
			const volume<float>& mask1,
			const volume<float>& mask2,
			float asym_time);

float fmap2pixshift_factor(const volume<float>& fmap, float pe_dwell_time,
			   const string& dir);

volume<float> yderiv(const volume<float>& vol);

volume<float> limit_pixshift(const volume<float>& pixshift, 
			     const volume<float>& mask, float mindiff);

volume<float> apply_pixshift(const volume<float>& epivol,
			     const volume<float>& pixshiftmap);

////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////


// TEMPLATE BODIES

template <class T>
void simple_erode(volume<T>& binaryvol)
{
  binaryvol.setpadvalue(1.0);
  binaryvol.setextrapolationmethod(constpad);
  ColumnVector structelement(3);
  structelement = 1.0/3.0;
  binaryvol = convolve_separable(binaryvol,structelement,
				 structelement,structelement);
  binaryvol.binarise(1.0 - 0.5/27.0);
}
  
template <class T>
void simple_dilate(volume<T>& binaryvol)
{
  binaryvol.setpadvalue(0.0);
  binaryvol.setextrapolationmethod(constpad);
  ColumnVector structelement(3);
  structelement = 1.0/3.0;
  binaryvol = convolve_separable(binaryvol,structelement,
				 structelement,structelement);
  binaryvol.binarise(0.5/27.0,100.0);
}

#endif