/* -*- mia-c++  -*-
 *
 * This file is part of MIA - a toolbox for medical image analysis 
 * Copyright (c) Leipzig, Madrid 1999-2016 Gert Wollny
 *
 * MIA is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with MIA; if not, see <http://www.gnu.org/licenses/>.
 *
 */

#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <fstream>
#include <cstdlib>
#include <cmath>
#include <string>
//#include <dlfcn.h>
#include <algorithm>

#include <mia/core/cmdlineparser.hh>
#include <mia/core/histogram.hh>
#include <mia/core/kmeans.hh>
#include <mia/core/cmeans.hh>
#include <mia/2d/fuzzyclustersolver_cg.hh>
#include <mia/2d/fuzzyclustersolver_sor.hh>
#include <mia/2d/fuzzyseg.hh>

NS_MIA_BEGIN
using namespace std;


/* maximum number of iterations for EM-Algorithm */
#define _MAXIT 400 


typedef vector<C2DFImage> C2DFImageVec;


class CSegment2d : public TFilter<C2DFImageVec> {
public:
	CSegment2d(const unsigned int& nClasses, const SFuzzySegParams& params);
	~CSegment2d ();
	P2DImage get_out_image () const;
	P2DImage get_gain_image () const;

	template <typename T>
	CSegment2d::result_type operator () (const T2DImage<T>& data);
private:
	unsigned int m_nClasses;
	SFuzzySegParams m_params; 
	P2DImage     m_out;
	P2DImage     m_gain_image;

};


/// maximum number of iterations for the solver
#define _MAX_ITER_PDE 	1000


using namespace std;


// solves the PDE  (W + lambda1 * H1 + lambda2 * H2) = f
void solvePDE (C2DFImage& weight_image, C2DFImage& force_image, C2DFImage& gain_image, const SFuzzySegParams& params)
{
	C2DFuzzyClusterSolver solver(weight_image,params.lambda1, params.lambda2, 1000);
	solver.solve (force_image, gain_image);
}

template <class Data2D>
int estimateGain (C2DFImage& gain_image, const Data2D& src_image, vector<C2DFImage>& cls_image,
		  vector<double> &clCenter, unsigned int classes, const SFuzzySegParams& params)
{

	const unsigned int nx = src_image.get_size().x;
	const unsigned int ny = src_image.get_size().y;
	int t=0;

	// precompute force (f) and weight matrix (w)
	C2DFImage force_image (src_image.get_size());
	C2DFImage weight_image (src_image.get_size());


	for (unsigned int y = 2; y < ny-2; y++)  {
		for (unsigned int x = 2; x < nx-2; x++)  {
			double forcePixel = 0;
			double weightPixel = 0;
			for (unsigned int k = 0; k < classes; k++)  {
				double uk = cls_image[k](x, y);
				double vk = clCenter[k];
				double v = uk * uk * vk;
				forcePixel += v;
				weightPixel += v * vk;
			};
			
			forcePixel *= src_image(x, y);
			force_image(x, y) = (float)(forcePixel);
			weight_image(x, y) = (float)(weightPixel);
		};
	};
	// C.Wolters:
	// now solve system using scaled CG
	solvePDE(weight_image, force_image, gain_image, params);

	return t;

};



CSegment2d::CSegment2d(const unsigned int& nClasses, const SFuzzySegParams& params):
	m_nClasses(nClasses), 
	m_params(params)
{
}

CSegment2d::~CSegment2d ()
{
}

P2DImage CSegment2d::get_out_image () const
{
	return m_out;
}

P2DImage CSegment2d::get_gain_image () const
{
	return m_gain_image;
}


/*! Functor operator
  \param data any data struture that hold an (STL- style) iterator
  \returns the corrected image, as well as the class-probability images
*/
template <typename T>
CSegment2d::result_type CSegment2d::operator () (const T2DImage<T>& data)
{

	const size_t nx = data.get_size().x;
	const size_t ny = data.get_size().y;
	const size_t noOfPixels = nx*ny;

	// number of pixels in image
	// TODO: was ist u ??
	vector<double> u(m_nClasses);

	// Field to store the border
	vector<char> border(noOfPixels);

	// get type of iterator
	typedef T itype;

	// maximum pixel value in image
	auto maximum =	max_element(data.begin(), data.end());
	
	assert(maximum == data.end() || *maximum >= 1);
	
	itype iMax = *maximum;

	cvmsg()  << " The Maximum pixel value is " << (double) iMax << endl;

	unsigned long k = 0;
	auto data_itr = data.begin();

	for( ; data_itr < data.end(); k++, data_itr++ ) {

		// initialize border information
		if ( fborder(k, nx, ny) )
			border[k] = 0;
		else
			border[k] = 1;

	}

	// Create and initialize gain-field
	C2DFImage gain_image( data.get_size(), data);

	fill (gain_image.begin(), gain_image.end(), 1.0);

	// class probability image, compute initial class centers
	vector<double> clCenter(m_nClasses);
	vector<unsigned short> buffer(data.size()); 
	
	kmeans(data.begin(), data.end(), buffer.begin(), clCenter); 

	cvmsg()  << "intl. class centers:" << clCenter << "\n"; 

	// Algorithm step 1
	// create class membership volumes

	C2DFImageVec cls_image;
	for (size_t i = 0; i < m_nClasses; ++i)  {
		cls_image.push_back(C2DFImage ( data.get_size(), data));
	}

	for (unsigned int t = 0; t < _MAXIT; t++)  {

		// Algorithm step 2:
		// estimate gain field

		estimateGain (gain_image, data, cls_image, clCenter, m_nClasses, m_params);

		// Algorithm step 3:
		// recompute class memberships

		cmeans_evaluate_probabilities(data, gain_image, clCenter, cls_image); 
		
		// Algorithm step 4:
		// recompute class clCenters
		double residuum = cmeans_update_class_centers(data, gain_image, cls_image, clCenter); 

		cvmsg() << "I[" << t << "]: cc=" << clCenter << ", r=" << residuum << "\n"; 
		if (residuum < 0.0001)
			break;
		
	};
	
	// compute corrected image
	T2DImage<T> *corrected_image = new T2DImage<T> (data.get_size(), data);
	C2DFImage::iterator gain_itr = gain_image.begin();
	typename T2DImage<T>::iterator corrected_itr = corrected_image->begin();
	
	for ( data_itr = data.begin(); data_itr < data.end();
	      gain_itr++, data_itr++, corrected_itr++) {
		
		double corrected_val = (double) *data_itr;
		if (*gain_itr != 0)
			corrected_val /= *gain_itr;
		*corrected_itr = (T) corrected_val;
	}

	corrected_image->set_attribute("class_centers",
				       PAttribute(new CVDoubleAttribute( clCenter)));
	m_out.reset(corrected_image);
	for (size_t i = 0; i < cls_image.size(); ++i) {
		cls_image[i].set_attribute("class_number",
					    PAttribute(new CIntAttribute( i )));
		cls_image[i].set_attribute("class_centers",
					    PAttribute(new CVDoubleAttribute( clCenter)));
	}
	m_gain_image.reset(new C2DFImage(gain_image)); 
	return cls_image;
}

template <>
CSegment2d::result_type CSegment2d::operator () (const C2DBitImage& /*data*/) {
	throw invalid_argument("Segemtation of binary images makes no sense");
}



EXPORT_2D P2DImage fuzzy_segment_2d(const C2DImage& src, size_t noOfClasses, const SFuzzySegParams& params, 
				    C2DImageVector& classes, P2DImage& gain)
{
	CSegment2d segment2D (noOfClasses, params);
	C2DFImageVec imagesVector = mia::accumulate (segment2D, src);

	for (size_t i=0; i < noOfClasses; i++) {
		classes.push_back( P2DImage(new C2DFImage(imagesVector[i])));
	}
	gain = segment2D.get_gain_image(); 
	return segment2D.get_out_image();
}

NS_MIA_END

